Index (Bio-Formats API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

a - Variable in class jj2000.j2k.entropy.decoder.MQDecoder: The current interval
a - Variable in class jj2000.j2k.entropy.encoder.MQCoder: The current interval
abort() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
About - Class in loci.plugins: Displays a small information dialog about the Bio-Formats Plugins package.
About() - Constructor for class loci.plugins.About
about() - Static method in class loci.plugins.About
abs() - Method in class loci.plugins.util.RecordedImageProcessor
absoluteTime - Variable in class loci.formats.in.PrairieMetadata.Frame: absoluteTime attribute of this <Frame>.
AbstractOMEXMLMetadata - Class in loci.formats.ome
AbstractOMEXMLMetadata() - Constructor for class loci.formats.ome.AbstractOMEXMLMetadata
ac - Variable in class loci.formats.in.FakeReader: Channel of last opened image plane.
accept(File) - Method in class loci.formats.gui.ComboFileFilter: Accepts files with the proper filename prefix.
accept(File) - Method in class loci.formats.gui.ExtensionFileFilter: Accepts files with the proper extensions.
accept(File) - Method in class loci.formats.gui.FormatFileFilter: Accepts files in accordance with the file format reader.
accept(File) - Method in class loci.formats.gui.NoExtensionFileFilter: Accepts files with no extension.
accept(String) - Method in class loci.formats.NumberFilter: Tests if a specified file should be included in a file list.
accept(File) - Method in class loci.formats.NumberFilter: Tests if a specified file should be included in a file list.
accumulate - Variable in class loci.formats.in.SDTInfo
ACCUMULATION - Static variable in class loci.formats.in.CellSensReader
ACCUMULATION_MODE - Static variable in class loci.formats.in.CellSensReader
acquire - Variable in class loci.formats.in.ZeissLSMReader.SubBlock
acquiredDate - Variable in class loci.formats.in.LIFReader
acquiredDate - Variable in class loci.formats.in.ZeissCZIReader
acquiredDate - Variable in class loci.formats.in.ZeissLSMReader
ACQUISITION_CYCLE_TIME - Static variable in class loci.formats.in.FluoviewReader
ACQUISITION_FILE - Static variable in class loci.formats.in.ScanrReader
ACQUISITION_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
ACQUISITION_TIME_TAG - Static variable in class loci.formats.in.FlowSightReader
acquisitionDate - Variable in class loci.formats.in.BaseZeissReader
acquisitionDate - Variable in class loci.formats.in.BioRadSCNReader
acquisitionDate - Variable in class loci.formats.in.ColumbusReader
acquisitionDate - Variable in class loci.formats.in.OIRReader
acquisitionDate - Variable in class loci.formats.in.SISReader
acquisitionDates - Variable in class loci.formats.in.FlexReader
acquisitionMode - Variable in class loci.formats.in.ZeissCZIReader.Channel
acquisitions - Variable in class loci.formats.in.ZeissCZIReader
acquisitionTime - Variable in class loci.formats.in.CellSensReader.Pyramid
act - Variable in class loci.formats.in.GIFReader: Active color table.
actionPerformed(ActionEvent) - Method in class loci.formats.gui.CacheComponent: Handles combo box changes.
actionPerformed(ActionEvent) - Method in class loci.formats.gui.DataConverter
actionPerformed(ActionEvent) - Method in class loci.formats.gui.ImageViewer: Handles menu commands.
actionPerformed(ActionEvent) - Method in class loci.formats.tools.EditTiffG
actionPerformed(ActionEvent) - Method in class loci.plugins.config.ConfigWindow
actionPerformed(ActionEvent) - Method in class loci.plugins.in.SeriesDialog
actionPerformed(ActionEvent) - Method in class loci.plugins.shortcut.ShortcutPanel: Handles button presses.
actionPerformed(ActionEvent) - Method in class loci.plugins.util.DataBrowser
actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow
actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow.SearchBox
active - Variable in class loci.formats.in.FV1000Reader.ChannelData
active - Variable in class loci.formats.in.LeicaHandler.Detector
active - Variable in class loci.formats.in.LeicaReader.Detector
ACTIVE_CHANNEL - Static variable in class loci.formats.in.CellSensReader
ACTIVE_LAYER_INDEX_VECTOR - Static variable in class loci.formats.in.CellSensReader
ACTIVE_LAYER_VECTOR - Static variable in class loci.formats.in.CellSensReader
ACTIVE_STACK_DIMENSION - Static variable in class loci.formats.in.CellSensReader
activeChannelIndices - Variable in class loci.formats.in.LeicaReader
activeChannels - Variable in class loci.formats.in.PrairieMetadata: Set of active channel indices.
activeDetector - Variable in class loci.formats.in.LIFReader
activePlane - Variable in class loci.formats.in.OperettaReader.OperettaHandler
activeSrcHeight - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: The height of the source region that will actually be copied into the destination image, taking into account all susbampling, offsetting, and clipping.
activeSrcMinX - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: The X coordinate of the upper-left source pixel that will actually be copied into the destination image, taking into account all subsampling, offsetting, and clipping.
activeSrcMinY - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: The Y coordinate of the upper-left source pixel that will actually be copied into the destination image, taking into account all subsampling, offsetting, and clipping.
activeSrcWidth - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: The width of the source region that will actually be copied into the destination image, taking into account all susbampling, offsetting, and clipping.
ACTUAL_TEMPERATURE - Static variable in class loci.formats.in.FluoviewReader
actualBytes - Variable in class jj2000.j2k.entropy.encoder.EBCOTLayer: The actual number of bytes which are consumed by the the current and any previous layers.
adcDE - Variable in class loci.formats.in.SDTInfo: ADC sample delay (SPC-930).
adcRE - Variable in class loci.formats.in.SDTInfo
adcResShift - Variable in class loci.formats.in.SPCReader
adcZoom - Variable in class loci.formats.in.SDTInfo
add(byte) - Method in class loci.formats.codec.ByteVector
add(byte[]) - Method in class loci.formats.codec.ByteVector
add(byte[], int, int) - Method in class loci.formats.codec.ByteVector
add(byte[], int, int, int, int) - Method in class loci.formats.codec.JPEGTileDecoder.TileCache
add(int[], int, int, int, int) - Method in class loci.formats.codec.JPEGTileDecoder.TileCache
add(double) - Method in class loci.plugins.util.RecordedImageProcessor
add(int) - Method in class loci.plugins.util.RecordedImageProcessor
add1DBits(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor: Get code for run and add to compressed bitstream.
add2DBits(byte[], int, int[][], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor: Place entry from mode table into compressed bitstream.
addAllowedTagSet(TIFFTagSet) - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam: Adds a TIFFTagSet object to the list of allowed tag sets.
addByteArray(byte[], int, int) - Method in class jj2000.j2k.entropy.decoder.ByteInputBuffer: Adds the specified data to the end of the byte array stream.
addCacheListener(CacheListener) - Method in class loci.formats.cache.Cache
addCacheListener(CacheListener) - Method in interface loci.formats.cache.CacheReporter: Adds a listener for status update events.
addCacheListener(CacheListener) - Method in class loci.formats.cache.CacheStrategy
AddCharString(short, byte) - Method in class com.sun.media.imageioimpl.common.LZWStringTable
addCheckbox(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog: Adds a checkbox to the given dialog object corresponding to the boolean option identified by the specified key.
addChildNode(IIOMetadataNode, String, Object) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
addChildNode(IIOMetadataNode, String, Object) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
addChoice(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog: Adds a choice to the given dialog object corresponding to the string option identified by the specified key.
addClass(int, Class<? extends T>) - Method in class loci.formats.ClassList: Adds the given class, which must be assignable to the base class, to the list.
addClass(Class<? extends T>) - Method in class loci.formats.ClassList: Adds the given class, which must be assignable to the base class, to the list.
addComment(String) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
addDirectory(String, int) - Method in class loci.formats.in.L2DReader: Recursively add all of the files in the given directory to the used file list.
addElements() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat: Adds the elements into this format object based on the XML schema and DTD.
addElements() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormat: Adds the elements into this format object based on the XML schema and DTD.
addEntry(Comparable<Object>, DefaultListModel) - Static method in class loci.plugins.config.ConfigWindow
addEOFB(byte[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor: Add an End-of-Facsimile-Block (EOFB == 0x001001) to the compressed bitstream.
addEOL(boolean, boolean, boolean, byte[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor: Add an End-of-Line (EOL == 0x001) to the compressed bitstream with optional byte alignment.
addFileToList(String, boolean) - Method in class loci.formats.in.DicomReader: Determine if the given file belongs in the same dataset as this file.
addGlobalMeta(String, Object) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, boolean) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, byte) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, short) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, int) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, long) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, float) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, double) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, char) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMetaList(String, Object) - Method in class loci.formats.FormatReader: Add the given key/value pair to the global metadata hashtable.
addInfo(int, String) - Method in class loci.formats.in.DicomReader
addInfo(int, int) - Method in class loci.formats.in.DicomReader
additionalMakeup - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
addMeta(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader: Adds an entry to the specified Hashtable.
addMetadataOnly(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService: Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in interface loci.formats.services.OMEXMLService: Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
addMetadataOnly(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in class loci.formats.services.OMEXMLServiceImpl
addMetaList(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader: Add the given key/value pair to the given hashtable.
addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in interface loci.formats.services.OMEXMLService: Adds ModuloAlong* annotations to the given OME-XML metadata object, using the given CoreMetadata object to determine modulo dimensions.
addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
addNode(Box) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
addNTP(int, int) - Method in class jj2000.j2k.codestream.reader.CBlkInfo: Adds the number of new truncation for specified layer.
addOption(String, String) - Method in class loci.formats.ClassList: Add a key/value pair to the list of options.
addOptPoint(float, int) - Method in class jj2000.j2k.entropy.encoder.LayersInfo: Adds a new optimization point, with target bitrate 'brate' and with 'elyrs' (unoptimized) extra layers after it.
addPossible(String) - Method in class loci.plugins.prefs.StringOption: Adds a possible value to the list.
addProp(HashMap<String, String>, String, String, HashMap<String, String>) - Method in class loci.plugins.config.ConfigWindow
addPtyFiles() - Method in class loci.formats.in.FV1000Reader
addScrollBars(Container) - Static method in class loci.plugins.util.WindowTools: Adds AWT scroll bars to the given container.
addSeriesMeta(String, Object) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, boolean) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, byte) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, short) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, int) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, long) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, float) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, double) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, char) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMetaList(String, Object) - Method in class loci.formats.FormatReader: Add the given key/value pair to the current series metadata hashtable.
addShortOrLongField(int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
addStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
addStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
addStringToTable(byte[], byte) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor: Add a new string to the string table.
addStringToTable(byte[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor: Add a new string to the string table.
addStringToTable(byte[], byte) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil: Add a new string to the string table.
addStringToTable(byte[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil: Add a new string to the string table.
addTagSet(TIFFTagSet) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory: Adds an element to the group of TIFFTagSets of which this directory is aware.
addTIFFField(TIFFField) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory: Adds a TIFF field to the directory.
addToHashtable() - Method in class loci.formats.in.ZeissLSMReader.SubBlock
addUsedFile(String, String) - Method in class loci.formats.in.PerkinElmerReader: Add the given file to the used files list.
addUserCommentMeta(Element, int) - Method in class loci.formats.in.LIFReader
addValueName(int, String) - Method in class com.sun.media.imageio.plugins.tiff.TIFFTag: Adds a mnemonic name for a particular value that this tag's data may take on.
addXYZPoints(IIOMetadataNode, String, double, double, double) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
adjust - Variable in class loci.formats.in.SlidebookReader
adjustBitDepths - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
adjustEndianness - Variable in class loci.formats.in.GatanReader
adjustForWhiteBalance(short, int) - Method in class loci.formats.in.DNGReader
adjustForWhiteBalance(short, int) - Method in class loci.formats.in.NikonReader
adjustmentValueChanged(AdjustmentEvent) - Method in class loci.plugins.util.DataBrowser
adjustWellDimensions() - Method in class loci.formats.in.ScanrReader
advanceBlock() - Method in class loci.formats.in.APNGReader.PNGInputStream
AE - Static variable in class loci.formats.in.DicomReader
AFIHandler() - Constructor for class loci.formats.in.AFIReader.AFIHandler
AFIReader - Class in loci.formats.in: AFIReader is the file format reader for Aperio AFI files.
AFIReader() - Constructor for class loci.formats.in.AFIReader: Constructs a new AFI reader.
AFIReader.AFIHandler - Class in loci.formats.in
ag - Variable in class loci.formats.FileStitcher.ExternalSeries
AIMReader - Class in loci.formats.in: AIMReader is the file format reader for .aim files.
AIMReader() - Constructor for class loci.formats.in.AIMReader: Constructs a new AIM reader.
airPressure - Variable in class loci.formats.in.ZeissCZIReader
AISF - Static variable in class loci.formats.in.VolocityClippingReader
AL3D_MAGIC_STRING - Static variable in class loci.formats.in.AliconaReader
AliconaReader - Class in loci.formats.in: AliconaReader is the file format reader for Alicona AL3D files.
AliconaReader() - Constructor for class loci.formats.in.AliconaReader: Constructs a new Alicona reader.
ALIGNMENT - Static variable in class loci.formats.in.ZeissCZIReader
alignROI - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava: By specifying this parameter, the ROI mask will be limited to covering only entire code-blocks.
aLine - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
ALL_DOMAINS - Static variable in class loci.formats.FormatTools: List of all supported domains.
ALL_TYPES - Static variable in class loci.formats.gui.GUITools: String to use for "all types" combination filter.
allBlockLengths - Variable in class loci.formats.in.SDTInfo
allBlockOffsets - Variable in class loci.formats.in.SDTInfo
allFiles - Variable in class loci.formats.in.BrukerReader
allFiles - Variable in class loci.formats.in.PerkinElmerReader: List of all files to open
allFiles - Variable in class loci.formats.in.SPCReader: List of all files to open
allocatedSize - Variable in class loci.formats.in.ZeissCZIReader.Segment
allocateRate() - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent: Allocates output bit-rate for each tile in parsing mode: The allocator simulates the truncation of a virtual layer-resolution progressive codestream.
ALLOW_AUTOSTITCHING_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
ALLOW_AUTOSTITCHING_KEY - Static variable in class loci.formats.in.ZeissCZIReader
allowAutostitching() - Method in class loci.formats.in.ZeissCZIReader
allowCZIAutostitch() - Static method in class loci.plugins.util.LociPrefs
allowedTagsByName - Variable in class com.sun.media.imageio.plugins.tiff.TIFFTagSet
allowedTagsByNumber - Variable in class com.sun.media.imageio.plugins.tiff.TIFFTagSet
allowedTagSets - Variable in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam
allowOpen - Variable in class loci.formats.gui.FormatFileFilter: Whether it is ok to open a file to determine its type.
allowOpen - Variable in class loci.formats.ImageReader
allowShow - Variable in class loci.plugins.util.DataBrowser
ALPHA - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7: The value of the first lifting step coefficient
ALPHA - Static variable in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7: The value of the first lifting step coefficient
ALPHABET_LENGTH - Static variable in class loci.formats.ResourceNamer
alphabeticIndexCount(String) - Static method in class loci.formats.ResourceNamer
alphaMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
alphaMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
alphaShort - Variable in class loci.formats.gui.Index16ColorModel: Lookup tables.
alreadyChecked() - Method in class loci.formats.UpgradeChecker: Return true if an upgrade check has already been performed in this JVM session.
altCodec - Variable in class loci.formats.in.NativeQTReader: Some movies use two video codecs -- this is the second codec.
alternateCenter - Variable in class loci.formats.in.LeicaHandler
alternateCenter - Variable in class loci.formats.in.LIFReader
ALTITUDE_REF_SEA_LEVEL - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet: A value to be used with the "GPSAltitudeRef" tag.
ALTITUDE_REF_SEA_LEVEL_REFERENCE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet: A value to be used with the "GPSAltitudeRef" tag.
altPlanes - Variable in class loci.formats.in.NativeQTReader: Number of frames that use the alternate codec.
AmiraParameters - Class in loci.formats.tools: AmiraParameters handles parsing and writing of AmiraMesh headers.
AmiraParameters(String) - Constructor for class loci.formats.tools.AmiraParameters
AmiraParameters(RandomAccessInputStream) - Constructor for class loci.formats.tools.AmiraParameters
AmiraReader - Class in loci.formats.in: This is a file format reader for AmiraMesh data.
AmiraReader() - Constructor for class loci.formats.in.AmiraReader
AmiraReader.ASCII - Class in loci.formats.in: This class provides a not-quite-efficient, but simple reader for planes stored in ASCII-encoded numbers.
AmiraReader.HxRLE - Class in loci.formats.in: This is the reader for RLE-compressed AmiraMeshes.
AmiraReader.HxZip - Class in loci.formats.in: This is the reader for GZip-compressed AmiraMeshes.
AmiraReader.PlaneReader - Interface in loci.formats.in: This is the common interface for all formats, compressed or not.
amplificationGain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
AnalysisFile() - Constructor for class loci.formats.in.MIASReader.AnalysisFile
analysisFiles - Variable in class loci.formats.in.MIASReader
analyze_hpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilter: Filters the input signal by this analysis filter, decomposing it in a low-pass and a high-pass signal.
analyze_hpf(float[], int, int, int, float[], int, int, float[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloat: A specific version of the analyze_hpf() method that works on int data.
analyze_hpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloat: The general version of the analyze_hpf() method, it just calls the specialized version.
analyze_hpf(float[], int, int, int, float[], int, int, float[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7: An implementation of the analyze_hpf() method that works on int data, for the forward 9x7 wavelet transform using the lifting scheme.
analyze_hpf(int[], int, int, int, int[], int, int, int[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterInt: A specific version of the analyze_hpf() method that works on int data.
analyze_hpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterInt: The general version of the analyze_hpf() method, it just calls the specialized version.
analyze_hpf(int[], int, int, int, int[], int, int, int[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3: An implementation of the analyze_hpf() method that works on int data, for the forward 5x3 wavelet transform using the lifting scheme.
analyze_lpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilter: Filters the input signal by this analysis filter, decomposing it in a low-pass and a high-pass signal.
analyze_lpf(float[], int, int, int, float[], int, int, float[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloat: A specific version of the analyze_lpf() method that works on int data.
analyze_lpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloat: The general version of the analyze_lpf() method, it just calls the specialized version.
analyze_lpf(float[], int, int, int, float[], int, int, float[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7: An implementation of the analyze_lpf() method that works on int data, for the forward 9x7 wavelet transform using the lifting scheme.
analyze_lpf(int[], int, int, int, int[], int, int, int[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterInt: A specific version of the analyze_lpf() method that works on int data.
analyze_lpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterInt: The general version of the analyze_lpf() method, it just calls the specialized version.
analyze_lpf(int[], int, int, int, int[], int, int, int[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3: An implementation of the analyze_lpf() method that works on int data, for the forward 5x3 wavelet transform using the lifting scheme.
AnalyzeReader - Class in loci.formats.in: AnalyzeReader is the file format reader for Analyze 7.5 files.
AnalyzeReader() - Constructor for class loci.formats.in.AnalyzeReader: Constructs a new Analyze reader.
anbytes - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent: Actual number of read bytes
and(int) - Method in class loci.plugins.util.RecordedImageProcessor
ANDOR_MAGIC_STRING - Static variable in class loci.formats.in.FluoviewReader
ANDOR_SHIFT_SPEED - Static variable in class loci.formats.in.CellSensReader
andTable - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
andTable - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
anGainExp - Variable in class jj2000.j2k.wavelet.Subband: The base 2 exponent of the analysis gain of the subband.
ANGLE - Static variable in class loci.formats.in.ZeissLSMReader
angle - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
angles - Variable in class loci.formats.in.ZeissCZIReader
anim - Variable in class loci.formats.gui.ImageViewer
anim - Variable in class loci.plugins.util.DataBrowser
animate - Variable in class loci.plugins.util.DataBrowser
ANIMATION_KEY - Static variable in class loci.formats.gui.ImageViewer
ANN_BOOLEAN_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_COMMENT_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_DOUBLE_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_LONG_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_TAG_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_TERM_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_TIME_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_XML_VALUE_END - Static variable in class loci.formats.in.FakeReader
ANN_XML_VALUE_START - Static variable in class loci.formats.in.FakeReader
annBool - Variable in class loci.formats.in.FakeReader
annComment - Variable in class loci.formats.in.FakeReader
annDouble - Variable in class loci.formats.in.FakeReader
annLong - Variable in class loci.formats.in.FakeReader
annMap - Variable in class loci.formats.in.FakeReader
ANNOTATION_NAMESPACE - Static variable in class loci.formats.in.FakeReader
ANNOTATION_PREFIX - Static variable in class loci.formats.in.FakeReader
annotationBoolCount - Variable in class loci.formats.in.FakeReader
annotationCommentCount - Variable in class loci.formats.in.FakeReader
annotationCount - Variable in class loci.formats.in.FakeReader
annotationDoubleCount - Variable in class loci.formats.in.FakeReader
annotationLongCount - Variable in class loci.formats.in.FakeReader
annotationMapCount - Variable in class loci.formats.in.FakeReader
annotationTagCount - Variable in class loci.formats.in.FakeReader
annotationTermCount - Variable in class loci.formats.in.FakeReader
annotationTimeCount - Variable in class loci.formats.in.FakeReader
annotationXmlCount - Variable in class loci.formats.in.FakeReader
annTag - Variable in class loci.formats.in.FakeReader
annTerm - Variable in class loci.formats.in.FakeReader
annTime - Variable in class loci.formats.in.FakeReader
annXml - Variable in class loci.formats.in.FakeReader
ANO_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
AnWTFilter - Class in jj2000.j2k.wavelet.analysis: This abstract class defines the methods of all analysis wavelet filters.
AnWTFilter() - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilter
AnWTFilterFloat - Class in jj2000.j2k.wavelet.analysis: This extends the analysis wavelet filter general definitions of AnWTFilter by adding methods that work for float data specifically.
AnWTFilterFloat() - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilterFloat
AnWTFilterFloatLift9x7 - Class in jj2000.j2k.wavelet.analysis: This class inherits from the analysis wavelet filter definition for int data.
AnWTFilterFloatLift9x7() - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
AnWTFilterInt - Class in jj2000.j2k.wavelet.analysis: This extends the analysis wavelet filter general definitions of AnWTFilter by adding methods that work for int data specifically.
AnWTFilterInt() - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilterInt
AnWTFilterIntLift5x3 - Class in jj2000.j2k.wavelet.analysis: This class inherits from the analysis wavelet filter definition for int data.
AnWTFilterIntLift5x3() - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
AnWTFilterSpec - Class in jj2000.j2k.wavelet.analysis: This class extends ModuleSpec class for analysis filters specification holding purpose.
AnWTFilterSpec(int, int, byte, QuantTypeSpec, J2KImageWriteParamJava, String) - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilterSpec: Constructs a new 'AnWTFilterSpec' for the specified number of components and tiles.
APERIO_IMAGE_DESCRIPTION_PREFIX - Static variable in class loci.formats.in.SVSReader: TIFF image description prefix for Aperio SVS files.
APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
ApertureValue() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ApertureValue
APLReader - Class in loci.formats.in: APLReader is the file format reader for Olympus APL files.
APLReader() - Constructor for class loci.formats.in.APLReader: Constructs a new APL reader.
APNGReader - Class in loci.formats.in: APNGReader is the file format reader for Animated Portable Network Graphics (APNG) images.
APNGReader() - Constructor for class loci.formats.in.APNGReader: Constructs a new APNGReader.
APNGReader.PNGBlock - Class in loci.formats.in
APNGReader.PNGInputStream - Class in loci.formats.in: InputStream implementation that stitches together IDAT blocks into a seamless zlib stream.
APNGWriter - Class in loci.formats.out: APNGWriter is the file format writer for PNG and APNG files.
APNGWriter() - Constructor for class loci.formats.out.APNGWriter
append(ClassList<T>) - Method in class loci.formats.ClassList: Appends a class list which must be assignable to the base class
append(List<Class<? extends T>>) - Method in class loci.formats.ClassList: Appends a list of classes which must be assignable to the base class
append(ILoggingEvent) - Method in class loci.plugins.util.IJStatusEchoer
appendChild(Node) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
appendedCompressionType - Variable in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam
appendServerMap(String, String) - Static method in class loci.formats.in.FlexReader: Add the path 'realName' to the mapping for the server named 'alias'.
applicationData - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
applicationIDs - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
applyCalibration(ImagePlus) - Method in class loci.plugins.in.Calibrator: Applies spatial calibrations to an image stack.
applyColors(List<ImagePlus>) - Method in class loci.plugins.in.Colorizer
applyColors(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
applyDisplayRanges(ImagePlus, int) - Method in class loci.plugins.in.Colorizer
applyMethodStack(List<RecordedImageProcessor.MethodEntry>) - Method in class loci.plugins.util.RecordedImageProcessor
applyTable(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
approximation - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
arate - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent: Actual decoding rate in bpp
ArbROIMaskGenerator - Class in jj2000.j2k.roi.encoder: This class generates the ROI bit-mask when, at least, one ROI is not rectangular.
ArbROIMaskGenerator(ROI[], int, Quantizer) - Constructor for class jj2000.j2k.roi.encoder.ArbROIMaskGenerator: The constructor of the arbitrary mask generator
arbShape - Variable in class jj2000.j2k.roi.encoder.ROI: Where or not the ROI shape is arbitrary
ARCHIVE - Static variable in class loci.formats.in.FlexReader
AreaInfo() - Constructor for class loci.formats.in.CellVoyagerReader.AreaInfo
areas - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
areIntArraysEqual(int[], int[]) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
areSampleSizesEqual(SampleModel) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: Returns whether all samples have the same number of bits.
ARFReader - Class in loci.formats.in: ARFReader is the file format reader for Axon Raw Format (ARF) files, produced by INDEC BioSystems's Imaging Workbench software.
ARFReader() - Constructor for class loci.formats.in.ARFReader: Constructs a new ARF reader.
arg - Variable in class loci.plugins.LociExporter: Argument passed to setup method.
arg - Variable in class loci.plugins.Slicer: Plugin options.
args - Static variable in class loci.plugins.shortcut.ShortcutPanel: Details for installed plugins.
args - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
ARRAY - Static variable in class loci.formats.in.GatanReader: Data types.
arrayToString(Array) - Method in class loci.formats.services.NetCDFServiceImpl
ArrayUtil - Class in jj2000.j2k.util: This class contains a colleaction of utility static methods for arrays.
ArrayUtil() - Constructor for class jj2000.j2k.util.ArrayUtil
ARROW - Static variable in class loci.formats.in.FV1000Reader
ARROW - Static variable in class loci.formats.in.LeicaHandler.ROI
ARROW - Static variable in class loci.formats.in.LIFReader.ROI
Artist() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Artist
ARTIST - Static variable in class loci.formats.tiff.IFD
AS - Static variable in class loci.formats.in.DicomReader
ascii - Variable in class loci.formats.in.AmiraReader
ASCII(int, int) - Constructor for class loci.formats.in.AmiraReader.ASCII
ascii - Variable in class loci.formats.tools.AmiraParameters
AsciiImage - Class in loci.formats.tools: A utility class for outputting a BufferedImage as ASCII text.
AsciiImage(BufferedImage) - Constructor for class loci.formats.tools.AsciiImage
asMap() - Method in class loci.formats.in.DeltavisionReader.DVExtHdrFields
asRetrieve(MetadataStore) - Method in interface loci.formats.services.OMEXMLService: Gets the given MetadataStore object as a MetadataRetrieve.
asRetrieve(MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
assertId(String, boolean, int) - Static method in class loci.formats.FormatTools: Asserts that the current file is either null, or not, according to the given flag.
assertStep(ImportStep) - Method in class loci.plugins.in.ImportProcess
assignL2Norm(float) - Method in class jj2000.j2k.wavelet.analysis.SubbandAn: Assigns the given L2-norm to the first leaf that does not have an L2-norm value yet (i.e.
assignPlaneIndices() - Method in class loci.formats.in.ZeissCZIReader
assignValues(double[]) - Method in class loci.formats.in.TextReader: Assigns values from the given row into the data array.
associations - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
associations - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
asStore(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService: Gets the given MetadataRetrieve object as a MetadataStore.
asStore(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
ASTRONOMY_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the astronomy domain.
AT - Static variable in class loci.formats.in.DicomReader
aTile - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc: The raster for a destination tile
attachCompanionFiles() - Method in class loci.formats.in.DicomReader: DICOM datasets produced by: http://www.ct-imaging.de/index.php/en/ct-systeme-e/mikro-ct-e.html contain a bunch of extra metadata and log files.
attachListeners(List<TextField>, List<Panel>) - Method in class loci.plugins.in.ColorDialog
Attachment(String, long) - Constructor for class loci.formats.in.ZeissCZIReader.Attachment
attachment - Variable in class loci.formats.in.ZeissCZIReader.Attachment
attachment - Variable in class loci.formats.in.ZeissCZIReader.Metadata
attachmentData - Variable in class loci.formats.in.ZeissCZIReader.Attachment
AttachmentDirectory() - Constructor for class loci.formats.in.ZeissCZIReader.AttachmentDirectory
attachmentDirectoryPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
AttachmentEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.AttachmentEntry
attachmentSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
attenuation - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
attr(Element, String) - Method in class loci.formats.in.PrairieMetadata: Gets the attribute value with the given name, or null if not defined.
ATTR_NAME_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
ATTR_NAME_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
ATTR_VALUE_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
ATTR_VALUE_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
attributeList - Variable in class loci.formats.services.NetCDFServiceImpl
attributeNames - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
attrInfoMap - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
authenticationCodes - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
AUTOEXPOSURE - Static variable in class loci.formats.in.CellSensReader
autoscale(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Perform autoscaling on the given BufferedImage.
autoscale(BufferedImage, int, int) - Static method in class loci.formats.gui.AWTImageTools: Perform autoscaling on the given BufferedImage; map min to 0 and max to 255.
autoscale(byte[], int, int, int, boolean) - Static method in class loci.formats.ImageTools: Perform autoscaling on the given byte array; map min to 0 and max to 255.
autoscaleBox - Variable in class loci.plugins.in.MainDialog
autoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
autoUpdate - Variable in class loci.formats.cache.Cache: Whether the cache should automatically update when a parameter changes.
available() - Method in class loci.formats.in.APNGReader.PNGInputStream
availMem - Variable in class loci.plugins.in.MemoryDialog: Remaining memory for the JVM.
avbits - Variable in class jj2000.j2k.codestream.writer.BitOutputBuffer: The number of available bits in the current byte
AVERAGE - Static variable in class loci.formats.in.APNGReader
AVERAGING - Static variable in class loci.formats.in.CellSensReader
AVI_MAGIC_STRING - Static variable in class loci.formats.in.AVIReader
AVIReader - Class in loci.formats.in: AVIReader is the file format reader for AVI files.
AVIReader() - Constructor for class loci.formats.in.AVIReader: Constructs a new AVI reader.
AVIWriter - Class in loci.formats.out: AVIWriter is the file format writer for AVI files.
AVIWriter() - Constructor for class loci.formats.out.AVIWriter
AWTImageTools - Class in loci.formats.gui: A utility class with convenience methods for manipulating images in BufferedImage form.
AWTImageTools() - Constructor for class loci.formats.gui.AWTImageTools
ax - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent: The horizontal coordinate of the image origin in the canvas system, on the reference grid.
axis - Variable in class loci.formats.gui.CacheIndicator
AxisGuesser - Class in loci.formats: AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T, C or S), potentially recommending an adjustment in dimension order within the files, depending on the confidence of each guess.
AxisGuesser(FilePattern, String, int, int, int, boolean) - Constructor for class loci.formats.AxisGuesser: Guesses dimensional axis assignments corresponding to the given file pattern, using the specified dimensional information from within each file as a guide.
axisTypes - Variable in class loci.formats.AxisGuesser: Guessed axis types.
ay - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent: The vertical coordinate of the image origin in the canvas system, on the reference grid.

B

b - Variable in class jj2000.j2k.entropy.decoder.MQDecoder: The last byte read
b - Variable in class jj2000.j2k.entropy.encoder.MQCoder: The last encoded byte of data
b(String) - Method in class loci.formats.in.PrairieMetadata: Converts the given string to a boolean.
BACK_MASK - Static variable in class loci.formats.codec.BitBuffer: Deprecated.

Various bitmasks for the 0000xxxx side of a byte.
BACKGROUND_TABLE - Static variable in class loci.formats.in.LiFlimReader
backgroundC - Variable in class loci.formats.in.LiFlimReader
backgroundColor - Variable in class loci.formats.in.CellSensReader
backgroundColorIndex - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
backgroundDatatype - Variable in class loci.formats.in.LiFlimReader
backgroundF - Variable in class loci.formats.in.LiFlimReader
backgroundP - Variable in class loci.formats.in.LiFlimReader
backgroundT - Variable in class loci.formats.in.LiFlimReader
backgroundX - Variable in class loci.formats.in.LiFlimReader
backgroundY - Variable in class loci.formats.in.LiFlimReader
backgroundZ - Variable in class loci.formats.in.LiFlimReader
backupHandler - Variable in class loci.formats.in.NativeND2Reader
BACKWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
backwardsStage - Variable in class loci.formats.in.DeltavisionReader: Whether or not the stage moved backwards.
BadFaxLines() - Constructor for class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet.BadFaxLines
bais - Variable in class jj2000.j2k.codestream.reader.PktHeaderBitReader: The byte array that is the source of data if the PktHeaderBitReader is instantiated with a buffer instead of a RandomAccessIO
bak_lblock - Variable in class jj2000.j2k.codestream.writer.PktEncoder: The saved base number of bits for sending code-block length information.
bak_prevtIdxs - Variable in class jj2000.j2k.codestream.writer.PktEncoder: The saved last encoded truncation point for each code-block.
baknBytes - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent: Backup of the number of bytes allocated to each tile.
bandOffsets - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
bandStride - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter: The strides for pixel, band, and scanline.
bandUsed - Variable in class loci.formats.in.NDPISReader
bankData - Variable in class loci.formats.gui.SignedByteBuffer
bankData - Variable in class loci.formats.gui.UnsignedIntBuffer
baos - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
baos - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder: The ByteArrayOutputStream to store header data.
barcode - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
barr - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc: Buffer for the 3 components of each pixel(in the current block)
barrierFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
base - Variable in class loci.formats.ClassList: Base class to which all classes are assignable.
base64Alphabet - Static variable in class loci.formats.codec.Base64Codec
Base64Codec - Class in loci.formats.codec: Implements encoding (compress) and decoding (decompress) methods for Base64.
Base64Codec() - Constructor for class loci.formats.codec.Base64Codec
BASE_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
BaseCodec - Class in loci.formats.codec: BaseCodec contains default implementation and testing for classes implementing the Codec interface, and acts as a base class for any of the compression classes.
BaseCodec() - Constructor for class loci.formats.codec.BaseCodec
basedir - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
BASELINE_CLAMP - Static variable in class loci.formats.in.FluoviewReader
BASELINE_OFFSET - Static variable in class loci.formats.in.FluoviewReader
BASELINE_OFFSET_CLAMP - Static variable in class loci.formats.in.CellSensReader
BaselineTIFFTagSet - Class in com.sun.media.imageio.plugins.tiff: A class representing the set of tags found in the baseline TIFF specification as well as some common additional tags.
BaselineTIFFTagSet() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet
BaselineTIFFTagSet.Artist - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.BitsPerSample - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.CellLength - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.CellWidth - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.ColorMap - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.Compression - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.Copyright - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.DateTime - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.DocumentName - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.DotRange - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.ExtraSamples - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.FillOrder - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.FreeByteCounts - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.FreeOffsets - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.GrayResponseCurve - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.GrayResponseUnit - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.HalftoneHints - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.HostComputer - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.ICCProfile - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.ImageDescription - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.ImageLength - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.ImageWidth - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.InkNames - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.InkSet - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.JPEGACTables - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.JPEGDCTables - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.JPEGInterchangeFormat - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.JPEGInterchangeFormatLength - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.JPEGLosslessPredictors - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.JPEGPointTransforms - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.JPEGProc - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.JPEGQTables - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.JPEGRestartInterval - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.JPEGTables - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.Make - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.MaxSampleValue - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.MinSampleValue - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.Model - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.NewSubfileType - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.NumberOfInks - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.Orientation - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.PageName - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.PageNumber - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.PhotometricInterpretation - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.PlanarConfiguration - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.Predictor - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.PrimaryChromaticities - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.ReferenceBlackWhite - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.ResolutionUnit - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.RowsPerStrip - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.SampleFormat - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.SamplesPerPixel - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.SMaxSampleValue - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.SMinSampleValue - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.Software - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.StripByteCounts - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.StripOffsets - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.SubfileType - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.T4Options - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.T6Options - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.TargetPrinter - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.Threshholding - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.TileByteCounts - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.TileLength - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.TileOffsets - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.TileWidth - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.TransferFunction - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.TransferRange - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.WhitePoint - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.XPosition - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.XResolution - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.YCbCrCoefficients - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.YCbCrPositioning - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.YCbCrSubSampling - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.YPosition - Class in com.sun.media.imageio.plugins.tiff
BaselineTIFFTagSet.YResolution - Class in com.sun.media.imageio.plugins.tiff
BaseMetadata - Interface in loci.formats.meta
baseName - Variable in class loci.formats.in.OIRReader
basename - Variable in class loci.formats.in.ZeissTIFFHandler.Plane
baseReader - Variable in class loci.plugins.in.ImportProcess
baseTiff - Variable in class loci.formats.in.MicromanagerReader.Position
BaseTiffReader - Class in loci.formats.in: BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
BaseTiffReader(String, String) - Constructor for class loci.formats.in.BaseTiffReader: Constructs a new BaseTiffReader.
BaseTiffReader(String, String[]) - Constructor for class loci.formats.in.BaseTiffReader: Constructs a new BaseTiffReader.
BaseZeissReader - Class in loci.formats.in: BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.
BaseZeissReader(String, String) - Constructor for class loci.formats.in.BaseZeissReader: Constructs a new ZeissZVI reader.
BaseZeissReader(String, String[]) - Constructor for class loci.formats.in.BaseZeissReader: Constructs a new ZeissZVI reader.
BaseZeissReader.Charset - Enum in loci.formats.in
BaseZeissReader.Context - Enum in loci.formats.in
BaseZeissReader.DrawStyle - Enum in loci.formats.in: Line drawing styles.
BaseZeissReader.FeatureType - Enum in loci.formats.in: Feature types.
BaseZeissReader.FillStyle - Enum in loci.formats.in: Fill styles.
BaseZeissReader.Layer - Class in loci.formats.in: Layer class representing an AxioVision layer; used to contain a collection of shapes.
BaseZeissReader.LineEndPositions - Enum in loci.formats.in
BaseZeissReader.LineEndStyle - Enum in loci.formats.in: Line ending styles.
BaseZeissReader.PointStyle - Enum in loci.formats.in: Point styles.
BaseZeissReader.Shape - Class in loci.formats.in: Shape class representing the metadata within an AxioVision Shape ROI
BaseZeissReader.Tag - Class in loci.formats.in: Content of a single tag from a Tags block.
BaseZeissReader.TextAlignment - Enum in loci.formats.in
bayerPattern - Variable in class loci.formats.in.MRWReader
bbox - Variable in class loci.formats.in.CellH5Reader
BBOX - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
bBox - Variable in class loci.formats.services.WlzServiceImpl
bbuf - Variable in class jj2000.j2k.codestream.reader.PktHeaderBitReader: The current bit buffer
bbuf - Variable in class jj2000.j2k.entropy.decoder.ByteToBitInput: The bit buffer
bbuf - Variable in class jj2000.j2k.entropy.encoder.BitToByteOutput: The bit buffer
BDReader - Class in loci.formats.in: BDReader is the file format reader for BD Pathway datasets.
BDReader() - Constructor for class loci.formats.in.BDReader: Constructs a new ScanR reader.
BEAM_SPLITTER_FILTER - Static variable in class loci.formats.in.ZeissLSMReader
BEAM_SPLITTER_FILTER_SET - Static variable in class loci.formats.in.ZeissLSMReader
BeamSplitter() - Constructor for class loci.formats.in.ZeissLSMReader.BeamSplitter
BEBufferedRandomAccessFile - Class in jj2000.j2k.io: This class defines a Buffered Random Access File, where all I/O is considered to be big-endian, and extends the BufferedRandomAccessFile class.
BEBufferedRandomAccessFile(File, String, int) - Constructor for class jj2000.j2k.io.BEBufferedRandomAccessFile: Constructor.
BEBufferedRandomAccessFile(File, String) - Constructor for class jj2000.j2k.io.BEBufferedRandomAccessFile: Constructor.
BEBufferedRandomAccessFile(String, String, int) - Constructor for class jj2000.j2k.io.BEBufferedRandomAccessFile: Constructor.
BEBufferedRandomAccessFile(String, String) - Constructor for class jj2000.j2k.io.BEBufferedRandomAccessFile: Constructor.
begin - Variable in class loci.formats.FilePatternBlock
beginDecoding() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: This routine is called prior to a sequence of calls to the decode method, in order to allow any necessary tables or other structures to be initialized based on metadata values.
beginDecoding() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor: Invokes the superclass method and then sets instance variables on the basis of the metadata set on this decompressor.
beginDecoding() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
beginDecoding() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullDecompressor
beginDecoding() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
BETA - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7: The value of the second lifting step coefficient
BETA - Static variable in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7: The value of the second lifting step coefficient
BEZIER_WITH_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
BF - Class in loci.plugins: Miscellaneous plugins utility methods.
BF() - Constructor for class loci.plugins.BF
bf_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor: output destination for bit codes
BFVirtualStack - Class in loci.plugins.util: Subclass of VirtualStack that uses Bio-Formats to read planes on demand.
BFVirtualStack(String, IFormatReader, boolean, boolean, boolean) - Constructor for class loci.plugins.util.BFVirtualStack
BGR - Static variable in class loci.formats.in.CellSensReader
BGR_24 - Static variable in class loci.formats.in.ZeissCZIReader
BGR_48 - Static variable in class loci.formats.in.ZeissCZIReader
BGR_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
BGRA_8 - Static variable in class loci.formats.in.ZeissCZIReader
bgrToRgb(byte[], boolean, int, int) - Static method in class loci.formats.ImageTools
BH_HEADER_CHKSUM - Static variable in class loci.formats.in.SDTInfo
BH_HEADER_NOT_VALID - Static variable in class loci.formats.in.SDTInfo
BH_HEADER_VALID - Static variable in class loci.formats.in.SDTInfo
bi - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader: The destination image.
bi - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader: The destination image.
BI_BITFIELDS - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
BI_JPEG - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
BI_PNG - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
BI_RGB - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
BI_RLE4 - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
BI_RLE8 - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
BIFormatReader - Class in loci.formats.in: BIFormatReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.
BIFormatReader(String, String) - Constructor for class loci.formats.in.BIFormatReader: Constructs a new BIFormatReader.
BIFormatReader(String, String[]) - Constructor for class loci.formats.in.BIFormatReader: Constructs a new BIFormatReader.
BIG - Static variable in class loci.formats.tiff.TiffConstants
BIG_ENDIAN - Static variable in interface jj2000.j2k.io.EndianType: Identifier for big-endian byte ordering (i.e.
BIG_TIFF - Static variable in class loci.formats.tiff.IFD
BIG_TIFF_BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants: The number of bytes in each IFD entry of a BigTIFF file.
BIG_TIFF_CUTOFF - Static variable in class loci.formats.out.TiffWriter: Number of bytes at which to automatically switch to BigTIFF This is approximately 3.9 GB instead of 4 GB, to allow space for the IFDs.
BIG_TIFF_MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
BIG_TIFF_SUFFIXES - Static variable in class loci.formats.out.TiffWriter
bigEndianString - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
bigEndianTransferSyntax - Variable in class loci.formats.in.DicomReader
bigTiff - Variable in class loci.formats.tiff.TiffParser: Whether or not the TIFF file contains BigTIFF data.
bigTiff - Variable in class loci.formats.tiff.TiffSaver: Whether or not to write BigTIFF data.
bin - Variable in class jj2000.j2k.codestream.reader.PktDecoder: The wrapper to read bits for the packet heads
bin - Variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder: The bit based input for arithmetic coding bypass (i.e.
bin - Variable in class loci.formats.in.InCellReader
binary - Variable in class loci.formats.in.EPSReader: Flag indicating binary data.
BINARY_SETUP - Static variable in class loci.formats.in.SDTInfo
BinaryDataInput - Interface in jj2000.j2k.io: This interface defines the input of binary data from streams and/or files.
BinaryDataOutput - Interface in jj2000.j2k.io: This interface defines the output of binary data to streams and/or files.
binData - Variable in class loci.formats.in.OMEXMLReader
BinData(int, int) - Constructor for class loci.formats.in.OMEXMLReader.BinData
binDataOffsets - Variable in class loci.formats.in.OMEXMLReader
binning - Variable in class loci.formats.in.BDReader
binning - Variable in class loci.formats.in.BioRadSCNReader
binning - Variable in class loci.formats.in.MetamorphHandler
binning - Variable in class loci.formats.in.MetamorphReader
binning - Variable in class loci.formats.in.MicromanagerReader.Position
binning - Variable in class loci.formats.in.ND2Handler
binning - Variable in class loci.formats.in.PCIReader
binning - Variable in class loci.formats.in.SimplePCITiffReader
binning - Variable in class loci.formats.in.ZeissLSMReader
binning - Variable in class loci.formats.in.ZeissLSMReader.Recording
binnings - Variable in class loci.formats.in.FlexReader
binnings - Variable in class loci.formats.in.ZeissCZIReader
binningX - Variable in class loci.formats.in.CellSensReader.Pyramid
binningY - Variable in class loci.formats.in.CellSensReader.Pyramid
binSize - Variable in class loci.formats.in.SPCReader
binX - Variable in class loci.formats.in.FlexReader: Camera binning values.
binX - Variable in class loci.formats.in.IvisionReader
binY - Variable in class loci.formats.in.FlexReader: Camera binning values.
binY - Variable in class loci.formats.in.IvisionReader
BioFormatsExtensionPrinter - Class in loci.formats.tools: This class is used to generate a text file containing all of the image file extensions supported by Bio-Formats.
BioFormatsExtensionPrinter() - Constructor for class loci.formats.tools.BioFormatsExtensionPrinter
BioRadGelReader - Class in loci.formats.in: BioRadGelReader is the file format reader for Bio-Rad gel files.
BioRadGelReader() - Constructor for class loci.formats.in.BioRadGelReader: Constructs a new Bio-Rad gel reader.
BioRadHandler() - Constructor for class loci.formats.in.BioRadReader.BioRadHandler
BioRadReader - Class in loci.formats.in: BioRadReader is the file format reader for Bio-Rad PIC files.
BioRadReader() - Constructor for class loci.formats.in.BioRadReader: Constructs a new BioRadReader.
BioRadReader.BioRadHandler - Class in loci.formats.in: SAX handler for parsing XML.
BioRadReader.Note - Class in loci.formats.in
BioRadSCNReader - Class in loci.formats.in: BioRadSCNReader is the reader for Bio-Rad .scn files
BioRadSCNReader() - Constructor for class loci.formats.in.BioRadSCNReader: Constructs a new Bio-Rad .scn reader.
BioRadSCNReader.SCNHandler - Class in loci.formats.in
biReader - Variable in class loci.formats.gui.DataConverter
bit - Variable in class loci.formats.codec.BitWriter: Deprecated.

Bit index into current byte of the buffer.
BIT - Static variable in class loci.formats.FormatTools: Identifies the BIT data type used to store pixel values.
BIT_DEPTH - Static variable in class loci.formats.in.CellSensReader
BitBuffer - Class in loci.formats.codec: Deprecated.
Use loci.common.RandomAccessInputStream instead
BitBuffer(byte[]) - Constructor for class loci.formats.codec.BitBuffer: Deprecated.

Default constructor.
bitDepth - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox
bitDepth - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox
bitDepth - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
bitDepth - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
bitDepth - Variable in class loci.formats.in.CellSensReader.Pyramid
bitDepths - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader: Various bit depth
bitDepthScale - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
BitFile - Class in com.sun.media.imageioimpl.common: Came from GIFEncoder initially.
BitFile(ImageOutputStream, boolean) - Constructor for class com.sun.media.imageioimpl.common.BitFile
bitmapFileSize - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
bitmapOffset - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
BITMASK_COMPRESSION - Static variable in class loci.formats.in.FlowSightReader
bitMasks - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
BitOutputBuffer - Class in jj2000.j2k.codestream.writer: This class implements a buffer for writing bits, with the required bit stuffing policy for the packet headers.
BitOutputBuffer() - Constructor for class jj2000.j2k.codestream.writer.BitOutputBuffer: Creates a new BitOutputBuffer width a buffer of length 'SZ_INIT'.
bitPointer - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
bitPos - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
bits - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor: Output bit buffer.
bits - Variable in class loci.formats.in.TargaReader
BITS_ALLOCATED - Static variable in class loci.formats.in.DicomReader
BITS_PER_COMPONENT_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
BITS_PER_SAMPLE - Static variable in class loci.formats.tiff.IFD
bitsLeft_ - Variable in class com.sun.media.imageioimpl.common.BitFile
BitsPerComponentBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000: This class is defined to represent a Bits Per Component Box of JPEG JP2 file format.
BitsPerComponentBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.BitsPerComponentBox: Counstructs a BitsPerComponentBox from the provided byte array containing the bit depths of each color component.
BitsPerComponentBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.BitsPerComponentBox: Constructs a BitsPerComponentBox based on the provide org.w3c.dom.Node.
bitsPerPixel - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
bitsPerPixel - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
bitsPerPixel - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
bitsPerPixel - Variable in class loci.formats.CoreMetadata: Number of valid bits per pixel.
bitsPerPixel - Variable in class loci.formats.in.DicomReader: Bits per pixel.
bitsPerPixel - Variable in class loci.formats.in.NativeQTReader: Pixel depth.
BitsPerSample() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.BitsPerSample
bitsPerSample - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: The value of the BitsPerSample tag.
bitsPerSample - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
bitsPerSample - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
bitsPerSample - Variable in class loci.formats.codec.CodecOptions: Number of bits per channel.
bitsPerSampleCache - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
bitsPerScanline - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
bitsToGet - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
bitsToGet - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
BitstreamReaderAgent - Class in jj2000.j2k.codestream.reader: This is the generic interface for bit stream reader agents.
BitstreamReaderAgent(HeaderDecoder, DecoderSpecs) - Constructor for class jj2000.j2k.codestream.reader.BitstreamReaderAgent: Initializes members of this class.
BitToByteOutput - Class in jj2000.j2k.entropy.encoder: This class provides an adapter to perform bit based output on byte based output objects that inherit from a 'ByteOutputBuffer' class.
BitToByteOutput(ByteOutputBuffer) - Constructor for class jj2000.j2k.entropy.encoder.BitToByteOutput: Instantiates a new 'BitToByteOutput' object that uses 'out' as the underlying byte based output.
BitWriter - Class in loci.formats.codec: Deprecated.
Use loci.common.RandomAccessOutputStream instead
BitWriter() - Constructor for class loci.formats.codec.BitWriter: Deprecated.

Constructs a new bit writer.
BitWriter(int) - Constructor for class loci.formats.codec.BitWriter: Deprecated.

Constructs a new bit writer with the given initial buffer size.
biWriter - Variable in class loci.formats.gui.DataConverter
bizarreMultichannelAcquisition - Variable in class loci.formats.in.MetamorphReader
BLACK - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor: The CCITT numerical definition of black.
black - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
blank(byte[]) - Method in class loci.formats.in.PrairieReader: Blanks out and returns the given buffer.
blankImage(int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Creates a blank image with the given dimensions and transfer type.
blankThumbBytes - Variable in class loci.formats.FileStitcher.ExternalSeries
BlkImgDataSrc - Interface in jj2000.j2k.image: This interface defines the methods to transfer image data in blocks, without following any particular order (random access).
block - Variable in class loci.formats.FilePatternBlock: String representation of this block.
block0 - Variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf: Block used to request component with index 0
block0 - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf: Block used to request component 0
block1 - Variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf: Block used to request component with index 1
block1 - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf: Block used to request component 1
block2 - Variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf: Block used to request component with index 2
block2 - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf: Block used to request component 2
BLOCK_END - Static variable in class loci.formats.FilePatternBlock: Identifies the end of a block.
BLOCK_START - Static variable in class loci.formats.FilePatternBlock: Identifies the start of a block.
blockAligned - Variable in class jj2000.j2k.roi.encoder.ROIScaler: Flag indicating if block aligned ROIs are used
blockData - Variable in class loci.formats.in.ZeissLSMReader.SubBlock
blockLength - Variable in class loci.formats.in.APNGReader.PNGInputStream
blockLength - Variable in class loci.formats.in.PQBinReader: No of timeBins pre-loaded as a block
blockLength - Variable in class loci.formats.in.SDTInfo: reserved2 now contains block (set) length.
blockLength - Variable in class loci.formats.in.SDTReader: No of timeBins pre-loaded as a block
blockNo - Variable in class loci.formats.in.SDTInfo: Number of the block in the file.
blockPointer - Variable in class loci.formats.in.APNGReader.PNGInputStream
blocks - Variable in class loci.formats.FilePattern: List of pattern blocks for this file pattern.
blocks - Variable in class loci.formats.in.APNGReader
blocks_ - Variable in class com.sun.media.imageioimpl.common.BitFile: note this also indicates gif format BITFile.
blockSize - Variable in class loci.formats.in.GIFReader: Block size.
blockSize - Variable in class loci.formats.in.VolocityReader.Stack
blocksPerPlane - Variable in class loci.formats.in.OIRReader
blockType - Variable in class loci.formats.in.APNGReader.PNGInputStream
blockType - Variable in class loci.formats.in.SDTInfo: See blockType defines below.
blue - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
blue - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
BLUE_GAIN - Static variable in class loci.formats.in.CellSensReader
BLUE_MIN - Static variable in class loci.plugins.in.Colorizer
BLUE_OFFSET - Static variable in class loci.formats.in.CellSensReader
BLUE_TO_GREEN_MIN - Static variable in class loci.plugins.in.Colorizer
blueGain - Variable in class loci.formats.in.CellSensReader.Pyramid
blueMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
blueMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
blueOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
blueOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
blueShort - Variable in class loci.formats.gui.Index16ColorModel: Lookup tables.
blueX - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
blueY - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
blueZ - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
BMP - Static variable in class loci.formats.in.CellSensReader
BMP_MAGIC_STRING - Static variable in class loci.formats.in.BMPReader
bmpBitsPerPixel - Variable in class loci.formats.in.AVIReader
bmpColorsUsed - Variable in class loci.formats.in.AVIReader
bmpCompression - Variable in class loci.formats.in.AVIReader
BMPConstants - Interface in com.sun.media.imageioimpl.plugins.bmp
BMPImageReader - Class in com.sun.media.imageioimpl.plugins.bmp: This class is the Java Image IO plugin reader for BMP images.
BMPImageReader(ImageReaderSpi) - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader: Constructs BMPImageReader from the provided ImageReaderSpi.
BMPImageReader.EmbeddedProgressAdapter - Class in com.sun.media.imageioimpl.plugins.bmp
BMPImageReaderSpi - Class in com.sun.media.imageioimpl.plugins.bmp
BMPImageReaderSpi() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
BMPImageWriteParam - Class in com.sun.media.imageio.plugins.bmp: A subclass of ImageWriteParam for encoding images in the BMP format.
BMPImageWriteParam(Locale) - Constructor for class com.sun.media.imageio.plugins.bmp.BMPImageWriteParam: Constructs a BMPImageWriteParam set to use a given Locale and with default values for all parameters.
BMPImageWriteParam() - Constructor for class com.sun.media.imageio.plugins.bmp.BMPImageWriteParam: Constructs an BMPImageWriteParam object with default values for all parameters and a null Locale.
BMPImageWriter - Class in com.sun.media.imageioimpl.plugins.bmp: The Java Image IO plugin writer for encoding a binary RenderedImage into a BMP format.
BMPImageWriter(ImageWriterSpi) - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter: Constructs BMPImageWriter based on the provided ImageWriterSpi.
BMPImageWriter.IIOWriteProgressAdapter - Class in com.sun.media.imageioimpl.plugins.bmp
BMPImageWriterSpi - Class in com.sun.media.imageioimpl.plugins.bmp
BMPImageWriterSpi() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
BMPMetadata - Class in com.sun.media.imageioimpl.plugins.bmp
BMPMetadata() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
BMPMetadata(IIOMetadata) - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
BMPMetadataFormat - Class in com.sun.media.imageioimpl.plugins.bmp
BMPMetadataFormat() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPMetadataFormat
BMPMetadataFormatResources - Class in com.sun.media.imageioimpl.plugins.bmp
BMPMetadataFormatResources() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPMetadataFormatResources
BMPReader - Class in loci.formats.in: BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
BMPReader() - Constructor for class loci.formats.in.BMPReader: Constructs a new BMP reader.
bmpScanLineSize - Variable in class loci.formats.in.AVIReader
bmpVersion - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
bmpWidth - Variable in class loci.formats.in.AVIReader
bms - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder: By-pass mode specifications
BogusColorSpace - Class in com.sun.media.imageioimpl.common: A dummy ColorSpace to enable ColorModel for image data which do not have an innate color representation.
BogusColorSpace(int) - Constructor for class com.sun.media.imageioimpl.common.BogusColorSpace: Constructs a bogus ColorSpace.
bold - Variable in class loci.formats.in.BaseZeissReader.Shape
BOOLEAN - Static variable in class loci.formats.in.CellSensReader
BooleanIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.BooleanIM3Record
BooleanOption - Class in loci.plugins.prefs: A boolean option for one of the plugins.
BooleanOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.BooleanOption: Constructs a boolean option with the parameters from the given map.
BooleanOption(String, boolean, String, String, boolean) - Constructor for class loci.plugins.prefs.BooleanOption: Constructs a boolean option with the given parameters.
BORDER - Static variable in class loci.plugins.shortcut.ShortcutPanel: Number of pixels for window border.
bordL - Variable in class loci.formats.in.SDTInfo
bordU - Variable in class loci.formats.in.SDTInfo
boundValues - Variable in class loci.formats.services.MDBServiceImpl
boutT - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder: The raw bit output used, for each thread
Box - Class in com.sun.media.imageioimpl.plugins.jpeg2000: This class is defined to create the box of JP2 file format.
Box(int, int, byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.Box: Constructs a Box instance using the provided the box type and the box content in byte array format.
Box(int, int, long, byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.Box: Constructs a Box instance using the provided the box type, the box extra length, and the box content in byte array format.
Box(ImageInputStream, int) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.Box: Constructs a Box instance from the provided ImageInputStream at the specified position.
Box(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.Box: Constructs a Box from an "unknown" Node.
BOX_SIZE - Static variable in class loci.formats.in.FakeReader
boxClasses - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.Box: A Hashtable contains the class names for each type of the boxes.
boxes - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata: The boxes of JP2 file used as meta data, i.
boxes - Variable in class loci.plugins.in.SeriesDialog
bpc - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter: Bits per component
BPC_LENGTH - Static variable in class jj2000.j2k.fileformat.writer.FileFormatWriter: base length of Bits Per Component box
bpcVaries - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter: Flag indicating whether number of bits per component varies
bpixels - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
bpos - Variable in class jj2000.j2k.codestream.reader.PktHeaderBitReader: The position of the next bit to read in the bit buffer (0 means empty, 8 full)
bpos - Variable in class jj2000.j2k.entropy.decoder.ByteToBitInput: The position of the next bit to get from the byte buffer.
bpos - Variable in class jj2000.j2k.entropy.encoder.BitToByteOutput: The position of the next bit to put in the bit buffer.
bpp - Variable in class loci.formats.in.BaseZeissReader: Number of bytes per pixel.
bpp - Variable in class loci.formats.in.BMPReader: Number of bits per pixel.
bpp - Variable in class loci.formats.in.MIASReader
bpp - Variable in class loci.formats.in.SPCReader
bpp - Variable in class loci.formats.out.CellH5Writer
branch - Variable in class loci.formats.codec.HuffmanCodec.Decoder
brand - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox: The element values.
breader - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
BRIGHT_FIELD - Static variable in class loci.formats.in.LegacyND2Reader
BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
BRIGHTNESS_VALUE - Static variable in class loci.formats.tiff.IFD
BrightnessValue() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.BrightnessValue
brokenNotes - Variable in class loci.formats.in.BioRadReader
BrowserOptionsWindow - Class in loci.plugins.util: Extension of JFrame that allows the user to adjust caching settings.
BrowserOptionsWindow(String, Cache, String[]) - Constructor for class loci.plugins.util.BrowserOptionsWindow
BrukerReader - Class in loci.formats.in: BrukerReader is the file format reader for Bruker MRI files.
BrukerReader() - Constructor for class loci.formats.in.BrukerReader: Constructs a new Bruker reader.
bsWriter - Variable in class jj2000.j2k.entropy.encoder.PostCompRateAllocator: The bit-stream writer
buf - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc: The line buffer.
buf - Variable in class jj2000.j2k.codestream.writer.BitOutputBuffer: The buffer where we store the data
buf - Variable in class jj2000.j2k.entropy.decoder.ByteInputBuffer: The byte array containing the data
buf - Variable in class jj2000.j2k.entropy.encoder.ByteOutputBuffer: The buffer where the data is stored
buf - Variable in class jj2000.j2k.image.input.ImgReaderPGM: The line buffer.
buf - Variable in class jj2000.j2k.util.ISRandomAccessIO
buf - Variable in class loci.formats.codec.BitWriter: Deprecated.

Buffer storing all bits written thus far.
BUF_DEF_LEN - Static variable in class jj2000.j2k.entropy.encoder.ByteOutputBuffer: The default initial buffer size
BUF_INC - Static variable in class jj2000.j2k.entropy.encoder.ByteOutputBuffer: The buffer increase size
buffer - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
buffer_ - Variable in class com.sun.media.imageioimpl.common.BitFile
BUFFER_SIZE - Static variable in class loci.formats.in.NativeND2Reader
BUFFER_SIZE - Static variable in class loci.formats.in.ZeissCZIReader
BufferedImageReader - Class in loci.formats.gui: A reader wrapper for reading image planes as BufferedImage objects.
BufferedImageReader() - Constructor for class loci.formats.gui.BufferedImageReader: Constructs a BufferedImageReader around a new image reader.
BufferedImageReader(IFormatReader) - Constructor for class loci.formats.gui.BufferedImageReader: Constructs a BufferedImageReader with the given reader.
BufferedImageSource - Class in loci.formats.gui: Retrieves BufferedImages from a data source using Bio-Formats.
BufferedImageSource(IFormatReader) - Constructor for class loci.formats.gui.BufferedImageSource
BufferedImageWriter - Class in loci.formats.gui: A writer wrapper for writing image planes from BufferedImage objects.
BufferedImageWriter() - Constructor for class loci.formats.gui.BufferedImageWriter: Constructs a BufferedImageWriter around a new image writer.
BufferedImageWriter(IFormatWriter) - Constructor for class loci.formats.gui.BufferedImageWriter: Constructs a BufferedImageWriter with the given writer.
BufferedRandomAccessFile - Class in jj2000.j2k.io: This class defines a Buffered Random Access File.
BufferedRandomAccessFile(File, String, int) - Constructor for class jj2000.j2k.io.BufferedRandomAccessFile: Constructor.
BufferedRandomAccessFile(File, String) - Constructor for class jj2000.j2k.io.BufferedRandomAccessFile: Constructor.
BufferedRandomAccessFile(String, String, int) - Constructor for class jj2000.j2k.io.BufferedRandomAccessFile: Constructor.
BufferedRandomAccessFile(String, String) - Constructor for class jj2000.j2k.io.BufferedRandomAccessFile: Constructor.
bufLength - Variable in class loci.formats.in.SPCReader
bufSize(int, int, int) - Static method in class org.libjpegturbo.turbojpeg.TJ: Returns the maximum size of the buffer (in bytes) required to hold a JPEG image with the given width and height, and level of chrominance subsampling.
bufSizeYUV(int, int, int) - Static method in class org.libjpegturbo.turbojpeg.TJ: Returns the size of the buffer (in bytes) required to hold a YUV planar image with the given width, height, and level of chrominance subsampling.
bugaddr - Static variable in class jj2000.j2k.JJ2KInfo: The bug reporting e-mail address
buildAndWriteLayers() - Method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator: This method builds all the bit stream layers and then writes them to the output bit stream.
BUILDER - Static variable in class loci.formats.meta.OriginalMetadataAnnotation
buildExtensions() - Method in class loci.plugins.macro.MacroFunctions: Builds the list of extensions, using reflection, from public methods of this class.
buildFileChooser(IFormatHandler) - Static method in class loci.formats.gui.GUITools: Constructs a file chooser for the given file format handler.
buildFileChooser(IFormatHandler, boolean) - Static method in class loci.formats.gui.GUITools: Constructs a file chooser for the given file format handler.
buildFileChooser(FileFilter[]) - Static method in class loci.formats.gui.GUITools: Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter.
buildFileChooser(FileFilter[], boolean) - Static method in class loci.formats.gui.GUITools: Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter, if one is not already specified.
buildFileFilters(IFormatHandler) - Static method in class loci.formats.gui.GUITools: Constructs a list of file filters for the given file format handler.
buildFiles(String, int, List<String>) - Method in class loci.formats.FilePattern
buildPalette() - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
buildTIFFList(int) - Method in class loci.formats.in.MicromanagerReader
buildTIFFList(int, String) - Method in class loci.formats.in.MicromanagerReader: Populate the list of TIFF files using the given file name as a pattern.
buildTime - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator: The wall time for the building of layers.
buildTypes() - Static method in class loci.formats.in.DicomReader: Assemble the data dictionary.
BurleighReader - Class in loci.formats.in: BurleighReader is the file format reader for Burleigh .img files.
BurleighReader() - Constructor for class loci.formats.in.BurleighReader: Constructs a new Burleigh reader.
bypass - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava: Uses the lazy coding mode with the entropy coder.
BYTE - Static variable in class loci.formats.in.GatanReader
BYTE_COUNT_OFFSET - Static variable in class loci.formats.out.QTWriter: Seek to this offset to update the total number of pixel bytes.
byteArraySet(byte[], byte) - Static method in class jj2000.j2k.util.ArrayUtil: Reinitializes a byte array to the given value in an optimized way.
ByteArraySource - Class in loci.formats.cache: Retrieves byte arrays from a data source (e.g., a file) using Bio-Formats.
ByteArraySource(IFormatReader) - Constructor for class loci.formats.cache.ByteArraySource: Constructs a byte array source from the given Bio-Formats reader.
ByteArraySource(String) - Constructor for class loci.formats.cache.ByteArraySource: Constructs a byte array source that draws from the given file.
bytebuf - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
byteBuffer - Variable in class com.sun.media.imageio.stream.FileChannelImageOutputStream: A ByteBuffer used for writing to the channel.
byteBuffer - Variable in class jj2000.j2k.io.BufferedRandomAccessFile: Buffer of bytes containing the part of the file that is currently being accessed
byteBuffer - Variable in class loci.formats.codec.BitBuffer: Deprecated.
byteBufferChanged - Variable in class jj2000.j2k.io.BufferedRandomAccessFile: Boolean keeping track of whether the byte buffer has been changed since it was read.
byteCount - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: The number of bytes of data from the source ImageInputStream to be decompressed.
byteIn() - Method in class jj2000.j2k.entropy.decoder.MQDecoder: This function gets one byte of compressed bits from the in-stream.
ByteInputBuffer - Class in jj2000.j2k.entropy.decoder: This class provides a byte input facility from byte buffers.
ByteInputBuffer(byte[]) - Constructor for class jj2000.j2k.entropy.decoder.ByteInputBuffer: Creates a new byte array input stream that reads data from the specified byte array.
ByteInputBuffer(byte[], int, int) - Constructor for class jj2000.j2k.entropy.decoder.ByteInputBuffer: Creates a new byte array input stream that reads data from the specified byte array.
byteOrder - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
byteOrder - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
byteOrder - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
byteOrder - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
byteOrdering - Variable in class jj2000.j2k.io.BufferedRandomAccessFile
byteOut() - Method in class jj2000.j2k.entropy.encoder.MQCoder: This function puts one byte of compressed bits in the out out stream.
ByteOutputBuffer - Class in jj2000.j2k.entropy.encoder: This class provides a buffering output stream similar to ByteArrayOutputStream, with some additional methods.
ByteOutputBuffer() - Constructor for class jj2000.j2k.entropy.encoder.ByteOutputBuffer: Creates a new byte array output stream.
ByteOutputBuffer(int) - Constructor for class jj2000.j2k.entropy.encoder.ByteOutputBuffer: Creates a new byte array output stream, with a buffer capacity of the specified size, in bytes.
bytePointer - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
bytes - Variable in class loci.formats.in.OBFReader.Frame
bytes - Variable in class loci.formats.tiff.TiffSaver: Output bytes.
BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants: The number of bytes in each IFD entry.
bytesFromReader(IFormatReader) - Method in class loci.formats.Memoizer.RandomAccessDeser
bytesPerAxis - Variable in class loci.formats.in.LeicaHandler
bytesPerElement - Variable in enum loci.formats.tiff.IFDType: Number of bytes per element of this type.
bytesPerLine - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
bytesPerLine - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
bytesPerLine - Variable in class loci.formats.in.PCXReader: Number of bytes per scan line - may be different than image width.
bytesPerPixel - Variable in class loci.formats.in.AmiraReader.ASCII
bytesPerPixel - Variable in class loci.formats.in.OpenlabRawReader: Number of bytes per pixel.
bytesPerPixel - Variable in class loci.formats.out.AVIWriter
bytesPerPlane - Variable in class loci.formats.in.AVIReader
byteTable - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
ByteToBitInput - Class in jj2000.j2k.entropy.decoder: This class provides an adapter to perform bit based input on byte based output obejcts that inherit from a 'ByteInputBuffer' class.
ByteToBitInput(ByteInputBuffer) - Constructor for class jj2000.j2k.entropy.decoder.ByteToBitInput: Instantiates a new 'ByteToBitInput' object that uses 'in' as the underlying byte based input.
byteValue() - Method in class loci.formats.tiff.TiffRational: Returns the value of the specified number as a byte.
ByteVector - Class in loci.formats.codec: A growable array of bytes.
ByteVector() - Constructor for class loci.formats.codec.ByteVector
ByteVector(int) - Constructor for class loci.formats.codec.ByteVector
ByteVector(byte[]) - Constructor for class loci.formats.codec.ByteVector

C

c - Variable in class jj2000.j2k.entropy.decoder.MQDecoder: The current bit code
c - Variable in class jj2000.j2k.entropy.encoder.MQCoder: The current bit code
c - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor: The component on which to compress
C - Static variable in class loci.formats.in.CellSensReader
c - Variable in class loci.formats.in.LeicaSCNReader.Dimension
c - Variable in class loci.formats.in.MicromanagerReader.Index
c - Variable in class loci.formats.in.OperettaReader.Plane
c - Variable in class loci.formats.tools.AmiraParameters
C01_MAGIC_BYTES - Static variable in class loci.formats.in.CellomicsReader
C_AXIS - Static variable in class loci.formats.AxisGuesser: Axis type for channels.
C_KEY - Static variable in class loci.formats.in.LiFlimReader
C_PREFIXES - Static variable in class loci.formats.AxisGuesser: Prefixes indicating channel dimension.
C_STRING - Static variable in class loci.formats.in.SDTInfo
Cache - Class in loci.formats.cache: Cache provides a means of managing subsets of large collections of image planes in memory.
Cache(ICacheStrategy, ICacheSource, boolean) - Constructor for class loci.formats.cache.Cache: Constructs an object cache with the given cache strategy and source.
cache - Variable in class loci.formats.cache.Cache: Master array containing cached objects.
cache - Variable in class loci.formats.cache.CacheUpdater
cache - Variable in class loci.formats.gui.CacheComponent: The cache that this component controls.
cache - Variable in class loci.formats.gui.CacheIndicator
cache - Variable in class loci.plugins.util.BFVirtualStack
CacheComponent - Class in loci.formats.gui: GUI component for managing a cache.
CacheComponent(Cache, String[]) - Constructor for class loci.formats.gui.CacheComponent: Creates a cache GUI component.
CacheComponent(Cache, String[], String) - Constructor for class loci.formats.gui.CacheComponent: Creates a cache GUI component with the ability to change between the various source types (mainly for debugging purposes).
CacheConsole - Class in loci.formats.tools: CacheConsole provides an interactive interpreter for testing the Bio-Formats caching implementation.
CacheConsole() - Constructor for class loci.formats.tools.CacheConsole
cachedDecoders - Variable in class loci.formats.codec.HuffmanCodec
cachedTileBuffer - Variable in class loci.formats.in.MIASReader: Cached tile buffer to avoid re-allocations when reading tiles.
cachedTileBuffer - Variable in class loci.formats.tiff.TiffParser: Cached tile buffer to avoid re-allocations when reading tiles.
CacheEvent - Class in loci.formats.cache: A event indicating a cache update.
CacheEvent(Object, int) - Constructor for class loci.formats.cache.CacheEvent: Constructs a cache event.
CacheEvent(Object, int, int) - Constructor for class loci.formats.cache.CacheEvent: Constructs a cache event.
CacheException - Exception in loci.formats.cache: CacheException is the exception thrown when something goes wrong performing a cache operation.
CacheException() - Constructor for exception loci.formats.cache.CacheException
CacheException(String) - Constructor for exception loci.formats.cache.CacheException
CacheException(String, Throwable) - Constructor for exception loci.formats.cache.CacheException
CacheException(Throwable) - Constructor for exception loci.formats.cache.CacheException
CacheIndicator - Class in loci.formats.gui: Indicator GUI component showing which planes are currently in the cache for a given dimensional axis at a particular dimensional position.
CacheIndicator(Cache, int) - Constructor for class loci.formats.gui.CacheIndicator: Creates a new cache indicator for the given cache.
CacheIndicator(Cache, int, Component, int, int) - Constructor for class loci.formats.gui.CacheIndicator: Creates a new cache indicator.
CacheListener - Interface in loci.formats.cache: A listener for cache updates.
CacheReporter - Interface in loci.formats.cache: Interface for components capable of reporting cache updates.
CacheSource - Class in loci.formats.cache: Superclass of cache sources that retrieve image planes from a data source (e.g., a file) using Bio-Formats.
CacheSource(IFormatReader) - Constructor for class loci.formats.cache.CacheSource: Constructs a cache source from the given Bio-Formats reader.
CacheSource(String) - Constructor for class loci.formats.cache.CacheSource: Constructs a cache source that draws from the given file.
CacheStrategy - Class in loci.formats.cache: Superclass of cache strategies.
CacheStrategy(int[]) - Constructor for class loci.formats.cache.CacheStrategy: Constructs a cache strategy.
cacheUpdated(CacheEvent) - Method in interface loci.formats.cache.CacheListener: Called when cache is updated.
cacheUpdated(CacheEvent) - Method in class loci.formats.gui.CacheComponent: Updates GUI to match latest cache state.
cacheUpdated(CacheEvent) - Method in class loci.formats.gui.CacheIndicator
CacheUpdater - Class in loci.formats.cache: Thread responsible for updating the cache (loading and dropping planes) in the background.
CacheUpdater(Cache) - Constructor for class loci.formats.cache.CacheUpdater
calcBasisWaveForms(float[][]) - Method in class jj2000.j2k.wavelet.analysis.SubbandAn: Calculates the basis waveform of the first leaf for which the L2-norm has not been calculated yet.
calcL2Norms() - Method in class jj2000.j2k.wavelet.analysis.SubbandAn: Calculates the L2-norm of the sythesis waveforms of every leaf in the tree.
calcMaxMagBits(J2KImageWriteParamJava) - Method in class jj2000.j2k.roi.encoder.ROIScaler: Calculates the maximum amount of magnitude bits for each tile-component, and stores it in the 'maxMagBits' array.
calcMixedBitDepths(int[], int, int[]) - Static method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf: Calculates the bitdepths of the transformed components, given the bitdepth of the un-transformed components and the component tranformation type.
calcMixedBitDepths(int[], int, int[]) - Static method in class jj2000.j2k.image.invcomptransf.InvCompTransf: Calculates the bitdepths of the transformed components, given the bitdepth of the un-transformed components and the component tranformation type.
calcPhotons - Variable in class loci.formats.in.SDTInfo: No of photons.
calcSbParams(SubbandAn, int) - Method in class jj2000.j2k.quantization.quantizer.Quantizer: Calculates the parameters of the SubbandAn objects that depend on the Quantizer.
calcSbParams(SubbandAn, int) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer: Calculates the parameters of the SubbandAn objects that depend on the Quantizer.
calcSkipMSBP(CBlkWTData, int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder: Calculates the number of magnitude bit-planes that are to be skipped, because they are non-significant.
calculateDimensions() - Method in class loci.formats.in.ZeissCZIReader
calculateDimensions(int, boolean) - Method in class loci.formats.in.ZeissCZIReader
CALIBRATION - Static variable in class loci.formats.in.OpenlabReader
calibrationTable - Variable in class loci.plugins.util.BFVirtualStack
calibrationUnit - Variable in class loci.formats.in.TiffReader
Calibrator - Class in loci.plugins.in: Logic for calibrating images.
Calibrator(ImportProcess) - Constructor for class loci.plugins.in.Calibrator
callLegacyReader() - Method in class loci.formats.DelegateReader
CAMERA_GAIN - Static variable in class loci.formats.in.CellSensReader
CAMERA_GAMMA - Static variable in class loci.formats.in.CellSensReader
CAMERA_OFFSET - Static variable in class loci.formats.in.CellSensReader
CAMERA_SERIAL_SETTING - Static variable in class loci.formats.in.FluoviewReader
cameraIDs - Variable in class loci.formats.in.FlexReader
cameraMode - Variable in class loci.formats.in.MicromanagerReader.Position
cameraModel - Variable in class loci.formats.in.ND2Handler
cameraName - Variable in class loci.formats.in.SimplePCITiffReader
cameraName - Variable in class loci.formats.in.SISReader
cameraRef - Variable in class loci.formats.in.MicromanagerReader.Position
cameraRefs - Variable in class loci.formats.in.FlexReader
cameraType - Variable in class loci.formats.in.SimplePCITiffReader
CAN_GROUP - Static variable in class loci.formats.FormatTools
CAN_GROUP - Static variable in interface loci.formats.IFormatReader
canAdjustDimensions - Variable in class loci.formats.in.ND2Handler
cancel - Variable in class loci.plugins.in.ImportProcess: Whether the process has been canceled.
cancel() - Method in class loci.plugins.in.ImportProcess: Cancels the import process.
canceled - Variable in class loci.plugins.LociImporter: Flag indicating whether last operation was canceled.
canceled - Variable in class loci.plugins.Slicer: Flag indicating whether last operation was canceled.
canceled - Variable in class loci.plugins.Updater: Flag indicating whether last operation was canceled.
canChangePattern() - Method in class loci.formats.FileStitcher
canCloseReader - Variable in class loci.formats.gui.ImageViewer
canCreatePalette(ImageTypeSpecifier) - Static method in class com.sun.media.imageioimpl.common.PaletteBuilder: Returns true if PaletteBuilder is able to create palette for given image type.
canCreatePalette(RenderedImage) - Static method in class com.sun.media.imageioimpl.common.PaletteBuilder: Returns true if PaletteBuilder is able to create palette for given rendered image.
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReaderSpi
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
canDoQT() - Method in class loci.formats.gui.LegacyQTTools: Whether QuickTime is available to this JVM.
canDoStacks() - Method in class loci.formats.FormatWriter
canDoStacks() - Method in interface loci.formats.IFormatWriter: Reports whether the writer can save multiple images to a single file.
canDoStacks() - Method in class loci.formats.ImageWriter
canDoStacks() - Method in class loci.formats.out.APNGWriter
canDoStacks() - Method in class loci.formats.out.AVIWriter
canDoStacks() - Method in class loci.formats.out.CellH5Writer
canDoStacks() - Method in class loci.formats.out.ICSWriter
canDoStacks() - Method in class loci.formats.out.JavaWriter
canDoStacks() - Method in class loci.formats.out.JPEG2000Writer: Overridden to indicate that stacks are not supported.
canDoStacks() - Method in class loci.formats.out.LegacyQTWriter
canDoStacks() - Method in class loci.formats.out.OMEXMLWriter
canDoStacks() - Method in class loci.formats.out.QTWriter
canDoStacks() - Method in class loci.formats.out.TiffWriter
canDoStacks() - Method in class loci.formats.out.V3DrawWriter
canDoStacks() - Method in class loci.formats.out.WlzWriter
canDoStacks() - Method in class loci.formats.WriterWrapper
canDoUpgradeCheck() - Method in class loci.formats.UpgradeChecker: Return whether or not we are ever allowed to perform an upgrade check.
canEncodeImage(ImageWriter, ImageTypeSpecifier) - Static method in class com.sun.media.imageioimpl.common.ImageUtil: Checks that the provided ImageWriter can encode the provided ImageTypeSpecifier or not.
canEncodeImage(ImageWriter, ColorModel, SampleModel) - Static method in class com.sun.media.imageioimpl.common.ImageUtil: Checks that the provided ImageWriter can encode the provided ColorModel and SampleModel.
canEncodeImage(int, ColorModel, SampleModel) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
canEncodeImage(int, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriterSpi
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
canImport(JComponent, DataFlavor[]) - Method in class loci.plugins.shortcut.ShortcutTransferHandler
canInsertEmpty(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
canInsertImage(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
canLookForND - Variable in class loci.formats.in.MetamorphReader
canMerge() - Method in class loci.formats.ChannelMerger: Determines whether the channels in the file can be merged.
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadataFormat
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadataFormat
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadataFormat
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormat
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadataFormat
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadataFormat
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadataFormat
CANNOT_GROUP - Static variable in class loci.formats.FormatTools
CANNOT_GROUP - Static variable in interface loci.formats.IFormatReader
CANON_TAG - Static variable in class loci.formats.in.DNGReader
CanonRawReader - Class in loci.formats.in: CanonRawReader is the file format reader for Canon RAW files.
CanonRawReader() - Constructor for class loci.formats.in.CanonRawReader: Constructs a new Canon RAW reader.
canParse - Variable in class loci.formats.in.LeicaHandler
canReadAttachments() - Method in class loci.formats.in.ZeissCZIReader
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
canReplacePixels(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
canUseBankDataDirectly(WritableRaster, int, Class<? extends DataBuffer>) - Static method in class loci.formats.gui.AWTImageTools: Whether we can return the data buffer's bank data without performing any copy or conversion operations.
canUsePrevious - Variable in class loci.formats.in.NativeQTReader: Flag indicating whether we can safely use prevPixels.
CANVAS_COLOR_1 - Static variable in class loci.formats.in.CellSensReader
CANVAS_COLOR_2 - Static variable in class loci.formats.in.CellSensReader
canWriteEmpty() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
canWriteRasters() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
canWriteRasters() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
canWriteRasters() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
canWriteRasters() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
canWriteRasters() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
canWriteSequence() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
canWriteSequence() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
CAPTURE_EDITOR_DATA - Static variable in class loci.formats.in.NikonReader
CAPTURE_RESOLUTION_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
cast(Class<?>) - Method in class loci.formats.ClassList: Cast the given class to something that extends the base class.
category - Variable in class loci.formats.in.BaseZeissReader.Tag
category - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
category - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
causalCXInfo - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava: Uses vertically stripe causal context formation.
cb0x - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder: The horizontal code-block partition origin
cb0x - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull: The horizontal coordinate of the code-block partition origin on the reference grid
cb0y - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder: The vertical code-block partition origin
cb0y - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull: The vertical coordinate of the code-block partition on the reference grid
cBegin - Variable in class loci.plugins.in.ImporterOptions
cbI - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent: Array containing info.
cbLength - Variable in class jj2000.j2k.codestream.reader.PktInfo: The length of the code-block in this packet (in bytes)
cblk - Variable in class jj2000.j2k.codestream.PrecInfo: Code-blocks belonging to this precinct in each subbands of the resolution level
CBlkCoordInfo - Class in jj2000.j2k.codestream: This class is used to store the coordinates of code-blocks.
CBlkCoordInfo() - Constructor for class jj2000.j2k.codestream.CBlkCoordInfo: Constructor.
CBlkCoordInfo(int, int) - Constructor for class jj2000.j2k.codestream.CBlkCoordInfo: Constructor.
CBlkInfo - Class in jj2000.j2k.codestream.reader: This class contains location of code-blocks' piece of codewords (there is one piece per layer) and some other information.
CBlkInfo(int, int, int, int, int) - Constructor for class jj2000.j2k.codestream.reader.CBlkInfo: Constructs a new instance with specified number of layers and code-block coordinates.
CBlkQuantDataSrcDec - Interface in jj2000.j2k.quantization.dequantizer: This interface defines a source of quantized wavelet coefficients and methods to transfer them in a code-block by code-block basis, fro the decoder side.
CBlkQuantDataSrcEnc - Interface in jj2000.j2k.quantization.quantizer: This interface defines a source of quantized wavelet coefficients and methods to transfer them in a code-block by code-block basis.
CBlkRateDistStats - Class in jj2000.j2k.entropy.encoder: This class stores coded (compressed) code-blocks with their associated rate-distortion statistics.
CBlkRateDistStats() - Constructor for class jj2000.j2k.entropy.encoder.CBlkRateDistStats: Creates a new CBlkRateDistStats object without allocating any space for 'truncRates', 'truncSlopes', 'truncDists' and 'truncIdxs' or 'data'.
CBlkRateDistStats(int, int, int, byte[], int[], double[], boolean[], int, boolean) - Constructor for class jj2000.j2k.entropy.encoder.CBlkRateDistStats: Creates a new CBlkRateDistStats object and initializes the valid truncation points, their rates and their slopes, from the 'rates' and 'dist' arrays.
cblks - Variable in class jj2000.j2k.codestream.reader.PktDecoder: List of code-blocks found in last read packet head (one list per subband)
cblks - Variable in class jj2000.j2k.decoder.DecoderSpecs: Code-blocks sizes specification
cblks - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator: 5D Array containing all the coded code-blocks: 1st index: tile index 2nd index: component index 3rd index: resolution level index 4th index: subband index 5th index: code-block index
cblks - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder: The code-block size specifications
cblks - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull: The code-block size specifications
CBlkSizeSpec - Class in jj2000.j2k.entropy: This class extends ModuleSpec class for code-blocks sizes holding purposes.
CBlkSizeSpec(int, int, byte) - Constructor for class jj2000.j2k.entropy.CBlkSizeSpec: Creates a new CBlkSizeSpec object for the specified number of tiles and components.
CBlkSizeSpec(int, int, byte, J2KImageWriteParamJava, String) - Constructor for class jj2000.j2k.entropy.CBlkSizeSpec: Creates a new CBlkSizeSpec object for the specified number of tiles and components and the parameters instance.
cblkToDecode - Variable in class jj2000.j2k.wavelet.synthesis.InvWTFull: The total number of code-blocks to decode
CBlkWTData - Class in jj2000.j2k.wavelet.analysis: This is a generic abstract class to store a code-block of wavelet data, be it quantized or not.
CBlkWTData() - Constructor for class jj2000.j2k.wavelet.analysis.CBlkWTData
CBlkWTDataFloat - Class in jj2000.j2k.wavelet.analysis: This is an implementation of the 'CBlkWTData' abstract class for 32 bit floating point data (float).
CBlkWTDataFloat() - Constructor for class jj2000.j2k.wavelet.analysis.CBlkWTDataFloat
CBlkWTDataInt - Class in jj2000.j2k.wavelet.analysis: This is an implementation of the 'CBlkWTData' abstract class for signed 32 bit integer data.
CBlkWTDataInt() - Constructor for class jj2000.j2k.wavelet.analysis.CBlkWTDataInt
CBlkWTDataSrc - Interface in jj2000.j2k.wavelet.analysis: This abstract class defines methods to transfer wavelet data in a code-block by code-block basis.
CBlkWTDataSrcDec - Interface in jj2000.j2k.wavelet.synthesis: This abstract class defines methods to transfer wavelet data in a code-block by code-block basis, for the decoder side.
cbOff - Variable in class jj2000.j2k.codestream.reader.PktInfo: The code-block offset in the codestream (for this packet)
ccb - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor: The object where to store the compressed code-block
CCD_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
cChoice - Variable in class loci.formats.gui.DataConverter
cChoice - Variable in class loci.plugins.in.SwapDialog
ccoc - Variable in class jj2000.j2k.codestream.HeaderInfo.COC
ccom - Variable in class jj2000.j2k.codestream.HeaderInfo.COM
cdata - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
cdata - Variable in class loci.formats.in.ZeissTIFFHandler
cdstreamStart - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
ce - Variable in class jj2000.j2k.entropy.Progression: Component index for the end of a progression.
CELL_LENGTH - Static variable in class loci.formats.tiff.IFD
CELL_WIDTH - Static variable in class loci.formats.tiff.IFD
CellH5Constants() - Constructor for class loci.formats.in.CellH5Reader.CellH5Constants
CellH5Coordinate(String, String, String) - Constructor for class loci.formats.in.CellH5Reader.CellH5Coordinate
CellH5PathsToImageData - Variable in class loci.formats.in.CellH5Reader
CellH5PositionList - Variable in class loci.formats.in.CellH5Reader
CellH5Reader - Class in loci.formats.in: Reader for CellH5 (HDF) files.
CellH5Reader() - Constructor for class loci.formats.in.CellH5Reader: Constructs a new CellH5 HDF reader.
CellH5Reader.CellH5Constants - Class in loci.formats.in
CellH5Reader.CellH5Coordinate - Class in loci.formats.in
CellH5Writer - Class in loci.formats.out: CellH5Writer is the file format writer for CellH5 format.
CellH5Writer() - Constructor for class loci.formats.out.CellH5Writer
CellH5Writer(String, String[]) - Constructor for class loci.formats.out.CellH5Writer
CellLength() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.CellLength
cellObjectNames - Variable in class loci.formats.in.CellH5Reader
cellomicsPattern - Variable in class loci.formats.in.CellomicsReader
CellomicsReader - Class in loci.formats.in: Reader for Cellomics C01 files.
CellomicsReader() - Constructor for class loci.formats.in.CellomicsReader: Constructs a new Cellomics reader.
CellSensReader - Class in loci.formats.in: CellSensReader is the file format reader for cellSens .vsi files.
CellSensReader() - Constructor for class loci.formats.in.CellSensReader: Constructs a new cellSens reader.
CellSensReader.Pyramid - Class in loci.formats.in
CellSensReader.TileCoordinate - Class in loci.formats.in
CellVoyagerReader - Class in loci.formats.in: A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).
CellVoyagerReader() - Constructor for class loci.formats.in.CellVoyagerReader
CellVoyagerReader.AreaInfo - Class in loci.formats.in
CellVoyagerReader.ChannelInfo - Class in loci.formats.in
CellVoyagerReader.FieldInfo - Class in loci.formats.in
CellVoyagerReader.WellInfo - Class in loci.formats.in
CellWidth() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.CellWidth
CellWorxReader - Class in loci.formats.in: CellWorxReader is the file format reader for CellWorx .pnl files.
CellWorxReader() - Constructor for class loci.formats.in.CellWorxReader: Constructs a new CellWorx reader.
cEnd - Variable in class loci.plugins.in.ImporterOptions
CENTERED_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
centerPixelValue - Variable in class loci.formats.in.DicomReader
centerX - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
centerY - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
cepoc - Variable in class jj2000.j2k.codestream.HeaderInfo.POC
certain - Variable in class loci.formats.AxisGuesser: Whether the guesser is confident that all axis types are correct.
certain - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane: Certainty flag, for dealing with unspecified NumPlanes.
cf - Variable in class org.libjpegturbo.turbojpeg.TJTransform: Custom filter instance
CFA_PATTERN - Static variable in class loci.formats.tiff.IFD
CFAPattern() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.CFAPattern
cfaPattern - Variable in class loci.formats.in.DNGReader
cfaPattern - Variable in class loci.formats.in.NikonReader
cfdHF - Variable in class loci.formats.in.SDTInfo
cfdLH - Variable in class loci.formats.in.SDTInfo
cfdLL - Variable in class loci.formats.in.SDTInfo
cfdZC - Variable in class loci.formats.in.SDTInfo
CFG_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
CFG_SUFFIX - Static variable in class loci.formats.in.PrairieReader
cfgFile - Variable in class loci.formats.in.PrairieReader: The associated XML files.
CHAINED_LAYERS - Static variable in class loci.formats.in.CellSensReader
chan - Variable in class loci.formats.in.SDTInfo: Routing channel number.
CHANDESC - Static variable in class loci.formats.in.LeicaReader
changedUpdate(DocumentEvent) - Method in class loci.plugins.config.FlexWidgets
changeOutputFile(String) - Method in class loci.formats.FormatWriter
changeOutputFile(String) - Method in interface loci.formats.IFormatWriter: Switch the output file for the current dataset.
changeOutputFile(String) - Method in class loci.formats.ImageWriter
changeOutputFile(String) - Method in class loci.formats.WriterWrapper
changingElemSize - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
chanMax - Variable in class loci.formats.MinMaxCalculator: Max values for each channel.
chanMin - Variable in class loci.formats.MinMaxCalculator: Min values for each channel.
channel - Variable in class com.sun.media.imageio.stream.FileChannelImageInputStream: The FileChannel data source.
channel - Variable in class com.sun.media.imageio.stream.FileChannelImageOutputStream: The FileChannel data destination.
CHANNEL - Static variable in class loci.formats.FormatTools: Identifies the Channel dimensional type, representing a generic channel dimension.
channel - Variable in class loci.formats.in.ColumbusReader.Plane
Channel() - Constructor for class loci.formats.in.LeicaHandler.Channel
channel - Variable in class loci.formats.in.LeicaHandler.Detector
channel - Variable in class loci.formats.in.LeicaHandler.MultiBand
Channel() - Constructor for class loci.formats.in.OIRReader.Channel
channel - Variable in class loci.formats.in.PrairieMetadata.PFile: channel of this <File>.
channel - Variable in class loci.formats.in.SPCReader
Channel() - Constructor for class loci.formats.in.ZeissCZIReader.Channel
Channel(int) - Constructor for class loci.formats.in.ZeissTIFFReader.Channel
CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_AMPLIFIER_GAIN - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
CHANNEL_COUNT_TAG - Static variable in class loci.formats.in.FlowSightReader
CHANNEL_DEFINITION_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
CHANNEL_DESCS_TAG - Static variable in class loci.formats.in.FlowSightReader
CHANNEL_DETECTOR_GAIN - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_DIM - Static variable in class loci.formats.in.CellSensReader
CHANNEL_FILTER - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_FILTER_SET - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
CHANNEL_INFO_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
CHANNEL_NAME - Static variable in class loci.formats.FormatTools
CHANNEL_NAME - Static variable in class loci.formats.in.CellSensReader
CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_NAMES_TAG - Static variable in class loci.formats.in.FlowSightReader
CHANNEL_NUM - Static variable in class loci.formats.FormatTools
CHANNEL_OVERFLOW - Static variable in class loci.formats.in.CellSensReader
CHANNEL_PINHOLE_DIAMETER - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_PRIORITIES - Static variable in class loci.formats.in.LIFReader
CHANNEL_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
CHANNEL_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
CHANNEL_TRANSPARENCY_VALUE - Static variable in class loci.formats.in.CellSensReader
CHANNEL_VISIBLE - Static variable in class loci.formats.in.CellSensReader
channelColor - Variable in class loci.formats.in.ColumbusReader.Plane
channelColor - Variable in class loci.formats.in.LeicaReader
channelColor - Variable in class loci.formats.in.ZeissLSMReader
channelColors - Variable in class loci.formats.in.BaseZeissReader
channelColors - Variable in class loci.formats.in.ImprovisionTiffReader
channelColors - Variable in class loci.formats.in.NativeND2Reader
ChannelData() - Constructor for class loci.formats.in.FV1000Reader.ChannelData
ChannelDefinitionBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000: This class is designed to represent a Channel Definition Box of JPEG JP2 file format.
ChannelDefinitionBox(ColorModel) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox: Constructs a ChannelDefinitionBox based on the provided ColorModel.
ChannelDefinitionBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox: Constructs a ChannelDefinitionBox based on the provided content in byte array.
ChannelDefinitionBox(short[], short[], short[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox: Constructs a ChannelDefinitionBox based on the provided channel definitions.
ChannelDefinitionBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox: Constructs a ChannelDefinitionBox based on the provided org.w3c.dom.Node.
channelDescs - Variable in class loci.formats.in.FlowSightReader
ChannelFiller - Class in loci.formats: For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
ChannelFiller() - Constructor for class loci.formats.ChannelFiller: Constructs a ChannelFiller around a new image reader.
ChannelFiller(IFormatReader) - Constructor for class loci.formats.ChannelFiller: Constructs a ChannelFiller with a given reader.
channelFiller - Variable in class loci.plugins.in.ImportProcess
channelId - Variable in class loci.formats.in.OIRReader.Detector
ChannelImageInputStreamSpi - Class in com.sun.media.imageioimpl.stream
ChannelImageInputStreamSpi() - Constructor for class com.sun.media.imageioimpl.stream.ChannelImageInputStreamSpi
ChannelImageOutputStreamSpi - Class in com.sun.media.imageioimpl.stream
ChannelImageOutputStreamSpi() - Constructor for class com.sun.media.imageioimpl.stream.ChannelImageOutputStreamSpi
channelIndices - Variable in class loci.formats.in.BaseZeissReader
ChannelInfo() - Constructor for class loci.formats.in.CellVoyagerReader.ChannelInfo
channelInfos - Variable in class loci.formats.in.CellVoyagerReader
channelLengths - Variable in class loci.formats.in.ICSReader: The length of each channel axis.
channelMap - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
channelMax - Variable in class loci.formats.in.ImarisHDFReader
ChannelMerger - Class in loci.formats: Logic to automatically merge channels in a file.
ChannelMerger() - Constructor for class loci.formats.ChannelMerger: Constructs a ChannelMerger around a new image reader.
ChannelMerger(IFormatReader) - Constructor for class loci.formats.ChannelMerger: Constructs a ChannelMerger with the given reader.
channelMin - Variable in class loci.formats.in.ImarisHDFReader
channelName - Variable in class loci.formats.in.BaseZeissReader
channelName - Variable in class loci.formats.in.ColumbusReader.Plane
channelName - Variable in class loci.formats.in.ImarisHDFReader
channelName - Variable in class loci.formats.in.MetamorphHandler
channelName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
channelName - Variable in class loci.formats.in.OperettaReader.Plane
channelName - Variable in class loci.formats.in.PrairieMetadata.PFile: channelName attribute of this <File>.
channelName - Variable in class loci.formats.in.SISReader
channelName - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
channelNames - Variable in class loci.formats.in.BDReader
channelNames - Variable in class loci.formats.in.CellSensReader.Pyramid
channelNames - Variable in class loci.formats.in.FlexReader
channelNames - Variable in class loci.formats.in.FlowSightReader
channelNames - Variable in class loci.formats.in.FluoviewReader
channelNames - Variable in class loci.formats.in.InCellReader
channelNames - Variable in class loci.formats.in.LeicaReader
channelNames - Variable in class loci.formats.in.LIFReader
channelNames - Variable in class loci.formats.in.MetamorphHandler
channelNames - Variable in class loci.formats.in.ND2Handler
channelNames - Variable in class loci.formats.in.ScanrReader
channelNames - Variable in class loci.formats.in.SlidebookTiffReader
channelNames - Variable in class loci.formats.in.VolocityReader.Stack
channelNames - Variable in class loci.formats.in.ZeissLSMReader
channelNumber - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
channelNumber - Variable in class loci.plugins.util.RecordedImageProcessor
channelOrder - Variable in class loci.formats.in.PhotoshopTiffReader
channels - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
channels - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader: Channel definitions
channels - Variable in class loci.formats.codec.CodecOptions: Number of channels.
channels - Variable in class loci.formats.in.FV1000Reader
channels - Variable in class loci.formats.in.LeicaHandler
channels - Variable in class loci.formats.in.LiFlimReader
channels - Variable in class loci.formats.in.MicromanagerReader.Position
channels - Variable in class loci.formats.in.OIRReader
channels - Variable in class loci.formats.in.PrairieReader: List of active channels.
channels - Variable in class loci.formats.in.SDTInfo
channels - Variable in class loci.formats.in.SDTReader: Number of spectral channels.
channels - Variable in class loci.formats.in.TextReader: List of channel labels.
channels - Variable in class loci.formats.in.ZeissCZIReader
channels - Variable in class loci.formats.in.ZeissTIFFReader
ChannelSeparator - Class in loci.formats: Logic to automatically separate the channels in a file.
ChannelSeparator() - Constructor for class loci.formats.ChannelSeparator: Constructs a ChannelSeparator around a new image reader.
ChannelSeparator(IFormatReader) - Constructor for class loci.formats.ChannelSeparator: Constructs a ChannelSeparator with the given reader.
channelSeparator - Variable in class loci.plugins.in.ImportProcess
channelsPerTimepoint - Variable in class loci.formats.in.InCellReader
channelTypes - Variable in class loci.formats.in.ICSReader: The type of each channel axis.
channelWavelengths - Variable in class loci.formats.in.CellSensReader.Pyramid
CHAR - Static variable in class loci.formats.in.CellSensReader
CHAR - Static variable in class loci.formats.in.GatanReader
characterCellHeight - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
characterCellWidth - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
characters(char[], int, int) - Method in class loci.formats.in.AFIReader.AFIHandler
characters(char[], int, int) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
characters(char[], int, int) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
characters(char[], int, int) - Method in class loci.formats.in.FEITiffReader.FEIHandler
characters(char[], int, int) - Method in class loci.formats.in.FlexReader.FlexHandler
characters(char[], int, int) - Method in class loci.formats.in.ImaconReader.ImaconHandler
characters(char[], int, int) - Method in class loci.formats.in.InCellReader.InCellHandler
characters(char[], int, int) - Method in class loci.formats.in.IvisionReader.IvisionHandler
characters(char[], int, int) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
characters(char[], int, int) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
characters(char[], int, int) - Method in class loci.formats.in.OperettaReader.OperettaHandler
characters(char[], int, int) - Method in class loci.formats.in.ScanrReader.ScanrHandler
characters(char[], int, int) - Method in class loci.formats.in.ZeissTIFFHandler
characters(char[], int, int) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
charData - Variable in class loci.formats.in.FlexReader.FlexHandler
CHARS - Static variable in class loci.formats.tools.AsciiImage
Charset(int, String) - Constructor for enum loci.formats.in.BaseZeissReader.Charset
charset - Variable in class loci.formats.in.BaseZeissReader.Shape
CHECK - Static variable in class loci.formats.in.ZeissLMSReader
checkBufferSize(IFormatReader, int) - Static method in class loci.formats.FormatTools
checkBufferSize(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools: Checks that the given buffer size is large enough to hold a w * h image as returned by the given reader.
checkBytePadding() - Method in class jj2000.j2k.entropy.decoder.ByteToBitInput: Checks for past errors in the decoding process by verifying the byte padding with an alternating sequence of 0's and 1's.
checkClass(String) - Static method in class loci.plugins.util.LibraryChecker: Checks whether the given class is available.
checkClassDependency(Class<? extends Object>) - Method in class loci.formats.services.WlzServiceImpl
checkCommentImageJ(String) - Method in class loci.formats.in.TiffReader
checkCommentMetamorph(String) - Method in class loci.formats.in.TiffReader
checkElement(Element, String) - Method in class loci.formats.in.PrairieMetadata: Checks that the given element has the specified name.
checkEndOfPassFF(byte[], int[], boolean[], int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder: Ensures that at the end of a non-terminated coding pass there is not a 0xFF byte, modifying the stored rates if necessary.
checkHeader() - Method in class loci.formats.tiff.TiffParser: Checks the TIFF header.
checkImageJ() - Static method in class loci.plugins.util.LibraryChecker: Checks whether ImageJ is new enough for the Bio-Formats plugins.
checkImageJ(String, String) - Static method in class loci.plugins.util.LibraryChecker: Returns true the current ImageJ version is greater than or equal to the specified version.
checkImageJ(String, String, String) - Static method in class loci.plugins.util.LibraryChecker: Returns true the current ImageJ version is greater than or equal to the specified version.
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
checkJava() - Static method in class loci.plugins.util.LibraryChecker: Checks for a new enough version of the Java Runtime Environment.
checkKey(String, String) - Method in class loci.formats.in.MetamorphHandler: Check if the value needs to be saved.
checkKey(String, String) - Method in class loci.plugins.in.ImporterOptions: Tests whether the given boolean key is set in the specified options.
checkLatest(String, String) - Static method in class loci.plugins.config.InstallWizard
checkLibrary() - Static method in class jj2000.j2k.util.NativeServices: Checks if the library SHLIB_NAME is already loaded and attempts to load if not yet loaded.
checkLibrary(LibraryChecker.Library, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker: Checks for a required library.
checkLibrary(String, String, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker: Checks whether the given class is available; if not, adds the specified JAR file name to the hash set (presumably to report it missing to the user).
checkMarkerLength(DataInputStream, String) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder: Checks that the marker segment length is correct.
checkMissing(HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker: Reports missing libraries in the given hash set to the user.
checkObsoleteOptions() - Method in class loci.plugins.in.ImporterOptions: Handles obsolete macro keys, for backward compatibility.
checkParams(int, byte[], int, int, int, int) - Method in class loci.formats.FormatWriter: Ensure that the arguments that are being passed to saveBytes(...) are valid.
checkParams - Variable in class loci.formats.out.TiffWriter: Whether or not to check the parameters passed to saveBytes.
checkParamsEmpty(ImageTypeSpecifier, int, int, List) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
checkPerformed - Static variable in class loci.plugins.in.UpgradeDialog: Whether an upgrade check has already been performed this session.
checkPlaneNumber(IFormatReader, int) - Static method in class loci.formats.FormatTools: Checks that the given plane number is valid for the given reader.
checkPlaneParameters(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools: Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given reader.
checkPoints(int) - Method in enum loci.formats.in.BaseZeissReader.FeatureType
checkPredTerm() - Method in class jj2000.j2k.entropy.decoder.MQDecoder: Checks for past errors in the decoding process using the predictable error resilient termination.
checkProgMode(String) - Method in class jj2000.j2k.entropy.ProgressionSpec: Check if the progression mode exists and if so, return its integer value.
checkQTLibrary() - Method in class loci.formats.gui.LegacyQTTools: Checks whether QTJava is available, throwing an exception if not.
checkReadParamBandSettingsWrapper(ImageReadParam, int, int) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader: Wrapper for the protected method checkReadParamBandSettings.
checkSampleModel(SampleModel) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
checkSampleModel(SampleModel) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
checkSuffix(String, String) - Static method in class loci.formats.FormatHandler: Performs suffix matching for the given filename.
checkSuffix(String, String[]) - Static method in class loci.formats.FormatHandler: Performs suffix matching for the given filename.
checkTargetErrors() - Method in class jj2000.j2k.util.ThreadPool: Checks that no error or runtime exception in any target have occurred so far.
checkTileSize(IFormatReader, int, int, int, int) - Static method in class loci.formats.FormatTools: Checks that the given tile size is valid for the given reader.
checkTime(long, int, long, long) - Method in class loci.formats.in.TextReader
checkUnit(String, String...) - Method in class loci.formats.in.ICSReader: Verifies that a unit matches the expected value.
checkUUIDInfoBox(Node, String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata: Check whether the child with a name childName exists.
childCount - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
childNames - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
childPolicy - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
children - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
CHIP_SIZE_X - Static variable in class loci.formats.in.FluoviewReader
CHIP_SIZE_Y - Static variable in class loci.formats.in.FluoviewReader
chksum - Variable in class loci.formats.in.SDTInfo
CHROMA_SUBSAMPLING - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGCompressor
chromaSubsampleH - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
chromaSubsampleV - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
CHUNK_SIZE - Static variable in class loci.formats.UpgradeChecker: Number of bytes to read from the CI server at a time.
ChunkMapEntry() - Constructor for class loci.formats.in.NativeND2Reader.ChunkMapEntry
chunkSizes - Variable in class loci.formats.in.NativeQTReader: Number of bytes in each plane.
CI_SERVER - Static variable in class loci.formats.UpgradeChecker: Location of the OME continuous integration server.
cIndex - Variable in class loci.formats.in.BaseZeissReader
cIndex - Variable in class loci.plugins.util.DataBrowser
CIRCLE - Static variable in class loci.formats.in.FV1000Reader
CIRCLE - Static variable in class loci.formats.in.ZeissLSMReader
CIRCLE_3POINT - Static variable in class loci.formats.in.ZeissLSMReader
cLabel - Variable in class loci.formats.gui.DataConverter
clamp(float) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFCIELabColorConverter
clamp(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
clamp2(float) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFCIELabColorConverter
CLASS_IMAGE_5D - Static variable in class loci.plugins.in.ImporterOptions
CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
CLASS_VIEW_5D - Static variable in class loci.plugins.in.ImporterOptions
classes - Variable in class loci.formats.ClassList: List of classes.
classes - Variable in class loci.formats.in.CellH5Reader
ClassList<T> - Class in loci.formats: ClassList is a list of classes for use with ImageReader or ImageWriter, parsed from a configuration file such as readers.txt or writers.txt.
ClassList(Class<T>) - Constructor for class loci.formats.ClassList: Constructs a list of classes, initially empty.
ClassList(String, Class<T>) - Constructor for class loci.formats.ClassList: Constructs a list of classes from the given configuration file.
ClassList(String, Class<T>, Class<?>) - Constructor for class loci.formats.ClassList: Constructs a list of classes from the given configuration file.
classList - Variable in class loci.formats.FileStitcher
CLEAN_FAX_DATA_ERRORS_CORRECTED - Static variable in class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet: A value to be used with the "CleanFaxData" tag.
CLEAN_FAX_DATA_ERRORS_UNCORRECTED - Static variable in class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet: A value to be used with the "CleanFaxData" tag.
CLEAN_FAX_DATA_NO_ERRORS - Static variable in class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet: A value to be used with the "CleanFaxData" tag.
CleanFaxData() - Constructor for class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet.CleanFaxData
cleanup() - Method in class loci.formats.Memoizer
cleanuppass(DataBlk, MQDecoder, int, int[], int[], boolean) - Method in class jj2000.j2k.entropy.decoder.StdEntropyDecoder: Performs the cleanup pass on the specified data and bit-plane.
cleanuppass(CBlkWTData, MQCoder, boolean, int, int[], int[], int[], int[], int[], int[], int, int, int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder: Performs the cleanup pass on the specified data and bit-plane.
clear() - Method in class loci.formats.codec.ByteVector
CLEAR_CODE - Static variable in class loci.formats.codec.LZWCodec
clearCode_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor: reserved clear code based on code size
clearDestImage() - Method in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
clearSeries() - Method in class loci.plugins.in.ImporterOptions
ClearTable(int) - Method in class com.sun.media.imageioimpl.common.LZWStringTable
clearTargetErrors() - Method in class jj2000.j2k.util.ThreadPool: Clears the current target error conditions, if any.
clearXML() - Method in class loci.formats.in.ZeissCZIReader.Metadata
clength - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter: Length of codestream
cLengths - Variable in class loci.plugins.util.DataBrowser
clip(int, int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
clip(int, int, int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
clipDestination(Rectangle) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
CLIPPING - Static variable in class loci.formats.in.CellSensReader
CLIPPING_MAGIC_STRING - Static variable in class loci.formats.in.VolocityClippingReader
CLIPPING_STATE - Static variable in class loci.formats.in.CellSensReader
clippingData - Variable in class loci.formats.in.VolocityReader.Stack
CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
clone() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory: Clones the directory and all the fields contained therein.
clone() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
clone() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
clone() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
clone() - Method in class jj2000.j2k.ModuleSpec
clone() - Method in class loci.formats.CoreMetadata
clone(IFormatReader, int) - Method in class loci.formats.CoreMetadata
clone() - Method in class loci.formats.SwappableMetadata
clone(IFormatReader, int) - Method in class loci.formats.SwappableMetadata
cloneImageReadParam(ImageReadParam, boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage: Creates a copy of param.
cloneNode(boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
close() - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream: Invokes the superclass method and sets the internal reference to the source FileChannel to null.
close() - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream: Invokes the superclass method, writes any unwritten data, and sets the internal reference to the source FileChannel to null.
close() - Method in class com.sun.media.imageio.stream.RawImageInputStream
close() - Method in class com.sun.media.imageioimpl.plugins.clib.InputStreamAdapter
close() - Method in class com.sun.media.imageioimpl.plugins.clib.OutputStreamAdapter
close() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
close() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
close() - Method in class jj2000.j2k.codestream.writer.CodestreamWriter: Closes the underlying resource (file, stream, network connection, etc.).
close() - Method in class jj2000.j2k.codestream.writer.FileCodestreamWriter: Writes the EOC marker and closes the underlying stream.
close() - Method in class jj2000.j2k.image.input.ImgReader: Closes the underlying file or network connection from where the image data is being read.
close() - Method in class jj2000.j2k.image.input.ImgReaderPGM: Closes the underlying RandomAccessFile from where the image data is being read.
close() - Method in class jj2000.j2k.io.BufferedRandomAccessFile: Closes the buffered random access file
close() - Method in interface jj2000.j2k.io.RandomAccessIO: Closes the I/O stream.
close() - Method in class jj2000.j2k.util.ISRandomAccessIO: Closes this object for reading as well as the wrapped InputStream, if not already closed.
close(boolean) - Method in class loci.formats.ChannelSeparator
close() - Method in class loci.formats.codec.JPEGTileDecoder
close(boolean) - Method in class loci.formats.DelegateReader
close() - Method in class loci.formats.FileStitcher
close(boolean) - Method in class loci.formats.FileStitcher
close(boolean) - Method in class loci.formats.FormatReader
close() - Method in class loci.formats.FormatReader
close() - Method in class loci.formats.FormatWriter
close() - Method in class loci.formats.gui.PreviewPane: Closes the underlying image reader.
close(boolean) - Method in interface loci.formats.IFormatReader: Closes the currently open file.
close(boolean) - Method in class loci.formats.ImageReader
close() - Method in class loci.formats.ImageReader
close() - Method in class loci.formats.ImageWriter
close(boolean) - Method in class loci.formats.in.AFIReader
close(boolean) - Method in class loci.formats.in.AIMReader
close(boolean) - Method in class loci.formats.in.AliconaReader
close(boolean) - Method in class loci.formats.in.AmiraReader
close(boolean) - Method in class loci.formats.in.AnalyzeReader
close(boolean) - Method in class loci.formats.in.APLReader
close(boolean) - Method in class loci.formats.in.APNGReader
close(boolean) - Method in class loci.formats.in.AVIReader
close(boolean) - Method in class loci.formats.in.BaseZeissReader
close(boolean) - Method in class loci.formats.in.BDReader
close(boolean) - Method in class loci.formats.in.BioRadReader
close(boolean) - Method in class loci.formats.in.BioRadSCNReader
close(boolean) - Method in class loci.formats.in.BMPReader
close(boolean) - Method in class loci.formats.in.BrukerReader
close(boolean) - Method in class loci.formats.in.BurleighReader
close(boolean) - Method in class loci.formats.in.CanonRawReader
close(boolean) - Method in class loci.formats.in.CellH5Reader
close(boolean) - Method in class loci.formats.in.CellomicsReader
close(boolean) - Method in class loci.formats.in.CellSensReader
close(boolean) - Method in class loci.formats.in.CellWorxReader
close(boolean) - Method in class loci.formats.in.ColumbusReader
close(boolean) - Method in class loci.formats.in.DeltavisionReader
close(boolean) - Method in class loci.formats.in.DicomReader
close(boolean) - Method in class loci.formats.in.DNGReader
close(boolean) - Method in class loci.formats.in.EPSReader
close(boolean) - Method in class loci.formats.in.FakeReader
close(boolean) - Method in class loci.formats.in.FEIReader
close(boolean) - Method in class loci.formats.in.FEITiffReader
close(boolean) - Method in class loci.formats.in.FilePatternReader
close() - Method in class loci.formats.in.FilePatternReader
close(boolean) - Method in class loci.formats.in.FitsReader
close(boolean) - Method in class loci.formats.in.FlexReader
close(boolean) - Method in class loci.formats.in.FlowSightReader
close(boolean) - Method in class loci.formats.in.FluoviewReader
close(boolean) - Method in class loci.formats.in.FujiReader
close(boolean) - Method in class loci.formats.in.FV1000Reader
close(boolean) - Method in class loci.formats.in.GatanDM2Reader
close(boolean) - Method in class loci.formats.in.GatanReader
close(boolean) - Method in class loci.formats.in.GIFReader
close(boolean) - Method in class loci.formats.in.HamamatsuVMSReader
close(boolean) - Method in class loci.formats.in.HitachiReader
close(boolean) - Method in class loci.formats.in.HRDGDFReader
close(boolean) - Method in class loci.formats.in.ICSReader
close(boolean) - Method in class loci.formats.in.IM3Reader
close(boolean) - Method in class loci.formats.in.ImaconReader
close(boolean) - Method in class loci.formats.in.ImageIOReader
close(boolean) - Method in class loci.formats.in.ImagicReader
close(boolean) - Method in class loci.formats.in.ImarisHDFReader
close(boolean) - Method in class loci.formats.in.ImarisReader
close(boolean) - Method in class loci.formats.in.IMODReader
close(boolean) - Method in class loci.formats.in.ImprovisionTiffReader
close(boolean) - Method in class loci.formats.in.ImspectorReader
close(boolean) - Method in class loci.formats.in.InCell3000Reader
close(boolean) - Method in class loci.formats.in.InCellReader
close(boolean) - Method in class loci.formats.in.InveonReader
close(boolean) - Method in class loci.formats.in.IPLabReader
close(boolean) - Method in class loci.formats.in.IPWReader
close(boolean) - Method in class loci.formats.in.IvisionReader
close(boolean) - Method in class loci.formats.in.JEOLReader
close(boolean) - Method in class loci.formats.in.JPEG2000Reader
close(boolean) - Method in class loci.formats.in.JPEGReader
close(boolean) - Method in class loci.formats.in.JPXReader
close(boolean) - Method in class loci.formats.in.KhorosReader
close(boolean) - Method in class loci.formats.in.KodakReader
close(boolean) - Method in class loci.formats.in.L2DReader
close(boolean) - Method in class loci.formats.in.LegacyQTReader
close(boolean) - Method in class loci.formats.in.LeicaReader
close(boolean) - Method in class loci.formats.in.LeicaSCNReader
close(boolean) - Method in class loci.formats.in.LiFlimReader
close(boolean) - Method in class loci.formats.in.LIFReader
close(boolean) - Method in class loci.formats.in.LIMReader
close(boolean) - Method in class loci.formats.in.MetamorphReader
close(boolean) - Method in class loci.formats.in.MetamorphTiffReader
close(boolean) - Method in class loci.formats.in.MIASReader
close(boolean) - Method in class loci.formats.in.MicromanagerReader
close(boolean) - Method in class loci.formats.in.MINCReader
close(boolean) - Method in class loci.formats.in.MinimalTiffReader
close(boolean) - Method in class loci.formats.in.MNGReader
close(boolean) - Method in class loci.formats.in.MolecularImagingReader
close(boolean) - Method in class loci.formats.in.MRCReader
close(boolean) - Method in class loci.formats.in.MRWReader
close(boolean) - Method in class loci.formats.in.NAFReader
close(boolean) - Method in class loci.formats.in.NativeND2Reader
close(boolean) - Method in class loci.formats.in.NativeQTReader
close(boolean) - Method in class loci.formats.in.NDPIReader
close(boolean) - Method in class loci.formats.in.NDPISReader
close(boolean) - Method in class loci.formats.in.NiftiReader
close(boolean) - Method in class loci.formats.in.NikonElementsTiffReader
close(boolean) - Method in class loci.formats.in.NikonReader
close(boolean) - Method in class loci.formats.in.NikonTiffReader
close(boolean) - Method in class loci.formats.in.NRRDReader
close(boolean) - Method in class loci.formats.in.OBFReader
close(boolean) - Method in class loci.formats.in.OIRReader
close(boolean) - Method in class loci.formats.in.OMETiffReader
close(boolean) - Method in class loci.formats.in.OMEXMLReader
close(boolean) - Method in class loci.formats.in.OpenlabRawReader
close(boolean) - Method in class loci.formats.in.OpenlabReader
close(boolean) - Method in class loci.formats.in.OperettaReader
close(boolean) - Method in class loci.formats.in.PCIReader
close(boolean) - Method in class loci.formats.in.PCORAWReader
close(boolean) - Method in class loci.formats.in.PCXReader
close(boolean) - Method in class loci.formats.in.PDSReader
close(boolean) - Method in class loci.formats.in.PerkinElmerReader
close(boolean) - Method in class loci.formats.in.PGMReader
close(boolean) - Method in class loci.formats.in.PhotoshopTiffReader
close(boolean) - Method in class loci.formats.in.PictReader
close(boolean) - Method in class loci.formats.in.PQBinReader
close(boolean) - Method in class loci.formats.in.PrairieReader
close(boolean) - Method in class loci.formats.in.PSDReader
close(boolean) - Method in class loci.formats.in.QuesantReader
close(boolean) - Method in class loci.formats.in.RHKReader
close(boolean) - Method in class loci.formats.in.SBIGReader
close(boolean) - Method in class loci.formats.in.ScanrReader
close(boolean) - Method in class loci.formats.in.ScreenReader
close(boolean) - Method in class loci.formats.in.SDTReader
close(boolean) - Method in class loci.formats.in.SIFReader
close(boolean) - Method in class loci.formats.in.SimplePCITiffReader
close(boolean) - Method in class loci.formats.in.SISReader
close(boolean) - Method in class loci.formats.in.SlidebookReader
close(boolean) - Method in class loci.formats.in.SlidebookTiffReader
close(boolean) - Method in class loci.formats.in.SPCReader
close(boolean) - Method in class loci.formats.in.SPEReader
close(boolean) - Method in class loci.formats.in.SpiderReader
close(boolean) - Method in class loci.formats.in.SVSReader
close(boolean) - Method in class loci.formats.in.TargaReader
close(boolean) - Method in class loci.formats.in.TCSReader
close(boolean) - Method in class loci.formats.in.TextReader
close(boolean) - Method in class loci.formats.in.TiffReader
close(boolean) - Method in class loci.formats.in.TileJPEGReader
close(boolean) - Method in class loci.formats.in.TillVisionReader
close(boolean) - Method in class loci.formats.in.TopometrixReader
close(boolean) - Method in class loci.formats.in.TrestleReader
close(boolean) - Method in class loci.formats.in.UBMReader
close(boolean) - Method in class loci.formats.in.UnisokuReader
close(boolean) - Method in class loci.formats.in.VarianFDFReader
close(boolean) - Method in class loci.formats.in.VeecoReader
close(boolean) - Method in class loci.formats.in.VisitechReader
close(boolean) - Method in class loci.formats.in.VolocityClippingReader
close(boolean) - Method in class loci.formats.in.VolocityReader
close(boolean) - Method in class loci.formats.in.WlzReader
close(boolean) - Method in class loci.formats.in.ZeissCZIReader
close() - Method in class loci.formats.in.ZeissCZIReader.Segment
close(boolean) - Method in class loci.formats.in.ZeissLMSReader
close(boolean) - Method in class loci.formats.in.ZeissLSMReader
close(boolean) - Method in class loci.formats.in.ZeissTIFFReader
close(boolean) - Method in class loci.formats.in.ZeissZVIReader
close(boolean) - Method in class loci.formats.in.ZipReader
close() - Method in class loci.formats.Memoizer
close(boolean) - Method in class loci.formats.Memoizer
close() - Method in interface loci.formats.Memoizer.Deser
close() - Method in class loci.formats.Memoizer.KryoDeser
close(boolean) - Method in class loci.formats.MinMaxCalculator
close() - Method in class loci.formats.out.APNGWriter
close() - Method in class loci.formats.out.AVIWriter
close() - Method in class loci.formats.out.CellH5Writer
close() - Method in class loci.formats.out.ICSWriter
close() - Method in class loci.formats.out.JavaWriter
close() - Method in class loci.formats.out.LegacyQTWriter
close() - Method in class loci.formats.out.OMETiffWriter
close() - Method in class loci.formats.out.OMEXMLWriter
close() - Method in class loci.formats.out.QTWriter
close() - Method in class loci.formats.out.TiffWriter
close() - Method in class loci.formats.out.V3DrawWriter
close() - Method in class loci.formats.out.WlzWriter
close(boolean) - Method in class loci.formats.ReaderWrapper
close() - Method in class loci.formats.ReaderWrapper
close() - Method in interface loci.formats.services.EXIFService
close() - Method in class loci.formats.services.EXIFServiceImpl
close() - Method in interface loci.formats.services.JHDFService: Closes and resets the service.
close() - Method in class loci.formats.services.JHDFServiceImpl
close() - Method in interface loci.formats.services.JPEGTurboService
close() - Method in class loci.formats.services.JPEGTurboServiceImpl
close() - Method in interface loci.formats.services.MDBService: Close the currently initialized file.
close() - Method in class loci.formats.services.MDBServiceImpl
close() - Method in interface loci.formats.services.MetakitService
close() - Method in class loci.formats.services.MetakitServiceImpl
close() - Method in interface loci.formats.services.NetCDFService: Closes and resets the service.
close() - Method in class loci.formats.services.NetCDFServiceImpl
close() - Method in interface loci.formats.services.POIService: Close the current POI file system.
close() - Method in class loci.formats.services.POIServiceImpl
close() - Method in interface loci.formats.services.WlzService: Closes the file.
close() - Method in class loci.formats.services.WlzServiceImpl
close() - Method in class loci.formats.tiff.OnDemandLongArray
close() - Method in class loci.formats.tiff.TiffSaver: Closes the output stream if not null.
close() - Method in class loci.formats.WriterWrapper
close() - Method in class loci.plugins.config.TextAreaWriter: Closing a TextAreaWriter does nothing.
close() - Method in class loci.plugins.macro.LociFunctions
close() - Method in class loci.plugins.util.VirtualImagePlus
close() - Method in class loci.plugins.util.VirtualReader
close() - Method in class org.libjpegturbo.turbojpeg.TJCompressor: Free the native structures associated with this compressor instance.
close() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor: Free the native structures associated with this decompressor instance.
CLOSED_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
CLOSED_BEZIER - Static variable in class loci.formats.in.ZeissLSMReader
CLOSED_POLYLINE - Static variable in class loci.formats.in.ZeissLSMReader
closeFileOnly() - Method in class loci.plugins.macro.LociFunctions
cm - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
cm - Variable in class loci.formats.FormatWriter: Default color model.
cNames - Variable in class loci.formats.in.ImprovisionTiffReader
co - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
co2Percent - Variable in class loci.formats.in.ZeissCZIReader
COARSE_FRAME_IFD - Static variable in class loci.formats.in.CellSensReader
COARSE_PYRAMID_LEVEL - Static variable in class loci.formats.in.CellSensReader
coc - Variable in class jj2000.j2k.codestream.HeaderInfo: Reference to the COC marker segments found in main and first tile-part header.
COC() - Constructor for class jj2000.j2k.codestream.HeaderInfo.COC
COC - Static variable in interface jj2000.j2k.codestream.Markers: Coding style component (COC): 0xFF53
COC_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder: Flag bit for COC marker segment found
cod - Variable in class jj2000.j2k.codestream.HeaderInfo: Reference to the COD marker segments found in main and first tile-part header.
COD() - Constructor for class jj2000.j2k.codestream.HeaderInfo.COD
COD - Static variable in interface jj2000.j2k.codestream.Markers: Coding style default (COD): 0xFF52
COD_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder: Flag bit for COD marker segment found
code - Variable in enum loci.formats.codec.CompressionType: Code for the compression.
code - Variable in enum loci.formats.codec.JPEG2000BoxType: Code for the box type.
code - Variable in enum loci.formats.codec.JPEG2000SegmentMarker: Code for the segment marker.
code - Variable in class loci.formats.in.FV1000Reader
code - Variable in enum loci.formats.tiff.IFDType: Code for the IFD type in the actual TIFF file.
code - Variable in enum loci.formats.tiff.PhotoInterp: Code for the IFD type in the actual TIFF file.
code - Variable in enum loci.formats.tiff.TiffCompression: Code for the TIFF compression in the actual TIFF file.
codeBlockSize - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam: Specifies the maximum code-block size to use for tile-component.
codeBlockSize - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava: Specifies the maximum code-block size to use for tile-component.
codeBlockSize - Variable in class loci.formats.codec.JPEG2000CodecOptions: The maximum code-block size to use per tile-component as it would be provided to: J2KImageWriteParam.setCodeBlockSize(int[]) (WRITE).
Codec - Interface in loci.formats.codec: This class is an interface for any kind of compression or decompression.
codec - Variable in class loci.formats.codec.JPEGTileDecoder.TileCache
codec - Variable in class loci.formats.gui.DataConverter
codec - Variable in class loci.formats.in.NativeND2Reader: Codec to use when decompressing pixel data.
codec - Variable in class loci.formats.in.NativeQTReader: Video codec used by this movie.
codec - Variable in class loci.formats.out.LegacyQTWriter: The codec to use.
codec - Variable in class loci.formats.out.QTWriter: The codec to use.
codec - Variable in enum loci.formats.tiff.TiffCompression: TIFF compression codec.
CODEC_ANIMATION - Static variable in class loci.formats.out.QTWriter: Value indicating Animation codec.
CODEC_CINEPAK - Static variable in class loci.formats.out.QTWriter: Value indicating Cinepak codec.
CODEC_H_263 - Static variable in class loci.formats.out.QTWriter: Value indicating H.263 codec.
CODEC_MOTION_JPEG_B - Static variable in class loci.formats.out.QTWriter: Value indicating Motion JPEG-B codec.
CODEC_MPEG_4 - Static variable in class loci.formats.out.QTWriter: Value indicating MPEG-4 codec.
CODEC_RAW - Static variable in class loci.formats.out.QTWriter: Value indicating Raw codec.
CODEC_SORENSON - Static variable in class loci.formats.out.QTWriter: Value indicating Sorenson codec.
CODEC_SORENSON_3 - Static variable in class loci.formats.out.QTWriter: Value indicating Sorenson 3 codec.
codecName - Variable in enum loci.formats.tiff.TiffCompression: Name of the TIFF compression codec.
CodecOptions - Class in loci.formats.codec: Options for compressing and decompressing data.
CodecOptions() - Constructor for class loci.formats.codec.CodecOptions: Construct a new CodecOptions.
CodecOptions(CodecOptions) - Constructor for class loci.formats.codec.CodecOptions: Construct a new CodecOptions using the given CodecOptions.
codecOptions - Variable in class loci.formats.tiff.TiffParser: Codec options to be used when decoding compressed pixel data.
CodedCBlk - Class in jj2000.j2k.entropy: This is the generic class to store coded (compressed) code-block.
CodedCBlk() - Constructor for class jj2000.j2k.entropy.CodedCBlk: Creates a new CodedCBlk object wit the default values and without allocating any space for its members.
CodedCBlk(int, int, int, byte[]) - Constructor for class jj2000.j2k.entropy.CodedCBlk: Creates a new CodedCBlk object with the specified values.
CodedCBlkDataSrcDec - Interface in jj2000.j2k.entropy.decoder: This interface defines a source of entropy coded data and methods to transfer it in a code-block by code-block basis.
CodedCBlkDataSrcEnc - Interface in jj2000.j2k.entropy.encoder: This interface defines a source of entropy coded data and methods to transfer it in a code-block by code-block basis.
codeSegSymbol - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava: Inserts an error resilience segmentation symbol in the MQ codeword at the end of each bit-plane (cleanup pass).
codeSize_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor: base underlying code size of data being compressed 8 for TIFF, 1 to 8 for GIF
codeStreamLength - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader: The lengths of the codestreams in the fileformat
CodestreamManipulator - Class in jj2000.j2k.util: This class takes a legal JPEG 2000 codestream and performs some manipulation on it.
CodestreamManipulator(File, int, int, boolean, boolean, boolean, boolean) - Constructor for class jj2000.j2k.util.CodestreamManipulator: Instantiates a codestream manipulator..
codestreamOffset - Variable in class loci.formats.in.JPEG2000MetadataParser: Offset to first contiguous codestream.
codestreamPixelType - Variable in class loci.formats.in.JPEG2000MetadataParser: Pixel type as specified in the JPEG 2000 codestream..
codeStreamPos - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader: The positions of the codestreams in the fileformat
codestreamSizeC - Variable in class loci.formats.in.JPEG2000MetadataParser: Number of channels the image as specified in the JPEG 2000 codestream.
codestreamSizeX - Variable in class loci.formats.in.JPEG2000MetadataParser: Width of the image as specified in the JPEG 2000 codestream.
codestreamSizeY - Variable in class loci.formats.in.JPEG2000MetadataParser: Height of the image as specified in the JPEG 2000 codestream.
CodestreamWriter - Class in jj2000.j2k.codestream.writer: This is the abstract class for writing to a bit stream.
CodestreamWriter(int) - Constructor for class jj2000.j2k.codestream.writer.CodestreamWriter: Allocates this object and initializes the maximum numner of bytes.
codeSymbol(int, int) - Method in class jj2000.j2k.entropy.encoder.MQCoder: This function performs the arithmetic encoding of one symbol.
codeSymbols(int[], int[], int) - Method in class jj2000.j2k.entropy.encoder.MQCoder: This function performs the arithmetic encoding of several symbols together.
codingRangeCbCr - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
codingRangeY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
codingRangeY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
col - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
col - Variable in class loci.formats.in.ColumbusReader.Plane
col - Variable in class loci.formats.in.OperettaReader.Plane
col - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
colCount - Variable in class loci.formats.in.BaseZeissReader
collection - Variable in class loci.formats.in.LeicaHandler
collection - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
COLLECTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
colName - Variable in class loci.formats.in.InCellReader
color - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
color - Variable in class loci.formats.in.LeicaHandler.ROI
color - Variable in class loci.formats.in.LIFReader.ROI
color - Variable in class loci.formats.in.OIRReader.Channel
color - Variable in class loci.formats.in.ZeissCZIReader.Channel
color16 - Variable in class loci.formats.in.IvisionReader
COLOR_BAR - Static variable in class loci.formats.in.FV1000Reader
COLOR_MAP - Static variable in class loci.formats.in.CanonRawReader
COLOR_MAP - Static variable in class loci.formats.in.DNGReader
COLOR_MAP - Static variable in class loci.formats.in.NikonReader
COLOR_MAP - Static variable in class loci.formats.tiff.IFD
COLOR_MAP_1 - Static variable in class loci.formats.in.MRWReader
COLOR_MAP_2 - Static variable in class loci.formats.in.MRWReader
COLOR_MODE - Static variable in class loci.formats.in.NikonReader
COLOR_MODE_COLORIZED - Static variable in class loci.plugins.in.ImporterOptions
COLOR_MODE_COMPOSITE - Static variable in class loci.plugins.in.ImporterOptions
COLOR_MODE_CUSTOM - Static variable in class loci.plugins.in.ImporterOptions
COLOR_MODE_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions
COLOR_MODE_GRAYSCALE - Static variable in class loci.plugins.in.ImporterOptions
COLOR_SPACE - Static variable in class loci.formats.in.CellSensReader
COLOR_SPACE - Static variable in class loci.formats.tiff.IFD
COLOR_SPACE_SRGB - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "ColorSpace" tag.
COLOR_SPACE_UNCALIBRATED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "ColorSpace" tag.
colorConvert - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
colorConverter - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: A TIFFColorConverter object describing the color space of the encoded pixel data, or null.
colorConverter - Variable in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam
colorConverter - Variable in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam
colorConverter - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
colorCount - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
ColorDialog - Class in loci.plugins.in: Bio-Formats Importer custom color chooser dialog box.
ColorDialog(ImportProcess) - Constructor for class loci.plugins.in.ColorDialog
colorize - Variable in class loci.plugins.util.BFVirtualStack
Colorizer - Class in loci.plugins.in: Logic for colorizing images.
Colorizer(ImportProcess) - Constructor for class loci.plugins.in.Colorizer
ColorMap() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ColorMap
colorMap - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: The value of the ColorMap tag.
colorMap - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
colorMap - Variable in class loci.formats.in.TargaReader
colorModeChoice - Variable in class loci.plugins.in.MainDialog
colorModel - Variable in class com.sun.media.imageioimpl.common.SimpleRenderedImage: The image's ColorModel.
colorModel - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
colorModel - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
colorModel - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
colorModel - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader: Create a IndexColorModel from the palette box if there is one
colorModel - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter: The color model of the image to be compressed.
colorModel - Variable in class loci.formats.codec.CodecOptions: Color model to use when constructing an image (WRITE).
ColorNode() - Constructor for class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
colorPlanes - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
colorPlanes - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
colorResolution - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
COLORS - Variable in class loci.formats.in.CellH5Reader
colors - Variable in class loci.formats.in.ImarisHDFReader
colors - Variable in class loci.formats.in.IMODReader
colors - Variable in class loci.formats.in.NativeND2Reader
colors - Variable in class loci.formats.in.ND2Handler
colorsImportant - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
ColorSpace() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ColorSpace
colorSpace - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
COLORSPACE - Static variable in class loci.formats.in.CellSensReader
colorSpaceNames - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
colorSpaceType - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader: Color specification
ColorSpecificationBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000: This class is defined to represent a Color Specification Box of JPEG JP2 file format.
ColorSpecificationBox(byte, byte, byte, int, ICC_Profile) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox: Creates a ColorSpecificationBox from the provided data elements.
ColorSpecificationBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox: Creates a ColorSpecificationBox from the provided byte array.
ColorSpecificationBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox: Constructs a ColorSpecificationBox based on the provided org.w3c.dom.Node.
colorsUsed - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
colorTables - Variable in class loci.formats.in.GIFReader
colorTableSizes - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
COLOUR_SPECIFICATION_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
cols - Variable in class loci.formats.in.CellSensReader
colT - Variable in class loci.formats.in.SDTInfo
ColumbusReader - Class in loci.formats.in: ColumbusReader is the file format reader for screens exported from PerkinElmer Columbus.
ColumbusReader() - Constructor for class loci.formats.in.ColumbusReader: Constructs a new Columbus reader.
ColumbusReader.MeasurementHandler - Class in loci.formats.in
ColumbusReader.Plane - Class in loci.formats.in
column - Variable in class loci.formats.in.FlexReader.FlexFile
column - Variable in class loci.formats.in.OMEXMLReader.BinData
column - Variable in class loci.formats.tools.AmiraParameters
COLUMNS - Static variable in class loci.formats.gui.DataConverter
COLUMNS - Static variable in class loci.formats.in.DicomReader
com - Variable in class jj2000.j2k.codestream.HeaderInfo: Reference to the COM marker segments found in main and tile-part headers.
COM() - Constructor for class jj2000.j2k.codestream.HeaderInfo.COM
COM - Static variable in interface jj2000.j2k.codestream.Markers: Comment (COM): 0xFF64
COM - Static variable in class loci.formats.codec.LosslessJPEGCodec
com.sun.media.imageio.plugins.bmp - package com.sun.media.imageio.plugins.bmp: Package containing the public classes used by the Sun BMP plug-in for the Image I/O Framework.
com.sun.media.imageio.plugins.jpeg2000 - package com.sun.media.imageio.plugins.jpeg2000: Package containing the public classes used by the Sun JPEG 2000 plug-in for the Image I/O Framework.
com.sun.media.imageio.plugins.pnm - package com.sun.media.imageio.plugins.pnm: Package containing the public classes used by the Sun PNM plug-in for the Image I/O Framework.
com.sun.media.imageio.plugins.tiff - package com.sun.media.imageio.plugins.tiff: Package containing the public classes used by the TIFF plug-in for the Image I/O Framework.
com.sun.media.imageio.stream - package com.sun.media.imageio.stream: Provides ImageInputStream and ImageOutputStream classes for use with the Java Image I/O Framework.
com.sun.media.imageioimpl.common - package com.sun.media.imageioimpl.common
com.sun.media.imageioimpl.plugins.bmp - package com.sun.media.imageioimpl.plugins.bmp
com.sun.media.imageioimpl.plugins.clib - package com.sun.media.imageioimpl.plugins.clib
com.sun.media.imageioimpl.plugins.gif - package com.sun.media.imageioimpl.plugins.gif
com.sun.media.imageioimpl.plugins.jpeg - package com.sun.media.imageioimpl.plugins.jpeg
com.sun.media.imageioimpl.plugins.jpeg2000 - package com.sun.media.imageioimpl.plugins.jpeg2000
com.sun.media.imageioimpl.plugins.pcx - package com.sun.media.imageioimpl.plugins.pcx
com.sun.media.imageioimpl.plugins.png - package com.sun.media.imageioimpl.plugins.png
com.sun.media.imageioimpl.plugins.pnm - package com.sun.media.imageioimpl.plugins.pnm
com.sun.media.imageioimpl.plugins.raw - package com.sun.media.imageioimpl.plugins.raw
com.sun.media.imageioimpl.plugins.tiff - package com.sun.media.imageioimpl.plugins.tiff
com.sun.media.imageioimpl.plugins.wbmp - package com.sun.media.imageioimpl.plugins.wbmp
com.sun.media.imageioimpl.stream - package com.sun.media.imageioimpl.stream
com.sun.media.jai.imageioimpl - package com.sun.media.jai.imageioimpl
com.sun.media.jai.operator - package com.sun.media.jai.operator: Provides JAI operations which read and write images using the Java Image I/O Framework.
COM_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder: Flag bit for COM marker segment found
ComboFileFilter - Class in loci.formats.gui: A file filter that recognizes files from a union of other filters.
ComboFileFilter(FileFilter[], String) - Constructor for class loci.formats.gui.ComboFileFilter: Constructs a new filter from a list of other filters.
COMMENT - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
comment - Variable in class loci.formats.in.FluoviewReader
comment - Variable in class loci.formats.in.MicromanagerReader.Position
comment - Variable in class loci.formats.in.QuesantReader
COMMENT_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
COMMENT_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
comments - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
comments - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
comments - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata: The comments.
comments - Variable in class loci.formats.in.JPEG2000MetadataParser: List of comments stored in the file.
comments - Variable in class loci.formats.in.SVSReader
commitBitstreamHeader(HeaderEncoder) - Method in class jj2000.j2k.codestream.writer.CodestreamWriter: Writes the header data to the bit stream, if it has not been already done.
commitBitstreamHeader(HeaderEncoder) - Method in class jj2000.j2k.codestream.writer.FileCodestreamWriter: Writes the header data in the codestream and actualize ndata with the header length.
comp - Variable in class jj2000.j2k.roi.encoder.ROI: The components for which the ROI is relevant
comp - Variable in class loci.formats.gui.CacheIndicator
COMP_POS_RES_LY_PROG - Static variable in interface jj2000.j2k.codestream.ProgressionType: The bit stream is Component/Position/Resolution/Layer progressive : 4
COMPANION_KEY - Static variable in class loci.formats.out.OMETiffWriter
COMPANION_SUFFIXES - Static variable in class loci.formats.in.TiffReader
companionFile - Variable in class loci.formats.in.TiffReader
companionFiles - Variable in class loci.formats.in.DicomReader
compare(Object, Object) - Method in class loci.formats.cache.CacheStrategy: Default comparator orders dimensional positions based on distance from the current position, taking into account axis priorities and planar ordering.
compare(String, String) - Method in class loci.formats.in.MetamorphTiffReader.NumericComparator
compareTo(Object) - Method in class com.sun.media.imageio.plugins.tiff.TIFFField: Compares this TIFFField with another TIFFField by comparing the tags.
compareTo(Object) - Method in class loci.formats.gui.ComboFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.ExtensionFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.FormatFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.NoExtensionFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.tiff.TiffIFDEntry
compareTo(TiffRational) - Method in class loci.formats.tiff.TiffRational: Compares this object with the specified object for order.
compareTo(Object) - Method in class loci.plugins.config.FormatEntry
compareTo(Object) - Method in class loci.plugins.config.LibraryEntry
compareTo(ThumbLoader.SeriesInfo) - Method in class loci.plugins.in.ThumbLoader.SeriesInfo
compareTokens(String[], int, String[], int) - Method in class loci.formats.in.ICSReader
compatibility - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox
compDef - Variable in class jj2000.j2k.ModuleSpec: The default value for each component.
compH - Variable in class jj2000.j2k.image.Tiler: The component height in the current active tile, for each component
compHeight - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ: Component heights
compIdx - Variable in class jj2000.j2k.image.ImgDataJoiner: The component index associated with each ImgData
compImageSize - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
complete - Variable in class jj2000.j2k.util.ISRandomAccessIO
completedComps - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder: The queue of completed compressors, for each component.
COMPLEX - Static variable in class loci.formats.in.CellSensReader
COMPLEX - Static variable in class loci.formats.in.ZeissCZIReader
COMPLEX_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
compMainDefDecompType - Variable in class jj2000.j2k.wavelet.WTDecompSpec: The component main default decomposition, for each component.
compMainDefLevels - Variable in class jj2000.j2k.wavelet.WTDecompSpec: The component main default decomposition levels, for each component
COMPONENT_HEIGHT - Static variable in class loci.formats.gui.CacheIndicator
COMPONENT_MAPPING_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
COMPONENT_WIDTH - Static variable in class loci.formats.gui.CacheIndicator
ComponentMappingBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000: This class is defined to represent a Color Specification Box of JPEG JP2 file format.
ComponentMappingBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox: Constructs a ComponentMappingBox from the provided content byte array.
ComponentMappingBox(short[], byte[], byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox: Constructs a ComponentMappingBox from the provided component mapping.
ComponentMappingBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox: Constructs a ComponentMappingBox based on the provided org.w3c.dom.Node.
components - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox: The data elements.
COMPONENTS_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
COMPONENTS_CONFIGURATION_B - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_CB - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_CR - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_DOES_NOT_EXIST - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_G - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_R - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_Y - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "ComponentsConfiguration" tag.
ComponentsConfiguration() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ComponentsConfiguration
componentTransformation - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam: Specifies to utilize the component transformation with some tiles.
componentTransformation - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava: Specifies to utilize the component transformation with some tiles.
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box: Composes the content byte array from the data elements.
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.SignatureBox
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDBox
compose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDListBox
composeString(byte[], byte) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor: Append newString to the end of oldString.
composeString(byte[], byte) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil: Append newString to the end of oldString.
COMPR_MASKS - Static variable in class loci.formats.codec.LZWCodec: Masks for writing bits in compressor.
compress(byte[], int, int) - Method in class com.sun.media.imageioimpl.common.LZWCompressor
compress(byte[], CodecOptions) - Method in class loci.formats.codec.Base64Codec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec: 2D data block encoding default implementation.
compress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec: Compresses a block of data.
compress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec: Compresses a block of data.
compress(byte[], CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEG2000Codec: The CodecOptions parameter should have the following fields set: width height bitsPerSample channels interleaved littleEndian lossless
compress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGCodec: The CodecOptions parameter should have the following fields set: width height channels bitsPerSample interleaved littleEndian signed
compress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.LosslessJPEGCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.LuraWaveCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.LZOCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.LZWCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.MJPBCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.MSRLECodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.MSVideoCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.NikonCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.PackbitsCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.PassthroughCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.QTRLECodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.RPZACodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.TargaRLECodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.ZlibCodec
compress(byte[]) - Method in class loci.formats.out.OMEXMLWriter: Compress the given byte array using the current codec.
compress(byte[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression: Encodes a strip of data.
compress(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor: Compress the uncompressed source image associated with this compressor instance and output a JPEG image to the given destination buffer.
compress(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor: Compress the uncompressed source image associated with this compressor instance and return a buffer containing a JPEG image.
compress(BufferedImage, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor: Compress the uncompressed source image stored in srcImage and output a JPEG image to the given destination buffer.
compress(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor: Compress the uncompressed source image stored in srcImage and return a buffer containing a JPEG image.
compress(byte[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
compress(int[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
compressBuffer(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer: Compresses the buffer.
compressCodeBlock(int, CBlkRateDistStats, CBlkWTData, MQCoder, BitToByteOutput, ByteOutputBuffer, int[], double[], int[], boolean[], int[], int[], int, boolean, int, int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder: Compresses the code-block in 'srcblk' and puts the results in 'ccb', using the specified options and temporary storage.
compressed - Variable in class loci.formats.in.NAFReader
compressed - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
compressed - Variable in class loci.formats.in.PSDReader
compressed - Variable in class loci.formats.in.SBIGReader
compressed - Variable in class loci.formats.in.TargaReader
COMPRESSED_BITS_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
CompressedBitsPerPixel() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.CompressedBitsPerPixel
compressedSize - Variable in class loci.formats.in.AmiraReader.HxRLE
compressedSize - Variable in class loci.formats.in.AmiraReader.HxZip
compressedSize - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
compressedTiles - Variable in class loci.formats.codec.JPEGTileDecoder.TileCache
Compression() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Compression
compression - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: The value of the Compression tag.
compression - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
compression - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
compression - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
compression - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
compression - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
compression - Variable in enum loci.formats.codec.CompressionType: The compression used.
compression - Variable in class loci.formats.FormatWriter: Current compression type.
compression - Variable in class loci.formats.in.AmiraReader
compression - Variable in class loci.formats.in.APNGReader
compression - Variable in class loci.formats.in.BMPReader: Compression type
compression - Variable in class loci.formats.in.LiFlimReader
compression - Variable in class loci.formats.in.OBFReader.Stack
compression - Variable in class loci.formats.in.OMEXMLReader
compression - Variable in class loci.formats.in.PhotoshopTiffReader
compression - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
COMPRESSION - Static variable in class loci.formats.tiff.IFD
COMPRESSION_CCITT_RLE - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet: A value to be used with the "Compression" tag.
COMPRESSION_CCITT_T_4 - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet: A value to be used with the "Compression" tag.
COMPRESSION_CCITT_T_6 - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet: A value to be used with the "Compression" tag.
COMPRESSION_DEFLATE - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet: A value to be used with the "Compression" tag.
COMPRESSION_GZIP - Static variable in class loci.formats.in.LiFlimReader
COMPRESSION_J2K - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_J2K_LOSSY - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_JPEG - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet: A value to be used with the "Compression" tag.
COMPRESSION_JPEG - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_KEY - Static variable in class loci.formats.in.LiFlimReader
COMPRESSION_LZW - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet: A value to be used with the "Compression" tag.
COMPRESSION_LZW - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_NONE - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet: A value to be used with the "Compression" tag.
COMPRESSION_NONE - Static variable in class loci.formats.in.LiFlimReader
COMPRESSION_OLD_JPEG - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet: A value to be used with the "Compression" tag.
COMPRESSION_PACKBITS - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet: A value to be used with the "Compression" tag.
COMPRESSION_SUFFIXES - Static variable in class loci.formats.FormatHandler: Suffixes for supported compression types.
COMPRESSION_UNCOMPRESSED - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_ZLIB - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet: A value to be used with the "Compression" tag.
compressionNumbers - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter: Compression tag values for known compression types.
compressionTagValue - Variable in class com.sun.media.imageio.plugins.tiff.TIFFCompressor: The value to be assigned to the TIFF Compression tag in the TIFF image metadata.
compressionType - Variable in class com.sun.media.imageio.plugins.tiff.TIFFCompressor: The name of the compression type supported by this compressor.
compressionType - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
compressionType - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox
compressionType - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
CompressionType - Enum in loci.formats.codec: An enumeration of compression types.
CompressionType(int, String) - Constructor for enum loci.formats.codec.CompressionType: Default constructor.
compressionType - Variable in class loci.formats.in.CellSensReader
compressionTypeNames - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
compressionTypes - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter: Known TIFF compression types.
compressionTypes - Variable in class loci.formats.FormatWriter: Available compression types.
compressionTypes - Variable in class loci.formats.ImageWriter: Compression types for all file format writers.
compressor - Variable in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam
compressor - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
Compressor(int) - Constructor for class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor: Creates a new compressor object with the given index.
comps - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader: Component mapping
compSize - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
CompTransfSpec - Class in jj2000.j2k.image: This class extends ModuleSpec class in order to hold tile specifications for component transformation
CompTransfSpec(int, int, byte) - Constructor for class jj2000.j2k.image.CompTransfSpec: Constructs an empty 'CompTransfSpec' with specified number of tile and components.
computeAxisLengths() - Method in class loci.formats.FileStitcher: Computes axis length arrays, and total axis lengths.
computeIndices(int) - Method in class loci.formats.FileStitcher: Gets the file index, and image index into that file, corresponding to the given global image index.
computeLength(ColorModel) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox: Computes the length of this box from the provided ColorModel.
computeLength(byte, ICC_Profile) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox: Computes the length of this box when profile is present.
computeLength(IndexColorModel) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox: Compute the length of this box.
computeLength(IIOMetadataNode) - Method in class jj2000.j2k.fileformat.writer.FileFormatWriter
computeNameAndLocation() - Method in class loci.plugins.in.ImportProcess: Initializes the idName and idLoc derived values.
computePhysicalSize(int, String, String) - Method in class loci.formats.in.VarianFDFReader: Return the physical size of a pixel, in microns, along an arbitrary axis based on the supplied physical and pixel lengths of the axis.
computeRegions(Rectangle, Dimension, ImageWriteParam) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter: Compute the source region and destination dimensions taking any parameter settings into account.
computeRegionsWrapper(ImageReadParam, boolean, int, int, BufferedImage, Rectangle, Rectangle) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader: Wrapper for the protected method computeRegions.
computeRegionsWrapper(ImageReadParam, int, int, BufferedImage, Rectangle, Rectangle) - Static method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader: Wrapper for the protected method computeRegions.
computeSeriesLabels(IFormatReader) - Method in class loci.plugins.in.ImportProcess
computeSizeT(int) - Method in class loci.formats.in.PrairieReader: Scans the parsed metadata to determine the number of actual time points versus the number of actual stage positions.
computeVariableTimeInterval(IMetadata, int) - Method in class loci.plugins.in.Calibrator
compW - Variable in class jj2000.j2k.image.Tiler: The component width in the current active tile, for each component
compWidth - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ: Component widths
concatenate(List<ImagePlus>) - Method in class loci.plugins.in.Concatenator: Concatenates the list of images as appropriate.
concatenate(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
concatenateBox - Variable in class loci.plugins.in.MainDialog
concatenateTokens(String[], int, int) - Method in class loci.formats.in.ICSReader
Concatenator - Class in loci.plugins.in: Logic for concatenating multiple images together.
Concatenator() - Constructor for class loci.plugins.in.Concatenator
conceal(DataBlk, int) - Method in class jj2000.j2k.entropy.decoder.StdEntropyDecoder: Conceals decoding errors detected in the last bit-plane.
CONCURRENCY_PROP_NAME - Static variable in class jj2000.j2k.util.ThreadPool: The name of the property that sets the concurrency level: jj2000.j2k.util.ThreadPool.concurrency
config - Variable in class loci.formats.in.PrairieMetadata: Key/value pairs from CFG and/or ENV files.
ConfigWindow - Class in loci.plugins.config: A window for managing configuration of the Bio-Formats plugins.
ConfigWindow() - Constructor for class loci.plugins.config.ConfigWindow
confirmFileType() - Method in class jj2000.j2k.image.input.ImgReaderPGM: Checks that the RandomAccessIO begins with 'P5'
ConsecutiveBadFaxLines() - Constructor for class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet.ConsecutiveBadFaxLines
constructDialog() - Method in class loci.plugins.in.ColorDialog
constructDialog() - Method in class loci.plugins.in.CropDialog
constructDialog() - Method in class loci.plugins.in.FilePatternDialog
constructDialog() - Method in class loci.plugins.in.IdDialog
constructDialog() - Method in class loci.plugins.in.ImporterDialog
constructDialog() - Method in class loci.plugins.in.LocationDialog
constructDialog() - Method in class loci.plugins.in.MainDialog
constructDialog() - Method in class loci.plugins.in.MemoryDialog
constructDialog() - Method in class loci.plugins.in.RangeDialog
constructDialog() - Method in class loci.plugins.in.SeriesDialog
constructDialog() - Method in class loci.plugins.in.SwapDialog
constructDialog() - Method in class loci.plugins.in.UpgradeDialog
constructImage(int, int, int, int, boolean, boolean, DataBuffer) - Static method in class loci.formats.gui.AWTImageTools: Creates an image with the given DataBuffer.
constructImage(int, int, int, int, boolean, boolean, DataBuffer, ColorModel) - Static method in class loci.formats.gui.AWTImageTools: Creates an image with the given DataBuffer.
constructImageTitle(IFormatReader, String, String, boolean) - Method in class loci.plugins.in.ImagePlusReader
constructLoader() - Static method in class loci.formats.gui.LegacyQTTools
constructSliceLabel(int, IFormatReader, IMetadata, int, int, int, int) - Method in class loci.plugins.in.ImagePlusReader
consumer - Variable in class loci.formats.codec.JPEGTileDecoder
CONTAINER_TYPES - Static variable in class loci.formats.in.NativeQTReader: List of identifiers for each container atom.
ContainerRecord(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.ContainerRecord
containsTIFFField(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory: Determines whether a TIFF field with the given tag number is contained in this directory.
contentFileType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
contentGUID - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
contents - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderResources
contents - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterResources
contents - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormatResources
contents - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormatResources
contents - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadataFormatResources
contents - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadataFormatResources
Context() - Constructor for enum loci.formats.in.BaseZeissReader.Context
context - Variable in class loci.formats.in.BaseZeissReader.Tag
CONTIGUOUS_CODESTREAM_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
Contrast() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.Contrast
CONTRAST - Static variable in class loci.formats.in.CellSensReader
CONTRAST - Static variable in class loci.formats.tiff.IFD
CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
CONTRAST_HARD - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "Contrast" tag.
CONTRAST_NORMAL - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "Contrast" tag.
CONTRAST_SOFT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "Contrast" tag.
CONTRAST_TARGET - Static variable in class loci.formats.in.CellSensReader
convert(String, String) - Static method in class loci.formats.FormatTools: Convenience method for converting the specified input file to the specified output file.
convert(IFormatReader, IFormatWriter, String) - Static method in class loci.formats.FormatTools: Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter.
convert - Variable in class loci.formats.gui.DataConverter
converter - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
converter2 - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
convertFactor - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTData: The value by which the absolute value of the data has to be divided in order to get the real absolute value.
convertFromExpMantissa(int) - Static method in class jj2000.j2k.quantization.quantizer.StdQuantizer: Converts the exponent-mantissa representation to its floating-point value.
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter: Creates a default image metadata object and merges in the supplied metadata.
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
convertMetadata(String, IIOMetadata, IIOMetadata) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter: Merges inData into outData.
convertMetadata(MetadataRetrieve, MetadataStore) - Static method in class loci.formats.meta.MetadataConverter: Deprecated.

Copies information from a metadata retrieval object (source) into a metadata store (destination).
convertMetadata(String, MetadataStore) - Method in interface loci.formats.services.OMEXMLService: Converts information from an OME-XML string (source) into a metadata store (destination).
convertMetadata(MetadataRetrieve, MetadataStore) - Method in interface loci.formats.services.OMEXMLService: Copies information from a metadata retrieval object (source) into a metadata store (destination).
convertMetadata(String, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
convertMetadata(MetadataRetrieve, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
convertNativeImageMetadata(IIOMetadata) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter: Converts a native com_sun_media_imageio_plugins_tiff_image_1.0 tree to a TIFFImageMetadata object.
convertObjectToString(Object) - Static method in class com.sun.media.imageioimpl.common.ImageUtil: Converts the provided object to String
convertPixelType(int) - Method in class loci.formats.in.CellSensReader
convertPixelType(int) - Method in class loci.formats.in.JPEG2000MetadataParser
convertPixelType(int) - Method in class loci.formats.in.TillVisionReader
convertPixelType(int) - Method in class loci.formats.in.ZeissCZIReader
convertPixelType(CoreMetadata, int) - Method in class loci.formats.in.ZeissCZIReader
convertRenderedImage(RenderedImage) - Static method in class loci.formats.gui.AWTImageTools: Converts a java.awt.image.RenderedImage into a java.awt.image.BufferedImage.
convertStandardImageMetadata(IIOMetadata) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter: Converts a standard javax_imageio_1.0 tree to a TIFFImageMetadata object.
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter: Creates a default stream metadata object and merges in the supplied metadata.
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
convertTo8Bit(short[][]) - Method in class loci.plugins.util.ImageProcessorReader
convertToByte(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
convertToExpMantissa(float) - Static method in class jj2000.j2k.quantization.quantizer.StdQuantizer: Converts the floating point value to its exponent-mantissa representation.
convertToFloat() - Method in class loci.plugins.util.RecordedImageProcessor
convertToRGB() - Method in class loci.plugins.util.RecordedImageProcessor
convertToShort(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
convertUnits(String) - Method in class loci.formats.in.GatanReader
convertUnits(int) - Method in class loci.formats.in.IMODReader
convolve(float[], int, int) - Method in class loci.plugins.util.RecordedImageProcessor
convolve3x3(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
COOKIE - Static variable in class loci.formats.in.IM3Reader: First 4 bytes of file is "1985"
COOLING_ON - Static variable in class loci.formats.in.CellSensReader
coordinate - Variable in class loci.formats.in.CellSensReader.TileCoordinate
Coordinate(int, int, int) - Constructor for class loci.formats.in.ZeissCZIReader.Coordinate
coordinates - Variable in class loci.formats.in.BaseZeissReader
CoordInfo - Class in jj2000.j2k.codestream: This class is used to store the coordinates of objects such as code-blocks or precincts.
CoordInfo(int, int, int, int) - Constructor for class jj2000.j2k.codestream.CoordInfo: Constructor.
CoordInfo() - Constructor for class jj2000.j2k.codestream.CoordInfo: Empty contructor
copyBits(ImageProcessor, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
copyData(WritableRaster) - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage: Copies an arbitrary rectangular region of the RenderedImage into a caller-supplied WritableRaster.
copyData(WritableRaster) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
copyInt(byte[], int, int) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box: Copies that four bytes of an integer into the byte array.
copyPixels(int, int, int, int, int, int, byte[], byte[], boolean) - Method in class loci.formats.in.NativeND2Reader
Copyright() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Copyright
copyright - Static variable in class jj2000.j2k.JJ2KInfo: The copyright message string.
COPYRIGHT - Static variable in class loci.formats.tiff.IFD
copyScaled(BufferedImage, BufferedImage, Object) - Static method in class loci.formats.gui.AWTImageTools: Copies the source image into the target, applying scaling.
core - Variable in class loci.formats.DimensionSwapper: Core metadata associated with this dimension swapper.
core - Variable in class loci.formats.FileStitcher: Core metadata.
core - Variable in class loci.formats.FormatReader: Core metadata values.
core - Variable in class loci.formats.in.LeicaHandler
core - Variable in class loci.formats.in.ND2Handler
core - Variable in class loci.formats.in.VolocityReader.Stack
coreIndex - Variable in class loci.formats.FileStitcher: The number of the current series.
coreIndex - Variable in class loci.formats.FormatReader: The number of the current series.
coreIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
coreIndexToSeries(int) - Method in class loci.formats.FileStitcher
coreIndexToSeries(int) - Method in class loci.formats.FormatReader
coreIndexToSeries(int) - Method in interface loci.formats.IFormatReader: Returns the series corresponding to the specified core index.
coreIndexToSeries(int) - Method in class loci.formats.ImageReader
coreIndexToSeries(int) - Method in class loci.formats.in.FilePatternReader
coreIndexToSeries(int) - Method in class loci.formats.ReaderWrapper
CoreMetadata - Class in loci.formats: Encompasses core metadata values.
CoreMetadata() - Constructor for class loci.formats.CoreMetadata
CoreMetadata(IFormatReader, int) - Constructor for class loci.formats.CoreMetadata
CoreMetadata(CoreMetadata) - Constructor for class loci.formats.CoreMetadata
coreMetaData - Static variable in class loci.formats.in.SPEReader
correction - Variable in class loci.formats.in.ND2Handler
correction - Variable in class loci.formats.in.NikonTiffReader
correction - Variable in class loci.formats.in.ZeissLSMReader.Recording
correctionCollar - Variable in class loci.formats.in.ZeissCZIReader
corrections - Variable in class loci.formats.in.LIFReader
correctUnits(Double, String) - Method in class loci.formats.in.ColumbusReader
CorruptedCodestreamException - Exception in jj2000.j2k.codestream: Thsi exception is thrown whenever an illegal value is read from a bit stream.
CorruptedCodestreamException() - Constructor for exception jj2000.j2k.codestream.CorruptedCodestreamException: Constructs a new CorruptedCodestreamException exception with no detail message.
CorruptedCodestreamException(String) - Constructor for exception jj2000.j2k.codestream.CorruptedCodestreamException: Constructs a new CorruptedCodestreamException exception with the specified detail message.
cortime - Variable in class loci.formats.in.SDTInfo: Correlation time [ms].
count - Variable in class com.sun.media.imageio.plugins.tiff.TIFFField: The number of data items present in the field.
count - Variable in class jj2000.j2k.entropy.decoder.ByteInputBuffer: The index one greater than the last valid character in the input stream buffer
count - Variable in class jj2000.j2k.entropy.encoder.ByteOutputBuffer: The number of valid bytes in the buffer
count - Variable in class loci.formats.in.LeicaHandler
count() - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
count - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
countBits(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
countedByteRead() - Method in class jj2000.j2k.image.input.ImgReaderPGM: Returns a byte read from the RandomAccessIO.
COUNTER_CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
countImages() - Method in class loci.formats.in.BaseZeissReader
countImages() - Method in class loci.formats.in.ZeissTIFFReader
countImages() - Method in class loci.formats.in.ZeissZVIReader
cqcc - Variable in class jj2000.j2k.codestream.HeaderInfo.QCC
cQuit - Variable in class jj2000.j2k.codestream.reader.PktDecoder: The component in which the ncb quit condition was reached
crc(byte[]) - Method in class loci.formats.out.APNGWriter
crc(byte[], int, int) - Method in class loci.formats.out.APNGWriter
createAngle(Double, Unit<Angle>) - Static method in class loci.formats.FormatTools
createAngle(Integer, Unit<Angle>) - Static method in class loci.formats.FormatTools
createAngle(T, Unit<Angle>) - Static method in class loci.formats.FormatTools
createArrayForType(int, int) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFField: Creates an array appropriate for the indicated data type.
createBaseReader() - Method in class loci.plugins.in.ImportProcess: Initializes an IFormatReader according to the current configuration.
createBitsPerComponentBoxFromStandardNode(Node) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
createBox(int, Node) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box: Creates a Box object with the provided type based on the provided Node object based on reflection.
createChannelDefinitionFromStandardNode(Node) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
createChannelPriorities() - Static method in class loci.formats.in.LIFReader
createCodec(boolean) - Method in class loci.formats.in.NativeND2Reader
createColorModel(SampleModel) - Static method in class com.sun.media.imageioimpl.common.ImageUtil: Creates a ColorModel that may be used with the specified SampleModel.
createColorModel(ColorSpace, SampleModel) - Static method in class com.sun.media.imageioimpl.common.ImageUtil
createColorModel() - Method in class loci.plugins.util.ImageProcessorReader
createColorSpecificationBoxFromStandardNode(Node) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
createColorTable(ColorModel, SampleModel) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter: Create a color table from the image ColorModel and SampleModel.
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.Index16ColorModel
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.SignedColorModel
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
createComponentCM(ColorSpace, int, int, boolean, boolean) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: Create a ComponentColorModel for use in creating an ImageTypeSpecifier.
created - Variable in class loci.formats.out.QTWriter: Time the file was created.
createDecoder(short[], int, int) - Method in class loci.formats.codec.HuffmanCodec.Decoder
createDecoder(HuffmanCodec.Decoder, short[], int, int) - Method in class loci.formats.codec.HuffmanCodec.Decoder
createDequantizer(CBlkQuantDataSrcDec, int[], DecoderSpecs) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder: Returns the dequantizer parameters.
createElectricPotential(Double, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
createElectricPotential(Integer, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
createElectricPotential(T, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
createEntropyDecoder(CodedCBlkDataSrcDec, J2KImageReadParamJava) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder: Creates and returns the entropy decoder corresponding to the information read from the codestream header and with the special additional parameters from the parameter list.
createFileInfo() - Method in class loci.plugins.in.ImagePlusReader
createFrequency(Double, Unit<Frequency>) - Static method in class loci.formats.FormatTools
createFrequency(Integer, Unit<Frequency>) - Static method in class loci.formats.FormatTools
createFrequency(T, Unit<Frequency>) - Static method in class loci.formats.FormatTools
createFromMetadata(IIOMetadata) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory: Creates a TIFFDirectory instance from the contents of an image metadata object.
createFromMetadataNode(TIFFTagSet, Node) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFField: Creates a TIFFField from a TIFF native image metadata node.
createGroup(String) - Method in interface loci.formats.services.JHDFService: Writes an array as sub-slice into an existing HDF5 dataset
createGroup(String) - Method in class loci.formats.services.JHDFServiceImpl
createHeaderBoxFromStandardNode(Node, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
createImage(String, List<ImageProcessor>) - Static method in class loci.plugins.in.ImagePlusReader: Creates an ImagePlus from the given image processors.
createImage(String, ImageStack, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader: Creates an ImagePlus from the given image stack.
createImage() - Method in class loci.plugins.util.RecordedImageProcessor
createIndexColorModel(RenderedImage) - Static method in class com.sun.media.imageioimpl.common.PaletteBuilder: Creates an palette representing colors from given image img.
createIndexedImage(RenderedImage) - Static method in class com.sun.media.imageioimpl.common.PaletteBuilder: Creates an image representing given image src using IndexColorModel.
createIndexMap(int) - Method in class loci.formats.in.FakeReader: Creates a mapping between indices and color values.
createInputStream() - Method in class loci.formats.out.TiffWriter
createInputStreamInstance(Object, boolean, File) - Method in class com.sun.media.imageioimpl.stream.ChannelImageInputStreamSpi
createInstance(RandomAccessIO, HeaderDecoder, J2KImageReadParamJava, DecoderSpecs, boolean, HeaderInfo) - Static method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent: Creates a bit stream reader of the correct type that works on the provided RandomAccessIO, with the special parameters from the parameter list.
createInstance(CBlkQuantDataSrcEnc, J2KImageWriteParamJava, CBlkSizeSpec, PrecinctSizeSpec, StringSpec, StringSpec, StringSpec, StringSpec, StringSpec, StringSpec, StringSpec) - Static method in class jj2000.j2k.entropy.encoder.EntropyCoder: Creates a EntropyCoder object for the appropriate entropy coding parameters in the parameter list 'pl', and having 'src' as the source of quantized data.
createInstance(CodedCBlkDataSrcEnc, float, CodestreamWriter, J2KImageWriteParamJava) - Static method in class jj2000.j2k.entropy.encoder.PostCompRateAllocator: Creates a PostCompRateAllocator object for the appropriate rate allocation parameters in the parameter list 'pl', having 'src' as the source of entropy coded data, 'rate' as the target bitrate and 'bw' as the bit stream writer object.
createInstance(CBlkWTDataSrc, J2KImageWriteParamJava) - Static method in class jj2000.j2k.quantization.quantizer.Quantizer: Creates a Quantizer object for the appropriate type of quantization specified in the options in the parameter list 'pl', and having 'src' as the source of data to be quantized.
createInstance(Quantizer, J2KImageWriteParamJava) - Static method in class jj2000.j2k.roi.encoder.ROIScaler: Creates a ROIScaler object.
createInstance(CBlkQuantDataSrcDec, J2KImageReadParamJava, DecoderSpecs) - Static method in class jj2000.j2k.roi.ROIDeScaler: Creates a ROIDeScaler object.
createInstance(BlkImgDataSrc, J2KImageWriteParamJava) - Static method in class jj2000.j2k.wavelet.analysis.ForwardWT: Creates a ForwardWT object with the specified filters, and with other options specified in the parameter list 'pl'.
createInstance(CBlkWTDataSrcDec, DecoderSpecs) - Static method in class jj2000.j2k.wavelet.synthesis.InverseWT: Creates an InverseWT object that works on the data type of the source, with the special additional parameters from the parameter list.
createInterleavedSM(int, int) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: Create a PixelInterleavedSampleModel for use in creating an ImageTypeSpecifier.
createKeys() - Static method in class loci.formats.in.ZeissLSMReader
createLargePalette(ColorModel) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
createLength(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
createLength(Integer, Unit<Length>) - Static method in class loci.formats.FormatTools
createLength(T, Unit<Length>) - Static method in class loci.formats.FormatTools
createLSID(String, int...) - Static method in class loci.formats.MetadataTools: Constructs an LSID, given the object type and indices.
createMask(int[], int) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
createMetadata(String, CoreMetadata) - Method in class loci.formats.tools.MakeTestOmeTiff
createModulo(OMEXMLMetadata, Modulo, StructuredAnnotations, Image, int, int, int) - Method in class loci.formats.services.OMEXMLServiceImpl: Create a ModuloAlong* annotation corresponding to the given Modulo.
createNodeIntoTree(IIOMetadataNode, String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
createOMEXMLMetadata() - Static method in class loci.formats.MetadataTools: Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.
createOMEXMLMetadata() - Method in interface loci.formats.services.OMEXMLService: Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.
createOMEXMLMetadata(String) - Method in interface loci.formats.services.OMEXMLService: Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package, wrapping a DOM representation of the given OME-XML string.
createOMEXMLMetadata(String, String) - Method in interface loci.formats.services.OMEXMLService: Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package, wrapping a DOM representation of the given OME-XML string.
createOMEXMLMetadata() - Method in class loci.formats.services.OMEXMLServiceImpl
createOMEXMLMetadata(String) - Method in class loci.formats.services.OMEXMLServiceImpl
createOMEXMLMetadata(String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
createOMEXMLRoot(String) - Method in interface loci.formats.services.OMEXMLService: Constructs an OME root node.
createOMEXMLRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl
createOutputStream() - Method in class loci.formats.FormatWriter
createOutputStreamInstance(Object, boolean, File) - Method in class com.sun.media.imageioimpl.stream.ChannelImageOutputStreamSpi
createPaletteBoxFromStandardNode(Node) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
createPlane(String, CoreMetadata, int) - Method in class loci.formats.tools.MakeTestOmeTiff
createPower(Double, Unit<Power>) - Static method in class loci.formats.FormatTools
createPower(Integer, Unit<Power>) - Static method in class loci.formats.FormatTools
createPower(T, Unit<Power>) - Static method in class loci.formats.FormatTools
createPressure(Double, Unit<Pressure>) - Static method in class loci.formats.FormatTools
createPressure(Integer, Unit<Pressure>) - Static method in class loci.formats.FormatTools
createPressure(T, Unit<Pressure>) - Static method in class loci.formats.FormatTools
createProcessor(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
createRawImage() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor: Creates a BufferedImage whose underlying data array will be suitable for holding the raw decoded output of the decodeRaw method.
createReaderInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
createReaderInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
createReaderInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
createReaderInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
createReaderInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReaderSpi
createReaderInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
createReaderInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
createResolutionBoxFromStandardNode(Node) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
createROIDeScaler(CBlkQuantDataSrcDec, J2KImageReadParamJava, DecoderSpecs) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder: Creates and returns the ROIDeScaler corresponding to the information read from the codestream header and with the special additional parameters from the parameter list.
createRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl: Constructs an OME root node.
createSmallPalette(ColorModel) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
createStack(List<ImageProcessor>, List<String>, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader: Creates an image stack from the given image processors.
createSwatch(Color) - Method in class loci.plugins.in.ColorDialog
createTemperature(Double, Unit<Temperature>) - Static method in class loci.formats.FormatTools
createTemperature(Integer, Unit<Temperature>) - Static method in class loci.formats.FormatTools
createTemperature(T, Unit<Temperature>) - Static method in class loci.formats.FormatTools
createTiffSaver() - Method in class loci.formats.out.TiffWriter
createTileParts() - Method in class jj2000.j2k.util.CodestreamManipulator: This method creates the tileparts from the buffered tile headers, packet headers and packet data
createTime(Double, Unit<Time>) - Static method in class loci.formats.FormatTools
createTime(Integer, Unit<Time>) - Static method in class loci.formats.FormatTools
createTime(T, Unit<Time>) - Static method in class loci.formats.FormatTools
createVirtualStack(ImportProcess, int, List<LUT>) - Method in class loci.plugins.in.ImagePlusReader
createWriter(String, CoreMetadata, String) - Method in class loci.formats.tools.MakeTestOmeTiff
createWriterInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
createWriterInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriterSpi
createWriterInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
createWriterInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
createWriterInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
createWriterInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
createWriterInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
createWriterInstance(Object) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
createXMLBoxFromStandardNode(Node) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
CREATION_TIME - Static variable in class loci.formats.in.CellSensReader
creationDate - Variable in class loci.formats.in.FV1000Reader
creationDate - Variable in class loci.formats.in.ImaconReader
creationDate - Variable in class loci.formats.in.InCellReader
creationDate - Variable in class loci.formats.in.IvisionReader
creationDate - Variable in class loci.formats.in.LeicaSCNReader.Image
creationDate - Variable in class loci.formats.in.PCIReader
CREATOR - Static variable in class loci.formats.FormatTools: Value to use when setting creator/software fields in exported files.
CREATOR_TAG - Static variable in class loci.formats.in.ImaconReader
crg - Variable in class jj2000.j2k.codestream.HeaderInfo: Reference to the CRG marker segment found in main header
CRG() - Constructor for class jj2000.j2k.codestream.HeaderInfo.CRG
CRG - Static variable in interface jj2000.j2k.codestream.Markers: Component registration (CRG): 0xFF63
CRG_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder: Flag bit for CRG marker segment found
crgn - Variable in class jj2000.j2k.codestream.HeaderInfo.RGN
crop() - Method in class loci.plugins.util.RecordedImageProcessor
cropBox - Variable in class loci.plugins.in.MainDialog
CropDialog - Class in loci.plugins.in: Bio-Formats Importer crop options dialog box.
CropDialog(ImportProcess) - Constructor for class loci.plugins.in.CropDialog: Creates a crop options dialog for the Bio-Formats Importer.
cropRegion - Variable in class loci.plugins.in.ImporterOptions
crossChan - Variable in class loci.formats.in.SDTInfo: Cross FCS routing channel number when chan = crossChan and mod == crossMod - Auto FCS otherwise - Cross FCS.
CrosshairStrategy - Class in loci.formats.cache: A crosshair strategy caches planes extending from the the current dimensional position along each individual axis, but not combinations of axes.
CrosshairStrategy(int[]) - Constructor for class loci.formats.cache.CrosshairStrategy: Constructs a crosshair strategy.
crossMod - Variable in class loci.formats.in.SDTInfo: Cross FCS module number.
crossMtResol - Variable in class loci.formats.in.SDTInfo: Macro time clock of cross FCS module in 0.1 ns units.
cs - Variable in class jj2000.j2k.entropy.Progression: Component index for the start of a progression
CS - Static variable in class loci.formats.in.DicomReader
CS_2C - Static variable in class loci.formats.gui.TwoChannelColorSpace
CSB_APPROX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
CSB_ENUM_GREY - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
CSB_ENUM_SRGB - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
CSB_ENUM_YCC - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
CSB_LENGTH - Static variable in class jj2000.j2k.fileformat.writer.FileFormatWriter: Length of Colour Specification Box
CSB_METH - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes: Colour Specification Box Fields
CSB_PREC - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
cScroll - Variable in class loci.plugins.util.DataBrowser
csiz - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ
cSlider - Variable in class loci.formats.gui.ImageViewer
cSliders - Variable in class loci.plugins.util.DataBrowser
cspoc - Variable in class jj2000.j2k.codestream.HeaderInfo.POC
csRGB - Variable in class com.sun.media.imageioimpl.common.InvertedCMYKColorSpace
csRGB - Variable in class com.sun.media.imageioimpl.common.SimpleCMYKColorSpace
css - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder: Causal stripes specifications
cStep - Variable in class loci.plugins.in.ImporterOptions
CSV_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
cT - Variable in class jj2000.j2k.entropy.decoder.MQDecoder: The bit code counter
cT - Variable in class jj2000.j2k.entropy.encoder.MQCoder: The bit code counter
ctp - Variable in class jj2000.j2k.codestream.reader.CBlkInfo: The cumulative number of truncation points
cts - Variable in class jj2000.j2k.decoder.DecoderSpecs: The component transformation specifications
cts - Variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf: The component transformations specifications
cts - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf: The component transformations specifications
cts - Variable in class jj2000.j2k.quantization.dequantizer.Dequantizer: The inverse component transformation specifications
ctX - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent: The current tile horizontal index
ctxtbufT - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder: Buffer for the contexts to use when sending buffered symbols to the MQ-coder, for each thread.
ctY - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent: The current tile vertical index
cType - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
culx - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent: The horizontal coordinates of the upper-left corner of the active tile, with respect to the canvas origin, in the component hi-res grid, for each component.
culy - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent: The vertical coordinates of the upper-left corner of the active tile, with respect to the canvas origin, in the component hi-res grid, for each component.
curbyte - Variable in class jj2000.j2k.codestream.writer.BitOutputBuffer: The position of the current byte to write
curCycle - Variable in class loci.formats.in.SDTInfo: Current cycle (accumulation cycle in FLOW mode) - (if multi-cycle measurement).
curPage - Variable in class loci.formats.in.SDTInfo: Current measured page.
currChangingElems - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
current - Variable in class loci.formats.ImageReader: Current form index.
current - Variable in class loci.formats.ImageWriter: Current form index.
current_layer - Variable in class loci.formats.in.ZeissTIFFHandler
current_scaling - Variable in class loci.formats.in.ZeissTIFFHandler
current_shape - Variable in class loci.formats.in.ZeissTIFFHandler
current_tag - Variable in class loci.formats.in.ZeissTIFFHandler
current_tagset - Variable in class loci.formats.in.ZeissTIFFHandler
currentBit - Variable in class loci.formats.codec.BitBuffer: Deprecated.
currentBlock - Variable in class loci.formats.in.APNGReader.PNGInputStream
currentBlock - Variable in class loci.formats.in.PQBinReader: Block of time bins currently stored for faster loading.
currentBlock - Variable in class loci.formats.in.SDTReader: Block of time bins currently stored for faster loading.
currentByte - Variable in class loci.formats.codec.BitBuffer: Deprecated.
currentCol - Variable in class loci.formats.in.InCellReader.InCellHandler
currentElement - Variable in class loci.formats.in.AFIReader.AFIHandler
currentElement - Variable in class loci.formats.in.IvisionReader.IvisionHandler
currentField - Variable in class loci.formats.in.InCellReader.InCellHandler
currentFile - Variable in class loci.formats.services.JHDFServiceImpl
currentFile - Variable in class loci.formats.services.NetCDFServiceImpl
currentFragment - Variable in class loci.formats.out.OMEXMLWriter
currentFrame - Variable in class loci.formats.in.SPCReader
currentIcsId - Variable in class loci.formats.in.ICSReader: Current filename.
currentId - Variable in class loci.formats.FormatHandler: Name of current file.
currentId - Variable in class loci.formats.ImageReader: Name of current file.
currentId - Variable in class loci.formats.ImageWriter: Name of current file.
currentIdsId - Variable in class loci.formats.in.ICSReader
currentImage - Variable in class loci.formats.in.InCellReader.InCellHandler
currentImage - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
currentImageFile - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
currentInflatedFrame - Variable in class loci.formats.in.OBFReader
currentLine - Variable in class loci.formats.in.SPCReader
currentName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
currentName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
currentNo - Variable in class loci.formats.in.AmiraReader.HxRLE
currentNo - Variable in class loci.formats.in.AmiraReader.HxZip
currentPixel - Variable in class loci.formats.in.SPCReader
currentPlane - Variable in class loci.formats.in.InCellReader.InCellHandler
currentPos - Variable in class loci.formats.cache.Cache: Current dimensional position.
currentProcessor - Variable in class loci.plugins.util.BFVirtualStack
currentQName - Variable in class loci.formats.in.InCellReader.InCellHandler
currentQName - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
currentRow - Variable in class loci.formats.in.InCellReader.InCellHandler
currentSlice - Variable in class loci.plugins.util.BFVirtualStack
currentSubband - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull: The subband being dealt with in each component
currentThumbnail - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
currentTile - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
currentTile - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
currentTileGrid - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
currentTileGrid - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
currentValue - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
currentValue - Variable in class loci.formats.in.OperettaReader.OperettaHandler
currentValue - Variable in class loci.formats.in.ScanrReader.ScanrHandler
currIndex - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
currLevel - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
currSize - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
curStep - Variable in class loci.formats.in.SDTInfo: Current step (if multi-step measurement).
curTilePart - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent: The current tile part being used
curve - Variable in class loci.formats.codec.NikonCodecOptions
CURVE - Static variable in class loci.formats.in.NikonReader
curve - Variable in class loci.formats.in.NikonReader
CUSTOM - Static variable in interface jj2000.j2k.wavelet.FilterTypes: User-defined filter: -1
CUSTOM_BITS - Static variable in class loci.formats.in.SimplePCITiffReader
CUSTOM_GRAYSCALE - Static variable in class loci.formats.in.CellSensReader
CUSTOM_RENDERED - Static variable in class loci.formats.tiff.IFD
CUSTOM_RENDERED_CUSTOM - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "CustomRendered" tag.
CUSTOM_RENDERED_NORMAL - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet: A value to be used with the "CustomRendered" tag.
customColors - Variable in class loci.plugins.in.ImporterOptions
customFilter(ShortBuffer, Rectangle, Rectangle, int, int, TJTransform) - Method in interface org.libjpegturbo.turbojpeg.TJCustomFilter: A callback function that can be used to modify the DCT coefficients after they are losslessly transformed but before they are transcoded to a new JPEG file.
CustomRendered() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.CustomRendered
cutIn - Variable in class loci.formats.in.LeicaHandler.MultiBand
cutInPopulated - Variable in class loci.formats.in.LeicaReader
cutIns - Variable in class loci.formats.in.LIFReader
cutOut - Variable in class loci.formats.in.LeicaHandler.MultiBand
cutOutPopulated - Variable in class loci.formats.in.LeicaReader
cutOuts - Variable in class loci.formats.in.LIFReader
cycle - Variable in class loci.formats.in.PrairieMetadata.Sequence: cycle of this <Sequence>.
cycleMax - Variable in class loci.formats.in.PrairieMetadata: Maximum cycle value.
cycleMin - Variable in class loci.formats.in.PrairieMetadata: Minimum cycle value.
cycles - Variable in class loci.formats.in.SDTInfo: Cycles (accumulation cycles in FLOW mode).
CYTELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader
CZI_MAGIC_STRING - Static variable in class loci.formats.in.ZeissCZIReader





D

d(String) - Method in class loci.formats.in.PrairieMetadata

Converts the given string to a Double, or null if
 incompatible.

DA - Static variable in class loci.formats.in.DicomReader
 
DAC - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
DAILY - Static variable in class loci.plugins.Updater
 
DAILY_BUILD - Static variable in class loci.formats.UpgradeChecker

Location of the JAR artifacts for Bio-Formats' daily build.

data - Variable in class com.sun.media.imageio.plugins.tiff.TIFFField

The field data.

data - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.Box
 
data - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
data - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
data - Variable in class jj2000.j2k.entropy.CodedCBlk

The compressed data

data - Variable in class jj2000.j2k.image.DataBlkFloat

The array where the data is stored

data - Variable in class jj2000.j2k.image.DataBlkInt

The array where the data is stored

data - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTDataFloat

The array where the data is stored

data - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTDataInt

The array where the data is stored

data - Variable in class loci.formats.codec.ByteVector
 
data - Variable in class loci.formats.in.ICSReader

Image data.

data - Variable in class loci.formats.in.IM3Reader
 
data - Variable in class loci.formats.in.TextReader

Because we have no way of indexing into the text file efficiently
 in general, we cheat and store the entire file's data in a giant array.

DATA_CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
 
DATA_CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
 
DATA_DIR - Static variable in class loci.formats.in.VolocityReader
 
DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo

For normal .sdt files (setup + data).

DATA_SIGNATURE - Static variable in class loci.formats.out.AVIWriter
 
DataBlk - Class in jj2000.j2k.image

This is a generic abstract class to store data from a block of an
 image.

DataBlk() - Constructor for class jj2000.j2k.image.DataBlk
 
DataBlkFloat - Class in jj2000.j2k.image

This is an implementation of the DataBlk interface for
 32 bit floating point data (float).

DataBlkFloat() - Constructor for class jj2000.j2k.image.DataBlkFloat

Creates a DataBlkFloat with 0 dimensions and no data array
 (i.e.

DataBlkFloat(int, int, int, int) - Constructor for class jj2000.j2k.image.DataBlkFloat

Creates a DataBlkFloat with the specified dimensions and
 position.

DataBlkFloat(DataBlkFloat) - Constructor for class jj2000.j2k.image.DataBlkFloat

Copy constructor.

DataBlkInt - Class in jj2000.j2k.image

This is an implementation of the DataBlk interface for
 signed 32 bit integral data.

DataBlkInt() - Constructor for class jj2000.j2k.image.DataBlkInt

Creates a DataBlkInt with 0 dimensions and no data array
 (i.e.

DataBlkInt(int, int, int, int) - Constructor for class jj2000.j2k.image.DataBlkInt

Creates a DataBlkInt with the specified dimensions and
 position.

DataBlkInt(DataBlkInt) - Constructor for class jj2000.j2k.image.DataBlkInt

Copy constructor.

dataBlockLength - Variable in class loci.formats.in.SDTInfo
 
dataBlockOffs - Variable in class loci.formats.in.SDTInfo

Offset of the first data block.

dataBlocks - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
DataBrowser - Class in loci.plugins.util

Extension of StackWindow with additional UI trimmings for animation,
 virtual stack caching options, metadata, and general beautification.

DataBrowser(ImagePlus) - Constructor for class loci.plugins.util.DataBrowser
 
DataBrowser(ImagePlus, ImageCanvas, String[], int[]) - Constructor for class loci.plugins.util.DataBrowser
 
DataBrowser(ImagePlus, ImageCanvas, String[], int[], XMLWindow) - Constructor for class loci.plugins.util.DataBrowser
 
DataChannel() - Constructor for class loci.formats.in.ZeissLSMReader.DataChannel
 
DataConverter - Class in loci.formats.gui

A utility for reorganizing and converting QuickTime movies,
 TIFF series and other 4D datasets.

DataConverter() - Constructor for class loci.formats.gui.DataConverter
 
DataConverter.RowPanel - Class in loci.formats.gui
 
DataEntryURLBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000

This class is defined to represent a Data Entry URL Box of JPEG JP2
  file format.

DataEntryURLBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox

Constructs a DataEntryURLBox from its content data.

DataEntryURLBox(byte, byte[], String) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox

Constructs a DataEntryURLBox from its data elements.

DataEntryURLBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox

Constructs a DataEntryURLBox from a Node.

dataFile - Variable in class loci.formats.in.NRRDReader

Name of data file, if the current extension is 'nhdr'.

dataId - Variable in class loci.formats.in.OIRReader.Laser
 
dataOffs - Variable in class loci.formats.in.SDTInfo

Offset of the data block from the beginning of the file.

dataOffset - Variable in class loci.formats.in.LiFlimReader

Offset to start of pixel data.

dataOffset - Variable in class loci.formats.in.ZeissCZIReader.Attachment
 
dataOffset - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
dataPointers - Variable in class loci.formats.in.InveonReader
 
datasetDescription - Variable in class loci.formats.FormatReader

Short description of the structure of the dataset.

dataSets - Variable in class loci.formats.in.IM3Reader
 
dataSize - Variable in class loci.formats.in.MRWReader
 
dataSize - Variable in class loci.formats.in.ZeissCZIReader.Attachment
 
dataSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
dataStore - Variable in class loci.formats.in.PQBinReader
 
dataStore - Variable in class loci.formats.in.SDTReader
 
dataType - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFAttrInfo
 
datatype - Variable in class loci.formats.in.LiFlimReader
 
DATATYPE_INT16 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_INT32 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_INT8 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_KEY - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_REAL32 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_REAL64 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_UINT16 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_UINT32 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_UINT8 - Static variable in class loci.formats.in.LiFlimReader
 
dataTypes - Variable in class com.sun.media.imageio.plugins.tiff.TIFFTag
 
DATE - Static variable in class loci.formats.FormatTools

Date on which this release was built.

DATE - Static variable in class loci.formats.in.CellSensReader
 
date - Variable in class loci.formats.in.DicomReader
 
date - Variable in class loci.formats.in.FEITiffReader
 
date - Variable in class loci.formats.in.FluoviewReader
 
date - Variable in class loci.formats.in.LEOReader
 
date - Variable in class loci.formats.in.MetamorphHandler
 
date - Variable in class loci.formats.in.ND2Handler
 
date - Variable in class loci.formats.in.PrairieMetadata

The date of the acquisition.

date - Variable in class loci.formats.in.QuesantReader
 
date - Variable in class loci.formats.in.SDTInfo

Date of creation.

date - Variable in class loci.formats.in.SimplePCITiffReader
 
date - Variable in class loci.formats.in.SVSReader
 
DATE_FORMAT - Static variable in class loci.formats.in.BrukerReader
 
DATE_FORMAT - Static variable in class loci.formats.in.CellWorxReader
 
DATE_FORMAT - Static variable in class loci.formats.in.DeltavisionReader

Deprecated.
Use DeltavisionReader.DATE_FORMATS instead


DATE_FORMAT - Static variable in class loci.formats.in.FEITiffReader
 
DATE_FORMAT - Static variable in class loci.formats.in.FluoviewReader

Date format

DATE_FORMAT - Static variable in class loci.formats.in.FujiReader
 
DATE_FORMAT - Static variable in class loci.formats.in.FV1000Reader
 
DATE_FORMAT - Static variable in class loci.formats.in.GelReader
 
DATE_FORMAT - Static variable in class loci.formats.in.HitachiReader
 
DATE_FORMAT - Static variable in class loci.formats.in.IvisionReader
 
DATE_FORMAT - Static variable in class loci.formats.in.KodakReader
 
DATE_FORMAT - Static variable in class loci.formats.in.L2DReader
 
DATE_FORMAT - Static variable in class loci.formats.in.LeicaReader

Format for dates.

DATE_FORMAT - Static variable in class loci.formats.in.MetamorphTiffReader
 
DATE_FORMAT - Static variable in class loci.formats.in.MicromanagerReader
 
DATE_FORMAT - Static variable in class loci.formats.in.MolecularImagingReader
 
DATE_FORMAT - Static variable in class loci.formats.in.ND2Handler
 
DATE_FORMAT - Static variable in class loci.formats.in.PDSReader
 
DATE_FORMAT - Static variable in class loci.formats.in.PerkinElmerReader
 
DATE_FORMAT - Static variable in class loci.formats.in.PrairieReader
 
DATE_FORMAT - Static variable in class loci.formats.in.SBIGReader
 
DATE_FORMAT - Static variable in class loci.formats.in.SimplePCITiffReader
 
DATE_FORMAT - Static variable in class loci.formats.in.SpiderReader
 
DATE_FORMAT - Static variable in class loci.formats.in.SVSReader
 
DATE_FORMAT - Static variable in class loci.formats.in.TCSReader
 
DATE_FORMATS - Static variable in class loci.formats.in.BaseTiffReader
 
DATE_FORMATS - Static variable in class loci.formats.in.DeltavisionReader
 
DATE_FORMATS - Static variable in class loci.formats.in.ICSReader
 
DATE_FORMATS - Static variable in class loci.formats.in.TillVisionReader
 
DATE_TIME - Static variable in class loci.formats.tiff.IFD
 
DATE_TIME_DIGITIZED - Static variable in class loci.formats.tiff.IFD
 
DATE_TIME_FORMAT - Static variable in class loci.formats.in.GelReader
 
DATE_TIME_ORIGINAL - Static variable in class loci.formats.tiff.IFD
 
dates - Variable in class loci.formats.in.TillVisionReader
 
datestamp - Variable in class loci.formats.in.TCSReader
 
DateTime() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.DateTime
 
DateTimeDigitized() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.DateTimeDigitized
 
DateTimeOriginal() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.DateTimeOriginal
 
datFile - Variable in class loci.formats.in.InveonReader
 
datFile - Variable in class loci.formats.in.UnisokuReader
 
dbi - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Data block used only to store coordinates of the buffered blocks

dbi - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf

Data block used only to store coordinates and progressiveness
        of the buffered blocks

dBlock - Variable in class loci.formats.in.GIFReader

Current data block.

DC_OFFSET - Static variable in class jj2000.j2k.image.input.ImgReaderPGM

DC offset value used when reading image

dcOffset - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
deadTimeComp - Variable in class loci.formats.in.SDTInfo
 
DEBUG - Static variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFDeflateDecompressor
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGCompressor
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
debug - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullDecompressor
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
DEBUG - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFPackBitsDecompressor
 
debug - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFPackBitsUtil
 
debug - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
debug(String) - Static method in class loci.plugins.BF
 
DEC_SPEC_COMP_DEF - Static variable in class jj2000.j2k.wavelet.WTDecompSpec

The identifier for "component default" specified decomposition

DEC_SPEC_MAIN_DEF - Static variable in class jj2000.j2k.wavelet.WTDecompSpec

The identifier for "main default" specified decomposition

DEC_SPEC_TILE_COMP - Static variable in class jj2000.j2k.wavelet.WTDecompSpec

The identifier for "tile and component specific" specified
        decomposition

DEC_SPEC_TILE_DEF - Static variable in class jj2000.j2k.wavelet.WTDecompSpec

The identifier for "tile specific default" specified decomposition

DecLyrdCBlk - Class in jj2000.j2k.entropy.decoder

This class stores coded (compressed) code-blocks that are organized
 in layers.

DecLyrdCBlk() - Constructor for class jj2000.j2k.entropy.decoder.DecLyrdCBlk
 
decode() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Decodes the input bit stream (located in the
 ImageInputStream stream, at offset
 offset, and continuing for byteCount
 bytes) into the output BufferedImage
 image.

decode(byte[], int, byte[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
decode(byte[], int, int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
decode() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullDecompressor
 
decode(byte[], int, byte[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFPackBitsDecompressor
 
decode(byte[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFPackBitsUtil
 
decode(RandomAccessInputStream) - Method in class loci.formats.codec.HuffmanCodec.Decoder
 
decode(APNGReader.PNGInputStream) - Method in class loci.formats.in.APNGReader
 
decode(APNGReader.PNGInputStream, int, int) - Method in class loci.formats.in.APNGReader
 
decode12BitCamera(byte[], int) - Method in class loci.formats.in.ZeissCZIReader
 
decodeBlackCodeWord() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
decodeDate(int) - Static method in class loci.formats.in.MetamorphReader

Converts a Julian date value into a human-readable string.

decodeImageData() - Method in class loci.formats.in.GIFReader

Decodes LZW image data into a pixel array.

decodeNextScanline(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
Decoder() - Constructor for class loci.formats.codec.HuffmanCodec.Decoder
 
Decoder(short[]) - Constructor for class loci.formats.codec.HuffmanCodec.Decoder
 
decoder - Variable in class loci.formats.in.TileJPEGReader
 
decodeRaw(byte[], int, int, int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Decodes the source data into the provided byte
 array b, starting at the offset given by
 dstOffset.

decodeRaw(short[], int, int, int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Decodes the source data into the provided short
 array s, starting at the offset given by
 dstOffset.

decodeRaw(int[], int, int, int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Decodes the source data into the provided int
 array i, starting at the offset given by
 dstOffset.

decodeRaw(float[], int, int, int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Decodes the source data into the provided float
 array f, starting at the offset given by
 dstOffset.

decodeRaw(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFDeflateDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLSBDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFPackBitsDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
decodeRLE() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
decodeRLE4(int, int, byte[], byte[]) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
decodeRLE8(int, int, byte[], byte[]) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
DecoderSpecs - Class in jj2000.j2k.decoder

This class holds references to each module specifications used in the
 decoding chain.

DecoderSpecs(int, int) - Constructor for class jj2000.j2k.decoder.DecoderSpecs

Initialize all members with the given number of tiles and components.

decodeSymbol(int) - Method in class jj2000.j2k.entropy.decoder.MQDecoder

Arithmetically decodes one symbol from the bit stream with the given
 context and returns its decoded value.

decodeSymbols(int[], int[], int) - Method in class jj2000.j2k.entropy.decoder.MQDecoder

This function performs the arithmetic decoding.

decodeT4() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
decodeT6() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
decodeTile(int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
decodeTile(int, int, int) - Method in class loci.formats.in.CellSensReader
 
decodeTime(int) - Static method in class loci.formats.in.MetamorphReader

Converts a time value in milliseconds into a human-readable string.

decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int) - Method in interface loci.formats.services.LuraWaveService

Wraps lwfDecoder.decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int).

decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int) - Method in class loci.formats.services.LuraWaveServiceImpl
 
decodeToMemoryGray8(byte[], int, int, int) - Method in interface loci.formats.services.LuraWaveService

Wraps lwfDecoder.decodeToMemoryGray8(byte[], int, int, int).

decodeToMemoryGray8(byte[], int, int, int) - Method in class loci.formats.services.LuraWaveServiceImpl
 
decodeWhiteCodeWord() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
decodingRate - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageReadParam

Specifies the decoding rate in bits per pixel (bpp) where the
  number of  pixels is related to the image's original size
  (Note: this number is not affected by resolution).

decomp(Subband, int, int, int) - Method in class jj2000.j2k.roi.encoder.ArbROIMaskGenerator

This function decomposes the mask for a node in the subband tree.

decomposedComps - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull

Block storing the full band decomposition for each component.

decompositionLevel - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies the number of wavelet decomposition levels to apply to
  the image.

DECOMPR_MASKS - Static variable in class loci.formats.codec.LZWCodec

Masks for reading bits in decompressor.

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.Base64Codec
 
decompress(byte[]) - Method in class loci.formats.codec.BaseCodec
 
decompress(byte[][]) - Method in class loci.formats.codec.BaseCodec
 
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.BaseCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.BaseCodec
 
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec

2D data block decoding default implementation.

decompress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec

Decompresses a block of data.

decompress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec

Decompresses a block of data.

decompress(byte[]) - Method in interface loci.formats.codec.Codec

Decompresses a block of data.

decompress(byte[][]) - Method in interface loci.formats.codec.Codec

Decompresses a block of data.

decompress(RandomAccessInputStream, CodecOptions) - Method in interface loci.formats.codec.Codec

Decompresses data from the given RandomAccessInputStream.

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec

The CodecOptions parameter must be an instance of
 HuffmanCodecOptions, and should have the following fields set:
   table
   bitsPerSample
   maxBytes

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.JPEG2000Codec

The CodecOptions parameter should have the following fields set:
 interleaved
 littleEndian

decompress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEG2000Codec

The CodecOptions parameter should have the following fields set:
 interleaved
 littleEndian

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.JPEGCodec

The CodecOptions parameter should have the following fields set:
  interleaved
  littleEndian

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
 
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec

The CodecOptions parameter should have the following fields set:
  maxBytes

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.LosslessJPEGCodec

The CodecOptions parameter should have the following fields set:
  interleaved
  littleEndian

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.LuraWaveCodec
 
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.LuraWaveCodec

The CodecOptions parameter should have the following fields set:
  maxBytes

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.LZOCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.LZWCodec

The CodecOptions parameter should have the following fields set:
  maxBytes

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.MJPBCodec

The CodecOptions parameter must be an instance of MJPBCodecOptions,
 and should have the following fields set:
  interlaced
  width
  height
  bitsPerSample
  littleEndian
  interleaved

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.MSRLECodec

The CodecOptions parameter should have the following fields set:
  width
  height
  previousImage

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.MSVideoCodec

The CodecOptions parameter should have the following fields set:
  width
  height
  bitsPerSample
  previousImage

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.NikonCodec

The CodecOptions parameter must be an instance of
 NikonCodecOptions, and should have the following fields set:
  lossless
  vPredictor
  curve
  split
  bitsPerSample
  maxBytes
  width
  height

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.PackbitsCodec

The CodecOptions parameter should have the following fields set:
  maxBytes

decompress(byte[], CodecOptions) - Method in class loci.formats.codec.PassthroughCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.PassthroughCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.QTRLECodec
 
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.QTRLECodec

The CodecOptions parameter should have the following fields set:
  width
  height
  bitsPerSample
  previousImage

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.RPZACodec

The CodecOptions parameter should have the following fields set:
  width
  height

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.TargaRLECodec

The CodecOptions parameter should have the following fields set:
  maxBytes
  CodecOptions.bitsPerSample

decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.ZlibCodec
 
decompress(byte[]) - Method in interface loci.formats.services.JPEGXRService

Decompress the given JPEG-XR compressed byte array and return as a byte array.

decompress(byte[]) - Method in class loci.formats.services.JPEGXRServiceImpl
 
decompress(byte[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression

Decodes a strip of data.

decompress(byte[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Decompress the JPEG source image associated with this decompressor
 instance and output a decompressed image to the given destination buffer.

decompress(int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Decompress the JPEG source image associated with this decompressor
 instance and return a buffer containing the decompressed image.

decompress(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Decompress the JPEG source image associated with this decompressor
 instance and output a decompressed image to the given
 BufferedImage instance.

decompress(int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Decompress the JPEG source image associated with this decompressor
 instance and return a BufferedImage instance containing the
 decompressed image.

decompress(byte[], int, byte[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
decompress(byte[], int, int[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
decompressHeader(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
decompressor - Variable in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam
 
decompressor - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
decompressor - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
decompressor - Variable in class loci.formats.in.AmiraReader.HxZip
 
decompressToYUV(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Decompress the JPEG source image associated with this decompressor
 instance and output a YUV planar image to the given destination buffer.

decompressToYUV(int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Decompress the JPEG source image associated with this decompressor
 instance and return a buffer containing a YUV planar image.

decompressToYUV(byte[], int, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
deconvolutionLogFile - Variable in class loci.formats.in.DeltavisionReader
 
decSpec - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
decSpec - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The decoder specifications

decSpec - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

The decoder specifications

decSpec - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Reference to decoder specifications

decSpec - Variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The decoder spec

decSpec - Variable in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

The decoder specifications

DEEP_GREY_10 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_11 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_12 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_13 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_14 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_15 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_16 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_9 - Static variable in class loci.formats.in.OpenlabReader
 
def - Variable in class jj2000.j2k.ModuleSpec

Default value for each tile-component

DEF_BUF_LEN - Static variable in class jj2000.j2k.codestream.writer.FileCodestreamWriter

The default buffer length, 1024 bytes

DEF_THREADS_NUM - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The default value for the property in THREADS_PROP_NAME: 0

DEFAULT_BACKGROUND_COLOR - Static variable in class loci.formats.in.CellSensReader
 
DEFAULT_BYTES_PER_STRIP - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
DEFAULT_CALLER - Static variable in class loci.formats.UpgradeChecker

Value of "bioformats.caller" for Bio-Formats utilities.

DEFAULT_COLORS - Static variable in class loci.plugins.in.ImporterOptions

Default custom colors for each channel.

DEFAULT_DIMENSION_ORDER - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_DISPLAY_RESOLUTION_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
DEFAULT_IMAGE - Static variable in class loci.formats.in.CellSensReader
 
DEFAULT_LINEARIZATION_TABLE - Static variable in class loci.formats.codec.NikonCodec
 
DEFAULT_MINIMUM_ELAPSED - Static variable in class loci.formats.Memoizer

Default value for Memoizer.minimumElapsed if none is provided in the
 constructor.

DEFAULT_PIXEL_TYPE - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_RANGE - Static variable in class loci.formats.cache.CacheStrategy

Default cache range.

DEFAULT_RGB_CHANNEL_COUNT - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_SAMPLE_IFD - Static variable in class loci.formats.in.CellSensReader
 
DEFAULT_SIZE_C - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_SIZE_T - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_SIZE_X - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_SIZE_Y - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_SIZE_Z - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_WRITE_BUFFER_SIZE - Static variable in class com.sun.media.imageio.stream.FileChannelImageOutputStream

The size of the write buffer.

defaultClasses - Static variable in class loci.formats.ImageReader

Default list of reader classes, for use with noargs constructor.

defaultClasses - Static variable in class loci.formats.ImageWriter

Default list of writer classes, for use with noargs constructor.

defaultDateEnabled - Static variable in class loci.formats.MetadataTools
 
defaultExposureTime - Variable in class loci.formats.in.CellSensReader.Pyramid
 
DefaultJPEGReader() - Constructor for class loci.formats.in.JPEGReader.DefaultJPEGReader
 
DefaultMetadataOptions - Class in loci.formats.in

Default implementation of MetadataOptions.

DefaultMetadataOptions() - Constructor for class loci.formats.in.DefaultMetadataOptions

Construct a new DefaultMetadataOptions.

DefaultMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DefaultMetadataOptions

Construct a new DefaultMetadataOptions.

defaultMinMax(int) - Static method in class loci.formats.FormatTools

Get the default range for the specified pixel type.

defaultValue - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFAttrInfo
 
defaultValue - Variable in class jj2000.j2k.entropy.CBlkSizeSpec
 
defaultValue - Variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransfSpec
 
defaultValue - Variable in class jj2000.j2k.quantization.GuardBitsSpec
 
defaultValue - Variable in class jj2000.j2k.quantization.QuantStepSizeSpec
 
defaultValue - Variable in class loci.plugins.prefs.BooleanOption

The option's default value.

defaultValue - Variable in class loci.plugins.prefs.DoubleOption

The option's default value.

defaultValue - Variable in class loci.plugins.prefs.StringOption

The option's default value.

defaultXMLSkip - Variable in class loci.formats.in.OIRReader
 
defimgn - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

Nominal range bit of the component defining default values in QCD for
 main header

DEFINITION - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
deflater - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFDeflater
 
defMsgLogger - Static variable in class jj2000.j2k.util.FacilityManager

The default logger, for threads that have none associated with them

deftilenr - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

Nominal range bit of the component defining default values in QCD for
 tile headers

defWatchProg - Static variable in class jj2000.j2k.util.FacilityManager

The default ProgressWatch for threads that have none
 associated with them.

delayTime - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
delegate - Variable in class loci.formats.in.SimplePCITiffReader
 
delegate - Variable in class loci.formats.services.LuraWaveServiceImpl

LuraWave decoder delegate.

DelegateReader - Class in loci.formats

DelegateReader is a file format reader that selects which reader to use
 for a format if there are two readers which handle the same format.

DelegateReader(String, String) - Constructor for class loci.formats.DelegateReader

Constructs a new delegate reader.

DelegateReader(String, String[]) - Constructor for class loci.formats.DelegateReader

Constructs a new delegate reader.

deleteQuietly(File) - Method in class loci.formats.Memoizer

Attempts to delete an existing file, logging at
 warn if the deletion returns false or at error
 if an exception is thrown.

delFF - Variable in class jj2000.j2k.entropy.encoder.BitToByteOutput

Flag that indicates if an FF has been delayed

delFF - Variable in class jj2000.j2k.entropy.encoder.MQCoder

If a 0xFF byte has been delayed and not yet been written to the output
 (in the MQ we can never have more than 1 0xFF byte in a row).

DELIMITERS - Static variable in class loci.formats.in.ImarisHDFReader
 
DELTA - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

The value of the fourth lifting step coefficient

DELTA - Static variable in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

The value of the fourth lifting step coefficient

deltaT - Variable in class loci.formats.in.ColumbusReader.Plane
 
deltaT - Variable in class loci.formats.in.FV1000Reader.PlaneData
 
deltaT - Variable in class loci.formats.in.InCellReader.Image
 
deltaT - Variable in class loci.formats.in.IvisionReader
 
deltaT - Variable in class loci.formats.in.NiftiReader
 
deltaT - Variable in class loci.formats.in.ScanrReader
 
DeltavisionReader - Class in loci.formats.in

DeltavisionReader is the file format reader for Deltavision files.

DeltavisionReader() - Constructor for class loci.formats.in.DeltavisionReader

Constructs a new Deltavision reader.

DeltavisionReader.DVExtHdrFields - Class in loci.formats.in

This private class structure holds the details for the extended header.

denom - Variable in class loci.formats.tiff.TiffRational

Components of the rational's fractional representation.

denom - Variable in class org.libjpegturbo.turbojpeg.TJScalingFactor

Denominator

denomH - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox
 
denomV - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox
 
depth - Variable in class loci.formats.tools.AmiraParameters
 
deq - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
Dequantizer - Class in jj2000.j2k.quantization.dequantizer

This is the abstract class from which all dequantizers must inherit.

Dequantizer(CBlkQuantDataSrcDec, int[], DecoderSpecs) - Constructor for class jj2000.j2k.quantization.dequantizer.Dequantizer

Initializes the source of compressed data.

DequantizerParams - Class in jj2000.j2k.quantization.dequantizer

This is the generic ineterface for dequantization parameters.

DequantizerParams() - Constructor for class jj2000.j2k.quantization.dequantizer.DequantizerParams
 
derived - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Whether or not the components in the current tile uses a derived
 quantization step size (only relevant in non reversible quantization
 mode).

desc - Variable in class loci.formats.gui.ComboFileFilter

Description.

desc - Variable in class loci.formats.gui.ExtensionFileFilter

Description.

desc - Variable in class loci.formats.gui.FormatFileFilter

Description.

description - Variable in class loci.formats.in.NiftiReader
 
description() - Method in interface loci.formats.in.PrairieMetadata.Value
 
description - Variable in class loci.formats.in.PrairieMetadata.ValueItem
 
description() - Method in class loci.formats.in.PrairieMetadata.ValueItem
 
description() - Method in class loci.formats.in.PrairieMetadata.ValueTable
 
description - Variable in class loci.formats.in.TiffReader
 
description - Variable in class loci.formats.in.VolocityReader.Stack
 
description - Variable in class loci.formats.in.ZeissCZIReader
 
description - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
descriptions - Variable in class loci.formats.in.LIFReader
 
DEST_DISTANCE_REF_KILOMETERS - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSDestDistanceRef" tag.

DEST_DISTANCE_REF_KNOTS - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSDestDistanceRef" tag.

DEST_DISTANCE_REF_MILES - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSDestDistanceRef" tag.

destBands - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

source and destination bands.

destBands - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader

source and destination bands.

destBitsPerSampleCache - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
destImage - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
destImage - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
destinationBands - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The sequence of destination bands to receive the source data.

destinationBands - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
destinationBands - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
destinationBands - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
destinationBandsCache - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
destinationRegion - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

The destination region.

destinationRegion - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
destinationRegion - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
destinationRegion - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader

The destination region.

destinationRegion - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
destinationRegion - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
destinationRegion - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

The destination bounds.

destroy() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
destroy() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
details - Variable in class loci.formats.in.PerkinElmerReader
 
DetectionChannel() - Constructor for class loci.formats.in.ZeissLSMReader.DetectionChannel
 
detector - Variable in class loci.formats.in.LeicaHandler.Channel
 
Detector() - Constructor for class loci.formats.in.LeicaHandler.Detector
 
Detector() - Constructor for class loci.formats.in.LeicaReader.Detector
 
Detector() - Constructor for class loci.formats.in.OIRReader.Detector
 
detector - Variable in class loci.formats.in.VolocityReader.Stack
 
detectorChannel - Variable in class loci.formats.in.LeicaHandler
 
detectorGain - Variable in class loci.formats.in.BaseZeissReader
 
detectorID - Variable in class loci.formats.in.MicromanagerReader.Position
 
detectorIndexes - Variable in class loci.formats.in.LIFReader
 
detectorIndices - Variable in class loci.formats.in.LeicaHandler
 
detectorManufacturer - Variable in class loci.formats.in.FluoviewReader
 
detectorManufacturer - Variable in class loci.formats.in.MicromanagerReader.Position
 
detectorModel - Variable in class loci.formats.in.MicromanagerReader.Position
 
detectorModels - Variable in class loci.formats.in.LIFReader
 
detectorOffset - Variable in class loci.formats.in.BaseZeissReader
 
detectorOffset - Variable in class loci.formats.in.OpenlabReader
 
detectorOffsets - Variable in class loci.formats.in.LIFReader
 
detectorRefs - Variable in class loci.formats.in.ZeissCZIReader
 
detectors - Variable in class loci.formats.in.FEITiffReader
 
detectors - Variable in class loci.formats.in.LeicaHandler
 
detectors - Variable in class loci.formats.in.LeicaReader
 
detectors - Variable in class loci.formats.in.OIRReader
 
detType - Variable in class loci.formats.in.SDTInfo

Detector type (SPC-930 in camera mode).

DEVICE_ID - Static variable in class loci.formats.in.CellSensReader
 
DEVICE_MANUFACTURER - Static variable in class loci.formats.in.CellSensReader
 
DEVICE_NAME - Static variable in class loci.formats.in.CellSensReader
 
DEVICE_SUBTYPE - Static variable in class loci.formats.in.CellSensReader
 
deviceIDs - Variable in class loci.formats.in.CellSensReader.Pyramid
 
deviceManufacturers - Variable in class loci.formats.in.CellSensReader.Pyramid
 
deviceNames - Variable in class loci.formats.in.CellSensReader.Pyramid
 
DeviceSettingDescription() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.DeviceSettingDescription
 
deviceTypes - Variable in class loci.formats.in.CellSensReader.Pyramid
 
devModel - Variable in class loci.formats.in.LeicaSCNReader.Image
 
devVersion - Variable in class loci.formats.in.LeicaSCNReader.Image
 
DHP - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
DHT - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
DHT - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
dialog - Variable in class loci.plugins.in.ThumbLoader
 
dichroic - Variable in class loci.formats.in.FlexReader.FilterGroup
 
dichroicMap - Variable in class loci.formats.in.FlexReader
 
dichroicModels - Variable in class loci.formats.in.NikonTiffReader
 
DICOM_MAGIC_STRING - Static variable in class loci.formats.in.DicomReader
 
DICOM_SUFFIXES - Static variable in class loci.formats.in.DicomReader
 
DicomReader - Class in loci.formats.in

DicomReader is the file format reader for DICOM files.

DicomReader() - Constructor for class loci.formats.in.DicomReader

Constructs a new DICOM reader.

diff - Variable in class loci.formats.in.BioRadGelReader
 
difference(byte[], IFD) - Static method in enum loci.formats.tiff.TiffCompression

Performs in-place differencing according to the given predictor value.

DIFFERENTIAL_CORRECTION_APPLIED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSDifferential" tag.

DIFFERENTIAL_CORRECTION_NONE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSDifferential" tag.

DIGITAL_ZOOM_RATIO - Static variable in class loci.formats.tiff.IFD
 
DigitalZoomRatio() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.DigitalZoomRatio
 
digits(int) - Static method in class loci.plugins.in.ImporterMetadata

Computes the given value's number of digits.

dilate() - Method in class loci.plugins.util.RecordedImageProcessor
 
DIM_INDEX_1 - Static variable in class loci.formats.in.CellSensReader
 
DIM_INDEX_2 - Static variable in class loci.formats.in.CellSensReader
 
DIMDESCR - Static variable in class loci.formats.in.LeicaReader
 
Dimension(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Dimension
 
dimension - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
Dimension(Integer) - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension

Constructor.

dimension - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
DIMENSION_DESCRIPTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_INCREMENT_ID - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_MEANING - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_NAME - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_NAMES - Static variable in class loci.formats.in.LeicaReader
 
DIMENSION_SIZE - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_START_ID - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_VALUE_ID - Static variable in class loci.formats.in.CellSensReader
 
dimensionCount - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
dimensionEntries - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
DimensionEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DimensionEntry
 
dimensionLength - Variable in class loci.formats.out.ICSWriter
 
dimensionM - Variable in class loci.formats.in.ZeissLSMReader
 
dimensionOffset - Variable in class loci.formats.out.ICSWriter
 
dimensionOrder - Variable in class loci.formats.CoreMetadata

Order in which dimensions are stored.

dimensionOrder - Variable in class loci.formats.in.FluoviewReader
 
dimensionOrdering - Variable in class loci.formats.in.CellSensReader.Pyramid
 
dimensionP - Variable in class loci.formats.in.ZeissLSMReader
 
DIMENSIONS_STRING - Static variable in class loci.formats.in.KodakReader
 
DimensionSwapper - Class in loci.formats

Handles swapping the dimension order of an image series.

DimensionSwapper() - Constructor for class loci.formats.DimensionSwapper

Constructs a DimensionSwapper around a new image reader.

DimensionSwapper(IFormatReader) - Constructor for class loci.formats.DimensionSwapper

Constructs a DimensionSwapper with the given reader.

dimensionSwapper - Variable in class loci.plugins.in.ImportProcess
 
dimensionTag - Variable in class loci.formats.in.CellSensReader
 
dimOrder - Variable in class loci.formats.AxisGuesser

Original ordering of internal dimensional axes.

dims - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
dims - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
 
dir - Variable in class loci.formats.in.VolocityReader
 
DIRECTION_REF_MAGNETIC - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSTrackRef", "GPSImgDirectionRef",
 and "GPSDestBearingRef" tags.

DIRECTION_REF_TRUE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSTrackRef", "GPSImgDirectionRef",
 and "GPSDestBearingRef" tags.

Directory() - Constructor for class loci.formats.in.ZeissCZIReader.Directory
 
directory - Variable in class loci.formats.Memoizer

Directory where all memo files should be created.

directory - Variable in class loci.formats.services.EXIFServiceImpl
 
DirectoryEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
directoryEntry - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
directoryList - Variable in class loci.formats.in.CellWorxReader
 
directoryPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
directoryRoot - Variable in class loci.formats.tools.FakeImage
 
dirty - Variable in class loci.formats.cache.CacheStrategy

Whether load order array needs to be recomputed
 before building the next load list.

DISPLAY_COLOR - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_LIMITS - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_LUT - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_MAPPING_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_PROCESSOR_TYPE - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_STACK_ID - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_STACK_INDEX - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_VISIBLE - Static variable in class loci.formats.in.CellSensReader
 
displayDataBrowser(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
 
displayDialog(GenericDialog) - Method in class loci.plugins.in.IdDialog

Asks user whether Bio-Formats should automatically check for upgrades,
 and if so, checks for an upgrade and prompts user to install it.

displayDialog(GenericDialog) - Method in class loci.plugins.in.ImporterDialog

Displays the dialog, or grabs values from macro options.

displayDialog(GenericDialog) - Method in class loci.plugins.in.SeriesDialog
 
displayDialog(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog

Asks user whether Bio-Formats should automatically check for upgrades,
 and if so, checks for an upgrade and prompts user to install it.

DISPLAYED_LUT_ID - Static variable in class loci.formats.in.CellSensReader
 
DisplayHandler - Class in loci.plugins.in

Logic for displaying images and metadata onscreen using ImageJ.

DisplayHandler(ImportProcess) - Constructor for class loci.plugins.in.DisplayHandler
 
displayImage(ImagePlus) - Method in class loci.plugins.in.DisplayHandler

Displays the given image according to the configured options.

displayImage5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
 
displayImages(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler

Displays the given images according to the configured options.

displayName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
displayNormal(ImagePlus) - Method in class loci.plugins.in.DisplayHandler

Displays in a normal ImageJ window.

displayOMEXML() - Method in class loci.plugins.in.DisplayHandler

Displays OME-XML metadata in a tree in its own window.

displayOriginalMetadata() - Method in class loci.plugins.in.DisplayHandler

Displays standard metadata in a table in its own window.

displayROIs(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler
 
displayTag - Variable in class loci.formats.in.BaseZeissReader.Shape
 
displayUsage() - Method in class loci.formats.tools.MakeTestOmeTiff
 
displayView5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
 
disposalMethod - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
disposalMethodNames - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
dispose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
dispose() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
dispose() - Method in class loci.formats.gui.CacheComponent
 
dispose - Variable in class loci.formats.in.GIFReader
 
distance(int, int) - Method in class loci.formats.cache.CacheStrategy

Computes the distance from the given axis value to the
 axis center, taking into account the axis ordering scheme.

distbufT - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The buffer for distortion values (avoids reallocation for each
        code-block), for each thread.

dither - Variable in class loci.formats.in.SDTInfo
 
dl - Variable in class jj2000.j2k.entropy.decoder.DecLyrdCBlk

The coded (compressed) data length.

DLL_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo

For .sdt files created using DLL function SPC_save_data_to_sdtfile
 (no setup, only data).

dls - Variable in class jj2000.j2k.decoder.DecoderSpecs

Number of decomposition levels specifications

dls - Variable in class jj2000.j2k.entropy.PrecinctSizeSpec

Reference to wavelet number of decomposition levels for each
 tile-component.

dls - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull

The number of decomposition levels specification

DM2_MAGIC_BYTES - Static variable in class loci.formats.in.GatanDM2Reader
 
DM3_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader
 
DM4_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader
 
DNGReader - Class in loci.formats.in

DNGReader is the file format reader for Canon DNG (TIFF) files.

DNGReader() - Constructor for class loci.formats.in.DNGReader

Constructs a new DNG reader.

DNL - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
DO_TIMING - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Whether to collect timing information or not: false.

DO_TIMING - Static variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Whether to collect timing information or not: false.

DO_TIMING - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Whether to collect timing information or not: false.

doc - Variable in class loci.formats.gui.XMLWindow
 
doCaching - Variable in class loci.formats.tiff.TiffParser
 
doChannels - Variable in class loci.formats.in.CellWorxReader
 
doCodestreamManipulation() - Method in class jj2000.j2k.util.CodestreamManipulator

This method performs the actual manipulation of the codestream which is
 the reparsing for tile parts and packed packet headers

doCrop() - Method in class loci.plugins.in.ImporterOptions
 
DOCUMENT_AUTHOR - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_COMPANY - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_BUILD_NUMBER - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_MAJOR_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_MINOR_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_NAME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_PACKAGE - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_SUB_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_KEYS - Static variable in class loci.formats.in.ICSReader
 
DOCUMENT_NAME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_NAME - Static variable in class loci.formats.tiff.IFD
 
DOCUMENT_NOTE - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PRODUCT - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PRODUCT_NAME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PRODUCT_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_THUMB - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_TIME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_TYPE_HINT - Static variable in class loci.formats.in.CellSensReader
 
DocumentName() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.DocumentName
 
documentUpdate() - Method in class loci.plugins.config.FlexWidgets
 
doer - Variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Flag to indicate if we should try to detect errors or just ignore any
 error resilient information

doFormatLayout(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
 
doInPlaceCaching - Variable in class loci.formats.Memoizer

If true, then all memo files will be created in the same
 directory as the original file.

domains - Variable in class loci.formats.FormatReader

List of domains in which this format is used.

doMustGroup() - Method in class loci.plugins.in.ImporterOptions
 
doNotChangePattern - Variable in class loci.formats.FileStitcher
 
doNotifyAll - Variable in class jj2000.j2k.util.ThreadPool.ThreadPoolThread
 
doRecording - Variable in class loci.plugins.util.RecordedImageProcessor
 
doStitchTiles() - Method in class loci.plugins.in.ImporterOptions
 
doT - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
DOT - Static variable in class loci.formats.ResourceNamer
 
DOT_RANGE - Static variable in class loci.formats.tiff.IFD
 
DotRange() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.DotRange
 
DOUBLE - Static variable in class loci.formats.FormatTools

Identifies the DOUBLE data type used to store pixel values.

DOUBLE - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE - Static variable in class loci.formats.in.GatanReader
 
DOUBLE_2 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_2_2 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_3 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_3_3 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_4 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_4_4 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_ARRAY_2 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_ARRAY_3 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_INTERVAL - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_RECT - Static variable in class loci.formats.in.CellSensReader
 
doubleCapacity() - Method in class loci.formats.codec.ByteVector
 
DoubleOption - Class in loci.plugins.prefs

A double option for one of the plugins.

DoubleOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.DoubleOption

Constructs a double option with the parameters from the given map.

DoubleOption(String, boolean, String, String, double) - Constructor for class loci.plugins.prefs.DoubleOption

Constructs a double option with the given parameters.

doubleValue() - Method in class loci.formats.tiff.TiffRational

Returns the value of the specified number as a double.

doUpgradeCheck() - Method in class loci.plugins.in.ImporterOptions
 
download(URLConnection) - Static method in class loci.plugins.config.InstallWizard
 
download(URLConnection, File) - Static method in class loci.plugins.config.InstallWizard
 
doZ - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
DP80_FRAME_CENTERING - Static variable in class loci.formats.in.CellSensReader
 
DQT - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
DQT - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
drawColour - Variable in class loci.formats.in.BaseZeissReader.Shape
 
drawDot(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawLine(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawRect(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawString(String) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawString(String, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
DrawStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.DrawStyle
 
drawStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
 
DRI - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
DRI - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
DRI - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
drivePictDecoder(int) - Method in class loci.formats.in.PictReader

Handles the opcodes in the PICT file.

DS - Static variable in class loci.formats.in.DicomReader
 
dstData - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
dstData - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
dstData - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFPackBitsUtil
 
dstHeight - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The height of the region of the destination image to be written.

dstHeight - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
dstIndex - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
dstIndex - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
dstIndex - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFPackBitsUtil
 
dstMinX - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The X coordinate of the upper left pixel to be written in the
 destination image.

dstMinX - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
dstMinY - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The Y coordinate of the upper left pixel to be written in the
 destination image.

dstMinY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
dstWidth - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The width of the region of the destination image to be written.

dstWidth - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
dstXOffset - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The horizontal destination offset used, along with
 sourceXOffset and subsampleX, to map
 between horizontal source and destination pixel coordinates.

dstXOffset - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
dstYOffset - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The vertical destination offset used, along with
 sourceYOffset and subsampleY, to map
 between horizontal source and destination pixel coordinates.

dstYOffset - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
DT - Static variable in class loci.formats.in.DicomReader
 
dtype - Variable in class jj2000.j2k.wavelet.synthesis.InvWTFull

Current data type

dualCamera - Variable in class loci.formats.in.MetamorphHandler
 
dualCamera - Variable in class loci.formats.in.MetamorphTiffReader
 
DUMMY_PIXEL - Static variable in class loci.formats.out.EPSWriter
 
DummyMetadata - Class in loci.formats.meta
 
DummyMetadata() - Constructor for class loci.formats.meta.DummyMetadata
 
dump(PrintStream) - Method in class com.sun.media.imageioimpl.common.LZWCompressor
 
dump(PrintStream) - Method in class com.sun.media.imageioimpl.common.LZWStringTable
 
duplicate(Class<? extends IFormatReader>) - Method in class loci.formats.ReaderWrapper

Performs a deep copy of the reader, including nested wrapped readers.

duplicate(Class<? extends IFormatWriter>) - Method in class loci.formats.WriterWrapper

Performs a deep copy of the writer, including nested wrapped writers.

duplicate() - Method in class loci.plugins.util.RecordedImageProcessor
 
duplicateRecurse(Class<? extends IFormatReader>) - Method in class loci.formats.ReaderWrapper
 
duplicateRecurse(Class<? extends IFormatWriter>) - Method in class loci.formats.WriterWrapper
 
DV_MAGIC_BYTES_1 - Static variable in class loci.formats.in.DeltavisionReader
 
DV_MAGIC_BYTES_2 - Static variable in class loci.formats.in.DeltavisionReader
 
DVExtHdrFields(RandomAccessInputStream) - Constructor for class loci.formats.in.DeltavisionReader.DVExtHdrFields
 
DWORD - Static variable in class loci.formats.in.CellSensReader
 
dwt - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

Reference to the DWT module

dyeName - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
dyeName - Variable in class loci.formats.in.LeicaHandler.MultiBand
 
dyes - Variable in class loci.formats.in.ND2Handler
 
DYNAMIC_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
DynamicMetadataOptions - Class in loci.formats.in

Configuration object for readers and writers.

DynamicMetadataOptions() - Constructor for class loci.formats.in.DynamicMetadataOptions

Creates an options object with metadata level set to DynamicMetadataOptions.METADATA_LEVEL_DEFAULT and file validation set to DynamicMetadataOptions.READER_VALIDATE_DEFAULT.

DynamicMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DynamicMetadataOptions

Creates an options object with metadata level set to the
 specified value and file validation set to DynamicMetadataOptions.READER_VALIDATE_DEFAULT





E

ealDE - Variable in class loci.formats.in.SDTInfo
 
EBCOTLayer - Class in jj2000.j2k.entropy.encoder

This class holds information about each layer that is to be, or has already
 been, allocated .

EBCOTLayer() - Constructor for class jj2000.j2k.entropy.encoder.EBCOTLayer
 
EBCOTRateAllocator - Class in jj2000.j2k.entropy.encoder

This implements the EBCOT post compression rate allocation algorithm.

EBCOTRateAllocator(CodedCBlkDataSrcEnc, LayersInfo, CodestreamWriter, J2KImageWriteParamJava) - Constructor for class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Initializes the EBCOT rate allocator of entropy coded data.

ECAT7_MAGIC - Static variable in class loci.formats.in.Ecat7Reader
 
ECAT7_MAGIC_REGEX - Static variable in class loci.formats.in.Ecat7Reader
 
Ecat7Reader - Class in loci.formats.in

Ecat7Reader is the file format reader for ECAT 7 files.

Ecat7Reader() - Constructor for class loci.formats.in.Ecat7Reader

Constructs a new ECAT7 reader.

ecopts - Variable in class jj2000.j2k.decoder.DecoderSpecs

The Entropy decoder options specifications

ecs - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
ECS_GRAY - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
ECS_sRGB - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox

The enumerated color space defined in JP2 file format.

ECS_YCC - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
EditTiffG - Class in loci.formats.tools

Provides a GUI for editing TIFF file comments.

EditTiffG() - Constructor for class loci.formats.tools.EditTiffG
 
effectiveFieldCount - Variable in class loci.formats.in.FlexReader
 
EFI_HEIGHT_MAP - Static variable in class loci.formats.in.CellSensReader
 
EFI_SHARPNESS_MAP - Static variable in class loci.formats.in.CellSensReader
 
EFI_STACK - Static variable in class loci.formats.in.CellSensReader
 
EFI_TEXTURE_MAP - Static variable in class loci.formats.in.CellSensReader
 
ehs - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Reference to the stream where to read from

el(NodeList, int) - Method in class loci.formats.in.PrairieMetadata

Gets the indexth element from the given list of nodes.

ELEMENT_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
 
ELEMENT_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
 
elementInfoMap - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
elementLength - Variable in class loci.formats.in.DicomReader
 
elementName - Variable in class loci.formats.in.LeicaHandler
 
elementNames - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox

Cache the element names for this box's xml definition

elementNames - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox

Cache the element names for this box's xml definition

elementNames - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox

Cache the element names for this box's xml definition

elementNames - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Cache the element names for this box's xml definition

elementNames - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDBox

Cache the element names for this box's xml definition

elementNames - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.XMLBox

Cache the element names for this box's xml definition

elements - Variable in class loci.formats.FilePatternBlock

Elements within this block, e.g.

ELLIPSE - Static variable in class loci.formats.in.FV1000Reader
 
ELLIPSE - Static variable in class loci.formats.in.ZeissLSMReader
 
ellipses - Variable in class loci.formats.in.FakeReader
 
EM_DAC - Static variable in class loci.formats.in.FluoviewReader
 
EM_DOMAIN - Static variable in class loci.formats.FormatTools

Identifies the electron microscopy domain.

EM_GAIN - Static variable in class loci.formats.in.CellSensReader
 
embedded_stream - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
EMBEDDED_STREAM - Static variable in class loci.formats.in.VolocityReader
 
embeddedImages - Variable in class loci.formats.in.TillVisionReader
 
embeddedOffset - Variable in class loci.formats.in.TillVisionReader
 
EmbeddedProgressAdapter() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader.EmbeddedProgressAdapter
 
emFilters - Variable in class loci.formats.in.InCellReader
 
emission - Variable in class loci.formats.in.FlexReader.FilterGroup
 
emission - Variable in class loci.formats.in.OIRReader.Channel
 
emission - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
emissionFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
emissionWavelength - Variable in class loci.formats.in.SVSReader
 
EMPTY_STRING - Static variable in class loci.formats.in.IM3Reader
 
EmptyImage - Class in com.sun.media.imageioimpl.plugins.tiff
 
EmptyImage(int, int, int, int, int, int, int, int, SampleModel, ColorModel) - Constructor for class com.sun.media.imageioimpl.plugins.tiff.EmptyImage
 
emWave - Variable in class loci.formats.in.BDReader
 
emWave - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
emWave - Variable in class loci.formats.in.ImarisHDFReader
 
emWave - Variable in class loci.formats.in.ND2Handler
 
emWave - Variable in class loci.formats.in.NikonTiffReader
 
emWavelen - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Emission filter wavelength.

emWavelength - Variable in class loci.formats.in.BaseZeissReader
 
emWavelength - Variable in class loci.formats.in.ColumbusReader.Plane
 
emWavelength - Variable in class loci.formats.in.MetamorphReader

The TIFF's emWavelength

emWavelength - Variable in class loci.formats.in.OperettaReader.Plane
 
emWaves - Variable in class loci.formats.in.InCellReader
 
emWaves - Variable in class loci.formats.in.LeicaReader
 
enableCT - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
 
enabledBox - Variable in class loci.plugins.config.ConfigWindow
 
encode(byte[], int, int, int, int[], int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Encodes the supplied image data, writing to the currently set
 ImageOutputStream.

encode(byte[], int, int, int, int[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
encode(byte[], int, int, int, int[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFDeflater
 
encode(byte[], int, int, int, int[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLSBCompressor
 
encode(byte[], int, int, int, int[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWCompressor
 
encode(byte[], int, int, int, int[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullCompressor
 
encode(byte[], int, int, int, int[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFPackBitsCompressor
 
encode(byte[], int, int, int, int[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRLECompressor
 
encode(byte[], int, int, int, int[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFT4Compressor
 
encode(byte[], int, int, int, int[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFT6Compressor
 
encode(int, int, int, BitOutputBuffer) - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Encodes information for the specified element of the tree,
 given the threshold and sends it to the 'out' stream.

encode1D(byte[], int, int, int, byte[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

One-dimensionally encode a row of data using CCITT Huffman compression.

encodeMainHeader() - Method in class jj2000.j2k.codestream.writer.HeaderEncoder

Write main header.

encodePacket(int, int, int, int, CBlkRateDistStats[][], int[][], BitOutputBuffer, byte[], int) - Method in class jj2000.j2k.codestream.writer.PktEncoder

Encodes a packet and returns the buffer containing the encoded packet
 header.

encodeRLE(byte[], int, int, int, byte[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRLECompressor

Encode a row of data using Modified Huffman Compression also known as
 CCITT RLE (Run Lenth Encoding).

encodeRLE4(byte[], int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
encodeRLE8(byte[], int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
encodeT4(boolean, boolean, byte[], int, int, int, int, byte[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFT4Compressor

Encode a buffer of data using CCITT T.4 Compression also known as
 Group 3 facsimile compression.

encodeT6(byte[], int, int, int, int, byte[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFT6Compressor

Encode a buffer of data using CCITT T.6 Compression also known as
 Group 4 facsimile compression.

encodeTilePartHeader(int, int) - Method in class jj2000.j2k.codestream.writer.HeaderEncoder

Writes tile-part header.

encodeYUV(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor

Encode the uncompressed source image associated with this compressor
 instance and output a YUV planar image to the given destination buffer.

encodeYUV(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor

Encode the uncompressed source image associated with this compressor
 instance and return a buffer containing a YUV planar image.

encodeYUV(BufferedImage, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor

Encode the uncompressed source image stored in srcImage
 and output a YUV planar image to the given destination buffer.

encodeYUV(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor

Encode the uncompressed source image stored in srcImage
 and return a buffer containing a YUV planar image.

encodeYUV(byte[], int, int, int, int, byte[], int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
encodeYUV(int[], int, int, int, int, byte[], int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
ENCODING - Static variable in interface com.sun.media.imageioimpl.plugins.pcx.PCXConstants
 
encoding - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
ENCODING - Static variable in class loci.formats.in.LIFReader

The encoding used in this file.

encoding - Variable in class loci.formats.in.NRRDReader

Data encoding.

encodingRate - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

The bitrate in bits-per-pixel for encoding.

encodingRate - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

The bitrate in bits-per-pixel for encoding.

end - Variable in class loci.formats.FilePatternBlock
 
END - Static variable in class loci.formats.in.GIFReader
 
end - Variable in class loci.formats.Modulo
 
endDocument() - Method in class loci.formats.in.ND2Handler
 
endDocument() - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
endElement(String, String, String) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
 
endElement(String, String, String) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
endElement(String, String, String) - Method in class loci.formats.in.FEITiffReader.FEIHandler
 
endElement(String, String, String) - Method in class loci.formats.in.FlexReader.FlexHandler
 
endElement(String, String, String) - Method in class loci.formats.in.InCellReader.InCellHandler
 
endElement(String, String, String) - Method in class loci.formats.in.InCellReader.MinimalInCellHandler
 
endElement(String, String, String) - Method in class loci.formats.in.IvisionReader.IvisionHandler
 
endElement(String, String, String) - Method in class loci.formats.in.LeicaHandler
 
endElement(String, String, String) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
endElement(String, String, String, Attributes) - Method in class loci.formats.in.ND2Handler
 
endElement(String, String, String) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
endElement(String, String, String) - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
endElement(String, String, String) - Method in class loci.formats.in.ScanrReader.ScanrHandler
 
endElement(String, String, String) - Method in class loci.formats.in.ZeissTIFFHandler
 
endElement(String, String, String) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
 
ENDIANNESS_OFFSET - Static variable in class loci.formats.in.MRCReader
 
EndianType - Interface in jj2000.j2k.io

This interface defines constants for the two types of byte
 ordering: little- and big-endian.

endIndex - Variable in class loci.formats.FilePattern

Indices into the pattern indicating the end of a numerical block.

endInsertEmpty() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
endOfFrameFlag - Variable in class loci.formats.in.SPCReader
 
endOfFrameList - Variable in class loci.formats.in.SPCReader
 
endOfInfo_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor

reserved end of data code based on code size

endPointer - Variable in class loci.formats.in.LIFReader
 
endPos - Variable in class loci.formats.out.AVIWriter
 
endReplacePixels() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
endTime - Variable in class loci.formats.in.SDTInfo

Macro time of the last photon.

endWriteEmpty() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
endWriteSequence() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
endWriteSequence() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
endX - Variable in class loci.formats.in.SPEReader.SpeROI
 
endY - Variable in class loci.formats.in.SPEReader.SpeROI
 
energyConvFactor - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Energy conversion factor.

ENHANCED_DYNAMIC_RANGE - Static variable in class loci.formats.in.CellSensReader
 
enJJ2KMarkSeg - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

Whether or not to write the JJ2000 COM marker segment

ensureCapacity(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
ensureCapacity(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFPackBitsUtil
 
ensureNonExisting(String) - Method in class loci.formats.tools.MakeTestOmeTiff
 
entdec - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
entensions - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
entensions - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
entensions - Static variable in class com.sun.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
entensions - Static variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
entensions - Static variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
entensions - Static variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
entries - Variable in class loci.formats.in.ZeissCZIReader.AttachmentDirectory
 
entries - Variable in class loci.formats.in.ZeissCZIReader.Directory
 
EntropyCoder - Class in jj2000.j2k.entropy.encoder

This abstract class provides the general interface for block-based entropy
 encoders.

EntropyCoder(CBlkQuantDataSrcEnc) - Constructor for class jj2000.j2k.entropy.encoder.EntropyCoder

Initializes the source of quantized wavelet coefficients.

EntropyDecoder - Class in jj2000.j2k.entropy.decoder

This is the abstract class from which all entropy decoders must
 inherit.

EntropyDecoder(CodedCBlkDataSrcDec) - Constructor for class jj2000.j2k.entropy.decoder.EntropyDecoder

Initializes the source of compressed data.

entryName - Variable in class loci.formats.in.ZipReader
 
entryToString(Object, String) - Static method in class loci.formats.tools.AmiraParameters
 
enumerations - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFAttrInfo
 
ENV_SUFFIX - Static variable in class loci.formats.in.PrairieReader
 
envFile - Variable in class loci.formats.in.PrairieReader

The associated XML files.

EOC - Static variable in interface jj2000.j2k.codestream.Markers

End of codestream (EOC): 0xFFD9

eofByte - Variable in class loci.formats.codec.BitBuffer

Deprecated.
 
eofFlag - Variable in class loci.formats.codec.BitBuffer

Deprecated.
 
EOI - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
EOI - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
EOI - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
EOI_CODE - Static variable in class loci.formats.codec.LZWCodec
 
EPH - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Specifies whether end of packet header (EPH) markers should be used.

EPH - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies whether end of packet header (EPH) markers should be used.

EPH - Static variable in interface jj2000.j2k.codestream.Markers

End of packet header (EPH): 0xFF92

EPH_LENGTH - Static variable in interface jj2000.j2k.codestream.Markers

Length of EPH marker (in bytes)

ephMarker - Variable in class jj2000.j2k.codestream.writer.FileCodestreamWriter

Array used to store the EPH markers values

ephs - Variable in class jj2000.j2k.decoder.DecoderSpecs

The End of Packet Headers (EPH) markers specifications

ephUsed - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Whether or not EPH marker are used

EPSReader - Class in loci.formats.in

Reader is the file format reader for Encapsulated PostScript (EPS) files.

EPSReader() - Constructor for class loci.formats.in.EPSReader

Constructs a new EPS reader.

EPSWriter - Class in loci.formats.out

EPSWriter is the file format writer for Encapsulated PostScript (EPS) files.

EPSWriter() - Constructor for class loci.formats.out.EPSWriter
 
epxDiv - Variable in class loci.formats.in.SDTInfo
 
equal(Length, Length) - Static method in class loci.formats.in.PrairieReader

Determines whether the two Length values are equal.

equalReaders(IFormatReader, IFormatReader) - Static method in class loci.formats.FormatTools

Check if the two given readers are equal.

equals(Object) - Method in class com.sun.media.imageioimpl.common.InvertedCMYKColorSpace
 
equals(Object) - Method in class com.sun.media.imageioimpl.common.SimpleCMYKColorSpace
 
equals(int[], int[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
equals(Object) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Tests if the 'obj' object is the same filter as this one.

equals(Object) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Tests if the 'obj' object is the same filter as this one.

equals(Object) - Method in class loci.formats.in.CellSensReader.TileCoordinate
 
equals(Object) - Method in class loci.formats.in.MetamorphTiffReader.Well
 
equals(Object) - Method in class loci.formats.in.ZeissCZIReader.Coordinate
 
equals(Node, Node) - Method in class loci.formats.services.OMEXMLServiceImpl

Compares two Elements for equality.

equals(Object) - Method in class loci.formats.tiff.TiffRational

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in class loci.formats.TileStitcher.TileCoordinate
 
equals(Object) - Method in class loci.plugins.config.FormatEntry
 
equals(Object) - Method in class loci.plugins.prefs.OptionsList
 
equals(TJScalingFactor) - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor

Returns true or false, depending on whether this instance and
 other have the same numerator and denominator.

equalStrips - Variable in class loci.formats.in.MinimalTiffReader
 
equalStrips - Variable in class loci.formats.tiff.TiffParser
 
erode() - Method in class loci.plugins.util.RecordedImageProcessor
 
err - Variable in class jj2000.j2k.util.StreamMsgLogger

The 'err' stream

ERROR - Static variable in interface jj2000.j2k.util.MsgLogger

Severity of message.

ers - Variable in class jj2000.j2k.decoder.DecoderSpecs

The error resilience specifications concerning the entropy
 decoder

ERS_SEG_SYMBOLS - Static variable in interface jj2000.j2k.codestream.Markers

The "segmentation symbols used" flag within Sers: 2

ERS_SOP - Static variable in interface jj2000.j2k.codestream.Markers

The "SOP marker segments used" flag within Sers: 1

estimateLayerThreshold(int, EBCOTLayer) - Method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

This function attempts to estimate a rate-distortion slope threshold
 which will achieve a target number of code bytes close the
 `targetBytes' value.

evalFile(String) - Method in class loci.formats.in.ZeissTIFFReader

Evaluate the metadata of a TIFF/XML file collection, and return this to the user.

excitation - Variable in class loci.formats.in.FlexReader.FilterGroup
 
excitation - Variable in class loci.formats.in.OIRReader.Channel
 
excitation - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
excitationFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
excitationWavelength - Variable in class loci.formats.in.SVSReader
 
exclude - Variable in class loci.formats.in.InCellReader
 
execute() - Method in class loci.plugins.in.ImportProcess

Performs the import preparation process,
 notifying status listeners at each step.

exFilters - Variable in class loci.formats.in.InCellReader
 
EXIF - Static variable in class loci.formats.tiff.IFD
 
EXIF_JPEG_COMPRESSION_TYPE - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
EXIF_VERSION - Static variable in class loci.formats.tiff.IFD
 
EXIF_VERSION_2_1 - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

An array of bytes containing the values {'0', '2', '1',
 '0'} to be used with the "EXIFVersion" tag to indicate
 EXIF version 2.1.

EXIF_VERSION_2_2 - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

An array of bytes containing the values {'0', '2', '2',
 '0'} to be used with the "EXIFVersion" tag to indicate
 EXIF version 2.2.

EXIFGPSTagSet - Class in com.sun.media.imageio.plugins.tiff

A class representing the tags found in an EXIF GPS Info IFD.

EXIFGPSTagSet() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet
 
EXIFGPSTagSet.GPSAltitude - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSAltitudeRef - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSAreaInformation - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDateStamp - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDestBearing - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDestBearingRef - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDestDistance - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDestDistanceRef - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDestLatitude - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDestLatitudeRef - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDestLongitude - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDestLongitudeRef - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDifferential - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSDOP - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSImgDirection - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSImgDirectionRef - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSLatitude - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSLatitudeRef - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSLongitude - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSLongitudeRef - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSMapDatum - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSMeasureMode - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSProcessingMethod - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSSatellites - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSSpeed - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSSpeedRef - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSStatus - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSTimeStamp - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSTrack - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSTrackRef - Class in com.sun.media.imageio.plugins.tiff
 
EXIFGPSTagSet.GPSVersionID - Class in com.sun.media.imageio.plugins.tiff
 
EXIFIFDPointer() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFParentTIFFTagSet.EXIFIFDPointer
 
EXIFInteroperabilityTagSet - Class in com.sun.media.imageio.plugins.tiff

A class representing the tags found in an EXIF Interoperability IFD.

EXIFInteroperabilityTagSet() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFInteroperabilityTagSet
 
EXIFInteroperabilityTagSet.InteroperabilityIndex - Class in com.sun.media.imageio.plugins.tiff
 
EXIFParentTIFFTagSet - Class in com.sun.media.imageio.plugins.tiff

A class containing the TIFF tags used to reference the EXIF and GPS IFDs.

EXIFParentTIFFTagSet() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFParentTIFFTagSet
 
EXIFParentTIFFTagSet.EXIFIFDPointer - Class in com.sun.media.imageio.plugins.tiff
 
EXIFParentTIFFTagSet.GPSInfoIFDPointer - Class in com.sun.media.imageio.plugins.tiff
 
EXIFService - Interface in loci.formats.services
 
EXIFServiceImpl - Class in loci.formats.services
 
EXIFServiceImpl() - Constructor for class loci.formats.services.EXIFServiceImpl
 
EXIFTIFFTagSet - Class in com.sun.media.imageio.plugins.tiff

A class representing the tags found in an EXIF IFD.

EXIFTIFFTagSet() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet
 
EXIFTIFFTagSet.ApertureValue - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.BrightnessValue - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.CFAPattern - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.ColorSpace - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.ComponentsConfiguration - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.CompressedBitsPerPixel - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.Contrast - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.CustomRendered - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.DateTimeDigitized - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.DateTimeOriginal - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.DeviceSettingDescription - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.DigitalZoomRatio - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.EXIFVersion - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.ExposureBiasValue - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.ExposureIndex - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.ExposureMode - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.ExposureProgram - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.ExposureTime - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.FileSource - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.Flash - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.FlashEnergy - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.FlashPixVersion - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.FNumber - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.FocalLength - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.FocalLengthIn35mmFilm - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.FocalPlaneResolutionUnit - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.FocalPlaneXResolution - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.FocalPlaneYResolution - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.GainControl - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.ImageUniqueID - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.InteroperabilityIFD - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.ISOSpeedRatings - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.LightSource - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.MakerNote - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.MaxApertureValue - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.MeteringMode - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.OECF - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.PixelXDimension - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.PixelYDimension - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.RelatedSoundFile - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.Saturation - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SceneCaptureType - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SceneType - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SensingMethod - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.Sharpness - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.ShutterSpeedValue - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SpatialFrequencyResponse - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SpectralSensitivity - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SubjectArea - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SubjectDistance - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SubjectDistanceRange - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SubjectLocation - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SubSecTime - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SubSecTimeDigitized - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.SubSecTimeOriginal - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.UserComment - Class in com.sun.media.imageio.plugins.tiff
 
EXIFTIFFTagSet.WhiteBalance - Class in com.sun.media.imageio.plugins.tiff
 
EXIFVersion() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.EXIFVersion
 
exists - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane

Whether or not the file meant to contain this plane exists.

exists(String) - Method in interface loci.formats.services.JHDFService

Checks if path in HDF5 file exists.

exists(String) - Method in class loci.formats.services.JHDFServiceImpl
 
exit() - Method in class loci.formats.tools.EditTiffG
 
exp - Variable in class jj2000.j2k.quantization.dequantizer.StdDequantizerParams

The quantization step "exponent" value, for each resolution level and
 subband, as it appears in the codestream.

EXP - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
exp() - Method in class loci.plugins.util.RecordedImageProcessor
 
expandCode(byte[], int, short, int) - Method in class com.sun.media.imageioimpl.common.LZWStringTable

If expanded data doesnt fit into array only what will fit is written
 to buf and the return value indicates how much of the expanded code has
 been written to the buf.

expandPixels(int, byte[], byte[], int) - Method in class loci.formats.in.PictReader

Expand an array of bytes.

EXPANSION_TABLE - Static variable in class loci.formats.in.PictReader

Table used in expanding pixels that use less than 8 bits.

EXPERIMENT - Static variable in class loci.formats.in.LeicaReader
 
EXPERIMENT_FILE - Static variable in class loci.formats.in.BDReader
 
EXPERIMENT_FILE - Static variable in class loci.formats.in.ScanrReader
 
experimenterName - Variable in class loci.formats.in.ImaconReader
 
expH - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox
 
EXPIRED_QT_MSG - Static variable in class loci.formats.gui.LegacyQTTools
 
expiredQT - Variable in class loci.formats.gui.LegacyQTTools

Flag indicating QuickTime for Java has expired.

explode() - Method in class loci.formats.FilePatternBlock
 
exporter - Variable in class loci.plugins.LociExporter
 
Exporter - Class in loci.plugins.out

Core logic for the Bio-Formats Exporter ImageJ plugin.

Exporter(LociExporter, ImagePlus) - Constructor for class loci.plugins.out.Exporter
 
exposure - Variable in class loci.formats.in.BDReader
 
exposure - Variable in class loci.formats.in.InCellReader.Image
 
exposure - Variable in class loci.formats.in.InCellReader.InCellHandler
 
exposure - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
EXPOSURE_BIAS_VALUE - Static variable in class loci.formats.tiff.IFD
 
EXPOSURE_INDEX - Static variable in class loci.formats.tiff.IFD
 
EXPOSURE_METERING_MODE - Static variable in class loci.formats.in.CellSensReader
 
EXPOSURE_MODE - Static variable in class loci.formats.tiff.IFD
 
EXPOSURE_MODE_AUTO_BRACKET - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureMode" tag.

EXPOSURE_MODE_AUTO_EXPOSURE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureMode" tag.

EXPOSURE_MODE_MANUAL_EXPOSURE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureMode" tag.

EXPOSURE_PROGRAM - Static variable in class loci.formats.tiff.IFD
 
EXPOSURE_PROGRAM_ACTION_PROGRAM - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureProgram" tag.

EXPOSURE_PROGRAM_APERTURE_PRIORITY - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureProgram" tag.

EXPOSURE_PROGRAM_CREATIVE_PROGRAM - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureProgram" tag.

EXPOSURE_PROGRAM_LANDSCAPE_MODE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureProgram" tag.

EXPOSURE_PROGRAM_MANUAL - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureProgram" tag.

EXPOSURE_PROGRAM_MAX_RESERVED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureProgram" tag.

EXPOSURE_PROGRAM_NORMAL_PROGRAM - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureProgram" tag.

EXPOSURE_PROGRAM_NOT_DEFINED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureProgram" tag.

EXPOSURE_PROGRAM_PORTRAIT_MODE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureProgram" tag.

EXPOSURE_PROGRAM_SHUTTER_PRIORITY - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "ExposureProgram" tag.

EXPOSURE_TIME - Static variable in class loci.formats.in.CellSensReader
 
EXPOSURE_TIME - Static variable in class loci.formats.in.FluoviewReader
 
EXPOSURE_TIME - Static variable in class loci.formats.tiff.IFD

EXIF tags.

ExposureBiasValue() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ExposureBiasValue
 
ExposureIndex() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ExposureIndex
 
ExposureMode() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ExposureMode
 
ExposureProgram() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ExposureProgram
 
exposures - Variable in class loci.formats.in.MetamorphHandler
 
exposures - Variable in class loci.formats.in.ScanrReader
 
exposureScale - Variable in class loci.formats.in.SVSReader
 
ExposureTime() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ExposureTime
 
exposureTime - Variable in class loci.formats.in.BaseZeissReader
 
exposureTime - Variable in class loci.formats.in.BioRadSCNReader
 
exposureTime - Variable in class loci.formats.in.FakeReader

exposure time per plane info

exposureTime - Variable in class loci.formats.in.FluoviewReader
 
exposureTime - Variable in class loci.formats.in.IvisionReader
 
exposureTime - Variable in class loci.formats.in.LeicaReader
 
exposureTime - Variable in class loci.formats.in.LiFlimReader
 
exposureTime - Variable in class loci.formats.in.MetamorphReader
 
exposureTime - Variable in class loci.formats.in.MicromanagerReader.Position
 
exposureTime - Variable in class loci.formats.in.NativeND2Reader
 
exposureTime - Variable in class loci.formats.in.ND2Handler
 
exposureTime - Variable in class loci.formats.in.SVSReader
 
exposureTime - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
exposureTimes - Variable in class loci.formats.in.CellSensReader.Pyramid
 
exposureTimes - Variable in class loci.formats.in.SimplePCITiffReader
 
exposureTimes - Variable in class loci.formats.in.TillVisionReader
 
exposureTimeUnit - Variable in class loci.formats.in.LiFlimReader
 
expTime - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Exposure time in seconds.

expTimes - Variable in class loci.formats.in.LIFReader
 
expV - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox
 
extCount - Variable in class loci.formats.in.PerkinElmerReader
 
EXTENSION - Static variable in class loci.formats.in.GIFReader
 
ExtensionFileFilter - Class in loci.formats.gui

A file filter based on file extensions, for use with a JFileChooser.

ExtensionFileFilter(String, String) - Constructor for class loci.formats.gui.ExtensionFileFilter

Constructs a new filter that accepts the given extension.

ExtensionFileFilter(String[], String) - Constructor for class loci.formats.gui.ExtensionFileFilter

Constructs a new filter that accepts the given extensions.

extensions - Static variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
extensions - Static variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
extensions - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
extensions - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
extensions - Static variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
extensions - Static variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
extensions - Variable in class loci.plugins.config.ConfigWindow
 
extensions - Variable in class loci.plugins.macro.MacroFunctions
 
EXTERNAL_DATA_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
EXTERNAL_FILE_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
externals - Variable in class loci.formats.FileStitcher
 
ExternalSeries(FilePattern) - Constructor for class loci.formats.FileStitcher.ExternalSeries
 
extHdrFields - Variable in class loci.formats.in.DeltavisionReader

Initialize an array of Extended Header Field structures.

extHeaderSize - Variable in class loci.formats.in.MRCReader

Size of extended header

extIndex - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
 
EXTRA_IMAGES - Static variable in class loci.formats.in.AFIReader
 
EXTRA_SAMPLES - Static variable in class loci.formats.in.CellSensReader
 
EXTRA_SAMPLES - Static variable in class loci.formats.tiff.IFD
 
EXTRA_SAMPLES_ASSOCIATED_ALPHA - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "ExtraSamples" tag.

EXTRA_SAMPLES_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
EXTRA_SAMPLES_UNASSOCIATED_ALPHA - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "ExtraSamples" tag.

EXTRA_SAMPLES_UNSPECIFIED - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "ExtraSamples" tag.

extractCoreMetaData() - Method in class loci.formats.tools.AmiraParameters
 
extractMainMarkSeg(short, RandomAccessIO) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

This method extract a marker segment from the main header and stores it
 into a byte buffer for the second pass.

extractTilePartMarkSeg(short, RandomAccessIO, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

This method extracts a marker segment in a tile-part header and stores
 it into a byte buffer for the second pass.

extractTokensFromFakeSeries(String) - Method in class loci.formats.in.FakeReader
 
extraFiles - Variable in class loci.formats.in.VolocityReader
 
extraImages - Variable in class loci.formats.in.ZeissCZIReader
 
extraLength - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.Box
 
extralyrs - Variable in class jj2000.j2k.entropy.encoder.LayersInfo

The number of extra layers to be added after an optimized layer.

extras - Variable in class loci.formats.in.LeicaHandler
 
ExtraSamples() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ExtraSamples
 
extraSamples - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The value of the ExtraSamples tag.

extraSamples - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
exts - Variable in class loci.formats.gui.ExtensionFileFilter

List of valid extensions.

extSize - Variable in class loci.formats.in.DeltavisionReader

Size of extended header.

exWave - Variable in class loci.formats.in.BDReader
 
exWave - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
exWave - Variable in class loci.formats.in.ImarisHDFReader
 
exWave - Variable in class loci.formats.in.LeicaHandler.Channel
 
exWave - Variable in class loci.formats.in.ND2Handler
 
exWave - Variable in class loci.formats.in.NikonTiffReader
 
exWavelen - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Excitation filter wavelength.

exWavelength - Variable in class loci.formats.in.BaseZeissReader
 
exWavelength - Variable in class loci.formats.in.ColumbusReader.Plane
 
exWavelength - Variable in class loci.formats.in.OperettaReader.Plane
 
exWaves - Variable in class loci.formats.in.InCellReader
 
exWaves - Variable in class loci.formats.in.LeicaReader
 
exWaves - Variable in class loci.formats.in.LIFReader
 




F

F_KEY - Static variable in class loci.formats.in.LiFlimReader
 
F_NUMBER - Static variable in class loci.formats.tiff.IFD
 
FacilityManager - Class in jj2000.j2k.util

This class manages common facilities for mutithreading environments, It can
 register different facilities for each thread, and also a default one, so
 that they can be referred by static methods, while possibly having
 different ones for different threads.

FacilityManager() - Constructor for class jj2000.j2k.util.FacilityManager
 
factor - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
factors - Variable in class loci.formats.in.FlexReader.FlexFile
 
factors - Variable in class loci.formats.in.FlexReader.FlexHandler
 
factory - Variable in class loci.formats.FormatReader
 
FAKE_EXT - Static variable in class loci.formats.ResourceNamer
 
fakeBigTiff - Variable in class loci.formats.tiff.TiffParser

Whether or not 64-bit offsets are used for non-BigTIFF files.

FakeImage - Class in loci.formats.tools

Generates fake image structures.

FakeImage(Location) - Constructor for class loci.formats.tools.FakeImage
 
FakeReader - Class in loci.formats.in

FakeReader is the file format reader for faking input data.

FakeReader() - Constructor for class loci.formats.in.FakeReader

Constructs a new fake reader.

fakeSeries - Variable in class loci.formats.in.FakeReader

List of used files if the fake is a SPW structure

falseColor - Variable in class loci.formats.CoreMetadata

Indicates whether or not we can ignore the color map (if present).

FAN_SPEED - Static variable in class loci.formats.in.CellSensReader
 
fastCodeSymbols(int, int, int) - Method in class jj2000.j2k.entropy.encoder.MQCoder

This method performs the coding of the symbol 'bit', using context
 'ctxt', 'n' times, using the MQ-coder speedup mode if possible.

fastDecodeSymbols(int[], int, int) - Method in class jj2000.j2k.entropy.decoder.MQDecoder

Decodes 'n' symbols from the bit stream using the same context
 'ctxt'.

fatal(Node, String) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
fatal(Node, String) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
fatal(Node, String) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
fatal(Node, String) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
FaxTIFFTagSet - Class in com.sun.media.imageio.plugins.tiff

A class representing the extra tags found in a
 
 TIFF-F (RFC 2036) file.

FaxTIFFTagSet() - Constructor for class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet
 
FaxTIFFTagSet.BadFaxLines - Class in com.sun.media.imageio.plugins.tiff
 
FaxTIFFTagSet.CleanFaxData - Class in com.sun.media.imageio.plugins.tiff
 
FaxTIFFTagSet.ConsecutiveBadFaxLines - Class in com.sun.media.imageio.plugins.tiff
 
fb - Variable in class loci.formats.in.BaseZeissReader.Shape
 
fcc - Variable in class loci.formats.in.AVIReader
 
FCS_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo

For .sdt files created in FIFO mode
 (setup, data blocks = Decay, FCS, FIDA, FILDA & MCS curves
 for each used routing channel).

fcsDecayCalc - Variable in class loci.formats.in.SDTInfo

Bit 0 = 1 - decay curve calculated.

fcsPoints - Variable in class loci.formats.in.SDTInfo

No of FCS values.

fcsType - Variable in class loci.formats.in.SDTInfo

0 - linear FCS with log binning (100 bins/log)
 when bit 15 = 1 (0x8000) - Multi-Tau FCS
 where bits 14-0 = ktau parameter.

fctlCount - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
FD - Static variable in class loci.formats.in.DicomReader
 
fdatValid - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
FEATURE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
FeatureType(int, int) - Constructor for enum loci.formats.in.BaseZeissReader.FeatureType
 
FEI_MAGIC_STRING - Static variable in class loci.formats.in.FEIReader
 
FEIHandler() - Constructor for class loci.formats.in.FEITiffReader.FEIHandler
 
FEIReader - Class in loci.formats.in

FEIReader is the file format reader for FEI and Philips .img files.

FEIReader() - Constructor for class loci.formats.in.FEIReader

Constructs a new FEI reader.

FEITiffReader - Class in loci.formats.in

FEITiffReader is the file format reader for TIFF files produced by various
 FEI software.

FEITiffReader() - Constructor for class loci.formats.in.FEITiffReader
 
FEITiffReader.FEIHandler - Class in loci.formats.in
 
fetchRow(MdbTableDef) - Method in class loci.formats.services.MDBServiceImpl

Fetches the next row from the table, ignoring potential parsing exceptions.

ff - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
fidaPoints - Variable in class loci.formats.in.SDTInfo

No of FIDA values.

fidaTime - Variable in class loci.formats.in.SDTInfo

Interval time [ms] for FIDA histogram.

field - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
field - Variable in class loci.formats.in.ColumbusReader.Plane
 
field - Variable in class loci.formats.in.FlexReader.FlexFile
 
field - Variable in class loci.formats.in.OperettaReader.Plane
 
FIELD - Static variable in class loci.formats.ResourceNamer
 
FIELD_AUX_FLAGS - Static variable in class loci.formats.in.IM3Reader
 
FIELD_BAND_INDEX - Static variable in class loci.formats.in.IM3Reader
 
FIELD_BANDS - Static variable in class loci.formats.in.IM3Reader
 
FIELD_CLASS_ID - Static variable in class loci.formats.in.IM3Reader
 
FIELD_DATA - Static variable in class loci.formats.in.IM3Reader
 
FIELD_DATA_SET - Static variable in class loci.formats.in.IM3Reader
 
FIELD_EXPOSURE - Static variable in class loci.formats.in.IM3Reader
 
FIELD_FILE_VERSION - Static variable in class loci.formats.in.IM3Reader
 
FIELD_FILTER_PAIR - Static variable in class loci.formats.in.IM3Reader
 
FIELD_FIXED_FILTER - Static variable in class loci.formats.in.IM3Reader
 
FIELD_HOMOGENEOUS - Static variable in class loci.formats.in.IM3Reader
 
FIELD_INDEX - Static variable in class loci.formats.in.ND2Handler
 
FIELD_MAGNITUDES - Static variable in class loci.formats.in.IM3Reader
 
FIELD_MANUFACTURER - Static variable in class loci.formats.in.IM3Reader
 
FIELD_MILLIMETERS_PER_PIXEL - Static variable in class loci.formats.in.IM3Reader
 
FIELD_NAME - Static variable in class loci.formats.in.IM3Reader
 
FIELD_NUANCE_FLAGS - Static variable in class loci.formats.in.IM3Reader
 
FIELD_OBJECTIVE - Static variable in class loci.formats.in.IM3Reader
 
FIELD_PART_NUMBER - Static variable in class loci.formats.in.IM3Reader
 
FIELD_PROTOCOL - Static variable in class loci.formats.in.IM3Reader
 
FIELD_PROXY_PARENT_FILE_NAME - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SAMPLE_ID - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SHAPE - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SOURCE_FILE_NAME - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SPECTRA - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SPECTRAL_BASIS_INFO - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SPECTRAL_LIBRARY - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SPECTRUM - Static variable in class loci.formats.in.IM3Reader
 
FIELD_THUMBNAIL - Static variable in class loci.formats.in.IM3Reader
 
FIELD_TIMESTAMP - Static variable in class loci.formats.in.IM3Reader
 
FIELD_TYPE - Static variable in class loci.formats.in.CellSensReader
 
FIELD_TYPE_ID - Static variable in class loci.formats.in.IM3Reader
 
FIELD_USER_COMMENTS - Static variable in class loci.formats.in.IM3Reader
 
FIELD_VALUES - Static variable in class loci.formats.in.IM3Reader
 
FIELD_WAVELENGTH - Static variable in class loci.formats.in.IM3Reader
 
FIELD_WAVELENGTHS - Static variable in class loci.formats.in.IM3Reader
 
fieldCol - Variable in class loci.formats.in.MetamorphTiffReader.Well
 
fieldCols - Variable in class loci.formats.in.BDReader
 
fieldColumnCount - Variable in class loci.formats.in.MetamorphTiffReader
 
fieldColumns - Variable in class loci.formats.in.ScanrReader
 
fieldCount - Variable in class loci.formats.in.CellWorxReader
 
fieldCount - Variable in class loci.formats.in.FlexReader
 
fieldCount - Variable in class loci.formats.in.InCellReader
 
fieldIndex - Variable in class loci.formats.in.FluoviewReader
 
fieldIndex - Variable in class loci.formats.in.NativeND2Reader
 
FieldInfo() - Constructor for class loci.formats.in.CellVoyagerReader.FieldInfo
 
fieldMap - Variable in class loci.formats.in.CellWorxReader
 
fieldOffsets - Variable in class loci.formats.in.FluoviewReader
 
fieldPositionX - Variable in class loci.formats.in.ScanrReader
 
fieldPositionY - Variable in class loci.formats.in.ScanrReader
 
fieldPosX - Variable in class loci.formats.in.LIFReader
 
fieldPosY - Variable in class loci.formats.in.LIFReader
 
fieldRow - Variable in class loci.formats.in.MetamorphTiffReader.Well
 
fieldRowCount - Variable in class loci.formats.in.MetamorphTiffReader
 
fieldRows - Variable in class loci.formats.in.BDReader
 
fieldRows - Variable in class loci.formats.in.ScanrReader
 
fields - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
 
fifoTyp - Variable in class loci.formats.in.SDTInfo
 
fildaPoints - Variable in class loci.formats.in.SDTInfo

No of FILDA values.

fildaTime - Variable in class loci.formats.in.SDTInfo

Interval time [ms] for FILDA histogram.

file - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter

The name of the file from which to read the codestream and to write
 the JP2 file

file - Variable in class jj2000.j2k.util.CodestreamManipulator

The name of the outfile

file - Variable in class loci.formats.in.ColumbusReader.Plane
 
file - Variable in class loci.formats.in.FlexReader.FlexFile
 
file - Variable in class loci.formats.tools.EditTiffG
 
FILE_LENGTH - Static variable in class loci.formats.in.CanonRawReader
 
FILE_MAGIC_STRING - Static variable in class loci.formats.in.OBFReader
 
FILE_SOURCE - Static variable in class loci.formats.tiff.IFD
 
FILE_SOURCE_DSC - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "FileSource" tag.

FILE_TYPE_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
FileBitstreamReaderAgent - Class in jj2000.j2k.codestream.reader

This class reads the bit stream (with the help of HeaderDecoder for tile
 headers and PktDecoder for packets header and body) and retrives location
 of all code-block's codewords.

FileBitstreamReaderAgent(HeaderDecoder, RandomAccessIO, DecoderSpecs, J2KImageReadParamJava, boolean, HeaderInfo) - Constructor for class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Reads all tiles headers and keep offset of their first
 packet.

fileBox - Variable in class loci.formats.tools.EditTiffG
 
FileChannelImageInputStream - Class in com.sun.media.imageio.stream

A class which implements ImageInputStream using a
 FileChannel as the eventual data source.

FileChannelImageInputStream(FileChannel) - Constructor for class com.sun.media.imageio.stream.FileChannelImageInputStream

Constructs a FileChannelImageInputStream from a
 FileChannel.

FileChannelImageOutputStream - Class in com.sun.media.imageio.stream

A class which implements ImageOutputStream using a
 FileChannel as the eventual data destination.

FileChannelImageOutputStream(FileChannel) - Constructor for class com.sun.media.imageio.stream.FileChannelImageOutputStream

Constructs a FileChannelImageOutputStream from a
 FileChannel.

FileCodestreamWriter - Class in jj2000.j2k.codestream.writer

This class implements a CodestreamWriter for Java streams.

FileCodestreamWriter(File, int) - Constructor for class jj2000.j2k.codestream.writer.FileCodestreamWriter

Opens the file 'file' for writing the bit stream, using the 'he' header
 encoder.

FileCodestreamWriter(String, int) - Constructor for class jj2000.j2k.codestream.writer.FileCodestreamWriter

Opens the file named 'fname' for writing the bit stream, using the 'he'
 header encoder.

FileCodestreamWriter(OutputStream, int) - Constructor for class jj2000.j2k.codestream.writer.FileCodestreamWriter

Uses the output stream 'os' for writing the bit stream, using the 'he'
 header encoder.

FileFormatBoxes - Interface in jj2000.j2k.fileformat

This class contains all the markers used in the JPEG 2000 Part I file format

FileFormatReader - Class in jj2000.j2k.fileformat.reader

This class reads the file format wrapper that may or may not exist around a
 valid JPEG 2000 codestream.

FileFormatReader(RandomAccessIO, J2KMetadata) - Constructor for class jj2000.j2k.fileformat.reader.FileFormatReader

The constructor of the FileFormatReader

FileFormatWriter - Class in jj2000.j2k.fileformat.writer

This class writes the file format wrapper that may or may not exist around
 a valid JPEG 2000 codestream.

FileFormatWriter(File, ImageOutputStream, int, int, int, int[], int, ColorModel, SampleModel, J2KMetadata) - Constructor for class jj2000.j2k.fileformat.writer.FileFormatWriter

The constructor of the FileFormatWriter.

fileGroupOption(String) - Method in class loci.formats.FormatReader
 
fileGroupOption(String) - Method in interface loci.formats.IFormatReader

Returns an int indicating that we cannot, must, or might group the files
 in a given dataset.

fileGroupOption(String) - Method in class loci.formats.ImageReader
 
fileGroupOption(String) - Method in class loci.formats.in.AFIReader
 
fileGroupOption(String) - Method in class loci.formats.in.AnalyzeReader
 
fileGroupOption(String) - Method in class loci.formats.in.APLReader
 
fileGroupOption(String) - Method in class loci.formats.in.BDReader
 
fileGroupOption(String) - Method in class loci.formats.in.BioRadReader
 
fileGroupOption(String) - Method in class loci.formats.in.BrukerReader
 
fileGroupOption(String) - Method in class loci.formats.in.CellomicsReader
 
fileGroupOption(String) - Method in class loci.formats.in.CellSensReader
 
fileGroupOption(String) - Method in class loci.formats.in.CellVoyagerReader
 
fileGroupOption(String) - Method in class loci.formats.in.ColumbusReader
 
fileGroupOption(String) - Method in class loci.formats.in.DicomReader
 
fileGroupOption(String) - Method in class loci.formats.in.FlexReader
 
fileGroupOption(String) - Method in class loci.formats.in.FujiReader
 
fileGroupOption(String) - Method in class loci.formats.in.FV1000Reader
 
fileGroupOption(String) - Method in class loci.formats.in.HitachiReader
 
fileGroupOption(String) - Method in class loci.formats.in.ICSReader
 
fileGroupOption(String) - Method in class loci.formats.in.ImagicReader
 
fileGroupOption(String) - Method in class loci.formats.in.InCellReader
 
fileGroupOption(String) - Method in class loci.formats.in.L2DReader
 
fileGroupOption(String) - Method in class loci.formats.in.LeicaReader
 
fileGroupOption(String) - Method in class loci.formats.in.MetamorphReader
 
fileGroupOption(String) - Method in class loci.formats.in.MIASReader
 
fileGroupOption(String) - Method in class loci.formats.in.MicromanagerReader
 
fileGroupOption(String) - Method in class loci.formats.in.NDPIReader
 
fileGroupOption(String) - Method in class loci.formats.in.NDPISReader
 
fileGroupOption(String) - Method in class loci.formats.in.NiftiReader
 
fileGroupOption(String) - Method in class loci.formats.in.NRRDReader
 
fileGroupOption(String) - Method in class loci.formats.in.OMETiffReader
 
fileGroupOption(String) - Method in class loci.formats.in.OperettaReader
 
fileGroupOption(String) - Method in class loci.formats.in.PerkinElmerReader
 
fileGroupOption(String) - Method in class loci.formats.in.PrairieReader
 
fileGroupOption(String) - Method in class loci.formats.in.ScanrReader
 
fileGroupOption(String) - Method in class loci.formats.in.ScreenReader
 
fileGroupOption(String) - Method in class loci.formats.in.SPCReader
 
fileGroupOption(String) - Method in class loci.formats.in.SVSReader
 
fileGroupOption(String) - Method in class loci.formats.in.TCSReader
 
fileGroupOption(String) - Method in class loci.formats.in.TillVisionReader
 
fileGroupOption(String) - Method in class loci.formats.in.TrestleReader
 
fileGroupOption(String) - Method in class loci.formats.in.VisitechReader
 
fileGroupOption(String) - Method in class loci.formats.in.ZeissLSMReader
 
fileGroupOption(String) - Method in class loci.formats.in.ZeissTIFFReader
 
fileGroupOption(String) - Method in class loci.formats.ReaderWrapper
 
fileGroupOption(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
fileGUID - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
FileHeader() - Constructor for class loci.formats.in.ZeissCZIReader.FileHeader
 
fileIndex - Variable in class loci.formats.in.ColumbusReader.Plane
 
FileInfo - Class in loci.formats

Encompasses basic metadata about a file.

FileInfo() - Constructor for class loci.formats.FileInfo
 
FILEINFO_STRING - Static variable in class loci.formats.in.KodakReader
 
fileLength - Variable in class loci.formats.in.LeicaReader

Length of each file name.

fileList - Variable in class loci.formats.in.DicomReader
 
fileMap - Variable in class loci.formats.in.CellSensReader
 
fileName - Variable in class jj2000.j2k.io.BufferedRandomAccessFile

The name of the current file

filename - Variable in class loci.formats.FileInfo

Absolute path to this file.

filename - Variable in class loci.formats.gui.ImageViewer
 
filename - Variable in class loci.formats.in.InCellReader.Image
 
filename - Variable in class loci.formats.in.MIASReader.AnalysisFile
 
filename - Variable in class loci.formats.in.OperettaReader.Plane
 
filename - Variable in class loci.formats.in.PrairieMetadata.PFile

filename attribute of this <File>.

filename - Variable in class loci.formats.in.ZeissCZIReader.Segment
 
filename - Variable in class loci.formats.in.ZeissTIFFReader.Plane
 
filename - Variable in class loci.formats.tiff.TiffSaver

Output filename.

fileNameMap - Variable in class loci.formats.in.MicromanagerReader.Position
 
filenames - Variable in class loci.formats.in.FV1000Reader
 
filePart - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
filePart - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
filePart - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
filePath - Variable in class loci.formats.services.POIServiceImpl
 
FilePattern - Class in loci.formats

Represents a collection of files meant to be part of the same
 data series.

FilePattern(Location) - Constructor for class loci.formats.FilePattern

Creates a pattern object using the given file as a template.

FilePattern(String, String) - Constructor for class loci.formats.FilePattern

Creates a pattern object using the given
 filename and directory path as a template.

FilePattern(String) - Constructor for class loci.formats.FilePattern

Creates a pattern object for files with the given pattern string.

FilePatternBlock - Class in loci.formats

FilePatternBlock represents a single block in a FilePattern.

FilePatternBlock(String) - Constructor for class loci.formats.FilePatternBlock

Builds a FilePatternBlock from a block string.

FilePatternDialog - Class in loci.plugins.in

Bio-Formats Importer file pattern dialog box.

FilePatternDialog(ImportProcess) - Constructor for class loci.plugins.in.FilePatternDialog

Creates a file pattern dialog for the Bio-Formats Importer.

FilePatternReader - Class in loci.formats.in
 
FilePatternReader() - Constructor for class loci.formats.in.FilePatternReader

Constructs a new pattern reader.

filePosition - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
filePosition - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
fileReader - Variable in class loci.formats.gui.ImageViewer

Reader for files on disk.

files - Variable in class loci.formats.FilePattern

File listing for this file pattern.

files - Variable in class loci.formats.FileStitcher.ExternalSeries
 
files - Variable in class loci.formats.in.CellomicsReader
 
files - Variable in class loci.formats.in.HamamatsuVMSReader
 
files - Variable in class loci.formats.in.ImprovisionTiffReader
 
files - Variable in class loci.formats.in.LeicaReader

Array of image file names.

files - Variable in class loci.formats.in.MetamorphTiffReader
 
files - Variable in class loci.formats.in.PerkinElmerReader

List of files to open.

files - Variable in class loci.formats.in.PrairieMetadata.Frame

<File> elements beneath this <Frame>, keyed on each
 file's channel.

files - Variable in class loci.formats.in.SlidebookTiffReader
 
files - Variable in class loci.formats.in.TrestleReader
 
files - Variable in class loci.formats.in.VarianFDFReader
 
files - Variable in class loci.formats.in.VisitechReader

Files in this dataset.

files - Variable in class loci.formats.in.ZeissZVIReader
 
files - Variable in class loci.formats.services.POIServiceImpl
 
fileSave - Variable in class loci.formats.gui.ImageViewer
 
fileSizes - Variable in class loci.formats.services.POIServiceImpl
 
FileSource() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.FileSource
 
FileStitcher - Class in loci.formats

Logic to stitch together files with similar names.

FileStitcher() - Constructor for class loci.formats.FileStitcher

Constructs a FileStitcher around a new image reader.

FileStitcher(boolean) - Constructor for class loci.formats.FileStitcher

Constructs a FileStitcher around a new image reader.

FileStitcher(IFormatReader) - Constructor for class loci.formats.FileStitcher

Constructs a FileStitcher with the given reader.

FileStitcher(IFormatReader, boolean) - Constructor for class loci.formats.FileStitcher

Constructs a FileStitcher with the given reader.

fileStitcher - Variable in class loci.plugins.in.ImportProcess
 
FileStitcher.ExternalSeries - Class in loci.formats
 
fileSystem - Variable in class loci.formats.services.POIServiceImpl
 
FileTypeBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000

This class is defined to represent a File Type Box of JPEG JP2 file
  format.

FileTypeBox(int, int, int[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox

Constructs a FileTypeBox from the provided brand, minor
  version and compatibility list.

FileTypeBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox

Constructs a FileTypeBox from the provided byte array.

FileTypeBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox

Constructs a FileTypeBox from
  org.w3c.dom.Node.

fileView - Variable in class loci.formats.gui.ImageViewer
 
fileWriter - Variable in class loci.formats.gui.ImageViewer

Writer for files on disk.

fill() - Method in class loci.plugins.util.RecordedImageProcessor
 
fill(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
 
FILL_ORDER - Static variable in class loci.formats.tiff.IFD
 
FILL_ORDER_LEFT_TO_RIGHT - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "FillOrder" tag.

FILL_ORDER_RIGHT_TO_LEFT - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "FillOrder" tag.

fillAcquisitionDate(MetadataStore, String, int) - Method in class loci.formats.in.FakeReader
 
fillAnnotations(MetadataStore, int) - Method in class loci.formats.in.FakeReader
 
fillBasedOnBands(int, boolean, short[], short[], short[]) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox

Fills the channel definitions into the arrays based on the number
  of components and isPremultiplied.

fillBits - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor

EOL padding flag: 1 if fill bits have been added before an EOL such
 that the EOL ends on a byte boundary, 0 otherwise.

fillColour - Variable in class loci.formats.in.BaseZeissReader.Shape
 
filled - Variable in class loci.formats.ChannelFiller

Whether to fill in the indices.

fillExposureTime(MetadataStore) - Method in class loci.formats.in.FakeReader
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Attachment
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.AttachmentDirectory
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Directory
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.FileHeader
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Metadata
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Segment
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
fillInIFD(IFD) - Method in class loci.formats.tiff.TiffParser

Fill in IFD entries that are stored at an arbitrary offset.

fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
 
fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
 
fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
 
fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
 
fillMetadataPass4(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
 
fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
 
fillMetadataPass6(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass7(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Store basic dimensions in model

FillOrder() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.FillOrder
 
fillOrder - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor

The logical order of bits within a byte.

fillOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
fillPhysicalSizes(MetadataStore) - Method in class loci.formats.in.FakeReader
 
fillPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
 
fillPrecInfo(int, int, int) - Method in class jj2000.j2k.codestream.reader.PktDecoder

Retrives precincts and code-blocks coordinates in the given resolution,
 level and component.

fillPrecInfo(int, int, int) - Method in class jj2000.j2k.codestream.writer.PktEncoder

Retrives precincts and code-blocks coordinates in the given resolution,
 component and tile.

fillRegions(MetadataStore, int) - Method in class loci.formats.in.FakeReader
 
FillStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.FillStyle
 
fillStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
 
filter - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Specifies which filters to use for the specified tile-components.

filter(Object) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGCompressor.JPEGSPIFilter
 
filter - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
 
filter - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
filter(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
FILTER_53 - Static variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

The filter for lossless compression.

FILTER_97 - Static variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

The filter for lossy compression.

FILTER_SPEC_COMP_DEF - Static variable in class jj2000.j2k.wavelet.WTFilterSpec

The identifier for "component default" specified filters

FILTER_SPEC_MAIN_DEF - Static variable in class jj2000.j2k.wavelet.WTFilterSpec

The identifier for "main default" specified filters

FILTER_SPEC_TILE_COMP - Static variable in class jj2000.j2k.wavelet.WTFilterSpec

The identifier for "tile and component specific" specified filters

FILTER_SPEC_TILE_DEF - Static variable in class jj2000.j2k.wavelet.WTFilterSpec

The identifier for "tile specific default" specified filters

FilterGroup() - Constructor for class loci.formats.in.FlexReader.FilterGroup
 
filterMap - Variable in class loci.formats.in.FlexReader
 
filterMetadata - Variable in class loci.formats.FormatReader

Whether or not to filter out invalid metadata.

FilterMetadata - Class in loci.formats.meta
 
FilterMetadata(MetadataStore, boolean) - Constructor for class loci.formats.meta.FilterMetadata
 
filterModels - Variable in class loci.formats.in.LIFReader
 
filterModels - Variable in class loci.formats.in.NikonTiffReader
 
filterRefPopulated - Variable in class loci.formats.in.LeicaReader
 
filters - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies which filters to use for the specified tile-components.

filters - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull

Wavelet filters for all components and tiles

filterSet - Variable in class loci.formats.in.FlexReader.FlexHandler
 
FILTERSET - Static variable in class loci.formats.in.LeicaReader
 
filterSet - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
 
filterSet - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
filterSetMap - Variable in class loci.formats.in.FlexReader
 
filterSetRef - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
filterSets - Variable in class loci.formats.in.FlexReader
 
FilterTypes - Interface in jj2000.j2k.wavelet

This interface defines the identifiers for the different types of
 filters that are supported.

filts - Variable in class loci.formats.gui.ComboFileFilter

List of filters to be combined.

finalize() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
finalize() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
finalize() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
finalize() - Method in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Prints the timing information, if collected, and calls 'finalize' on
 the super class.

finalize() - Method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Prints the timing information, if collected, and calls 'finalize' on
 the super class.

finalize() - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Prints the timing information, if collected, and calls 'finalize' on
 the super class.

finalize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
finalize() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
find(String[]) - Method in class loci.formats.in.PrairieReader

Finds the first file with one of the given suffixes.

find(String, String) - Static method in class loci.plugins.Updater
 
FindCharString(short, byte) - Method in class com.sun.media.imageioimpl.common.LZWStringTable
 
findChildWithID(Node, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl

Return the child node with specified value for the "ID" attribute.

findColorIndex(PaletteBuilder.ColorNode, Color) - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
 
findEdges() - Method in class loci.plugins.util.RecordedImageProcessor
 
findFiles(Location) - Method in class loci.formats.in.FlexReader

Search for files that correspond to the given file.

findFiles(Location, String[]) - Method in class loci.formats.in.FlexReader
 
findImages(RandomAccessInputStream) - Method in class loci.formats.in.TillVisionReader
 
findKeyValue(String[], String[][]) - Method in class loci.formats.in.ICSReader
 
findKeyValueForCategory(String[], String[][]) - Method in class loci.formats.in.ICSReader
 
findKeyValueOther(String[], String[][]) - Method in class loci.formats.in.ICSReader
 
findLEIFile(String) - Method in class loci.formats.in.LeicaReader

Find the .lei file that belongs to the same dataset as the given file.

findLogFiles() - Method in class loci.formats.in.DeltavisionReader

Find the log files.

findLogFiles() - Method in class loci.formats.in.FakeReader
 
findMetadataFiles() - Method in class loci.formats.in.PrairieReader
 
findNextBlock() - Method in class loci.formats.in.OpenlabReader
 
findNextLine() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
findNextOffset(RandomAccessInputStream) - Method in class loci.formats.in.TillVisionReader
 
findNextOffset(RandomAccessInputStream, byte[]) - Method in class loci.formats.in.TillVisionReader
 
findOffset() - Method in class loci.formats.in.ImspectorReader

Find the offset to the next block of pixel data.

findOffset(boolean) - Method in class loci.formats.in.ImspectorReader
 
findOIFFile(String) - Method in class loci.formats.in.FV1000Reader
 
findPaletteEntry(PaletteBuilder.ColorNode, int, byte[], byte[], byte[]) - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
 
findPattern(String) - Static method in class loci.formats.FilePattern

Identifies the group pattern from a given file within that group.

findPattern(Location) - Static method in class loci.formats.FilePattern

Identifies the group pattern from a given file within that group.

findPattern(File) - Static method in class loci.formats.FilePattern

Identifies the group pattern from a given file within that group.

findPattern(String, String) - Static method in class loci.formats.FilePattern

Identifies the group pattern from a given filename and directory.

findPattern(String, String, String[]) - Static method in class loci.formats.FilePattern

Identifies the group pattern from a given filename, directory and
 list of candidate filenames.

findPattern(String, String, String[], int[]) - Static method in class loci.formats.FilePattern

Identifies the group pattern from a given filename, directory and
 list of candidate filenames.

findPattern(String[]) - Static method in class loci.formats.FilePattern

Generate a pattern from a list of file names.

findPattern(String, String[], int, int, String) - Static method in class loci.formats.FilePattern
 
findPattern(String) - Method in class loci.formats.FileStitcher
 
findPatterns(String) - Method in class loci.formats.FileStitcher

Finds the file pattern for the given ID, based on the state of the file
 stitcher.

findPixelOffsets() - Method in class loci.formats.in.JPXReader
 
findPixelsOffset(int) - Method in class loci.formats.in.VisitechReader
 
findRootNode(Node) - Method in class loci.formats.services.OMEXMLServiceImpl

Return the absolute root node for the specified child node.

findSeriesPatterns(String) - Static method in class loci.formats.FilePattern

Works like FilePattern.findSeriesPatterns(String, String, String[]),
 but dir and nameList are inferred from the given file's absolute
 path.

findSeriesPatterns(String, String, String[]) - Static method in class loci.formats.FilePattern

Similar to FilePattern.findPattern(String, String, String[]), but
 this does not merge series indices into a pattern block.

findString(String) - Method in class loci.formats.in.KodakReader
 
findTIFFs() - Method in class loci.formats.in.MetamorphTiffReader
 
findTruncIndices(int, int, int, int, SubbandAn, float, int) - Method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

This function finds the new truncation points indices for a packet.

findXML(String) - Static method in class loci.formats.in.ColumbusReader
 
finish(ImportProcess) - Method in class loci.plugins.in.Importer
 
finishedTileComponent - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

A flag indicating for each component if all the code-blocks of the *
        current tile have been returned.

finishLengthCalculation(int[], int) - Method in class jj2000.j2k.entropy.encoder.MQCoder

Terminates the calculation of the required length for each coding
 pass.

finishTime - Variable in class loci.formats.in.PerkinElmerReader
 
finishTiming() - Method in class loci.plugins.in.ImagePlusReader
 
FIRMWARE_VERSION - Static variable in class loci.formats.in.NikonReader
 
FIRST_BYPASS_PASS_IDX - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The index of the first "raw" pass, if bypass mode is on.

FIRST_CODE - Static variable in class loci.formats.codec.LZWCodec
 
firstAvailable(int...) - Method in class loci.plugins.in.SwapDialog
 
firstDataStream - Variable in class loci.formats.tools.AmiraParameters
 
firstFile - Variable in class loci.formats.in.PrairieMetadata.Frame

The first actual <File> element for this <Frame>.

firstFrame - Variable in class loci.formats.in.PrairieMetadata.Sequence

The first actual <Frame> element for this <Sequence>.

firstIFD - Variable in class loci.formats.tiff.TiffParser

Cached first IFD in the current file.

firstIndex - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
 
firstLowBit(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
firstPackOff - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Offset of the first packet in each tile-part in each tile

firstSequence - Variable in class loci.formats.in.PrairieMetadata

The first actual <Sequence> element.

firstSeriesChannels - Variable in class loci.formats.in.MetamorphReader
 
firstStamp - Variable in class loci.formats.in.LeicaHandler
 
firstTilePartHeadLen - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

First tile part header length

firstTimeLoop - Variable in class loci.formats.in.ND2Handler
 
firstWellPlanes() - Method in class loci.formats.in.FlexReader

Returns the number of planes in the first well that has data.

fis - Variable in class loci.formats.Memoizer.KryoDeser
 
FitsReader - Class in loci.formats.in

FitsReader is the file format reader for
 Flexible Image Transport System (FITS) images.

FitsReader() - Constructor for class loci.formats.in.FitsReader

Constructs a new FitsReader.

fixed - Variable in class loci.formats.FilePatternBlock

Whether or not this is a fixed-width block.

FL - Static variable in class loci.formats.in.DicomReader
 
FLAG_ACCURATEDCT - Static variable in class org.libjpegturbo.turbojpeg.TJ

Use the most accurate DCT/IDCT algorithm available in the underlying
 codec.

FLAG_BOTTOMUP - Static variable in class org.libjpegturbo.turbojpeg.TJ

The uncompressed source/destination image is stored in bottom-up (Windows,
 OpenGL) order, not top-down (X11) order.

FLAG_FASTDCT - Static variable in class org.libjpegturbo.turbojpeg.TJ

Use the fastest DCT/IDCT algorithm available in the underlying codec.

FLAG_FASTUPSAMPLE - Static variable in class org.libjpegturbo.turbojpeg.TJ

When decompressing, use the fastest chrominance upsampling algorithm
 available in the underlying codec.

FLAG_FORCEMMX - Static variable in class org.libjpegturbo.turbojpeg.TJ

Turn off CPU auto-detection and force TurboJPEG to use MMX code
 (if the underlying codec supports it.)

FLAG_FORCESSE - Static variable in class org.libjpegturbo.turbojpeg.TJ

Turn off CPU auto-detection and force TurboJPEG to use SSE code
 (if the underlying codec supports it.)

FLAG_FORCESSE2 - Static variable in class org.libjpegturbo.turbojpeg.TJ

Turn off CPU auto-detection and force TurboJPEG to use SSE2 code
 (if the underlying codec supports it.)

FLAG_FORCESSE3 - Static variable in class org.libjpegturbo.turbojpeg.TJ

Turn off CPU auto-detection and force TurboJPEG to use SSE3 code
 (if the underlying codec supports it.)

flags - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
 
flags - Variable in class loci.formats.in.BaseZeissReader.Layer
 
flags - Variable in class loci.formats.in.SDTInfo

Scan clocks bits 2-0 (frame, line, pixel), rates_read - bit 15.

Flash() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.Flash
 
FLASH - Static variable in class loci.formats.tiff.IFD
 
FLASH_COMPENSATION - Static variable in class loci.formats.in.NikonReader
 
FLASH_DID_NOT_FIRE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "Flash" tag, indicating that the
 flash did not fire.

FLASH_ENERGY - Static variable in class loci.formats.tiff.IFD
 
FLASH_FIRED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "Flash" tag, indicating that the
 flash fired, but the strobe return status is unknown.

FLASH_MASK_FIRED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A mask to be used with the "Flash" tag, indicating that the
 flash fired.

FLASH_MASK_FUNCTION_NOT_PRESENT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A mask to be used with the "Flash" tag, indicating no flash function
 present.

FLASH_MASK_MODE_AUTO - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A mask to be used with the "Flash" tag, indicating auto mode.

FLASH_MASK_MODE_FLASH_FIRING - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A mask to be used with the "Flash" tag, indicating compulsory flash
 firing mode.

FLASH_MASK_MODE_FLASH_SUPPRESSION - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A mask to be used with the "Flash" tag, indicating compulsory flash
 suppression mode.

FLASH_MASK_RED_EYE_REDUCTION - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A mask to be used with the "Flash" tag, indicating red-eye reduction
 supported.

FLASH_MASK_RETURN_DETECTED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A mask to be used with the "Flash" tag, indicating strobe return
 light detected.

FLASH_MASK_RETURN_NOT_DETECTED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A mask to be used with the "Flash" tag, indicating strobe return
 light not detected.

FLASH_MODE - Static variable in class loci.formats.in.NikonReader
 
FLASH_PIX_VERSION - Static variable in class loci.formats.tiff.IFD
 
FLASH_SETTING - Static variable in class loci.formats.in.NikonReader
 
FLASH_STROBE_RETURN_LIGHT_DETECTED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "Flash" tag, indicating that the
 flash fired, and the strobe return light was detected.

FLASH_STROBE_RETURN_LIGHT_NOT_DETECTED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "Flash" tag, indicating that the
 flash fired, but the strobe return light was not detected.

FLASH_USED - Static variable in class loci.formats.in.NikonReader
 
FlashEnergy() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.FlashEnergy
 
FlashPixVersion() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.FlashPixVersion
 
flattenedResolutions - Variable in class loci.formats.FormatReader

Whether or not resolutions are flattened.

flattenHashtables() - Method in class loci.formats.FormatReader

Call FormatReader.updateMetadataLists(Hashtable) on
 all metadata hashtables.

flbckX - Variable in class loci.formats.in.SDTInfo
 
flbckY - Variable in class loci.formats.in.SDTInfo
 
FLEX - Static variable in class loci.formats.in.FlexReader

Custom IFD entry for Flex XML.

flex - Variable in class loci.formats.in.FlexReader.MeaHandler
 
FLEX_SUFFIX - Static variable in class loci.formats.in.FlexReader
 
FlexFile() - Constructor for class loci.formats.in.FlexReader.FlexFile
 
flexFiles - Variable in class loci.formats.in.FlexReader
 
FlexHandler(List<String>, List<String>, MetadataStore, boolean, int, int) - Constructor for class loci.formats.in.FlexReader.FlexHandler
 
FlexReader - Class in loci.formats.in

FlexReader is a file format reader for Evotec Flex files.

FlexReader() - Constructor for class loci.formats.in.FlexReader

Constructs a new Flex reader.

FlexReader.FilterGroup - Class in loci.formats.in

Stores a grouping of filters.

FlexReader.FlexFile - Class in loci.formats.in
 
FlexReader.FlexHandler - Class in loci.formats.in

SAX handler for parsing XML.

FlexReader.MeaHandler - Class in loci.formats.in

SAX handler for parsing XML from .mea files.

FlexReader.ResHandler - Class in loci.formats.in

SAX handler for parsing XML from .res files.

FlexWidgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats Flex support.

FlexWidgets() - Constructor for class loci.plugins.config.FlexWidgets
 
FLIM_DOMAIN - Static variable in class loci.formats.FormatTools

Identifies the fluorescence-lifetime domain.

flip - Variable in class loci.formats.in.NativeQTReader
 
flipHorizontal() - Method in class loci.plugins.util.RecordedImageProcessor
 
flipTable - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
flipTable - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLSBDecompressor

Table for flipping bytes from LSB-to-MSB to MSB-to-LSB.

flipVertical() - Method in class loci.plugins.util.RecordedImageProcessor
 
FLOAT - Static variable in class loci.formats.FormatTools

Identifies the FLOAT data type used to store pixel values.

FLOAT - Static variable in class loci.formats.in.CellSensReader
 
FLOAT - Static variable in class loci.formats.in.GatanReader
 
FLOAT - Static variable in class loci.formats.in.SPEReader
 
FLOAT_ABS_PRECISION - Static variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

The precision for float data type, in an absolute sense.

FLOAT_REL_PRECISION - Static variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

The relative precision for float data.

FloatIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.FloatIM3Record
 
floatValue() - Method in class loci.formats.tiff.TiffRational

Returns the value of the specified number as a float.

FLOW_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo

For .sdt files created automatically in Continuous Flow mode measurement
 (no setup, only data).

FlowSightReader - Class in loci.formats.in
 
FlowSightReader() - Constructor for class loci.formats.in.FlowSightReader
 
fluor - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
FLUOVIEW_MAGIC_STRING - Static variable in class loci.formats.in.FluoviewReader

String identifying a Fluoview file.

FluoviewReader - Class in loci.formats.in

FluoviewReader is the file format reader for
 Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.

FluoviewReader() - Constructor for class loci.formats.in.FluoviewReader

Constructs a new Fluoview TIFF reader.

flush() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
flush() - Method in class com.sun.media.imageioimpl.common.BitFile
 
flush() - Method in class com.sun.media.imageioimpl.common.LZWCompressor

Indicate to compressor that no more data to go so write out
 any remaining buffered data.

flush() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO

A null operation as writing is not supported.

flush() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
flush() - Method in class jj2000.j2k.entropy.decoder.ByteToBitInput

Flushes (i.e.

flush() - Method in class jj2000.j2k.entropy.encoder.BitToByteOutput

Writes the contents of the bit buffer and byte aligns the output by
 filling bits with an alternating sequence of 0's and 1's.

flush() - Method in interface jj2000.j2k.io.BinaryDataOutput

Any data that has been buffered must be written, and the stream should
 be realigned at the byte level.

flush() - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Any data that has been buffered must be written (including
 buffering at the bit level), and the stream should be realigned
 at the byte level.

flush() - Method in class jj2000.j2k.util.ISRandomAccessIO

Does nothing since this class does not implement data output.

flush() - Method in interface jj2000.j2k.util.MsgLogger

Writes any buffered data from the println() method to the device.

flush() - Method in class jj2000.j2k.util.StreamMsgLogger

Writes any buffered data from the print() and println() methods to the
 device.

flush() - Method in class loci.plugins.config.TextAreaWriter

Flushing a TextAreaWriter does nothing .

flushBefore(long) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
flushBuffer() - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream

Write to the FileChannel any remaining bytes in
 the byte output buffer.

FM_LOSSLESS - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Distortion estimation lookup table for bits coded using the
 magnitude-refinement (MR) primative, for lossless coding and last
 bit-plane.

FM_LOSSY - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Distortion estimation lookup table for bits coded using the
 magnitude-refinement (MR) primative, for lossy coding (i.e.

fmt - Variable in class loci.formats.in.GelReader
 
fmt - Variable in class loci.formats.in.OpenlabReader
 
FNumber() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.FNumber
 
FOCAL_LENGTH - Static variable in class loci.formats.tiff.IFD
 
FOCAL_LENGTH_35MM_FILM - Static variable in class loci.formats.tiff.IFD
 
FOCAL_PLANE_RESOLUTION_UNIT - Static variable in class loci.formats.tiff.IFD
 
FOCAL_PLANE_RESOLUTION_UNIT_CENTIMETER - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "FocalPlaneXResolution" tag.

FOCAL_PLANE_RESOLUTION_UNIT_INCH - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "FocalPlaneXResolution" tag.

FOCAL_PLANE_RESOLUTION_UNIT_NONE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "FocalPlaneResolutionUnit" tag.

FOCAL_PLANE_X_RESOLUTION - Static variable in class loci.formats.tiff.IFD
 
FOCAL_PLANE_Y_RESOLUTION - Static variable in class loci.formats.tiff.IFD
 
FocalLength() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.FocalLength
 
FocalLengthIn35mmFilm() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.FocalLengthIn35mmFilm
 
FocalPlaneResolutionUnit() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.FocalPlaneResolutionUnit
 
FocalPlaneXResolution() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.FocalPlaneXResolution
 
FocalPlaneYResolution() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.FocalPlaneYResolution
 
FOCUS_IMAGE - Static variable in class loci.formats.in.CellSensReader
 
FOCUS_MODE - Static variable in class loci.formats.in.NikonReader
 
focusGained(FocusEvent) - Method in class loci.plugins.in.MainDialog

Handles information pane updates when component focus changes.

focusLost(FocusEvent) - Method in class loci.plugins.in.MainDialog
 
font - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
 
fontName - Variable in class loci.formats.in.BaseZeissReader.Shape
 
fontName - Variable in class loci.formats.in.LeicaHandler.ROI
 
fontName - Variable in class loci.formats.in.LIFReader.ROI
 
fontSize - Variable in class loci.formats.in.BaseZeissReader.Shape
 
fontSize - Variable in class loci.formats.in.LeicaHandler.ROI
 
fontSize - Variable in class loci.formats.in.LIFReader.ROI
 
fontWeight - Variable in class loci.formats.in.BaseZeissReader.Shape
 
FOOTER_SIZE - Static variable in class loci.formats.in.SIFReader
 
footerPointer - Variable in class loci.formats.out.APNGWriter
 
force - Variable in class loci.formats.gui.DataConverter
 
forceType - Variable in class loci.formats.gui.DataConverter
 
forkFile - Variable in class loci.formats.in.NativeQTReader
 
format - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata

cache the metadata format

format - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter

cache the J2KMetadataFormat

format - Variable in class loci.formats.FormatHandler

Name of this file format.

formatCompression(IFD) - Method in class loci.formats.out.TiffWriter

Sets the compression code for the specified IFD.

FormatEntry - Class in loci.plugins.config

A list entry for the configuration window's Formats tab.

FormatEntry(PrintWriter, Object) - Constructor for class loci.plugins.config.FormatEntry
 
FormatException - Exception in loci.formats

FormatException is the exception thrown when something
 goes wrong performing a file format operation.

FormatException() - Constructor for exception loci.formats.FormatException
 
FormatException(String) - Constructor for exception loci.formats.FormatException
 
FormatException(String, Throwable) - Constructor for exception loci.formats.FormatException
 
FormatException(Throwable) - Constructor for exception loci.formats.FormatException
 
FormatFileFilter - Class in loci.formats.gui

A file filter for a biological file format, for use with a JFileChooser.

FormatFileFilter(IFormatReader) - Constructor for class loci.formats.gui.FormatFileFilter

Constructs a new filter that accepts files of the given reader's type.

FormatFileFilter(IFormatReader, boolean) - Constructor for class loci.formats.gui.FormatFileFilter

Constructs a new filter that accepts files of the given reader's type,
 allowing the reader to open files only if the allowOpen flag is set.

FormatHandler - Class in loci.formats

Abstract superclass of all biological file format readers and writers.

FormatHandler(String, String) - Constructor for class loci.formats.FormatHandler

Constructs a format handler with the given name and default suffix.

FormatHandler(String, String[]) - Constructor for class loci.formats.FormatHandler

Constructs a format handler with the given name and default suffixes.

formatInfo - Variable in class loci.plugins.config.ConfigWindow
 
formatLabel - Variable in class loci.formats.gui.PreviewPane

Labels containing thumbnail and dimensional information.

formatName - Variable in class loci.plugins.config.FormatEntry
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
formatNames - Static variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
FormatReader - Class in loci.formats

Abstract superclass of all biological file format readers.

FormatReader(String, String) - Constructor for class loci.formats.FormatReader

Constructs a format reader with the given name and default suffix.

FormatReader(String, String[]) - Constructor for class loci.formats.FormatReader

Constructs a format reader with the given name and default suffixes.

FORMATS - Static variable in class loci.formats.in.GelReader
 
formatsList - Variable in class loci.plugins.config.ConfigWindow
 
formatsListModel - Variable in class loci.plugins.config.ConfigWindow
 
formatTag(int) - Method in class loci.formats.in.DicomReader
 
formatText - Variable in class loci.formats.gui.PreviewPane
 
formatTip - Variable in class loci.formats.gui.PreviewPane
 
FormatTools - Class in loci.formats

A utility class for format reader and writer implementations.

FormatTools() - Constructor for class loci.formats.FormatTools
 
FormatWriter - Class in loci.formats

Abstract superclass of all biological file format writers.

FormatWriter(String, String) - Constructor for class loci.formats.FormatWriter

Constructs a format writer with the given name and default suffix.

FormatWriter(String, String[]) - Constructor for class loci.formats.FormatWriter

Constructs a format writer with the given name and default suffixes.

FORW_ICT - Static variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Identifier for the Forward Irreversible Component
        Transformation (FORW_ICT).

FORW_RCT - Static variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Identifier for the Forward Reversible Component Transformation
        (FORW_RCT).

FORWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
 
forwardWarningMessage(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader

Package scope method to allow decompressors, for example, to
 emit warning messages.

ForwardWT - Class in jj2000.j2k.wavelet.analysis

This abstract class represents the forward wavelet transform functional
 block.

ForwardWT(ImgData) - Constructor for class jj2000.j2k.wavelet.analysis.ForwardWT

Initializes this object for the specified number of tiles 'nt' and
 components 'nc'.

ForwCompTransf - Class in jj2000.j2k.image.forwcomptransf

This class apply component transformations to the tiles depending
 on user specifications.

ForwCompTransf(BlkImgDataSrc, J2KImageWriteParamJava) - Constructor for class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Constructs a new ForwCompTransf object that operates on the
 specified source of image data.

ForwCompTransfSpec - Class in jj2000.j2k.image.forwcomptransf

This class extends CompTransfSpec class in order to hold encoder specific
 aspects of CompTransfSpec.

ForwCompTransfSpec(int, int, byte, AnWTFilterSpec, J2KImageWriteParamJava, String) - Constructor for class jj2000.j2k.image.forwcomptransf.ForwCompTransfSpec

Constructs a new 'ForwCompTransfSpec' for the specified number of
 components and tiles and the arguments of optName
 option.

forwICT(DataBlk, int) - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Apply forward irreversible component transformation to obtain requested
 component from specified block of data.

forwRCT(DataBlk, int) - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Apply forward component transformation to obtain requested component
 from specified block of data.

ForwWT - Interface in jj2000.j2k.wavelet.analysis

This interface extends the WaveletTransform with the
 specifics of forward wavelet transforms.

ForwWTDataProps - Interface in jj2000.j2k.wavelet.analysis

This interface extends the ImgData interface with methods that are
 necessary for forward wavelet data (i.e.

ForwWTFull - Class in jj2000.j2k.wavelet.analysis

This class implements the ForwardWT with the full-page approach to be used
 either with integer or floating-point filters

ForwWTFull(BlkImgDataSrc, J2KImageWriteParamJava, int, int) - Constructor for class jj2000.j2k.wavelet.analysis.ForwWTFull

Initializes this object with the given source of image data and with
 all the decompositon parameters

fos - Variable in class loci.formats.Memoizer.KryoDeser
 
found - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
 
foundChannelTag - Variable in class loci.formats.in.CellSensReader
 
foundPlateLayout - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
foundPositions - Variable in class loci.formats.in.ScanrReader
 
fp - Variable in class jj2000.j2k.image.ImgDataConverter

The number of fraction bits in the casted ints

fp - Variable in class loci.formats.AxisGuesser

File pattern identifying dimensional axis blocks.

fp - Variable in class loci.plugins.in.FilePatternDialog
 
fps - Variable in class loci.formats.FormatWriter

Frame rate to use when writing in frames per second, if applicable.

fps - Variable in class loci.formats.gui.DataConverter
 
fps - Variable in class loci.formats.gui.ImageViewer
 
fpsSpin - Variable in class loci.plugins.util.DataBrowser
 
FRAC_BITS - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
FRAC_SCALE - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
fracBits - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
Frame() - Constructor for class loci.formats.in.OBFReader.Frame
 
Frame(PrairieMetadata.Sequence, Element) - Constructor for class loci.formats.in.PrairieMetadata.Frame

Creates a new frame by parsing the given <Frame> element.

frame - Variable in class loci.formats.in.PrairieMetadata.PFile

The <Frame> containing this <File>.

FRAME_OFFSET - Static variable in class loci.formats.out.AVIWriter
 
FRAME_OFFSET_2 - Static variable in class loci.formats.out.AVIWriter
 
FRAME_ORIGIN - Static variable in class loci.formats.in.CellSensReader
 
FRAME_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
FRAME_SCALE - Static variable in class loci.formats.in.CellSensReader
 
FRAME_SIZE - Static variable in class loci.formats.in.CellSensReader
 
FRAME_TRANSFER - Static variable in class loci.formats.in.CellSensReader
 
FRAME_TYPE - Static variable in class loci.formats.in.CellSensReader
 
frameClockList - Variable in class loci.formats.in.SPCReader
 
frameCoordinates - Variable in class loci.formats.in.APNGReader
 
frameIndex(PrairieMetadata.Sequence, int, int, int) - Method in class loci.formats.in.PrairieReader

Gets the frame index associated with the given (Z, T) position of the
 specified series.

frames - Variable in class loci.formats.in.PrairieMetadata.Sequence

<Frame> elements beneath this <Sequence>, keyed on each
 frame's index.

framesAreTime - Variable in class loci.formats.in.PrairieReader

Whether a series uses Frames as time points rather than focal
 planes (i.e., sizeZ and sizeT values inverted).

frameValues - Variable in class loci.formats.in.PrairieMetadata.Frame

Table of key/value pairs for this <Frame>.

FREE_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
 
FREE_LINE - Static variable in class loci.formats.in.FV1000Reader
 
FREE_OFFSETS - Static variable in class loci.formats.tiff.IFD
 
FREE_SHAPE - Static variable in class loci.formats.in.FV1000Reader
 
FreeByteCounts() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.FreeByteCounts
 
FreeOffsets() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.FreeOffsets
 
freeTree(PaletteBuilder.ColorNode) - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
 
frequencies - Variable in class loci.formats.in.LiFlimReader
 
FREQUENCY - Static variable in class loci.formats.FormatTools

Identifies the Frequency dimensional type,
 representing a dimension consisting of frequencies.

fromCIEXYZ(float[]) - Method in class com.sun.media.imageioimpl.common.BogusColorSpace
 
fromCIEXYZ(float[]) - Method in class com.sun.media.imageioimpl.common.InvertedCMYKColorSpace
 
fromCIEXYZ(float[]) - Method in class com.sun.media.imageioimpl.common.SimpleCMYKColorSpace
 
fromCIEXYZ(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
 
fromISO8859(String) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableImageMetadata
 
fromRGB(float, float, float, float[]) - Method in class com.sun.media.imageio.plugins.tiff.TIFFColorConverter

Converts an RGB triple into the native color space of this
 TIFFColorConverter, and stores the result in the first three
 entries of the result array.

fromRGB(float[]) - Method in class com.sun.media.imageioimpl.common.BogusColorSpace
 
fromRGB(float[]) - Method in class com.sun.media.imageioimpl.common.InvertedCMYKColorSpace
 
fromRGB(float[]) - Method in class com.sun.media.imageioimpl.common.SimpleCMYKColorSpace
 
fromRGB(float, float, float, float[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFCIELabColorConverter
 
fromRGB(float, float, float, float[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
fromRGB(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
 
FRONT_MASK - Static variable in class loci.formats.codec.BitBuffer

Deprecated.
Various bitmasks for the xxxx0000 side of a byte.

FS_LOSSLESS - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Distortion estimation lookup table for bits coded using the sign-code
 (SC) primative, for lossless coding and last bit-plane.

FS_LOSSY - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Distortion estimation lookup table for bits coded using the sign-code
 (SC) primative, for lossy coding (i.e.

FT_BR - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes

File Type Fields

FTB_LENGTH - Static variable in class jj2000.j2k.fileformat.writer.FileFormatWriter

Length of File Type Box

ftpIdx - Variable in class jj2000.j2k.entropy.decoder.DecLyrdCBlk

The index of the first truncation point returned

FujiReader - Class in loci.formats.in

FujiReader is the file format reader for Fuji LAS 3000 datasets.

FujiReader() - Constructor for class loci.formats.in.FujiReader

Constructs a new Fuji reader.

fullImage - Variable in class loci.formats.in.MRWReader
 
FV1000_MAGIC_STRING_1 - Static variable in class loci.formats.in.FV1000Reader
 
FV1000_MAGIC_STRING_2 - Static variable in class loci.formats.in.FV1000Reader
 
FV1000_SUFFIXES - Static variable in class loci.formats.in.FV1000Reader
 
FV1000Reader - Class in loci.formats.in

FV1000Reader is the file format reader for Fluoview FV 1000 OIB and
 Fluoview FV 1000 OIF files.

FV1000Reader() - Constructor for class loci.formats.in.FV1000Reader

Constructs a new FV1000 reader.

FV1000Reader.ChannelData - Class in loci.formats.in
 
FV1000Reader.PlaneData - Class in loci.formats.in
 




G

gain - Variable in class loci.formats.in.BDReader
 
gain - Variable in class loci.formats.in.BioRadReader
 
gain - Variable in class loci.formats.in.BioRadSCNReader
 
gain - Variable in class loci.formats.in.CellSensReader.Pyramid
 
gain - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
gain - Variable in class loci.formats.in.ImarisHDFReader
 
gain - Variable in class loci.formats.in.InCellReader
 
gain - Variable in class loci.formats.in.IvisionReader
 
gain - Variable in class loci.formats.in.LeicaHandler.Channel
 
gain - Variable in class loci.formats.in.MetamorphHandler
 
gain - Variable in class loci.formats.in.MetamorphReader
 
gain - Variable in class loci.formats.in.MicromanagerReader.Position
 
gain - Variable in class loci.formats.in.ND2Handler
 
gain - Variable in class loci.formats.in.NikonTiffReader
 
gain - Variable in class loci.formats.in.OIRReader.Detector
 
gain - Variable in class loci.formats.in.OpenlabReader
 
gain - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
gain - Variable in class loci.formats.in.ZeissCZIReader
 
gain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
GAIN_CONTROL - Static variable in class loci.formats.tiff.IFD
 
GAIN_CONTROL_HIGH_GAIN_DOWN - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "GainControl" tag.

GAIN_CONTROL_HIGH_GAIN_UP - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "GainControl" tag.

GAIN_CONTROL_LOW_GAIN_DOWN - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "GainControl" tag.

GAIN_CONTROL_LOW_GAIN_UP - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "GainControl" tag.

GAIN_CONTROL_NONE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "GainControl" tag.

GAIN_UNIT - Static variable in class loci.formats.in.CellSensReader
 
GainControl() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.GainControl
 
gains - Variable in class loci.formats.in.FluoviewReader
 
gains - Variable in class loci.formats.in.LIFReader
 
GAMMA - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

The value of the third lifting step coefficient

GAMMA - Static variable in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

The value of the third lifting step coefficient

gamma - Variable in class loci.formats.in.GatanReader
 
gamma(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
 
gammaBlue - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
gammaGreen - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
gammaRed - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
GatanDM2Reader - Class in loci.formats.in

GatanDM2Reader is the file format reader for Gatan .dm2 files.

GatanDM2Reader() - Constructor for class loci.formats.in.GatanDM2Reader

Constructs a new Gatan .dm2 reader.

GatanReader - Class in loci.formats.in

GatanReader is the file format reader for Gatan files.

GatanReader() - Constructor for class loci.formats.in.GatanReader

Constructs a new Gatan reader.

gb - Variable in class jj2000.j2k.codestream.HeaderInfo.QCC
 
gb - Variable in class jj2000.j2k.codestream.HeaderInfo.QCD
 
gb - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Number of guard bits off all component in the current tile.

gbs - Variable in class jj2000.j2k.decoder.DecoderSpecs

Number of guard bits specifications

gbs - Variable in class jj2000.j2k.quantization.dequantizer.StdDequantizer

The number of guard bits spec

gbs - Variable in class jj2000.j2k.quantization.quantizer.StdQuantizer

The guard bits specifications

gcd(int, int) - Static method in class jj2000.j2k.util.MathUtil

Method that calculates the Greatest Common Divisor (GCD) of two
 positive integer numbers.

gcd(int[]) - Static method in class jj2000.j2k.util.MathUtil

Method that calculates the Greatest Common Divisor (GCD) of several
 positive integer numbers.

gct - Variable in class loci.formats.in.GIFReader

Global color table.

GEL_DOMAIN - Static variable in class loci.formats.FormatTools

Identifies the gel and blot imaging domain.

GelReader - Class in loci.formats.in

GelReader is the file format reader for
 Molecular Dynamics GEL TIFF files.

GelReader() - Constructor for class loci.formats.in.GelReader

Constructs a new GEL reader.

generateScreen(int, int, int, int, int) - Method in class loci.formats.tools.FakeImage

Creates a fake SPW file/directory structure.

GeoAsciiParams() - Constructor for class com.sun.media.imageio.plugins.tiff.GeoTIFFTagSet.GeoAsciiParams
 
GeoDoubleParams() - Constructor for class com.sun.media.imageio.plugins.tiff.GeoTIFFTagSet.GeoDoubleParams
 
GeoKeyDirectory() - Constructor for class com.sun.media.imageio.plugins.tiff.GeoTIFFTagSet.GeoKeyDirectory
 
GeoTIFFTagSet - Class in com.sun.media.imageio.plugins.tiff

A class representing the tags found in a GeoTIFF IFD.

GeoTIFFTagSet() - Constructor for class com.sun.media.imageio.plugins.tiff.GeoTIFFTagSet
 
GeoTIFFTagSet.GeoAsciiParams - Class in com.sun.media.imageio.plugins.tiff
 
GeoTIFFTagSet.GeoDoubleParams - Class in com.sun.media.imageio.plugins.tiff
 
GeoTIFFTagSet.GeoKeyDirectory - Class in com.sun.media.imageio.plugins.tiff
 
GeoTIFFTagSet.ModelPixelScale - Class in com.sun.media.imageio.plugins.tiff
 
GeoTIFFTagSet.ModelTiePoint - Class in com.sun.media.imageio.plugins.tiff
 
GeoTIFFTagSet.ModelTransformation - Class in com.sun.media.imageio.plugins.tiff
 
get(int) - Method in class loci.formats.codec.ByteVector
 
get(int) - Static method in enum loci.formats.codec.CompressionType

Retrieves the compression by reverse lookup of its "code".

get(int) - Static method in enum loci.formats.codec.JPEG2000BoxType

Retrieves the box type by reverse lookup of its "code".

get(int) - Static method in enum loci.formats.codec.JPEG2000SegmentMarker

Retrieves the segment marker by reverse lookup of its "code".

get(int, int, int, int) - Method in class loci.formats.codec.JPEGTileDecoder.TileCache
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.Charset
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.DrawStyle
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.FeatureType
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.FillStyle
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.LineEndPositions
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.LineEndStyle
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.PointStyle
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.TextAlignment
 
get(String) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name.

get(String, String) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name.

get(Object) - Method in interface loci.formats.in.PrairieMetadata.Value
 
get(int) - Method in interface loci.formats.in.PrairieMetadata.Value
 
get(Object) - Method in class loci.formats.in.PrairieMetadata.ValueItem
 
get(int) - Method in class loci.formats.in.PrairieMetadata.ValueItem
 
get(int) - Method in class loci.formats.in.PrairieMetadata.ValueTable
 
get(int) - Static method in enum loci.formats.tiff.IFDType

Retrieves a IFD type by reverse lookup of its "code".

get(int) - Method in class loci.formats.tiff.OnDemandLongArray
 
get(int) - Static method in enum loci.formats.tiff.PhotoInterp

Retrieves a photometric interpretation by reverse lookup of its "code".

get(int) - Static method in enum loci.formats.tiff.TiffCompression

Retrieves a TIFF compression instance by code.

get(List<T>, int, T) - Method in class loci.plugins.in.ImporterOptions
 
get(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
get(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
get16BitLookupTable() - Method in class loci.formats.ChannelFiller
 
get16BitLookupTable() - Method in class loci.formats.DelegateReader
 
get16BitLookupTable() - Method in class loci.formats.FileStitcher
 
get16BitLookupTable() - Method in class loci.formats.FormatReader
 
get16BitLookupTable() - Method in interface loci.formats.IFormatReader

Gets the 16-bit color lookup table associated with
 the most recently opened image.

get16BitLookupTable() - Method in class loci.formats.ImageReader
 
get16BitLookupTable() - Method in class loci.formats.in.BaseZeissReader
 
get16BitLookupTable() - Method in class loci.formats.in.DicomReader
 
get16BitLookupTable() - Method in class loci.formats.in.FakeReader
 
get16BitLookupTable() - Method in class loci.formats.in.FilePatternReader
 
get16BitLookupTable() - Method in class loci.formats.in.FV1000Reader
 
get16BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader
 
get16BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader
 
get16BitLookupTable() - Method in class loci.formats.in.InCellReader
 
get16BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
 
get16BitLookupTable() - Method in class loci.formats.in.JPXReader
 
get16BitLookupTable() - Method in class loci.formats.in.LeicaReader
 
get16BitLookupTable() - Method in class loci.formats.in.LIFReader
 
get16BitLookupTable() - Method in class loci.formats.in.MIASReader
 
get16BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
 
get16BitLookupTable() - Method in class loci.formats.in.NativeND2Reader
 
get16BitLookupTable() - Method in class loci.formats.in.OIRReader
 
get16BitLookupTable() - Method in class loci.formats.in.OMETiffReader
 
get16BitLookupTable() - Method in class loci.formats.in.PDSReader
 
get16BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader
 
get16BitLookupTable() - Method in class loci.formats.in.ScreenReader
 
get16BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader
 
get16BitLookupTable() - Method in class loci.formats.in.TCSReader
 
get16BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader
 
get16BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
 
get16BitLookupTable() - Method in class loci.formats.in.ZipReader
 
get16BitLookupTable() - Method in class loci.formats.ReaderWrapper
 
get8BitLookupTable() - Method in class loci.formats.ChannelFiller
 
get8BitLookupTable() - Method in class loci.formats.DelegateReader
 
get8BitLookupTable() - Method in class loci.formats.FileStitcher
 
get8BitLookupTable() - Method in class loci.formats.FormatReader
 
get8BitLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools

Converts an IndexColorModel to a 2D byte array.

get8BitLookupTable() - Method in interface loci.formats.IFormatReader

Gets the 8-bit color lookup table associated with
 the most recently opened image.

get8BitLookupTable() - Method in class loci.formats.ImageReader
 
get8BitLookupTable() - Method in class loci.formats.in.AmiraReader
 
get8BitLookupTable() - Method in class loci.formats.in.APNGReader
 
get8BitLookupTable() - Method in class loci.formats.in.AVIReader
 
get8BitLookupTable() - Method in class loci.formats.in.BaseZeissReader
 
get8BitLookupTable() - Method in class loci.formats.in.BioRadReader
 
get8BitLookupTable() - Method in class loci.formats.in.BMPReader
 
get8BitLookupTable() - Method in class loci.formats.in.CellH5Reader
 
get8BitLookupTable() - Method in class loci.formats.in.DicomReader
 
get8BitLookupTable() - Method in class loci.formats.in.FakeReader
 
get8BitLookupTable() - Method in class loci.formats.in.FilePatternReader
 
get8BitLookupTable() - Method in class loci.formats.in.GIFReader
 
get8BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader
 
get8BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader
 
get8BitLookupTable() - Method in class loci.formats.in.InCellReader
 
get8BitLookupTable() - Method in class loci.formats.in.IPWReader
 
get8BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
 
get8BitLookupTable() - Method in class loci.formats.in.JPXReader
 
get8BitLookupTable() - Method in class loci.formats.in.KhorosReader
 
get8BitLookupTable() - Method in class loci.formats.in.LeicaReader
 
get8BitLookupTable() - Method in class loci.formats.in.LIFReader
 
get8BitLookupTable() - Method in class loci.formats.in.MIASReader
 
get8BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
 
get8BitLookupTable() - Method in class loci.formats.in.NativeND2Reader
 
get8BitLookupTable() - Method in class loci.formats.in.OIRReader
 
get8BitLookupTable() - Method in class loci.formats.in.OMETiffReader
 
get8BitLookupTable() - Method in class loci.formats.in.OpenlabReader
 
get8BitLookupTable() - Method in class loci.formats.in.PCXReader
 
get8BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader
 
get8BitLookupTable() - Method in class loci.formats.in.PictReader
 
get8BitLookupTable() - Method in class loci.formats.in.PSDReader
 
get8BitLookupTable() - Method in class loci.formats.in.ScreenReader
 
get8BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader
 
get8BitLookupTable() - Method in class loci.formats.in.TargaReader
 
get8BitLookupTable() - Method in class loci.formats.in.TCSReader
 
get8BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader
 
get8BitLookupTable() - Method in class loci.formats.in.ZeissLMSReader
 
get8BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
 
get8BitLookupTable() - Method in class loci.formats.in.ZipReader
 
get8BitLookupTable() - Method in class loci.formats.ReaderWrapper
 
getAbortRequest() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

This method wraps the protected method abortRequested
  to allow the abortions be monitored by J2KReadState.

getAbortRequest() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter

This method wraps the protected method abortRequested
  to allow the abortions be monitored by J2KRenderedImage.

getAbortRequest() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader

This method wraps the protected method abortRequested
  to allow the abortions be monitored by J2KReadState.

getAbsoluteTime() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the absoluteTime associated with this Frame.

getAcquisitionMode(String) - Method in class loci.formats.FormatReader

Retrieves an AcquisitionMode enumeration
 value for the given String.

getActiveChannels() - Method in class loci.formats.in.PrairieMetadata

Gets the list of active channel indices, in sorted order.

getActualNbytes() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Return the actual number of read bytes.

getActualRate() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Return the actual decoding rate in bits per pixel.

getAdjustedIndex(int) - Method in class loci.formats.FileStitcher

Gets the local reader index for use with the given image plane.

getAdjustedOrder() - Method in class loci.formats.AxisGuesser

Gets the adjusted dimension order.

getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
 
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
 
getAdvancedSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader

Returns an array of FileInfo objects representing the files needed to
 open the current series.

getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
 
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
 
getAdvancedUsedFiles(boolean) - Method in class loci.formats.FileStitcher
 
getAdvancedUsedFiles(boolean) - Method in class loci.formats.FormatReader
 
getAdvancedUsedFiles(boolean) - Method in interface loci.formats.IFormatReader

Returns an array of FileInfo objects representing the files needed
 to open this dataset.

getAdvancedUsedFiles(boolean) - Method in class loci.formats.ImageReader
 
getAdvancedUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
 
getAlignROI() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets alignROI

getAllChildren(Integer) - Method in class loci.formats.in.VolocityReader
 
getAllCodeBlocks() - Method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

This method gets all the coded code-blocks from the EBCOT entropy coder
 for every component and every tile.

getAllFiles(String) - Method in class loci.formats.FilePattern
 
getAllNodes(IIOMetadataNode, List) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
getAllowedTagSets() - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam

Returns a List containing the allowed
 TIFFTagSet objects.

getAlpha(int) - Method in class loci.formats.gui.Index16ColorModel
 
getAlpha(int) - Method in class loci.formats.gui.SignedColorModel
 
getAlpha(Object) - Method in class loci.formats.gui.SignedColorModel
 
getAlpha(int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getAlpha(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getAlphas() - Method in class loci.formats.gui.Index16ColorModel

Return the array of alpha color components.

getAnHighNegSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the negative support of the high-pass analysis
 filter.

getAnHighNegSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the negative support of the high-pass analysis filter.

getAnHighNegSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns the negative support of the high-pass analysis filter.

getAnHighNegSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns the negative support of the high-pass analysis filter.

getAnHighNegSupport() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the negative support of the high-pass analysis
 filter.

getAnHighPosSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the positive support of the high-pass analysis
 filter.

getAnHighPosSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the positive support of the high-pass analysis filter.

getAnHighPosSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns the positive support of the high-pass analysis filter.

getAnHighPosSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns the positive support of the high-pass analysis filter.

getAnHighPosSupport() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the positive support of the high-pass analysis
 filter.

getAnLowNegSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the negative support of the low-pass analysis
 filter.

getAnLowNegSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the negative support of the low-pass analysis
 filter.

getAnLowNegSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns the negative support of the low-pass analysis filter.

getAnLowNegSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns the negative support of the low-pass analysis filter.

getAnLowNegSupport() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the negative support of the low-pass analysis
 filter.

getAnLowPosSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the positive support of the low-pass analysis
 filter.

getAnLowPosSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the positive support of the low-pass analysis filter.

getAnLowPosSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns the positive support of the low-pass analysis filter.

getAnLowPosSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns the positive support of the low-pass analysis filter.

getAnLowPosSupport() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the positive support of the low-pass analysis
 filter.

getAnSubbandTree(int, int) - Method in class jj2000.j2k.entropy.encoder.EntropyCoder

Returns a reference to the root of subband tree structure representing
 the subband decomposition for the specified tile-component.

getAnSubbandTree(int, int) - Method in class jj2000.j2k.quantization.quantizer.Quantizer

Returns a reference to the subband tree structure representing the
 subband decomposition for the specified tile-component.

getAnSubbandTree(int, int) - Method in class jj2000.j2k.roi.encoder.ROIScaler

Returns a reference to the subband tree structure representing the
 subband decomposition for the specified tile-component.

getAnSubbandTree(int, int) - Method in interface jj2000.j2k.wavelet.analysis.ForwWTDataProps

Returns a reference to the root of subband tree structure representing
 the subband decomposition for the specified tile-component.

getAnSubbandTree(int, int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns a reference to the subband tree structure representing the
 subband decomposition for the specified tile-component of the source.

getApproximationAccuracy() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox

Returns ApproximationAccuracy.

getArcType(String) - Method in class loci.formats.FormatReader

Retrieves an ArcType enumeration
 value for the given String.

getArray(String, int[], int[]) - Method in interface loci.formats.services.NetCDFService

Retrieves an HDF path's values.

getArray(String, int[], int[]) - Method in class loci.formats.services.NetCDFServiceImpl
 
getAsBytes() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns the data as an uninterpreted array of
 bytes.

getAsChars() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns TIFFTag.TIFF_SHORT data as an array of
 chars (unsigned 16-bit integers).

getAsDouble(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns data in any format as a double.

getAsDoubles() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns TIFFTag.TIFF_DOUBLE data as an array of
 doubles (64-bit floating-point values).

getAsFloat(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns data in any format as a float.

getAsFloats() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns TIFFTag.TIFF_FLOAT data as an array of
 floats (32-bit floating-point values).

getAsInt(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns data in any format as an int.

getAsInts() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns TIFFTag.TIFF_SLONG data as an array of
 ints (signed 32-bit integers).

getAsLong(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns data in any format as a long.

getAsLongs() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns TIFFTag.TIFF_LONG or
 TIFF_IFD_POINTER data as an array of
 longs (signed 64-bit integers).

getAsMetadata() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Converts the directory to a metadata object.

getAsNativeNode() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns the TIFFField as a node named either
 "TIFFField" or "TIFFIFD" as described in the
 TIFF native image metadata specification.

getAsRational(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns a TIFFTag.TIFF_RATIONAL data item as a two-element array
 of ints.

getAsRationals() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns TIFFTag.TIFF_RATIONAL data as an array of
 2-element arrays of longs.

getAsShorts() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns TIFFTag.TIFF_SSHORT data as an array of
 shorts (signed 16-bit integers).

getAssociation() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox

Returns the association which associates a color channel to a color
  component in the color space of the image.

getAsSRational(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns a TIFFTag.TIFF_SRATIONAL data item as a
 two-element array of ints.

getAsSRationals() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns TIFFTag.TIFF_SRATIONAL data as an array of
 2-element arrays of ints.

getAsString(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns a TIFFTag.TIFF_ASCII value as a
 String.

getAsTree(String) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getAsTree(String) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getAsTree(String) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getAsTree(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getAsTree(String) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
getAsTree(String) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getAsTree(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getAsTree(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
getAsTree(String) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
getAttribute(Node, String) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFField
 
getAttribute(Node, String) - Static method in class com.sun.media.imageio.stream.RawImageInputStream

Gets the attribute from the node.

getAttribute(Node, String, String, boolean) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getAttribute(Node, String) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getAttribute(Node, String, String, boolean) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getAttribute(Node, String) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getAttribute(Node, String) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Extracts the value of the attribute from name.

getAttribute(Node, String) - Static method in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
getAttribute(Node, String) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getAttribute(Node, String) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getAttributeDataType(String, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeDefaultValue(String, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeDescription(String, String, Locale) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeEnumerations(String, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeList() - Method in interface loci.formats.services.NetCDFService

Retrieves an exhaustive list of the HDF paths for all attributes in the
 HDF document.

getAttributeList() - Method in class loci.formats.services.NetCDFServiceImpl
 
getAttributeListMaxLength(String, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeListMinLength(String, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeMaxValue(String, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeMinValue(String, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeNames(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeValue(String) - Method in interface loci.formats.services.NetCDFService

Retrieves an attribute's value.

getAttributeValue(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getAttributeValueType(String, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttrInfo(String, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAutoscaleInfo() - Method in class loci.plugins.in.ImporterOptions
 
getAutoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
getAutoThreshold(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
getAvailableMemory() - Method in class loci.plugins.in.MemoryDialog
 
getAxisCount(int) - Method in class loci.formats.AxisGuesser

Gets the number of axes in the pattern of the given type.

getAxisCountC() - Method in class loci.formats.AxisGuesser

Gets the number of C axes in the pattern.

getAxisCountS() - Method in class loci.formats.AxisGuesser

Gets the number of S axes in the pattern.

getAxisCountT() - Method in class loci.formats.AxisGuesser

Gets the number of T axes in the pattern.

getAxisCountZ() - Method in class loci.formats.AxisGuesser

Gets the number of Z axes in the pattern.

getAxisGuesser() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getAxisGuesser() - Method in class loci.formats.FileStitcher

Gets the axis guesser object used to guess
 which dimensional axes are which.

getAxisType(String) - Static method in class loci.formats.AxisGuesser

Convert the given label to an axis type.

getAxisTypes() - Method in class loci.formats.AxisGuesser

Gets the guessed axis type for each dimensional block.

getAxisTypes() - Method in class loci.formats.FileStitcher

Gets the axis type for each dimensional block.

getBackgroundValue() - Method in class loci.plugins.util.RecordedImageProcessor
 
getBandSize(SampleModel) - Static method in class com.sun.media.imageioimpl.common.ImageUtil
 
getBaseReader() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getBestIndex(Color) - Method in class loci.plugins.util.RecordedImageProcessor
 
getBinaryOnlyOMEXML(String, String, String) - Method in class loci.formats.out.OMETiffWriter
 
getBinning(String) - Method in class loci.formats.FormatReader

Retrieves an Binning enumeration
 value for the given String.

getBinning() - Method in class loci.formats.in.MetamorphHandler
 
getBinnings() - Method in class loci.formats.in.ND2Handler
 
getBitDepth() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.BitsPerComponentBox

Returns the bit depths for all the image components.

getBitDepth() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Returns the bit depth for all the image components.

getBitDepth() - Method in class loci.formats.in.PrairieMetadata

Gets the bitDepth recorded in the configuration.

getBitDepths() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

Return the bit depths for all the color components.

getBitOffset() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
getBits(int) - Method in class loci.formats.codec.BitBuffer

Deprecated.
Returns an int value representing the value of the bits read from
 the byte array, from the current position.

getBitsPerPixel(SampleModel) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Returns the number of bits per pixel.

getBitsPerPixel() - Method in class loci.formats.FileStitcher
 
getBitsPerPixel() - Method in class loci.formats.FormatReader
 
getBitsPerPixel() - Method in interface loci.formats.IFormatReader

Gets the number of valid bits per pixel.

getBitsPerPixel() - Method in class loci.formats.ImageReader
 
getBitsPerPixel() - Method in class loci.formats.in.FilePatternReader
 
getBitsPerPixel(int) - Method in class loci.formats.in.OBFReader
 
getBitsPerPixel() - Method in class loci.formats.ReaderWrapper
 
getBitsPerSample() - Method in class loci.formats.tiff.IFD

Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given
 TIFF IFD.

getBlankThumbBytes() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getBlock(int) - Method in class loci.formats.FilePattern

Gets the specified file pattern block (e.g., <0-9>).

getBlock() - Method in class loci.formats.FilePatternBlock

Gets the block string.

getBlock(int, String) - Method in class loci.formats.in.ScanrReader
 
getBlockAligned() - Method in class jj2000.j2k.roi.encoder.ROIScaler

This function returns the blockAligned flag

getBlocks() - Method in class loci.formats.FilePattern

Gets all file pattern blocks.

getBlue(int) - Method in class loci.formats.gui.Index16ColorModel
 
getBlue(int) - Method in class loci.formats.gui.SignedColorModel
 
getBlue(Object) - Method in class loci.formats.gui.SignedColorModel
 
getBlue(int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getBlue(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getBlueOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ

For the given pixel format, returns the number of bytes that the blue
 component is offset from the start of the pixel.

getBlues() - Method in class loci.formats.gui.Index16ColorModel

Return the array of blue color components.

getBoolean(Node, String) - Static method in class com.sun.media.imageio.stream.RawImageInputStream

Gets the boolean type attribute.

getBoolean(String) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a Boolean.

getBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a Boolean.

getBooleanAttribute(Node, String, boolean, boolean) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getBooleanAttribute(Node, String) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getBooleanOption(String) - Method in class loci.plugins.prefs.OptionsList

Gets the boolean option with the given key.

getBooleanValue(String) - Method in class loci.plugins.Slicer

Gets the value of the given macro key as a boolean.

getBounds() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns a Rectangle indicating the image bounds.

getBounds(BigInteger[], boolean) - Static method in class loci.formats.FilePattern

Gets a string containing start, end and step values
 for a sorted list of numbers.

getBoxClass(int) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Returns the Box class for the box with the provided type.

getBranchIndex(Color, int) - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
 
getBrand() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox

Returns the brand of this file type box.

getBuffer() - Method in class jj2000.j2k.codestream.writer.BitOutputBuffer

Returns the byte buffer.

getBuffer() - Method in class jj2000.j2k.codestream.writer.HeaderEncoder

Returns the byte-buffer used to store the codestream header.

getBufferedImage() - Method in class loci.plugins.util.RecordedImageProcessor
 
getBufferLength() - Method in class jj2000.j2k.codestream.writer.HeaderEncoder

Returns the number of bytes used in the codestream header's
 buffer.

getBuildDate(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getBypass() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets bypass

getByte(int) - Method in class jj2000.j2k.entropy.encoder.ByteOutputBuffer

Returns the byte buffered at the given position in the buffer.

getByte(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader

Method used to retrieve data values for Byte entries into the SPE header table

getByte(int) - Method in class loci.formats.in.SPEReader.SpeHeader

Private method used to retrieve a Byte value from the SPE header

getByteArray(Node, String) - Static method in class com.sun.media.imageio.stream.RawImageInputStream

Gets the integer type attribute.

getByteArrayElementValue(Node) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Gets the byte array from an IIOMetadataNode.

getByteBuffer() - Method in class loci.formats.codec.BitBuffer

Deprecated.
Return the backing byte array.

getByteElementValue(Node) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Gets its byte value from an IIOMetadataNode.

getByteInputBuffer() - Method in class jj2000.j2k.entropy.decoder.MQDecoder

Returns the underlying 'ByteInputBuffer' from where the MQ
 coded input bytes are read.

getByteOrder() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
getByteOrdering() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
getByteOrdering() - Method in interface jj2000.j2k.io.BinaryDataInput

Returns the endianess (i.e., byte ordering) of the implementing
 class.

getByteOrdering() - Method in interface jj2000.j2k.io.BinaryDataOutput

Returns the endianness (i.e., byte ordering) of the implementing
 class.

getByteOrdering() - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Returns the endianess (i.e., byte ordering) of the implementing
 class.

getByteOrdering() - Method in class jj2000.j2k.util.ISRandomAccessIO

Returns the endianess (i.e., byte ordering) of multi-byte I/O
 operations.

getBytes(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of unsigned bytes, one per channel.

getBytes(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of unsigned bytes, one per channel.

getBytes(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of unsigned bytes, one per channel.

getBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools

Get the bytes from an image, merging the channels as necessary.

getBytesPerElement() - Method in enum loci.formats.tiff.IFDType

Retrieves the number of bytes per element.

getBytesPerPixel(int) - Static method in class loci.formats.FormatTools

Retrieves how many bytes per pixel the current plane or section has.

getBytesPerPixel(String) - Static method in class loci.formats.FormatTools

Retrieves the number of bytes per pixel in the current plane.

getBytesPerPixel(int) - Method in class loci.formats.in.LegacyND2Reader
 
getBytesPerSample() - Method in class loci.formats.tiff.IFD

Retrieves the image's bytes per sample (derived from tag BitsPerSample)
 from this IFD.

getByteValue(Node) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getC() - Method in class loci.formats.gui.ImageViewer

Gets the C value of the currently displayed image.

getCache() - Method in class loci.formats.gui.CacheComponent
 
getCache() - Method in class loci.plugins.util.BFVirtualStack
 
getCacheListeners() - Method in class loci.formats.cache.Cache
 
getCacheListeners() - Method in interface loci.formats.cache.CacheReporter

Gets a list of all registered status update listeners.

getCacheListeners() - Method in class loci.formats.cache.CacheStrategy
 
getCalibrationTable() - Method in class loci.plugins.util.RecordedImageProcessor
 
getCameraModel() - Method in class loci.formats.in.ND2Handler
 
getCategory() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getCausalCXInfo() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets causalCXInfo

getCBegin(int) - Method in class loci.plugins.in.ImporterOptions
 
getCBegin(int) - Method in class loci.plugins.in.ImportProcess
 
getCBlkHeight(byte, int, int) - Method in class jj2000.j2k.entropy.CBlkSizeSpec

Returns the code-block height:

 
 for the specified tile/component
 for the specified tile
 for the specified component
 default value
 

 The value returned depends on the value of the variable 'type' which
 can take the following values :

 
 SPEC_DEF -> Default value is returned.

getCBlkHeight(int, int) - Method in class jj2000.j2k.entropy.encoder.EntropyCoder

Returns the code-block height for the specified tile and component.

getCBlkHeight(int, int) - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Returns the code-block height for the specified tile and component.

getCBlkInfo() - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Gets the reference to the CBlkInfo array

getCBlkWidth(byte, int, int) - Method in class jj2000.j2k.entropy.CBlkSizeSpec

Returns the code-block width :

 
 for the specified tile/component
 for the specified tile
 for the specified component
 default value
 

 The value returned depends on the value of the variable 'type' which
 can take the following values :


 
 SPEC_DEF -> Default value is returned.

getCBlkWidth(int, int) - Method in class jj2000.j2k.entropy.encoder.EntropyCoder

Returns the code-block width for the specified tile and component.

getCBlkWidth(int, int) - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Returns the code-block width for the specified tile and component.

getCbULX() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the vertical code-block partition origin.

getCbULX() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the horizontal code-block partition origin.Allowable values are
 0 and 1, nothing else.

getCbULX() - Method in class jj2000.j2k.entropy.decoder.EntropyDecoder

Returns the horizontal code-block partition origin.

getCbULX() - Method in class jj2000.j2k.entropy.encoder.EntropyCoder

Returns the horizontal offset of the code-block partition.

getCbULX() - Method in class jj2000.j2k.quantization.dequantizer.Dequantizer

Returns the horizontal code-block partition origin.

getCbULX() - Method in class jj2000.j2k.quantization.quantizer.Quantizer

Returns the horizontal offset of the code-block partition.

getCbULX() - Method in class jj2000.j2k.roi.encoder.ROIScaler

Returns the horizontal offset of the code-block partition.

getCbULX() - Method in class jj2000.j2k.roi.ROIDeScaler

Returns the horizontal code-block partition origin.

getCbULX() - Method in interface jj2000.j2k.wavelet.analysis.ForwWTDataProps

Returns the horizontal offset of the code-block partition.

getCbULX() - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the horizontal offset of the code-block partition.

getCbULX() - Method in interface jj2000.j2k.wavelet.synthesis.InvWTData

Returns the horizontal code-block partition origin.

getCbULY() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the vertical code-block partition origin.

getCbULY() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the vertical code-block partition origin.

getCbULY() - Method in class jj2000.j2k.entropy.decoder.EntropyDecoder

Returns the vertical code-block partition origin.

getCbULY() - Method in class jj2000.j2k.entropy.encoder.EntropyCoder

Returns the vertical offset of the code-block partition.

getCbULY() - Method in class jj2000.j2k.quantization.dequantizer.Dequantizer

Returns the vertical code-block partition origin.

getCbULY() - Method in class jj2000.j2k.quantization.quantizer.Quantizer

Returns the vertical offset of the code-block partition.

getCbULY() - Method in class jj2000.j2k.roi.encoder.ROIScaler

Returns the vertical offset of the code-block partition.

getCbULY() - Method in class jj2000.j2k.roi.ROIDeScaler

Returns the vertical code-block partition origin.

getCbULY() - Method in interface jj2000.j2k.wavelet.analysis.ForwWTDataProps

Returns the vertical offset of the code-block partition.

getCbULY() - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the vertical offset of the code-block partition.

getCbULY() - Method in interface jj2000.j2k.wavelet.synthesis.InvWTData

Returns the vertical code-block partition origin Allowable values are 0
 and 1, nothing else.

getCCount(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.SERIES.

getCEnd(int) - Method in class loci.plugins.in.ImporterOptions
 
getCEnd(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getChannel() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox

Returns the defined channels.

getChannel(String) - Method in class loci.formats.in.CellomicsReader
 
getChannel() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the channel associated with this File.

getChannel(int) - Method in class loci.formats.in.ZeissTIFFReader
 
getChannelColor(int) - Method in class loci.formats.in.LIFReader
 
getChannelColorFromFile(String) - Method in class loci.formats.in.MIASReader

Get the color associated with the given file's channel.

getChannelColors() - Method in class loci.formats.in.ND2Handler
 
getChannelCount() - Method in class loci.formats.in.SDTReader

Gets the number of spectral channels.

getChannelDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
 
getChannelDimCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getChannelDimLength(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getChannelDimType(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getChannelFiller() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getChannelGlobalMaximum(int) - Method in class loci.formats.MinMaxCalculator

Retrieves a specified channel's global maximum.

getChannelGlobalMinimum(int) - Method in class loci.formats.MinMaxCalculator

Retrieves a specified channel's global minimum.

getChannelIndex(Element) - Method in class loci.formats.in.LIFReader
 
getChannelIndexOfCellObjectName(String) - Method in class loci.formats.in.CellH5Reader
 
getChannelKnownMaximum(int) - Method in class loci.formats.MinMaxCalculator

Retrieves the specified channel's maximum based on the images that
 have been read.

getChannelKnownMinimum(int) - Method in class loci.formats.MinMaxCalculator

Retrieves the specified channel's minimum based on the images that have
 been read.

getChannelLabel(int) - Method in class loci.formats.in.TextReader

Gets the label for the given channel.

getChannelName(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getChannelName() - Method in class loci.formats.in.MetamorphHandler
 
getChannelName() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the channelName associated with this File.

getChannelNames() - Method in class loci.formats.in.MetamorphHandler
 
getChannelNames() - Method in class loci.formats.in.ND2Handler
 
getChannels(int) - Method in class loci.formats.in.LegacyND2Reader
 
getChannelSeparator() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getChar(int) - Method in class loci.formats.tools.AsciiImage
 
getCheckboxes(GenericDialog) - Static method in class loci.plugins.util.WindowTools
 
getChild(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
 
getChild(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
 
getChild() - Method in class loci.plugins.util.RecordedImageProcessor
 
getChildIndex(Integer, String) - Method in class loci.formats.in.VolocityReader
 
getChildNames(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getChildNode(Node, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getChildNodes(Element) - Method in class loci.formats.in.OBFReader
 
getChildPolicy(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getChildren(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
 
getChildText(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
 
getChildText(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
 
getChoices(GenericDialog) - Static method in class loci.plugins.util.WindowTools
 
getClass(String) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a class.

getClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a class.

getClasses() - Method in class loci.formats.ClassList

Gets the list of classes as an array.

getCode() - Method in enum loci.formats.codec.CompressionType

Implemented as specified by the CodedEnum I/F.

getCode() - Method in enum loci.formats.codec.JPEG2000BoxType

Implemented as specified by the CodedEnum I/F.

getCode() - Method in enum loci.formats.codec.JPEG2000SegmentMarker

Implemented as specified by the CodedEnum I/F.

getCode() - Method in enum loci.formats.tiff.IFDType
 
getCode() - Method in enum loci.formats.tiff.PhotoInterp
 
getCode() - Method in enum loci.formats.tiff.TiffCompression
 
getCodeBlock(int, int, int, SubbandSyn, int, int, DecLyrdCBlk) - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Returns the specified coded code-block, for the specified component, in
 the current tile.

getCodeBlock(int, int, int, SubbandSyn, int, int, DecLyrdCBlk) - Method in interface jj2000.j2k.entropy.decoder.CodedCBlkDataSrcDec

Returns the specified coded code-block, for the specified component, in
 the current tile.

getCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Returns the specified code-block in the current tile for the specified
 component, as a copy (see below).

getCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in interface jj2000.j2k.quantization.dequantizer.CBlkQuantDataSrcDec

Returns the specified code-block in the current tile for the specified
 component, as a copy (see below).

getCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in class jj2000.j2k.quantization.dequantizer.StdDequantizer

Returns the specified code-block in the current tile for the specified
 component, as a copy (see below).

getCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in class jj2000.j2k.roi.ROIDeScaler

Returns the specified code-block in the current tile for the specified
 component, as a copy (see below).

getCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in interface jj2000.j2k.wavelet.synthesis.CBlkWTDataSrcDec

Returns the specified code-block in the current tile for the specified
 component, as a copy (see below).

getCodeBlockSize() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Gets codeBlockSize.

getCodeBlockSize() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets codeBlockSize

getCodecName(int) - Method in class loci.formats.in.AVIReader
 
getCodecName() - Method in enum loci.formats.tiff.TiffCompression

Retrieves the name of the TIFF compression codec.

getCodecOptions() - Method in class loci.formats.tiff.TiffParser

Retrieves the current set of codec options being used to decompress pixel
 data.

getCodeSegSymbol() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets codeSegSymbol

getCodestreamOffset() - Method in class loci.formats.in.JPEG2000MetadataParser

Retrieves the offset to the first contiguous codestream.

getCodestreamPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser

Returns the pixel type as specified in the header.

getCodeStreamPos() - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method creates and returns an array of positions to contiguous
 codestreams in the file

getCodestreamSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser

Returns the number of channels the image has as specified in the header.

getCodestreamSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser

Returns the width of the image as specified in the header.

getCodestreamSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser

Returns the height of the image as specified in the header.

getColorConverter() - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam

Returns the currently set TIFFColorConverter object,
 or null if none is set.

getColorConverter() - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam

Returns the current TIFFColorConverter object that
 will be used to perform color conversion when writing the
 image, or null if none is set.

getColorMap(IFD) - Method in class loci.formats.tiff.TiffParser

Retrieve the color map associated with the given IFD.

getColorMode() - Method in class loci.plugins.in.ImporterOptions
 
getColorModeInfo() - Method in class loci.plugins.in.ImporterOptions
 
getColorModel() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the ColorModel of the image.

getColorModel() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getColorModel() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getColorModel() - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

Returns the color model created from the palette box.

getColorModel() - Method in class loci.formats.FormatWriter
 
getColorModel() - Method in interface loci.formats.IFormatWriter

Gets the color model.

getColorModel() - Method in class loci.formats.ImageWriter
 
getColorModel() - Method in class loci.formats.WriterWrapper
 
getColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
 
getColorModes() - Method in class loci.plugins.in.ImporterOptions
 
getColorSpace(Node) - Static method in class com.sun.media.imageio.stream.RawImageInputStream
 
getColorTable(Node, String, boolean, int) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getColorValue(TextField) - Method in class loci.plugins.in.ColorDialog
 
getColumn() - Method in class loci.formats.in.OMEXMLReader.BinData
 
getColumn(String) - Method in class loci.formats.in.ScreenReader
 
getColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getColumNames(int) - Method in interface loci.formats.services.MetakitService
 
getColumNames(int) - Method in class loci.formats.services.MetakitServiceImpl
 
getColumnNames(String) - Method in interface loci.formats.services.MetakitService
 
getColumnNames(String) - Method in class loci.formats.services.MetakitServiceImpl
 
getColumnTypes(int) - Method in interface loci.formats.services.MetakitService
 
getColumnTypes(String) - Method in interface loci.formats.services.MetakitService
 
getColumnTypes(int) - Method in class loci.formats.services.MetakitServiceImpl
 
getColumnTypes(String) - Method in class loci.formats.services.MetakitServiceImpl
 
getComment(int, int) - Method in class loci.formats.in.MetamorphReader
 
getComment() - Method in class loci.formats.tiff.IFD

Convenience method for obtaining the ImageDescription from this IFD.

getComment() - Method in class loci.formats.tiff.TiffParser

Convenience method for obtaining a stream's first ImageDescription.

getComments() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getComments() - Method in class loci.formats.in.JPEG2000MetadataParser

Retrieves the list of comments stored in the file.

getCompanion() - Method in class loci.formats.out.OMETiffWriter
 
getCompatibilityList() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox

Returns the compatibilty list of this file type box.

getCompData(DataBlk, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns, in the blk argument, a block of image data containing the
 specifed rectangular area, in the specified component.

getCompData(DataBlk, int) - Method in interface jj2000.j2k.image.BlkImgDataSrc

Returns, in the blk argument, a block of image data containing the
 specifed rectangular area, in the specified component.

getCompData(DataBlk, int) - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Apply forward component transformation associated with the current
 tile.

getCompData(DataBlk, int) - Method in class jj2000.j2k.image.ImgDataConverter

Returns, in the blk argument, a block of image data containing the
 specifed rectangular area, in the specified component, using the
 'transfer type' specified in the block given as argument.

getCompData(DataBlk, int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns, in the blk argument, a block of image data containing the
 specifed rectangular area, in the specified component.

getCompData(DataBlk, int) - Method in class jj2000.j2k.image.input.ImgReaderPGM

Returns, in the blk argument, a block of image data containing the
 specifed rectangular area, in the specified component.

getCompData(DataBlk, int) - Method in class jj2000.j2k.image.invcomptransf.InvCompTransf

Apply inverse component transformation associated with the current
 tile.

getCompData(DataBlk, int) - Method in class jj2000.j2k.image.Tiler

Returns, in the blk argument, a block of image data containing the
 specifed rectangular area, in the specified component.

getCompData(DataBlk, int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTFull

Returns a block of image data containing the specifed rectangular area,
 in the specified component, as a copy (see below).

getCompDef(int) - Method in class jj2000.j2k.ModuleSpec

Gets default value of the specified component.

getCompHeight(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the height in pixels of the specified component in the current
 tile.

getCompImgHeight(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the height in pixels of the specified component in the overall
 image.

getCompImgHeight(int) - Method in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
getCompImgHeight(int, int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the height in pixels of the specified component in the overall
 image, for the given (component) resolution level.

getCompImgHeight(int) - Method in interface jj2000.j2k.image.ImgData

Returns the height in pixels of the specified component in the overall
 image.

getCompImgHeight(int) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the height in pixels of the specified component in the overall
 image.

getCompImgHeight(int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the height in pixels of the specified component in the
 overall image.

getCompImgHeight(int) - Method in class jj2000.j2k.image.input.ImgReader

Returns the height in pixels of the specified component in the overall
 image.

getCompImgHeight(int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the height in pixels of the specified component in the overall
 image.

getCompImgHeight(int, int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the height in pixels of the specified component in the overall
 image, for the given resolution level.

getCompImgHeight(int, int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the height in pixels of the specified component in the overall
 image, for the given resolution level.

getCompImgWidth(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the width in pixels of the specified component in the overall
 image.

getCompImgWidth(int) - Method in class jj2000.j2k.codestream.HeaderInfo.SIZ

Width of the specified tile-component

getCompImgWidth(int, int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the width in pixels of the specified component in the overall
 image, for the given (component) resolution level.

getCompImgWidth(int) - Method in interface jj2000.j2k.image.ImgData

Returns the width in pixels of the specified component in the overall
 image.

getCompImgWidth(int) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the width in pixels of the specified component in the overall
 image.

getCompImgWidth(int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the width in pixels of the specified component in the overall
 image.

getCompImgWidth(int) - Method in class jj2000.j2k.image.input.ImgReader

Returns the width in pixels of the specified component in the overall
 image.

getCompImgWidth(int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the width in pixels of the specified component in the overall
 image.

getCompImgWidth(int, int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the width in pixels of the specified component in the overall
 image, for the given resolution level.

getCompImgWidth(int, int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the width in pixels of the specified component in the overall
 image, for the given resolution level.

getComponent() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
 
getComponent(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getComponentAssociation() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
 
getComponentTransformation() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Gets componentTransformation.

getComponentTransformation() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets componentTransformation

getComponentType() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
 
getCompressedSize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor

Returns the size of the image (in bytes) generated by the most recent
 compress/encode operation.

getCompression() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getCompression() - Method in enum loci.formats.codec.CompressionType

Returns the compression.

getCompression(String) - Method in class loci.formats.FormatReader

Retrieves an Compression enumeration
 value for the given String.

getCompression() - Method in class loci.formats.FormatWriter
 
getCompression() - Method in interface loci.formats.IFormatWriter

Gets the current compression type.

getCompression() - Method in class loci.formats.ImageWriter
 
getCompression(int) - Method in class loci.formats.in.OBFReader
 
getCompression() - Method in class loci.formats.tiff.IFD

Retrieves the image's compression type (TIFF tag Compression) from
 this IFD.

getCompression() - Method in class loci.formats.WriterWrapper
 
getCompressionCodecOptions(IFD) - Method in enum loci.formats.tiff.TiffCompression

Creates a set of codec options for compression.

getCompressionCodecOptions(IFD, CodecOptions) - Method in enum loci.formats.tiff.TiffCompression

Creates a set of codec options for compression.

getCompressionMap() - Static method in enum loci.formats.tiff.TiffCompression
 
getCompressionTagValue() - Method in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Retrieve the value to be assigned to the TIFF Compression tag
 in the TIFF image metadata.

getCompressionType() - Method in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Retrieve the name of the compression type supported by this compressor.

getCompressionType(String) - Static method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
getCompressionType() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Returns the compression type.

getCompressionTypes() - Method in class loci.formats.FormatWriter
 
getCompressionTypes() - Method in interface loci.formats.IFormatWriter

Gets the available compression types.

getCompressionTypes() - Method in class loci.formats.ImageWriter
 
getCompressionTypes() - Method in class loci.formats.WriterWrapper
 
getCompSize(IndexColorModel) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

Gets the size of the components or the bit depth for all the color
  coomponents.

getCompSubsX(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the component subsampling factor in the horizontal direction,
 for the specified component.

getCompSubsX(int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the component subsampling factor in the horizontal direction,
 for the specified component.

getCompSubsX(int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the component sub-sampling factor, with respect to the
 reference grid, along the horizontal direction for the specified
 component.

getCompSubsX(int) - Method in interface jj2000.j2k.image.ImgData

Returns the component subsampling factor in the horizontal direction,
 for the specified component.

getCompSubsX(int) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the component subsampling factor in the horizontal direction,
 for the specified component.

getCompSubsX(int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the component subsampling factor in the horizontal direction,
 for the specified component.

getCompSubsX(int) - Method in class jj2000.j2k.image.input.ImgReader

Returns the component subsampling factor in the horizontal direction,
 for the specified component.

getCompSubsX(int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the component subsampling factor in the horizontal
 direction, for the specified component.

getCompSubsX(int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the component subsampling factor in the horizontal direction,
 for the specified component.

getCompSubsX(int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the component subsampling factor in the horizontal direction,
 for the specified component.

getCompSubsY(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the component subsampling factor in the vertical direction, for
 the specified component.

getCompSubsY(int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the component subsampling factor in the vertical direction, for
 the specified component.

getCompSubsY(int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the component sub-sampling factor, with respect to the
 reference grid, along the vertical direction for the specified
 component.

getCompSubsY(int) - Method in interface jj2000.j2k.image.ImgData

Returns the component subsampling factor in the vertical direction, for
 the specified component.

getCompSubsY(int) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the component subsampling factor in the vertical direction, for
 the specified component.

getCompSubsY(int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the component subsampling factor in the vertical direction, for
 the specified component.

getCompSubsY(int) - Method in class jj2000.j2k.image.input.ImgReader

Returns the component subsampling factor in the vertical direction, for
 the specified component.

getCompSubsY(int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the component subsampling factor in the vertical
 direction, for the specified component.

getCompSubsY(int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the component subsampling factor in the vertical direction, for
 the specified component.

getCompSubsY(int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the component subsampling factor in the vertical direction, for
 the specified component.

getCompULX(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the horizontal coordinate of the upper-left corner of the
 active tile, with respect to the canvas origin, in the component
 coordinates, for the specified component.

getCompULX(int) - Method in interface jj2000.j2k.image.ImgData

Returns the horizontal coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULX(int) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the horizontal coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULX(int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the horizontal coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULX(int) - Method in class jj2000.j2k.image.input.ImgReader

Returns the horizontal coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULX(int) - Method in class jj2000.j2k.image.Tiler

Returns the horizontal coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULX(int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the horizontal coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULY(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the vertical coordinate of the upper-left corner of the active
 tile, with respect to the canvas origin, in the component coordinates,
 for the specified component.

getCompULY(int) - Method in interface jj2000.j2k.image.ImgData

Returns the vertical coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULY(int) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the vertical coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULY(int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the vertical coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULY(int) - Method in class jj2000.j2k.image.input.ImgReader

Returns the vertical coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULY(int) - Method in class jj2000.j2k.image.Tiler

Returns the vertical coordinate of the upper-left corner of the
 specified component in the current tile.

getCompULY(int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the vertical coordinate of the upper-left corner of the
 specified component in the current tile.

getCompWidth(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the width in pixels of the specified component in the current
 tile.

getConcatenateInfo() - Method in class loci.plugins.in.ImporterOptions
 
getConfig(String) - Method in class loci.formats.in.PrairieMetadata

Gets the value of the given configuration key.

getConfig() - Method in class loci.formats.in.PrairieMetadata

Gets the map of configuration key/value pairs.

getConstraintsForCell(int, int, Container, int) - Static method in class loci.plugins.config.SpringUtilities
 
getContent() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Returns the box content in byte array.

getContents() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadataFormatResources
 
getContents() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadataFormatResources
 
getContents() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadataFormatResources
 
getContents() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderResources
 
getContents() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterResources
 
getContents() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormatResources
 
getContents() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormatResources
 
getContents() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadataFormatResources
 
getContents() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadataFormatResources
 
getContrastMethod(String) - Method in class loci.formats.FormatReader

Retrieves an ContrastMethod enumeration
 value for the given String.

getCopy() - Method in class jj2000.j2k.codestream.HeaderInfo.COD
 
getCopy(int) - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a copy of this object

getCopy() - Method in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
getCopy() - Method in class jj2000.j2k.decoder.DecoderSpecs

Returns a copy of the current object.

getCopy() - Method in class jj2000.j2k.ModuleSpec
 
getCoreIndex() - Method in class loci.formats.FileStitcher
 
getCoreIndex() - Method in class loci.formats.FormatReader
 
getCoreIndex() - Method in interface loci.formats.IFormatReader

Return the index into CoreMetadata of the current resolution/series.

getCoreIndex() - Method in class loci.formats.ImageReader
 
getCoreIndex() - Method in class loci.formats.in.FilePatternReader
 
getCoreIndex() - Method in class loci.formats.ReaderWrapper
 
getCoreMetadataList() - Method in class loci.formats.DimensionSwapper
 
getCoreMetadataList() - Method in class loci.formats.FileStitcher
 
getCoreMetadataList() - Method in class loci.formats.FormatReader
 
getCoreMetadataList() - Method in interface loci.formats.IFormatReader

Obtains the core metadata values for the current file.

getCoreMetadataList() - Method in class loci.formats.ImageReader
 
getCoreMetadataList() - Method in class loci.formats.in.FilePatternReader
 
getCoreMetadataList() - Method in class loci.formats.in.LeicaHandler
 
getCoreMetadataList() - Method in class loci.formats.in.ND2Handler
 
getCoreMetadataList() - Method in class loci.formats.ReaderWrapper
 
getCorrection(String) - Method in class loci.formats.FormatReader

Retrieves an Correction enumeration
 value for the given String.

getCorrection() - Method in class loci.formats.in.ND2Handler
 
getCount() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns the number of data items present in the field.

getCount() - Method in class loci.formats.FilePattern

Gets the number of elements for each pattern block.

getCreationDate() - Method in interface loci.formats.services.EXIFService
 
getCreationDate() - Method in class loci.formats.services.EXIFServiceImpl
 
getCropInfo() - Method in class loci.plugins.in.ImporterOptions
 
getCropRegion(int) - Method in class loci.plugins.in.ImporterOptions
 
getCropRegion(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getCStep(int) - Method in class loci.plugins.in.ImporterOptions
 
getCStep(int) - Method in class loci.plugins.in.ImportProcess
 
getCurrentColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
 
getCurrentFile() - Method in class loci.formats.FormatReader
 
getCurrentFile() - Method in interface loci.formats.IFormatReader

Returns the current file.

getCurrentFile() - Method in class loci.formats.ImageReader
 
getCurrentFile() - Method in class loci.formats.ReaderWrapper
 
getCurrentFile() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getCurrentFile(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getCurrentPos() - Method in class loci.formats.cache.Cache

Gets the current dimensional position.

getCustomColor(int, int) - Method in class loci.plugins.in.ImporterOptions
 
getCustomColorKey(int, int) - Method in class loci.plugins.in.ImporterOptions
 
getCutIn(Double) - Static method in class loci.formats.FormatTools
 
getCutOut(Double) - Static method in class loci.formats.FormatTools
 
getCycle() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the cycle associated with this Sequence.

getCycleCount() - Method in class loci.formats.in.PrairieMetadata

Gets the number of recorded cycles.

getCycleMax() - Method in class loci.formats.in.PrairieMetadata

Gets the maximum cycle value.

getCycleMin() - Method in class loci.formats.in.PrairieMetadata

Gets the minimum cycle value.

getCZTag(IFD) - Method in class loci.formats.in.ZeissLSMReader
 
getData() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns a reference to the data object associated with the field.

getData() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the entire image in a single Raster.

getData(Rectangle) - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns an arbitrary rectangular region of the RenderedImage
 in a Raster.

getData() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDBox

Returns the UUID data of this box.

getData() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getData(Rectangle) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getData() - Method in class jj2000.j2k.image.DataBlk

Returns the array containing the data, or null if there is no
 data.

getData() - Method in class jj2000.j2k.image.DataBlkFloat

Returns the array containing the data, or null if there is no
 data array.

getData() - Method in class jj2000.j2k.image.DataBlkInt

Returns the array containing the data, or null if there is no
 data array.

getData(DataBlk, int, boolean) - Method in class jj2000.j2k.image.ImgDataConverter

Implements the 'getInternCompData()' and the 'getCompData()'
 methods.

getData() - Method in class jj2000.j2k.wavelet.analysis.CBlkWTData

Returns the array containing the data, or null if there is no data.

getData() - Method in class jj2000.j2k.wavelet.analysis.CBlkWTDataFloat

Returns the array containing the data, or null if there is no
 data array.

getData() - Method in class jj2000.j2k.wavelet.analysis.CBlkWTDataInt

Returns the array containing the data, or null if there is no
 data array.

getData() - Method in class loci.formats.gui.SignedByteBuffer
 
getData(int) - Method in class loci.formats.gui.SignedByteBuffer
 
getData() - Method in class loci.formats.gui.SignedShortBuffer
 
getData(int) - Method in class loci.formats.gui.SignedShortBuffer
 
getData() - Method in class loci.formats.gui.UnsignedIntBuffer
 
getData(int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getDataElements(int, Object) - Method in class loci.formats.gui.Index16ColorModel
 
getDataElements(int, Object) - Method in class loci.formats.gui.SignedColorModel
 
getDataElements(int, Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getDataFloat() - Method in class jj2000.j2k.image.DataBlkFloat

Returns the array containing the data, or null if there is no
 data array.

getDataFloat() - Method in class jj2000.j2k.wavelet.analysis.CBlkWTDataFloat

Returns the array containing the data, or null if there is no
 data array.

getDataInt() - Method in class jj2000.j2k.image.DataBlkInt

Returns the array containing the data, or null if there is no
 data array.

getDataInt() - Method in class jj2000.j2k.wavelet.analysis.CBlkWTDataInt

Returns the array containing the data, or null if there is no
 data array.

getDatasetStructureDescription() - Method in class loci.formats.FormatReader
 
getDatasetStructureDescription() - Method in interface loci.formats.IFormatReader

Returns a short description of the dataset structure.

getDatasetStructureDescription() - Method in class loci.formats.ImageReader
 
getDatasetStructureDescription() - Method in class loci.formats.in.FilePatternReader
 
getDatasetStructureDescription() - Method in class loci.formats.ReaderWrapper
 
getDataType() - Method in class jj2000.j2k.image.DataBlk

Returns the data type of the DataBlk object, as
 defined in this class.

getDataType() - Method in class jj2000.j2k.image.DataBlkFloat

Returns the identifier of this data type, TYPE_FLOAT,
 as defined in DataBlk.

getDataType() - Method in class jj2000.j2k.image.DataBlkInt

Returns the identifier of this data type, TYPE_INT,
 as defined in DataBlk.

getDataType() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloat

Returns the type of data on which this filter works, as defined
 in the DataBlk interface, which is always TYPE_FLOAT for this
 class.

getDataType() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterInt

Returns the type of data on which this filter works, as defined
 in the DataBlk interface, which is always TYPE_INT for this
 class.

getDataType() - Method in class jj2000.j2k.wavelet.analysis.CBlkWTData

Returns the data type of the CBlkWTData object, as
 defined in the DataBlk class.

getDataType() - Method in class jj2000.j2k.wavelet.analysis.CBlkWTDataFloat

Returns the identifier of this data type, TYPE_FLOAT,
 as defined in DataBlk.

getDataType() - Method in class jj2000.j2k.wavelet.analysis.CBlkWTDataInt

Returns the data type of this object, always DataBlk.TYPE_INT.

getDataType(int, int) - Method in interface jj2000.j2k.wavelet.analysis.CBlkWTDataSrc

Return the data type of this CBlkWTDataSrc for the given
  component in the current tile.

getDataType(int, int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Return the data type of this CBlkWTDataSrc.

getDataType() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloat

Returns the type of data on which this filter works, as defined
 in the DataBlk interface, which is always TYPE_FLOAT for this
 class.

getDataType() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterInt

Returns the type of data on which this filter works, as defined
 in the DataBlk interface, which is always TYPE_INT for this
 class.

getDataType() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the type of data on which this filter works, as defined
 in the DataBlk interface.

getDataTypeFromNumBits(int, boolean) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
getDataTypes() - Method in class com.sun.media.imageio.plugins.tiff.TIFFTag

Returns a bit mask indicating the set of data types that may
 be used to store the data associated with the tag.

getDataTypeSize(int) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Return the number of bits occupied by dataType
 which must be one of the DataBuffer TYPEs.

getDate() - Method in class loci.formats.in.MetamorphHandler
 
getDate() - Method in class loci.formats.in.ND2Handler
 
getDate() - Method in class loci.formats.in.PrairieMetadata

Gets the date of the acquisition.

getDatestamp() - Method in class loci.formats.in.SVSReader
 
getDecoderSpecs() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Return the DecoderSpecs instance filled when reading the headers

getDecodingRate() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageReadParam

Gets decodingRate.

getDecomp(int, int) - Method in interface jj2000.j2k.wavelet.analysis.ForwWT

Returns the wavelet tree decomposition.

getDecomp(int, int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the wavelet tree decomposition.

getDecompLevels(int, int) - Method in interface jj2000.j2k.wavelet.analysis.ForwWT

Returns the number of decomposition levels that are applied to
 obtain the LL band, in the specified tile-component.

getDecompLevels(int, int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the number of decomposition levels that are applied to the LL
 band, in the specified tile-component.

getDecompositionLevel() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets decompositionLevel

getDecompressedStream(String) - Method in class loci.formats.in.CellomicsReader
 
getDecompType(int) - Method in class jj2000.j2k.wavelet.WTDecompSpec

Returns the decomposition type to be used in component 'n' and tile
 't'.

getDecSpecType(int) - Method in class jj2000.j2k.wavelet.WTDecompSpec

Returns the type of specification for the decomposition in the
 specified component and tile.

getDefault() - Method in class jj2000.j2k.ModuleSpec

Gets default value for this module.

getDefault() - Method in class loci.plugins.prefs.BooleanOption

Gets the default value of the option.

getDefault() - Method in class loci.plugins.prefs.DoubleOption

Gets the default value of the option.

getDefault() - Method in class loci.plugins.prefs.StringOption

Gets the default value of the option.

getDefaultColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
 
getDefaultConfiguration() - Static method in class loci.formats.gui.AWTImageTools

Gets the default graphics configuration for the environment.

getDefaultCustomColor(int) - Method in class loci.plugins.in.ImporterOptions
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
getDefaultOptions() - Static method in class loci.formats.codec.CodecOptions

Return CodecOptions with reasonable default values.

getDefaultOptions() - Static method in class loci.formats.codec.JPEG2000CodecOptions

Return JPEG2000CodecOptions with reasonable default values.

getDefaultOptions(CodecOptions) - Static method in class loci.formats.codec.JPEG2000CodecOptions

Return JPEG2000CodecOptions using the given CodecOptions as the default.

getDefaultReaderClasses() - Static method in class loci.formats.ImageReader
 
getDefaultReadParam() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
getDefaultReadParam() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getDefaultReadParam() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
getDefaultReadParam() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
getDefaultReadParam() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getDefaultReadParam() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
getDefaultValue(String) - Method in class loci.plugins.prefs.OptionsList

Gets the default value of the string option with the given key.

getDefaultWriteParam() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
getDefaultWriteParam() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
getDefaultWriteParam() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
getDefaultWriteParam() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
getDefaultWriteParam() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
getDefaultWriteParam() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
getDefaultWriterClasses() - Static method in class loci.formats.ImageWriter
 
getDenom() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor

Returns denominator

getDenominator() - Method in class loci.formats.tiff.TiffRational

Gets this number's denominator.

getDequantizerType() - Method in class jj2000.j2k.quantization.dequantizer.DequantizerParams

Returns the type of the dequantizer for which the parameters are.

getDequantizerType() - Method in class jj2000.j2k.quantization.dequantizer.StdDequantizerParams

Returns the type of the dequantizer for which the parameters are.

getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.stream.ChannelImageInputStreamSpi
 
getDescription(Locale) - Method in class com.sun.media.imageioimpl.stream.ChannelImageOutputStreamSpi
 
getDescription() - Method in class loci.formats.gui.ComboFileFilter

Returns the filter's description.

getDescription() - Method in class loci.formats.gui.ExtensionFileFilter

Gets the filter's description.

getDescription() - Method in class loci.formats.gui.FormatFileFilter

Gets the filter's description.

getDescription() - Method in class loci.formats.gui.NoExtensionFileFilter

Gets the filter's description.

getDeser() - Method in class loci.formats.Memoizer

Returns a configured Kryo instance.

getDestination(ImageReadParam, Iterator, int, int) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getDestinationRegion() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getDestinationType(ImageReadParam, Iterator) - Static method in class com.sun.media.imageioimpl.common.ImageUtil

Gets the destination image type.

getDetectorType(String) - Method in class loci.formats.FormatReader

Retrieves an DetectorType enumeration
 value for the given String.

getDeviceSubtype(String) - Method in class loci.formats.in.CellSensReader
 
getDimension(String) - Method in class loci.formats.in.ZeissTIFFHandler.Scaling

Get a dimension by its index.

getDimension(String) - Method in interface loci.formats.services.NetCDFService

Retrieves the length of a dimension.

getDimension(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getDimensionDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
 
getDimensionOrder() - Method in class loci.formats.ChannelMerger
 
getDimensionOrder() - Method in class loci.formats.ChannelSeparator
 
getDimensionOrder() - Method in class loci.formats.DimensionSwapper
 
getDimensionOrder() - Method in class loci.formats.FileStitcher
 
getDimensionOrder() - Method in class loci.formats.FormatReader
 
getDimensionOrder(String) - Method in class loci.formats.FormatReader

Retrieves an DimensionOrder enumeration
 value for the given String.

getDimensionOrder() - Method in interface loci.formats.IFormatReader

Gets a five-character string representing the
 dimension order in which planes will be returned.

getDimensionOrder() - Method in class loci.formats.ImageReader
 
getDimensionOrder() - Method in class loci.formats.in.FilePatternReader
 
getDimensionOrder() - Method in class loci.formats.ReaderWrapper
 
getDimensionOrder(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getDimensionSwapper() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getDirectory(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getDirectoryAsIFD(TIFFDirectory) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Converts a TIFFDirectory to a TIFFIFD.

getDocument() - Method in class loci.formats.gui.XMLWindow

Gets the XML document currently being displayed within the window.

getDocumentBytes(String) - Method in interface loci.formats.services.POIService

Retrieve all of the raw bytes that correspond to the given file name.

getDocumentBytes(String, int) - Method in interface loci.formats.services.POIService

Retrieve at most 'length' bytes that correspond to the given file name.

getDocumentBytes(String) - Method in class loci.formats.services.POIServiceImpl
 
getDocumentBytes(String, int) - Method in class loci.formats.services.POIServiceImpl
 
getDocumentList() - Method in interface loci.formats.services.POIService

Retrieve a list of all files in the current POI file system.

getDocumentList() - Method in class loci.formats.services.POIServiceImpl
 
getDocumentStream(String) - Method in interface loci.formats.services.POIService

Retrieve a RandomAccessInputStream corresponding to the given file name.

getDocumentStream(String) - Method in class loci.formats.services.POIServiceImpl
 
getDomains() - Method in class loci.formats.FormatReader
 
getDomains() - Method in interface loci.formats.IFormatReader

Returns the list of domains represented by the current file.

getDomains() - Method in class loci.formats.ImageReader
 
getDomains() - Method in class loci.formats.in.CellomicsReader
 
getDomains() - Method in class loci.formats.in.FilePatternReader
 
getDomains() - Method in class loci.formats.in.ICSReader
 
getDomains() - Method in class loci.formats.in.MetamorphTiffReader
 
getDomains() - Method in class loci.formats.in.NiftiReader
 
getDomains() - Method in class loci.formats.in.OMETiffReader
 
getDomains() - Method in class loci.formats.in.OMEXMLReader
 
getDomains() - Method in class loci.formats.ReaderWrapper
 
getDouble(String) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a Double.

getDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a Double.

getDoubleAttribute(Node, String, double, boolean) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getDoubleAttribute(Node, String) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getDoubles(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of doubles, one per channel.

getDoubles(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of doubles, one per channel.

getDoubles(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of doubles, one per channel.

getDoubleValue(Node) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getDoubleValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
getDT(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getDX(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getDY(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getDZ(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getEffectiveSeries(int) - Method in class loci.formats.in.ZeissLSMReader
 
getEffectiveSizeC() - Method in class loci.formats.FormatReader
 
getEffectiveSizeC() - Method in interface loci.formats.IFormatReader

Gets the effective size of the C dimension, guaranteeing that
 getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount()
 regardless of the result of isRGB().

getEffectiveSizeC() - Method in class loci.formats.ImageReader
 
getEffectiveSizeC() - Method in class loci.formats.in.FilePatternReader
 
getEffectiveSizeC() - Method in class loci.formats.ReaderWrapper
 
getEffectiveSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getElem(int) - Method in class loci.formats.gui.SignedByteBuffer
 
getElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
 
getElem(int, int) - Method in class loci.formats.gui.SignedShortBuffer
 
getElem(int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getElemDouble(int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getElemDouble(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getElement(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getElementDescription(String, Locale) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getElementInfo(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getElementMaxChildren(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getElementMinChildren(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getElementNames() - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox

This method will be called by the getNativeNodeForSimpleBox of the
  class Box to get the element names.

getElementNames() - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox

This method will be called by the getNativeNodeForSimpleBox of the
  class Box to get the element names.

getElementNames() - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox

This method will be called by the getNativeNodeForSimpleBox of the
  class Box to get the element names.

getElementNames() - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

This method will be called by the getNativeNodeForSimpleBox of the
  class Box to get the element names.

getElementNames() - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDBox

This method will be called by the getNativeNodeForSimpleBox of the
  class Box to get the element names.

getElementNames() - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.XMLBox

This method will be called by the getNativeNodeForSimpleBox of the
  class Box to get the element names.

getElements() - Method in class loci.formats.FilePattern

Gets individual elements for each pattern block.

getElements() - Method in class loci.formats.FilePatternBlock

Gets all block elements.

getElementSize(SampleModel) - Static method in class com.sun.media.imageioimpl.common.ImageUtil
 
getElementSize(String) - Method in interface loci.formats.services.JHDFService

Retrieves the Element Size of a dataset in Byte.

getElementSize(String) - Method in class loci.formats.services.JHDFServiceImpl
 
getElemFloat(int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getElemFloat(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getEmission() - Method in class loci.formats.in.SVSReader
 
getEmissionWavelength(Double) - Static method in class loci.formats.FormatTools
 
getEmissionWavelengths() - Method in class loci.formats.in.ND2Handler
 
getEncodingRate() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Gets encodingRate.

getEncodingRate() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets encodingRate

getEndX() - Method in class loci.formats.in.SPEReader.SpeROI
 
getEndY() - Method in class loci.formats.in.SPEReader.SpeROI
 
getEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record

Return all entries as an array

getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record

Get the boolean value at the given index

getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.FloatIM3Record

Get the floating-point value at the given index

getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.IntIM3Record

Get the integer value at the given index

getEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as an enumerated type.

getEnumeratedAttribute(Node, String, String[], int, boolean) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getEnumeratedAttribute(Node, String, String[]) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getEnumeratedColorSpace() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox

Returns the enumerated color space.

getEPH() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Gets EPH.

getEPH() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets EPH

getErrorMessage() - Method in class loci.formats.FilePattern

Gets the file pattern error message, if any.

getExcitation() - Method in class loci.formats.in.SVSReader
 
getExcitationWavelength(Double) - Static method in class loci.formats.FormatTools
 
getExcitationWavelengths() - Method in class loci.formats.in.ND2Handler
 
getExifIFDs() - Method in class loci.formats.tiff.TiffParser

Returns EXIF IFDs.

getExifTagName(int) - Static method in class loci.formats.in.BaseTiffReader
 
getExperimenterName() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getExperimentType(String) - Method in class loci.formats.FormatReader

Retrieves an ExperimentType enumeration
 value for the given String.

getExposures() - Method in class loci.formats.in.MetamorphHandler
 
getExposureTime() - Method in class loci.formats.in.SVSReader
 
getExposureTimes() - Method in class loci.formats.in.ND2Handler
 
getExtension() - Method in class loci.formats.gui.ExtensionFileFilter

Gets the filter's first valid extension.

getExtensionFunctions() - Method in class loci.plugins.macro.MacroFunctions
 
getExtensions() - Method in class loci.formats.gui.ExtensionFileFilter

Gets the filter's valid extensions.

getExternalSeries() - Method in class loci.formats.FileStitcher
 
getExternalSeries(int) - Method in class loci.formats.FileStitcher
 
getExtraLayers(int) - Method in class jj2000.j2k.entropy.encoder.LayersInfo

Returns the number of extra layers to add after the optimization point
 'n', but before optimization point 'n+1'.

getExtraLength() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Returns the box extra length.

getExtraSeries(String) - Method in class loci.formats.in.ZeissLSMReader
 
getf(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getf(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getField(String) - Method in class loci.formats.in.CellomicsReader
 
getField(String) - Method in class loci.formats.in.FlexReader
 
getField(int) - Method in class loci.formats.in.FluoviewReader
 
getField(String) - Method in class loci.formats.in.MetamorphTiffReader
 
getFieldFromSeries(int) - Method in class loci.formats.in.InCellReader
 
getFieldIndex() - Method in class loci.formats.in.ND2Handler
 
getFieldName(int) - Static method in class loci.formats.tiff.IFD

This method uses reflection to scan the values of this class's
 static fields, returning the first matching field's name.

getFilamentType(String) - Method in class loci.formats.FormatReader

Retrieves an FilamentType enumeration
 value for the given String.

getFile(int, int) - Method in class loci.formats.in.CellWorxReader

Retrieve the .pnl file corresponding to the given series.

getFile(String) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a file object.

getFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a file object.

getFile(String) - Method in class loci.formats.in.FV1000Reader
 
getFile(int) - Method in class loci.formats.in.MicromanagerReader.Position
 
getFile(String, int, int, int, int, int) - Method in class loci.formats.in.MicromanagerReader.Position
 
getFile(int) - Method in class loci.formats.in.PerkinElmerReader
 
getFile(int) - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the File with the given channel.

getFile(int, int, int) - Method in class loci.formats.in.PrairieMetadata

Gets the Frame at the given (cycle, index,
 channel).

getFile(int, int) - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the Frame at the given (cycle, index,
 channel).

getFile(Integer, Location) - Method in class loci.formats.in.VolocityReader
 
getFile() - Method in interface loci.formats.services.JHDFService

Retrieves the current initialized file path.

getFile() - Method in class loci.formats.services.JHDFServiceImpl
 
getFile() - Method in interface loci.formats.services.NetCDFService

Retrieves the current initialized file path.

getFile() - Method in class loci.formats.services.NetCDFServiceImpl
 
getFileHandle(String) - Method in class loci.formats.in.FlexReader
 
getFileIndex(int) - Method in class loci.formats.in.PerkinElmerReader
 
getFilename(int, int, IFormatReader, String) - Static method in class loci.formats.FormatTools
 
getFilename(int, int, IFormatReader, String, boolean) - Static method in class loci.formats.FormatTools
 
getFilename(int, int, MetadataRetrieve, String, boolean) - Static method in class loci.formats.FormatTools
 
getFilename(int, int) - Method in class loci.formats.in.BDReader
 
getFilename() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the filename associated with this File.

getFilenames(String, IFormatReader) - Static method in class loci.formats.FormatTools
 
getFilePattern() - Method in class loci.formats.AxisGuesser

Gets the file pattern.

getFilePattern() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getFilePattern() - Method in class loci.formats.FileStitcher

Gets the file pattern object used to build the list of files.

getFiles() - Method in class loci.formats.FilePattern

Gets a listing of all files matching this file pattern.

getFiles() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getFileSize(String) - Method in interface loci.formats.services.POIService

Retrieve the total number of bytes in the given file.

getFileSize(String) - Method in class loci.formats.services.POIServiceImpl
 
getFileStitcher() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getFileVersion(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
 
getFillRule(String) - Method in class loci.formats.FormatReader

Retrieves an FillRule enumeration
 value for the given String.

getFilter() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Gets filters.

getFilters() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets filters

getFilters() - Method in class loci.formats.gui.ComboFileFilter

Gets the list of file filters forming this filter combination.

getFilterType(int, AnWTFilterSpec) - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransfSpec

Get the filter type common to all component of a given tile.

getFilterType() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilter

Returns the type of filter used according to the FilterTypes
 interface.

getFilterType() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the type of filter used according to the FilterTypes
 interface(W9x7).

getFilterType() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the type of filter used according to the FilterTypes interface
 (W5x3).

getFilterType(String) - Method in class loci.formats.FormatReader

Retrieves an FilterType enumeration
 value for the given String.

getFirst() - Method in class loci.formats.FilePattern

Gets the START element for all blocks.

getFirst() - Method in class loci.formats.FilePatternBlock

Gets the first element in a range block.

getFirstChannel(String) - Method in class loci.formats.in.SlidebookTiffReader
 
getFirstChild() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getFirstChild(Element, String) - Method in class loci.formats.in.OIRReader
 
getFirstChild(Element, String) - Method in class loci.formats.in.PrairieMetadata

Gets the first child element with the given name.

getFirstCodeStreamLength() - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method returns the length of the first contiguous codestreams in
 the file

getFirstCodeStreamPos() - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method returns the position of the first contiguous codestreams in
 the file

getFirstComment(int) - Method in class loci.formats.in.MetamorphReader

Returns the TIFF comment from the first IFD of the first STK file in the
 given series.

getFirstFile() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the first File of the Sequence.

getFirstFrame() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the first Frame of the Sequence.

getFirstIFD() - Method in class loci.formats.tiff.TiffParser

Gets the first IFD within the TIFF file, or null
 if the input source is not a valid TIFF file.

getFirstIFDEntry(int) - Method in class loci.formats.tiff.TiffParser

Retrieve a given entry from the first IFD in the stream.

getFirstNode(Element, String) - Method in class loci.formats.in.ZeissCZIReader
 
getFirstNodeValue(Element, String) - Method in class loci.formats.in.ZeissCZIReader
 
getFirstOffset() - Method in class loci.formats.tiff.TiffParser

Gets offset to the first IFD, or -1 if stream is not TIFF.

getFirstSequence() - Method in class loci.formats.in.PrairieMetadata

Gets the first Sequence.

getFirstTimeInfo() - Method in class loci.plugins.in.ImporterOptions
 
getFixedHeader() - Method in class loci.formats.services.JPEGTurboServiceImpl
 
getFixedPoint(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the position of the fixed point in the specified component
 (i.e.

getFixedPoint(int) - Method in interface jj2000.j2k.image.BlkImgDataSrc

Returns the position of the fixed point in the specified component, or
 equivalently the number of fractional bits.

getFixedPoint(int) - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Returns the position of the fixed point in the specified
 component.

getFixedPoint(int) - Method in class jj2000.j2k.image.ImgDataConverter

Returns the position of the fixed point in the specified
 component.

getFixedPoint(int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the position of the fixed point in the specified
 component.

getFixedPoint(int) - Method in class jj2000.j2k.image.input.ImgReaderPGM

Returns the position of the fixed point in the specified component
 (i.e.

getFixedPoint(int) - Method in class jj2000.j2k.image.invcomptransf.InvCompTransf

Returns the position of the fixed point in the specified
 component.

getFixedPoint(int) - Method in class jj2000.j2k.image.Tiler

Returns the position of the fixed point in the specified
 component.

getFixedPoint(int) - Method in class jj2000.j2k.quantization.dequantizer.StdDequantizer

Returns the position of the fixed point in the output data for the
 specified component.

getFixedPoint(int) - Method in interface jj2000.j2k.wavelet.analysis.CBlkWTDataSrc

Returns the position of the fixed point in the specified component, or
 equivalently the number of fractional bits.

getFixedPoint(int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the position of the fixed point in the specified
 component.

getFixedPoint(int) - Method in interface jj2000.j2k.wavelet.synthesis.CBlkWTDataSrcDec

Returns the position of the fixed point in the specified component, or
 equivalently the number of fractional bits.

getFixedPoint(int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTFull

Returns the position of the fixed point in the specified
 component.

getFlags() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox

Returns the Flags data element.

getFlexFiles() - Method in class loci.formats.in.FlexReader.MeaHandler
 
getFloat(String) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a Float.

getFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a Float.

getFloatArray() - Method in class loci.plugins.util.RecordedImageProcessor
 
getFloatAttribute(Node, String, float, boolean) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getFloatAttribute(Node, String) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getFloats(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of floats, one per channel.

getFloats(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of floats, one per channel.

getFloats(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of floats, one per channel.

getFloatValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
getFlushedPosition() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
getFontFamily(String) - Method in class loci.formats.FormatReader

Retrieves an FontFamily enumeration
 value for the given String.

getFontMetrics() - Method in class loci.plugins.util.RecordedImageProcessor
 
getFontSize(Integer) - Static method in class loci.formats.FormatTools
 
getFontStyle(String) - Method in class loci.formats.FormatReader

Retrieves an FontStyle enumeration
 value for the given String.

getForceThumbnailsInfo() - Method in class loci.plugins.in.ImporterOptions
 
getFormat() - Method in class loci.formats.FormatHandler
 
getFormat() - Method in interface loci.formats.IFormatHandler

Gets the name of this file format.

getFormat(String) - Method in class loci.formats.ImageReader

Gets a string describing the file format for the given file.

getFormat() - Method in class loci.formats.ImageReader
 
getFormat(String) - Method in class loci.formats.ImageWriter

Gets a string describing the file format for the given file.

getFormat() - Method in class loci.formats.ImageWriter
 
getFormat() - Method in class loci.formats.ReaderWrapper
 
getFormat() - Method in class loci.formats.WriterWrapper
 
getFormat(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
getFormatName() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getFrame(int, int) - Method in class loci.formats.in.PrairieMetadata

Gets the Frame at the given (cycle and index).

getFrame() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the <Frame> containing this <File>.

getFrame(int) - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the Frame with the given index.

getFramesPerSecond() - Method in class loci.formats.FormatWriter
 
getFramesPerSecond() - Method in interface loci.formats.IFormatWriter

Gets the frames per second to use when writing.

getFramesPerSecond() - Method in class loci.formats.ImageWriter
 
getFramesPerSecond() - Method in class loci.formats.WriterWrapper
 
getFromParam() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getGain() - Method in class loci.formats.in.MetamorphHandler
 
getGain(int) - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the cth gain for this Frame.

getGains() - Method in class loci.formats.in.ND2Handler
 
getGifPaletteSize(int) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter

According do GIF specification size of clor table (palette here) 
 must be in range from 2 to 256 and must be power of 2.

getGlobalMeta(String) - Method in class loci.formats.FormatReader

Gets a value from the global metadata table.

getGlobalMetadata() - Method in class loci.formats.FormatReader
 
getGlobalMetadata() - Method in interface loci.formats.IFormatReader

Obtains the hashtable containing the metadata field/value pairs from
 the current file.

getGlobalMetadata() - Method in class loci.formats.ImageReader
 
getGlobalMetadata() - Method in class loci.formats.in.FilePatternReader
 
getGlobalMetadata() - Method in class loci.formats.in.LeicaHandler
 
getGlobalMetadata() - Method in class loci.formats.ReaderWrapper
 
getGrandchildren(Element, String) - Method in class loci.formats.in.ZeissCZIReader
 
getGrandchildren(Element, String, String) - Method in class loci.formats.in.ZeissCZIReader
 
getGreen(int) - Method in class loci.formats.gui.Index16ColorModel
 
getGreen(int) - Method in class loci.formats.gui.SignedColorModel
 
getGreen(Object) - Method in class loci.formats.gui.SignedColorModel
 
getGreen(int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getGreen(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getGreenOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ

For the given pixel format, returns the number of bytes that the green
 component is offset from the start of the pixel.

getGreens() - Method in class loci.formats.gui.Index16ColorModel

Return the array of green color components.

getGroup(String) - Method in class loci.formats.services.NetCDFServiceImpl

Retrieves a group based on its fully qualified path.

getGroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getGroupX() - Method in class loci.formats.in.SPEReader.SpeROI
 
getGroupY() - Method in class loci.formats.in.SPEReader.SpeROI
 
getGuardBits() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets guardBits

getHeader() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getHeader() - Method in class loci.formats.in.SPEReader.SpeHeader
 
getHeaderInfo(int, String) - Method in class loci.formats.in.DicomReader
 
getHeaderPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser

Returns the pixel type as specified in the header.

getHeaderSize() - Method in class loci.formats.in.SPEReader.SpeHeader
 
getHeaderSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser

Returns the number of channels the image has as specified in the header.

getHeaderSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser

Returns the width of the image as specified in the header.

getHeaderSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser

Returns the height of the image as specified in the header.

getHeight() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the height of the image.

getHeight(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
getHeight() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Returns the height of the image.

getHeight(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getHeight() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getHeight(int) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
getHeight(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
getHeight(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
getHeight() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
getHeight() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getHeight(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getHeight() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getHeight(int) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getHeight() - Method in class jj2000.j2k.codestream.reader.TagTreeDecoder

Returns the number of leafs along the vertical direction.

getHeight() - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Returns the number of leafs along the vertical direction.

getHeight() - Method in class loci.formats.codec.JPEGTileDecoder
 
getHeight() - Method in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
getHeight(int) - Method in class loci.formats.in.LegacyND2Reader
 
getHeight() - Method in interface loci.formats.services.LuraWaveService

Wraps lwfDecoder.getHeight()

getHeight() - Method in class loci.formats.services.LuraWaveServiceImpl
 
getHeight(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack
 
getHeight() - Method in class loci.plugins.util.BFVirtualStack
 
getHeight() - Method in class loci.plugins.util.RecordedImageProcessor
 
getHeight() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Returns the height of the JPEG image associated with this decompressor
 instance.

getHFilters(int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterSpec

Returns the horizontal analysis filters to be used in component 'n' and
 tile 't'.

getHFilters(int, int) - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterSpec

Returns the horizontal analysis filters to be used in component 'n' and
 tile 't'.

getHH() - Method in class jj2000.j2k.wavelet.analysis.SubbandAn

Returns the HH child subband of this subband.

getHH() - Method in class jj2000.j2k.wavelet.Subband

Returns the HH child subband of this subband.

getHH() - Method in class jj2000.j2k.wavelet.synthesis.SubbandSyn

Returns the HH child subband of this subband.

getHistogram() - Method in class loci.plugins.util.RecordedImageProcessor
 
getHistogramMax() - Method in class loci.plugins.util.RecordedImageProcessor
 
getHistogramMin() - Method in class loci.plugins.util.RecordedImageProcessor
 
getHistogramSize() - Method in class loci.plugins.util.RecordedImageProcessor
 
getHL() - Method in class jj2000.j2k.wavelet.analysis.SubbandAn

Returns the HL (horizontal high-pass) child subband of this
 subband.

getHL() - Method in class jj2000.j2k.wavelet.Subband

Returns the HL (horizontal high-pass) child subband of this subband.

getHL() - Method in class jj2000.j2k.wavelet.synthesis.SubbandSyn

Returns the HL (horizontal high-pass) child subband of this
 subband.

getHorAnWaveletFilters(int, int) - Method in interface jj2000.j2k.wavelet.analysis.ForwWT

Returns the horizontal analysis wavelet filters used in each
 level, for the specified tile-component.

getHorAnWaveletFilters(int, int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the horizontal analysis wavelet filters used in each level, for
 the specified component and tile.

getHorizontalResolution() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox

Return the horizontal resolution.

getHorWFilter() - Method in class jj2000.j2k.wavelet.analysis.SubbandAn

This function returns the horizontal wavelet filter relevant to this
 subband

getHorWFilter() - Method in class jj2000.j2k.wavelet.Subband

This function returns the horizontal wavelet filter relevant to this
 subband

getHorWFilter() - Method in class jj2000.j2k.wavelet.synthesis.SubbandSyn

This function returns the horizontal wavelet filter relevant to this
 subband

getHPSynthesisFilter() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilter

Returns the time-reversed high-pass synthesis waveform of the
 filter, which is the high-pass filter.

getHPSynthesisFilter() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the time-reversed high-pass synthesis waveform of the
 filter, which is the high-pass filter.

getHPSynthesisFilter() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the time-reversed high-pass synthesis waveform of the filter,
 which is the high-pass filter.

getHPSynWaveForm(float[], float[]) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilter

Returns the equivalent high-pass synthesis waveform of a
 cascade of filters, given the syhthesis waveform of the
 previous stage.

getICCProfile() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox

Returns the ICC color profile in this color specification box.

getId(String) - Method in class loci.formats.tools.MakeTestOmeTiff
 
getId() - Method in class loci.plugins.in.ImporterOptions
 
getIdInfo() - Method in class loci.plugins.in.ImporterOptions
 
getIdle(boolean) - Method in class jj2000.j2k.util.ThreadPool

Returns and idle thread and removes it from the list of idle
 threads.

getIdLocation() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getIdName() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getIdx() - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor

Returns the index of this compressor.

getIFD(long) - Method in class loci.formats.tiff.TiffParser

Gets the IFD stored at the given offset.

getIFDAsTree(TIFFIFD, String, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getIFDIndex(int, int) - Method in class loci.formats.in.NDPIReader
 
getIFDIndex(int) - Method in class loci.formats.in.SVSReader
 
getIFDIntArray(int) - Method in class loci.formats.tiff.IFD

Gets the given directory entry values in int format
 from this IFD, performing some error checking.

getIFDIntValue(int) - Method in class loci.formats.tiff.IFD

Gets the given directory entry value in int format from this IFD,
 or -1 if the given directory does not exist.

getIFDIntValue(int, int) - Method in class loci.formats.tiff.IFD

Gets the given directory entry value in int format from this IFD,
 performing some error checking.

getIFDLongArray(int) - Method in class loci.formats.tiff.IFD

Gets the given directory entry values in long format
 from this IFD, performing some error checking.

getIFDLongValue(int, long) - Method in class loci.formats.tiff.IFD

Gets the given directory entry value in long format from this IFD,
 performing some error checking.

getIFDOffsets() - Method in class loci.formats.tiff.TiffParser

Gets the offsets to every IFD in the file.

getIFDRationalValue(int) - Method in class loci.formats.tiff.IFD

Gets the given directory entry value in rational format from this IFD,
 performing some error checking.

getIFDs() - Method in class loci.formats.in.MinimalTiffReader

Gets the list of IFDs associated with the current TIFF's image planes.

getIFDs() - Method in class loci.formats.tiff.TiffParser

Returns all IFDs in the file.

getIFDShortArray(int) - Method in class loci.formats.tiff.IFD

Gets the given directory entry values in short format
 from this IFD, performing some error checking.

getIFDStringValue(int) - Method in class loci.formats.tiff.IFD

Gets the given directory entry value as a string from this IFD,
 performing some error checking.

getIFDTagName(int) - Static method in class loci.formats.tiff.IFD

Gets the name of the IFD tag encoded by the given number.

getIFDTextValue(int) - Method in class loci.formats.tiff.IFD

Gets the given directory entry value as a string (regardless of type).

getIFDValue(int) - Method in class loci.formats.tiff.IFD

Gets the given directory entry value from this IFD.

getIFDValue(int, Class) - Method in class loci.formats.tiff.IFD

Gets the given directory entry value from this IFD,
 performing some error checking.

getIFDValue(TiffIFDEntry) - Method in class loci.formats.tiff.TiffParser

Retrieve the value corresponding to the given TiffIFDEntry.

getIlluminationType(String) - Method in class loci.formats.FormatReader

Retrieves an IlluminationType enumeration
 value for the given String.

getImage() - Method in class loci.formats.gui.ImageViewer

Gets the currently displayed image.

getImage(byte[], int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getImageCount() - Method in class loci.formats.ChannelMerger
 
getImageCount() - Method in class loci.formats.ChannelSeparator
 
getImageCount() - Method in class loci.formats.FileStitcher
 
getImageCount() - Method in class loci.formats.FormatReader
 
getImageCount() - Method in interface loci.formats.IFormatReader

Determines the number of image planes in the current file.

getImageCount() - Method in class loci.formats.ImageReader
 
getImageCount() - Method in class loci.formats.in.FilePatternReader
 
getImageCount() - Method in class loci.formats.ReaderWrapper
 
getImageCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getImageCreationDate() - Method in class loci.formats.in.BaseTiffReader

Retrieves the image creation date.

getImageCreationDate(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getImageData(int, int, int) - Method in class loci.formats.in.CellH5Reader
 
getImageData(int, int, int, int, int) - Method in class loci.formats.in.ImarisHDFReader

Retrieve an array corresponding to the specified image tile.

getImageDescription(Element) - Method in class loci.formats.in.LIFReader
 
getImageDimension(int) - Method in class com.sun.media.imageio.stream.RawImageInputStream

Retrieves the dimnsion of the imageIndexth image.

getImageIndex() - Method in class loci.formats.gui.ImageViewer

Gets the index of the currently displayed image.

getImageIndex(int) - Method in class loci.formats.in.FluoviewReader
 
getImageIndex(String) - Method in class loci.formats.in.PCIReader

Get the image index from the image file name.

getImageInputStream() - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream

Returns an ImageInputStream for reading.

getImageLength() - Method in class loci.formats.tiff.IFD

Retrieves the image's length (TIFF tag ImageLength) from a given TIFF IFD.

getImageMetadata(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
getImageMetadata(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getImageMetadata(int) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
getImageMetadata(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
getImageMetadata(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
getImageMetadata(boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor

Retrieves image metadata with non-core nodes removed.

getImageMetadata(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getImageMetadata(int) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getImageName() - Method in class loci.formats.in.MetamorphHandler
 
getImageNumber(String, int) - Method in class loci.formats.in.ZeissZVIReader
 
getImageOffset(int) - Method in class com.sun.media.imageio.stream.RawImageInputStream

Retrieves the image offset of the imageIndexth image.

getImageReader() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getImageSequence(int) - Method in class loci.formats.in.DeltavisionReader

Get the image sequence string.

getImagesPerFile() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getImagesPerFile(String, IFormatReader) - Static method in class loci.formats.FormatTools
 
getImageType() - Method in class com.sun.media.imageio.stream.RawImageInputStream

Retrieves the image type.

getImageType(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getImageType() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getImageTypes(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
getImageTypes(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getImageTypes(int) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
getImageTypes(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
getImageTypes(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
getImageTypes(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getImageTypes(int) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getImageWidth() - Method in class loci.formats.tiff.IFD

Retrieves the image's width (TIFF tag ImageWidth) from a given TIFF IFD.

getImagingDevice() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the imaging device associated with this Frame.

getImgHeight() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the overall height of the image in pixels.

getImgHeight(int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the overall height of the image in pixels, for the given
 resolution level.

getImgHeight() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the image height in the reference grid.

getImgHeight() - Method in interface jj2000.j2k.image.ImgData

Returns the overall height of the image in pixels.

getImgHeight() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the overall height of the image in pixels.

getImgHeight() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the overall height of the image in pixels.

getImgHeight() - Method in class jj2000.j2k.image.input.ImgReader

Returns the overall height of the image in pixels.

getImgHeight() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the overall height of the image in pixels.

getImgHeight(int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the overall height of the image in pixels, for the given
 resolution level.

getImgHeight(int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the overall height of the image in pixels, for the given
 resolution level.

getImgRes() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the image resolution level to reconstruct from the
 codestream.

getImgULX() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the horizontal coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULX(int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the horizontal coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid at the specified
 resolution level.

getImgULX() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Return the horizontal upper-left coordinate of the image in the
 reference grid.

getImgULX() - Method in interface jj2000.j2k.image.ImgData

Returns the horizontal coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULX() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the horizontal coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULX() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the horizontal coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULX() - Method in class jj2000.j2k.image.input.ImgReader

Returns the horizontal coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULX() - Method in class jj2000.j2k.image.Tiler

Returns the horizontal coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULX() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the horizontal coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULX(int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the horizontal coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid at the specified
 resolution level.

getImgULX(int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the horizontal coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid at the specified
 resolution level.

getImgULY() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the vertical coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULY(int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the vertical coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid at the specified
 resolution level.

getImgULY() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Return the vertical upper-left coordinate of the image in the reference
 grid.

getImgULY() - Method in interface jj2000.j2k.image.ImgData

Returns the vertical coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULY() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the vertical coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULY() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the vertical coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULY() - Method in class jj2000.j2k.image.input.ImgReader

Returns the vertical coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULY() - Method in class jj2000.j2k.image.Tiler

Returns the vertical coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULY() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the vertical coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid.

getImgULY(int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the vertical coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid at the specified
 resolution level.

getImgULY(int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the vertical coordinate of the image origin, the top-left
 corner, in the canvas system, on the reference grid at the specified
 resolution level.

getImgWidth() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the overall width of the image in pixels.

getImgWidth(int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the overall width of the image in pixels, for the given (image)
 resolution level.

getImgWidth() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the image width in the reference grid.

getImgWidth() - Method in interface jj2000.j2k.image.ImgData

Returns the overall width of the image in pixels.

getImgWidth() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the overall width of the image in pixels.

getImgWidth() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the overall width of the image in pixels.

getImgWidth() - Method in class jj2000.j2k.image.input.ImgReader

Returns the overall width of the image in pixels.

getImgWidth() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the overall width of the image in pixels.

getImgWidth(int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the overall width of the image in pixels, for the given
 resolution level.

getImgWidth(int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the overall width of the image in pixels, for the given
 resolution level.

getImmersion(String) - Method in class loci.formats.FormatReader

Retrieves an Immersion enumeration
 value for the given String.

getImmersion() - Method in class loci.formats.in.ND2Handler
 
getImmersion() - Method in class loci.formats.in.PrairieMetadata.Frame

Extracts the immersion from the objective lens string.

getImplementationType(int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the implementation type of this wavelet transform, WT_IMPL_FULL
 (full-page based transform).

getImplementationType(int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTFull

Returns the implementation type of this wavelet transform, WT_IMPL_FULL
 (full-page based transform).

getImplementationType(int) - Method in interface jj2000.j2k.wavelet.WaveletTransform

Returns the implementation type of this wavelet transform
 (WT_IMPL_LINE or WT_IMPL_FRAME) for the specified component, 
 in the current tile.

getImplType() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the implementation type of this filter, as defined in
 this class, such as WT_FILTER_INT_LIFT, WT_FILTER_FLOAT_LIFT,
 WT_FILTER_FLOAT_CONVOL.

getImplType() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the implementation type of this filter, as defined in this
 class, such as WT_FILTER_INT_LIFT, WT_FILTER_FLOAT_LIFT,
 WT_FILTER_FLOAT_CONVOL.

getImplType() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns the implementation type of this filter, as defined in this
 class, such as WT_FILTER_INT_LIFT, WT_FILTER_FLOAT_LIFT,
 WT_FILTER_FLOAT_CONVOL.

getImplType() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns the implementation type of this filter, as defined in this
 class, such as WT_FILTER_INT_LIFT, WT_FILTER_FLOAT_LIFT,
 WT_FILTER_FLOAT_CONVOL.

getImplType() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the implementation type of this filter, as defined in
 this class, such as WT_FILTER_INT_LIFT, WT_FILTER_FLOAT_LIFT,
 WT_FILTER_FLOAT_CONVOL.

getIndex() - Method in class loci.formats.cache.CacheEvent

Gets the index relevant to the cache update, if any.

getIndex(int, int, int, int, int, int) - Method in class loci.formats.ChannelMerger
 
getIndex(int, int, int) - Method in class loci.formats.ChannelMerger
 
getIndex(int, int, int) - Method in class loci.formats.ChannelSeparator
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ChannelSeparator
 
getIndex(int, int, int) - Method in class loci.formats.DimensionSwapper
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.DimensionSwapper
 
getIndex(int, int, int) - Method in class loci.formats.FileStitcher
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.FileStitcher
 
getIndex(int, int, int) - Method in class loci.formats.FormatReader
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.FormatReader
 
getIndex(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools

Gets the rasterized index corresponding
 to the given Z, C and T coordinates (real sizes).

getIndex(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools

Gets the rasterized index corresponding to the given Z, C, T,
 ModuloZ, ModuloC and ModuloT coordinates (effective sizes).

getIndex(String, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools

Gets the rasterized index corresponding
 to the given Z, C and T coordinates (real sizes).

getIndex(String, int, int, int, int, int, int, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools

Gets the rasterized index corresponding to the given Z, C, T,
 ModuloZ, ModuloC, ModuloT coordinates (effective sizes).

getIndex(int, int, int) - Method in interface loci.formats.IFormatReader

Gets the rasterized index corresponding
 to the given Z, C and T coordinates (real sizes).

getIndex(int, int, int, int, int, int) - Method in interface loci.formats.IFormatReader

Gets the rasterized index corresponding to the given Z, C, T,
 moduloZ, moduloC and moduloT coordinates (effective sizes).

getIndex(int, int, int) - Method in class loci.formats.ImageReader
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ImageReader
 
getIndex() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getIndex(int, int, int) - Method in class loci.formats.in.FilePatternReader
 
getIndex() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the index associated with this Frame.

getIndex(int, int, int) - Method in class loci.formats.ReaderWrapper
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
 
getIndex(Double, Double, Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getIndexColorModel() - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
 
getIndexCount() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the number of recorded indices at this Sequence.

getIndexedImage() - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
 
getIndexMax() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the maximum index value.

getIndexMin() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the minimum index value.

getInfo() - Method in class loci.formats.in.SDTReader

Gets object containing SDT header information.

getInfo() - Method in class loci.plugins.prefs.Option

Gets documentation about the option.

getInfo(String) - Method in class loci.plugins.prefs.OptionsList

Gets the documentation for the option with the given key.

getIniFile(String) - Method in class loci.formats.in.FV1000Reader
 
getInputOrder() - Method in class loci.formats.DimensionSwapper
 
getInputOrder(int) - Method in class loci.plugins.in.ImporterOptions
 
getInputStream(String) - Method in interface loci.formats.services.POIService

Retrieve an InputStream corresponding to the given file name.

getInputStream(String) - Method in class loci.formats.services.POIServiceImpl
 
getInstance() - Static method in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

Returns a shared instance of a BaselineTIFFTagSet.

getInstance() - Static method in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

Returns a shared instance of an EXIFGPSTagSet.

getInstance() - Static method in class com.sun.media.imageio.plugins.tiff.EXIFInteroperabilityTagSet

Returns the shared instance of
 EXIFInteroperabilityTagSet.

getInstance() - Static method in class com.sun.media.imageio.plugins.tiff.EXIFParentTIFFTagSet

Returns a shared instance of an EXIFParentTIFFTagSet.

getInstance() - Static method in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

Returns a shared instance of an EXIFTIFFTagSet.

getInstance() - Static method in class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet

Returns a shared instance of a FaxTIFFTagSet.

getInstance() - Static method in class com.sun.media.imageio.plugins.tiff.GeoTIFFTagSet

Returns a shared instance of a GeoTIFFTagSet.

getInstance() - Static method in class com.sun.media.imageioimpl.common.InvertedCMYKColorSpace
 
getInstance() - Static method in class com.sun.media.imageioimpl.common.SimpleCMYKColorSpace
 
getInstance() - Static method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadataFormat
 
getInstance() - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadataFormat
 
getInstance() - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadataFormat
 
getInstance() - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
getInstance() - Static method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormat
 
getInstance() - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadataFormat
 
getInstance() - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadataFormat
 
getInstance() - Static method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadataFormat
 
getInstance(int) - Static method in class loci.formats.gui.TwoChannelColorSpace
 
getInt(Node, String) - Static method in class com.sun.media.imageio.stream.RawImageInputStream

Gets the integer type attribute.

getInt(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader

Method used to retrieve data values for Integer entries into the SPE header table

getInt(int) - Method in class loci.formats.in.SPEReader.SpeHeader

Private method used to retrieve an Integer value from the SPE header

getIntArray(Node, String) - Static method in class com.sun.media.imageio.stream.RawImageInputStream

Gets the integer type attribute.

getIntArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader

Method used to retrieve data values for Integer Array entries into the SPE header table

getIntArray() - Method in class loci.plugins.util.RecordedImageProcessor
 
getIntArrayElementValue(Node) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Gets the integer array from an IIOMetadataNode.

getIntAttribute(Node, String, int, boolean) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getIntAttribute(Node, String) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getIntAttribute(Node, String, int, boolean, boolean, int, int) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getIntAttribute(Node, String, boolean, int, int) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getInteger(String) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as an Integer.

getInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as an Integer.

getIntegerValue(Node) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getIntElementValue(Node) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Gets its integer value from an IIOMetadataNode.

getIntellectualProperty() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Returns the IntellectualProperty flag.

getInternCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Returns the specified code-block in the current tile for the specified
 component (as a reference or copy).

getInternCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in interface jj2000.j2k.quantization.dequantizer.CBlkQuantDataSrcDec

Returns the specified code-block in the current tile for the specified
 component (as a reference or copy).

getInternCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in class jj2000.j2k.quantization.dequantizer.StdDequantizer

Returns the specified code-block in the current tile for the specified
 component (as a reference or copy).

getInternCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in class jj2000.j2k.roi.ROIDeScaler

Returns the specified code-block in the current tile for the specified
 component (as a reference or copy).

getInternCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in interface jj2000.j2k.wavelet.synthesis.CBlkWTDataSrcDec

Returns the specified code-block in the current tile for the specified
 component (as a reference or copy).

getInternCompData(DataBlk, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns, in the blk argument, the block of image data containing the
 specifed rectangular area, in the specified component.

getInternCompData(DataBlk, int) - Method in interface jj2000.j2k.image.BlkImgDataSrc

Returns, in the blk argument, a block of image data containing the
 specifed rectangular area, in the specified component.

getInternCompData(DataBlk, int) - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Apply the component transformation associated with the current tile.

getInternCompData(DataBlk, int) - Method in class jj2000.j2k.image.ImgDataConverter

Returns, in the blk argument, a block of image data containing the
 specifed rectangular area, in the specified component, using the
 'transfer type' defined in the block given as argument.

getInternCompData(DataBlk, int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns, in the blk argument, a block of image data containing the
 specifed rectangular area, in the specified component.

getInternCompData(DataBlk, int) - Method in class jj2000.j2k.image.input.ImgReaderPGM

Returns, in the blk argument, the block of image data containing the
 specifed rectangular area, in the specified component.

getInternCompData(DataBlk, int) - Method in class jj2000.j2k.image.invcomptransf.InvCompTransf

Apply the inverse component transformation associated with the current
 tile.

getInternCompData(DataBlk, int) - Method in class jj2000.j2k.image.Tiler

Returns, in the blk argument, a block of image data containing the
 specifed rectangular area, in the specified component.

getInternCompData(DataBlk, int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTFull

Returns a block of image data containing the specifed rectangular area,
 in the specified component, as a reference to the internal buffer (see
 below).

getInterpolate() - Method in class loci.plugins.util.RecordedImageProcessor
 
getInterpolatedPixel(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
getInts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of signed integers, one per channel.

getInts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of signed integers, one per channel.

getInts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of signed integers, one per channel.

getIntValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
getJDKImageReaderWriterSPI(ServiceRegistry, String, boolean) - Static method in class com.sun.media.imageioimpl.common.ImageUtil
 
getJPEGBuf() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Returns the JPEG image buffer associated with this decompressor instance.

getJPEGSize() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Returns the size of the JPEG image (in bytes) associated with this
 decompressor instance.

getJPEGTablesReader() - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGCompressor

Retrieves a JPEG reader which supports native JPEG stream metadata.

getKerSpecType(int) - Method in class jj2000.j2k.wavelet.WTFilterSpec

Returns the type of specification for the filters in the specified
 component and tile.

getKey() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getKey(int) - Method in class loci.formats.in.BaseZeissReader.Tag

Return the string corresponding to the given ID.

getKey(int) - Method in class loci.formats.in.MetamorphReader
 
getKey() - Method in class loci.formats.meta.OriginalMetadataAnnotation
 
getKey() - Method in class loci.plugins.prefs.Option

Gets the option's key name.

getKeyID() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getLabel() - Method in class loci.plugins.prefs.Option

Gets label describing the option.

getLabel(String) - Method in class loci.plugins.prefs.OptionsList

Gets the label for the option with the given key.

getLabels() - Method in class loci.plugins.config.FlexWidgets
 
getLabels() - Method in interface loci.plugins.config.IFormatWidgets
 
getLabels() - Method in class loci.plugins.config.LIFWidgets
 
getLabels() - Method in class loci.plugins.config.ND2Widgets
 
getLabels() - Method in class loci.plugins.config.PictWidgets
 
getLabels() - Method in class loci.plugins.config.QTWidgets
 
getLabels() - Method in class loci.plugins.config.SDTWidgets
 
getLabels() - Method in class loci.plugins.config.TiffDelegateWidgets
 
getLabels() - Method in class loci.plugins.config.ZeissCZIWidgets
 
getLaserMedium(String) - Method in class loci.formats.FormatReader

Retrieves an LaserMedium enumeration
 value for the given String.

getLaserPower() - Method in class loci.formats.in.PrairieMetadata

Gets the first laserPower recorded in the configuration.

getLaserType(String) - Method in class loci.formats.FormatReader

Retrieves an LaserType enumeration
 value for the given String.

getLast() - Method in class loci.formats.FilePattern

Gets the STOP element for all blocks.

getLast() - Method in class loci.formats.FilePatternBlock

Gets the last element in a range block.

getLastBodyBuf() - Method in class jj2000.j2k.codestream.writer.PktEncoder

Returns the buffer of the body of the last encoded packet.

getLastBodyLen() - Method in class jj2000.j2k.codestream.writer.PktEncoder

Returns the length of the body of the last encoded packet, in
 bytes.

getLastChild() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getLastPosition() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD
 
getLatestVersion() - Method in interface loci.formats.services.OMEXMLService

Retrieves the latest supported version of the OME-XML schema.

getLatestVersion() - Method in class loci.formats.services.OMEXMLServiceImpl
 
getLayers() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets layers

getLeafChildCount() - Method in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
getLength() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Returns the box length.

getLength() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getLength() - Method in class jj2000.j2k.codestream.writer.BitOutputBuffer

Returns the current length of the buffer, in bytes.

getLength() - Method in class jj2000.j2k.codestream.writer.CodestreamWriter

Returns the current length of the entire bit stream.

getLength() - Method in class jj2000.j2k.codestream.writer.FileCodestreamWriter

Returns the current length of the entire bit stream.

getLength() - Method in class jj2000.j2k.codestream.writer.HeaderEncoder

Returns the length of the header.

getLength(RandomAccessInputStream, int) - Method in class loci.formats.in.DicomReader
 
getLength(long) - Method in class loci.formats.in.OBFReader
 
getLengths() - Method in class loci.formats.cache.CacheStrategy
 
getLengths() - Method in interface loci.formats.cache.ICacheStrategy

Gets the lengths of all the axes.

getLengths(IFormatReader) - Static method in class loci.formats.tools.CacheConsole

Helper utility for constructing lengths array, used by main.

getLensNA() - Method in class loci.formats.in.MetamorphHandler
 
getLensRI() - Method in class loci.formats.in.MetamorphHandler
 
getLetter() - Method in class loci.formats.ResourceNamer

Returns a String representing a single letter (in the case
 where the class instance has been initialized with a resource count lower
 than 26) or a concatenation of two letters (if resource count is higher
 than 26).

getLevels(int) - Method in class jj2000.j2k.wavelet.WTDecompSpec

Returns the decomposition number of levels in component 'n' and tile
 't'.

getLH() - Method in class jj2000.j2k.wavelet.analysis.SubbandAn

Returns the LH (vertical high-pass) child subband of this
 subband.

getLH() - Method in class jj2000.j2k.wavelet.Subband

Returns the LH (vertical high-pass) child subband of this subband.

getLH() - Method in class jj2000.j2k.wavelet.synthesis.SubbandSyn

Returns the LH (vertical high-pass) child subband of this
 subband.

getLicenseCode() - Method in interface loci.formats.services.LuraWaveService

Retrieves the current license code as a string.

getLicenseCode() - Method in class loci.formats.services.LuraWaveServiceImpl
 
getLimitedSIndexFromSlope(float) - Static method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Returns the index of a slope for the summary table, limiting to the
 admissible values.

getLine(double, double, double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
getLinesPerFrame() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the lines per frame for this Frame.

getLineWidth() - Method in class jj2000.j2k.util.MsgPrinter

Returns the line width that is used for formatting.

getLL() - Method in class jj2000.j2k.wavelet.analysis.SubbandAn

Returns the LL child subband of this subband.

getLL() - Method in class jj2000.j2k.wavelet.Subband

Returns the LL child subband of this subband.

getLL() - Method in class jj2000.j2k.wavelet.synthesis.SubbandSyn

Returns the LL child subband of this subband.

getLoadList(int[]) - Method in class loci.formats.cache.CacheStrategy
 
getLoadList(int[]) - Method in interface loci.formats.cache.ICacheStrategy

Gets the indices of the objects to cache,
 surrounding the object at the given position.

getLocation() - Method in class loci.plugins.in.ImporterOptions
 
getLocationFromResourceName(Location, String, int, String) - Method in class loci.formats.ResourceNamer

Creates a new Location instance using the provided parent path and
 child node name.

getLocationInfo() - Method in class loci.plugins.in.ImporterOptions
 
getLocations() - Method in class loci.plugins.in.ImporterOptions
 
getLong(String) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a Long.

getLong(String, Long) - Method in class loci.formats.in.DynamicMetadataOptions

Get the value of property name as a Long.

getLong(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader

Method used to retrieve data values for Long enteries into the SPE header table

getLong(int) - Method in class loci.formats.in.SPEReader.SpeHeader

Private method used to retrieve a Long value from the SPE header

getLongArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader

Method used to retrieve data values for Long Array entries into the SPE header table

getLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools

Convers an Index16ColorModel to a 2D short array.

getLookupTable(Map) - Method in class loci.formats.in.AmiraReader
 
getLookupTable() - Method in class loci.formats.in.JPEG2000MetadataParser

Returns the color lookup table stored in the file, or null if a lookup
 table is not present.

getLookupTableComponentCount() - Method in class loci.formats.ChannelFiller

Gets the number of color components in the lookup table.

getLossless() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Gets lossless.

getLossless() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets encodingRate

getLPSynthesisFilter() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilter

Returns the time-reversed low-pass synthesis waveform of the
 filter, which is the low-pass filter.

getLPSynthesisFilter() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the time-reversed low-pass synthesis waveform of the
 filter, which is the low-pass filter.

getLPSynthesisFilter() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the time-reversed low-pass synthesis waveform of the filter,
 which is the low-pass filter.

getLPSynWaveForm(float[], float[]) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilter

Returns the equivalent low-pass synthesis waveform of a cascade
 of filters, given the syhthesis waveform of the previous
 stage.

getLSMFileFromSeries(int) - Method in class loci.formats.in.ZeissLSMReader
 
getLUT(IndexColorModel) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

Gets the LUT from the IndexColorModel as an two-dimensional
  byte array.

getLUT() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

Return the LUT.

getLutNames() - Method in class loci.formats.in.LeicaHandler
 
getLutUpdateMode() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMagnification(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getMagnification() - Method in class loci.formats.in.ND2Handler
 
getMagnification() - Method in class loci.formats.in.PrairieMetadata.Frame

Extracts the magnification from the objective lens string.

getMagnification() - Method in class loci.formats.in.SVSReader
 
getMagnitudes() - Method in class loci.formats.in.IM3Reader.Spectrum
 
getMainDefDecompType() - Method in class jj2000.j2k.wavelet.WTDecompSpec

Returns the main default decomposition type.

getMainDefLevels() - Method in class jj2000.j2k.wavelet.WTDecompSpec

Returns the main default decomposition number of levels.

getMap() - Method in class loci.formats.tools.AmiraParameters
 
getMappedBuffer(int) - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream

Returns a MappedByteBuffer which memory maps
 at least from the channel position corresponding to the
 current stream position to len bytes beyond.

getMarker(String) - Method in class loci.formats.FormatReader

Retrieves an Marker enumeration
 value for the given String.

getMask() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMaskArray() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMax() - Method in class jj2000.j2k.IntegerSpec

Get the maximum value of each tile-component

getMax() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMaxAvailableBytes() - Method in class jj2000.j2k.codestream.writer.CodestreamWriter

Returns the number of bytes remaining available in the bit stream.

getMaxAvailableBytes() - Method in class jj2000.j2k.codestream.writer.FileCodestreamWriter

Returns the number of bytes remaining available in the bit stream.

getMaxBitDepth() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getMaxCBlkHeight() - Method in class jj2000.j2k.entropy.CBlkSizeSpec

Returns the maximum code-block's height

getMaxCBlkWidth() - Method in class jj2000.j2k.entropy.CBlkSizeSpec

Returns the maximum code-block's width

getMaxCompHeight() - Method in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
getMaxCompImgHeight() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Return the maximum height among all components

getMaxCompImgWidth() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Return the maximum width among all components

getMaxCompWidth() - Method in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
getMaxFieldCount(Integer) - Static method in class loci.formats.FormatTools
 
getMaximumSize() - Method in class loci.formats.gui.CacheIndicator
 
getMaximumSize() - Method in class loci.formats.gui.DataConverter.RowPanel
 
getMaxInComp(int) - Method in class jj2000.j2k.IntegerSpec

Get the maximum value of each tile for specified component

getMaxInTile(int) - Method in class jj2000.j2k.IntegerSpec

Get the maximum value of each component in specified tile

getMaxMagBits(int) - Method in class jj2000.j2k.quantization.quantizer.Quantizer

Returns the maximum number of magnitude bits in any subband in the
 current tile.

getMaxMagBits(int) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer

Returns the maximum number of magnitude bits in any subband of the
 current tile.

getMaxMagBitsDerived(Subband, int, int) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer

Returns the maximum number of magnitude bits in any subband in the
 given tile-component if derived quantization is used

getMaxMagBitsExpounded(Subband, int, int) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer

Returns the maximum number of magnitude bits in any subband in the
 given tile-component if expounded quantization is used

getMaxMagBitsRev(Subband, int) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer

Returns the maximum number of magnitude bits in any subband of the
 current tile if reversible quantization is used

getMaxThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMaxTileX() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the horizontal index of the rightmost column of tiles.

getMaxTileX() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
getMaxTileY() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the vertical index of the bottom row of tiles.

getMaxTileY() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
getMaxValue() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
getMaxValue() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getMaxX() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the X coordinate of the column immediatetely to the
 right of the rightmost column of the image.

getMaxY() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the Y coordinate of the row immediately below the
 bottom row of the image.

getMCUHeight(int) - Static method in class org.libjpegturbo.turbojpeg.TJ

Returns the MCU block height for the given level of chrominance
 subsampling.

getMCUWidth(int) - Static method in class org.libjpegturbo.turbojpeg.TJ

Returns the MCU block width for the given level of chrominance
 subsampling.

getMDBFile(String) - Method in class loci.formats.in.ZeissLSMReader
 
getMeasurementID() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getMeasurementName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getMeasurementTime() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getMedium(String) - Method in class loci.formats.FormatReader

Retrieves an Medium enumeration
 value for the given String.

getMember(String) - Method in interface loci.formats.services.JHDFService

Retrieves the all members of a group.

getMember(String) - Method in class loci.formats.services.JHDFServiceImpl
 
getMemoFile(String) - Method in class loci.formats.Memoizer

Constructs a File object from id string.

getMemoryUsage() - Method in class loci.plugins.in.ImportProcess

Gets a projection of required memory in bytes.

getMessage() - Method in enum loci.plugins.in.ImportStep
 
getMetadata() - Method in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Returns the current IIOMetadata object.

getMetadata() - Method in class loci.formats.in.ND2Handler
 
getMetadataLevel() - Method in class loci.formats.in.DefaultMetadataOptions
 
getMetadataLevel() - Method in class loci.formats.in.DynamicMetadataOptions
 
getMetadataLevel() - Method in interface loci.formats.in.MetadataOptions

Get the configured metadata level.

getMetadataOptions() - Method in class loci.formats.DelegateReader
 
getMetadataOptions() - Method in class loci.formats.FormatHandler
 
getMetadataOptions() - Method in class loci.formats.ImageReader
 
getMetadataOptions() - Method in class loci.formats.ImageWriter
 
getMetadataOptions() - Method in interface loci.formats.IMetadataConfigurable
 
getMetadataOptions() - Method in class loci.formats.ReaderWrapper
 
getMetadataOptions() - Method in class loci.formats.WriterWrapper
 
getMetadataRetrieve() - Method in class loci.formats.FormatWriter
 
getMetadataRetrieve() - Method in interface loci.formats.IFormatWriter

Retrieves the current metadata retrieval object for this writer.

getMetadataRetrieve() - Method in class loci.formats.ImageWriter
 
getMetadataRetrieve() - Method in class loci.formats.WriterWrapper
 
getMetadataRoot(String) - Method in class loci.formats.in.LIFReader
 
getMetadataStore() - Method in class loci.formats.FileStitcher
 
getMetadataStore() - Method in class loci.formats.FormatReader
 
getMetadataStore() - Method in interface loci.formats.IFormatReader

Retrieves the current metadata store for this reader.

getMetadataStore() - Method in class loci.formats.ImageReader
 
getMetadataStore() - Method in class loci.formats.in.FilePatternReader
 
getMetadataStore() - Method in class loci.formats.Memoizer
 
getMetadataStore() - Method in class loci.formats.ReaderWrapper
 
getMetadataStoreForConversion() - Method in class loci.formats.in.OMETiffReader

Deprecated.
Use the general FormatReader.getMetadataStore() method.


getMetadataStoreForDisplay() - Method in class loci.formats.in.OMETiffReader

Deprecated.
Use the general FormatReader.getMetadataStore() method.


getMetadataStoreRoot() - Method in class loci.formats.FileStitcher
 
getMetadataStoreRoot() - Method in class loci.formats.FormatReader
 
getMetadataStoreRoot() - Method in interface loci.formats.IFormatReader

Retrieves the current metadata store's root object.

getMetadataStoreRoot() - Method in class loci.formats.ImageReader
 
getMetadataStoreRoot() - Method in class loci.formats.in.FilePatternReader
 
getMetadataStoreRoot() - Method in class loci.formats.ReaderWrapper
 
getMetadataString(String) - Method in class loci.plugins.in.ImporterMetadata

Returns a string with each key/value pair on its own line.

getMetadataType() - Method in enum loci.formats.tiff.PhotoInterp

Retrieves the metadata type of the photometric interpretation.

getMetadataValue(String) - Method in class loci.formats.FormatReader
 
getMetadataValue(String) - Method in interface loci.formats.IFormatReader

Obtains the specified metadata field's value for the current file.

getMetadataValue(String) - Method in class loci.formats.ImageReader
 
getMetadataValue(String) - Method in class loci.formats.in.FilePatternReader
 
getMetadataValue(String) - Method in class loci.formats.ReaderWrapper
 
getMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
getMethod() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox

Returns the method to define the color space.

getMethodForMQLengthCalc() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets methodForMQLengthCalc

getMethodForMQTermination() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets methodForMQTermination

getMethodStack() - Method in class loci.plugins.util.BFVirtualStack
 
getMethodStack() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMicrobeamManipulationType(String) - Method in class loci.formats.FormatReader

Retrieves an MicrobeamManipulationType
 enumeration value for the given String.

getMicronsPerPixelX() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the microns per pixel along X for this Frame.

getMicronsPerPixelY() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the microns per pixel along Y for this Frame.

getMicroscopeType(String) - Method in class loci.formats.FormatReader

Retrieves an MicroscopeType enumeration
 value for the given String.

getMin() - Method in class jj2000.j2k.IntegerSpec

Get the minimum value of each tile-component

getMin() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMinimumSize() - Method in class loci.formats.gui.CacheIndicator
 
getMinInComp(int) - Method in class jj2000.j2k.IntegerSpec

Get the minimum value of each tile for specified component

getMinInTile(int) - Method in class jj2000.j2k.IntegerSpec

Get the minimum value of each component in specified tile

getMinMaxCalculator() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getMinMaxStore() - Method in class loci.formats.MinMaxCalculator

Retrieves the current active min-max store for the calculator.

getMinorVersion() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox

Returns the minor version of this file type box.

getMinThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMinTileX() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the horizontal index of the leftmost column of tiles.

getMinTileX() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
getMinTileX() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getMinTileY() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the vertical index of the uppermost row of tiles.

getMinTileY() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
getMinTileY() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getMinX() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the X coordinate of the leftmost column of the image.

getMinX() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets minX

getMinX() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getMinY() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the X coordinate of the uppermost row of the image.

getMinY() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets minY

getMinY() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getModalities() - Method in class loci.formats.in.ND2Handler
 
getModality(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getModuloAlong(OMEXMLMetadata, String, int) - Method in class loci.formats.services.OMEXMLServiceImpl

Create a Modulo corresponding to the given ModuloAlong* tag.

getModuloAlongC(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService

Retrieve the ModuloAlongC annotation in the given Image in the given
 OME-XML metadata object.

getModuloAlongC(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getModuloAlongT(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService

Retrieve the ModuloAlongT annotation in the given Image in the given
 OME-XML metadata object.

getModuloAlongT(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getModuloAlongZ(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService

Retrieve the ModuloAlongZ annotation in the given Image in the given
 OME-XML metadata object.

getModuloAlongZ(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getModuloC() - Method in class loci.formats.FormatReader
 
getModuloC() - Method in interface loci.formats.IFormatReader
 
getModuloC() - Method in class loci.formats.ImageReader
 
getModuloC() - Method in class loci.formats.in.FilePatternReader
 
getModuloC() - Method in class loci.formats.ReaderWrapper
 
getModuloT() - Method in class loci.formats.FormatReader
 
getModuloT() - Method in interface loci.formats.IFormatReader
 
getModuloT() - Method in class loci.formats.ImageReader
 
getModuloT() - Method in class loci.formats.in.FilePatternReader
 
getModuloT() - Method in class loci.formats.ReaderWrapper
 
getModuloZ() - Method in class loci.formats.FormatReader
 
getModuloZ() - Method in interface loci.formats.IFormatReader
 
getModuloZ() - Method in class loci.formats.ImageReader
 
getModuloZ() - Method in class loci.formats.in.FilePatternReader
 
getModuloZ() - Method in class loci.formats.ReaderWrapper
 
getMontage(int) - Method in class loci.formats.in.FluoviewReader
 
getMsgLogger() - Static method in class jj2000.j2k.util.FacilityManager

Returns the MsgLogger registered with the current thread (the
 thread that calls this method).

getMsgLogger(Thread) - Static method in class jj2000.j2k.util.FacilityManager

Returns the MsgLogger registered with the thread 't' (the thread
 that calls this method).

getMustGroupInfo() - Method in class loci.plugins.in.ImporterOptions
 
getNA(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getName() - Method in class com.sun.media.imageio.plugins.tiff.TIFFTag

Returns the name of the tag, as it will appear in image metadata.

getName(int) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Returns the XML tag name defined in JP2 XML xsd/dtd for the box
  with the provided type.

getName() - Method in enum loci.formats.codec.JPEG2000BoxType

Returns the name of the box type.

getName() - Method in enum loci.formats.codec.JPEG2000SegmentMarker

Returns the name of the segment marker.

getName(int) - Method in class loci.formats.gui.TwoChannelColorSpace
 
getName() - Method in enum loci.formats.in.BaseZeissReader.Charset
 
getName() - Method in class loci.formats.in.IM3Reader.Spectrum
 
getName(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getName() - Method in enum loci.formats.tiff.PhotoInterp

Retrieves the given name of the photometric interpretation.

getNamingConvention(String) - Method in class loci.formats.FormatReader

Retrieves an NamingConvention enumeration
 value for the given String.

getNativeDataType() - Method in class loci.formats.ChannelFiller
 
getNativeDataType() - Method in class loci.formats.ChannelMerger
 
getNativeDataType() - Method in class loci.formats.ChannelSeparator
 
getNativeDataType() - Method in class loci.formats.FormatHandler
 
getNativeDataType() - Method in interface loci.formats.IFormatHandler

Returns the native data type of image planes for this reader, as returned
 by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object).

getNativeDataType() - Method in class loci.formats.ImageReader
 
getNativeDataType() - Method in class loci.formats.ImageWriter
 
getNativeDataType() - Method in class loci.formats.in.BIFormatReader
 
getNativeDataType() - Method in class loci.formats.in.FilePatternReader
 
getNativeDataType() - Method in class loci.formats.in.TextReader
 
getNativeDataType() - Method in class loci.formats.MinMaxCalculator
 
getNativeDataType() - Method in class loci.formats.out.ImageIOWriter
 
getNativeDataType() - Method in class loci.formats.out.LegacyQTWriter
 
getNativeDataType() - Method in class loci.formats.ReaderWrapper
 
getNativeDataType() - Method in class loci.formats.TileStitcher
 
getNativeDataType() - Method in class loci.formats.WriterWrapper
 
getNativeDataType() - Method in class loci.plugins.util.ImageProcessorReader
 
getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Creates an IIOMetadataNode from this
  box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox

Creates an IIOMetadataNode from this channel definition
  box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox

Creates an IIOMetadataNode from this color specification
  box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox

Creates an IIOMetadataNode from this component mapping
  box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox

Creates an IIOMetadataNode from this data entry URL
  box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox

Creates an IIOMetadataNode from this file type box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Creates an IIOMetadataNode from this image header box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

creates an IIOMetadataNode from this palette box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox

Creates an IIOMetadataNode from this resolution
  box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.SignatureBox

Creates an IIOMetadataNode from this signature
  box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDBox

Creates an IIOMetadataNode from this UUID
  box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDListBox

Creates an IIOMetadataNode from this UUID list
  box.

getNativeNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.XMLBox

Creates an IIOMetadataNode from this XML
  box.

getNativeNodeForSimpleBox() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Creates an IIOMetadataNode from this
  box.

getNativeTree() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getNativeTree() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getNativeTree() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getNativeTree() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getNativeTree() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getNativeTree() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getNativeTree() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
getNChannels() - Method in class loci.plugins.util.RecordedImageProcessor
 
getNewCOC() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a new instance of COC

getNewCOD() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a new instance of COD

getNewCOM() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a new instance of COM

getNewCRG() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a new instance of CRG

getNewPOC() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a new instance of POC

getNewQCC() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a new instance of QCC

getNewQCD() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a new instance of QCD

getNewRGN() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a new instance of RGN

getNewSIZ() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a new instance of SIZ

getNewSOT() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns a new instance of SOT

getNextChangingElement(int, boolean, int[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
getNextCode() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
getNextCode() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
getNextCodeBlock(int, CBlkRateDistStats) - Method in interface jj2000.j2k.entropy.encoder.CodedCBlkDataSrcEnc

Returns the next coded code-block in the current tile for the specified
 component, as a copy (see below).

getNextCodeBlock(int, CBlkRateDistStats) - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Returns the next coded code-block in the current tile for the specified
 component, as a copy (see below).

getNextCodeBlock(int, CBlkWTData) - Method in interface jj2000.j2k.quantization.quantizer.CBlkQuantDataSrcEnc

Returns the next code-block in the current tile for the specified
 component, as a copy (see below).

getNextCodeBlock(int, CBlkWTData) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer

Returns the next code-block in the current tile for the specified
 component, as a copy (see below).

getNextCodeBlock(int, CBlkWTData) - Method in class jj2000.j2k.roi.encoder.ROIScaler

This function gets a datablk from the entropy coder.

getNextCodeBlock(int, CBlkWTData) - Method in interface jj2000.j2k.wavelet.analysis.CBlkWTDataSrc

Returns the next code-block in the current tile for the specified
 component, as a copy (see below).

getNextCodeBlock(int, CBlkWTData) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the next code-block in the current tile for the specified
 component, as a copy (see below).

getNextInternCodeBlock(int, CBlkWTData) - Method in interface jj2000.j2k.quantization.quantizer.CBlkQuantDataSrcEnc

Returns the next code-block in the current tile for the specified
 component.

getNextInternCodeBlock(int, CBlkWTData) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer

Returns the next code-block in the current tile for the specified
 component.

getNextInternCodeBlock(int, CBlkWTData) - Method in class jj2000.j2k.roi.encoder.ROIScaler

This function gets a datablk from the entropy coder.

getNextInternCodeBlock(int, CBlkWTData) - Method in interface jj2000.j2k.wavelet.analysis.CBlkWTDataSrc

Returns the next code-block in the current tile for the specified
 component.

getNextInternCodeBlock(int, CBlkWTData) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the next code-block in the current tile for the specified
 component.

getNextLine(List<String>) - Method in class loci.formats.in.TextReader
 
getNextOffset(long) - Method in class loci.formats.tiff.TiffParser

Read a file offset.

getNextResLevel() - Method in class jj2000.j2k.wavelet.Subband

Returns the first leaf subband element in the next higher resolution
 level.

getNextSibling() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getNextSubband(int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the next subband that will be used to get the next code-block
 to return by the getNext[Intern]CodeBlock method.

getNextTag(RandomAccessInputStream) - Method in class loci.formats.in.DicomReader
 
getNextTag(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
 
getNodeFromTree(IIOMetadataNode, String, String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getNodeName(TIFFField) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getNodes(Element, String) - Method in class loci.formats.in.LIFReader
 
getNomRangeBits(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the number of bits corresponding to the nominal range of the
 data in the specified component.

getNomRangeBits(int) - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Returns the number of bits, referred to as the "range bits",
 corresponding to the nominal range of the data in the specified
 component and in the current tile.

getNomRangeBits(int) - Method in interface jj2000.j2k.image.ImgData

Returns the number of bits, referred to as the "range bits",
 corresponding to the nominal range of the image data in the specified
 component.

getNomRangeBits(int) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the number of bits, referred to as the "range bits",
 corresponding to the nominal range of the image data in the specified
 component.

getNomRangeBits(int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the number of bits, referred to as the "range bits",
 corresponding to the nominal range of the data in the specified
 component.

getNomRangeBits(int) - Method in class jj2000.j2k.image.input.ImgReaderPGM

Returns the number of bits corresponding to the nominal range of the
 data in the specified component.

getNomRangeBits(int) - Method in class jj2000.j2k.image.invcomptransf.InvCompTransf

Returns the number of bits, referred to as the "range bits",
 corresponding to the nominal range of the data in the specified
 component.

getNomRangeBits(int) - Method in class jj2000.j2k.quantization.dequantizer.Dequantizer

Returns the number of bits, referred to as the "range bits",
 corresponding to the nominal range of the data in the specified
 component.

getNomRangeBits(int) - Method in interface jj2000.j2k.wavelet.synthesis.CBlkWTDataSrcDec

Returns the number of bits, referred to as the "range bits",
 corresponding to the nominal range of the data in the specified
 component.

getNomRangeBits(int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTFull

Returns the number of bits, referred to as the "range bits",
 corresponding to the nominal range of the data in the specified
 component.

getNomTileHeight() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getNomTileHeight() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the nominal tile height

getNomTileHeight() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the nominal width of the tiles in the reference grid.

getNomTileHeight() - Method in interface jj2000.j2k.image.ImgData

Returns the nominal tiles height

getNomTileHeight() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the nominal tiles height

getNomTileHeight() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the nominal tiles height

getNomTileHeight() - Method in class jj2000.j2k.image.input.ImgReader

Returns the nominal tiles height

getNomTileHeight() - Method in class jj2000.j2k.image.Tiler

Returns the nominal width of the tiles in the reference grid.

getNomTileHeight() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the nominal height of tiles

getNomTileHeight() - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the nominal tiles height

getNomTileHeight() - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the nominal tiles height

getNomTileWidth() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getNomTileWidth() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the nominal tile width

getNomTileWidth() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the nominal width of the tiles in the reference grid.

getNomTileWidth() - Method in interface jj2000.j2k.image.ImgData

Returns the nominal tiles width

getNomTileWidth() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the nominal tiles width

getNomTileWidth() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the nominal tiles width

getNomTileWidth() - Method in class jj2000.j2k.image.input.ImgReader

Returns the nominal tiles width

getNomTileWidth() - Method in class jj2000.j2k.image.Tiler

Returns the nominal width of the tiles in the reference grid.

getNomTileWidth() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the nominal width of tiles

getNomTileWidth() - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the nominal tiles width

getNomTileWidth() - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the nominal tiles width

getNonThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser

Returns non-thumbnail IFDs.

getNOptPoints() - Method in class jj2000.j2k.entropy.encoder.LayersInfo

Returns the number of layers to optimize, or optimization points, as
 specified by this object.

getNoROIDescaling() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava

Gets noROIDescaling

getNoWlzMsg() - Method in interface loci.formats.services.WlzService

Gets the text string for when Woolz has not been found.

getNoWlzMsg() - Method in class loci.formats.services.WlzServiceImpl
 
getNum() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor

Returns numerator

getNumBands() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getNumber() - Method in class com.sun.media.imageio.plugins.tiff.TIFFTag

Returns the integer used to represent the tag.

getNumber(String) - Method in class loci.formats.NumberFilter

Gets numbers filling the asterisk positions.

getNumBits(int) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter

The number of bits represented by the value which should be a
 legal length for a color table.

getNumBits(int) - Static method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
getNumBytes(int) - Method in class loci.formats.in.GatanReader
 
getNumCodedBytes() - Method in class jj2000.j2k.entropy.encoder.MQCoder

Returns the number of bytes that are necessary from the compressed
 output stream to decode all the symbols that have been coded this
 far.

getNumCOM() - Method in class jj2000.j2k.codestream.HeaderInfo

Returns the number of found COM marker segments

getNumComp() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

Return the number of color components.

getNumComponents() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Returns the number of image components.

getNumComponents() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets the number of components

getNumComponents() - Method in class loci.formats.gui.TwoChannelColorSpace
 
getNumComps() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the number of components in the image.

getNumComps() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the number of components in the image.

getNumComps() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the number of components in the image.

getNumComps() - Method in interface jj2000.j2k.image.ImgData

Returns the number of components in the image.

getNumComps() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the number of components in the image.

getNumComps() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the number of components in the image.

getNumComps() - Method in class jj2000.j2k.image.input.ImgReader

Returns the number of components in the image.

getNumComps() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the number of components in the image.

getNumComps() - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the number of components in the image.

getNumComps() - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the number of components in the image.

getNumCtxts() - Method in class jj2000.j2k.entropy.decoder.MQDecoder

Returns the number of contexts in the arithmetic coder.

getNumCtxts() - Method in class jj2000.j2k.entropy.encoder.MQCoder

Returns the number of contexts in the arithmetic coder.

getNumDecompositionLevels() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Gets numDecompositionLevels.

getNumEntries() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

Return the number of palette entries.

getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record

Get the # of boolean values in this record

getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record

Get the # of floating-point values in this record

getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.IntIM3Record

Get the # of integer values in this record

getNumerator() - Method in class loci.formats.tiff.TiffRational

Gets this number's numerator.

getNumericalAperture() - Method in class loci.formats.in.ND2Handler
 
getNumericFields(GenericDialog) - Method in class loci.plugins.in.ColorDialog
 
getNumericFields(GenericDialog) - Static method in class loci.plugins.util.WindowTools
 
getNumFoundMarkSeg() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the number of found marker segments in the current header.

getNumGuardBits() - Method in class jj2000.j2k.codestream.HeaderInfo.QCC
 
getNumGuardBits() - Method in class jj2000.j2k.codestream.HeaderInfo.QCD
 
getNumGuardBits(int, int) - Method in class jj2000.j2k.quantization.quantizer.Quantizer

Returns the number of guard bits used by this quantizer in the
 given tile-component.

getNumGuardBits(int, int) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer

Returns the number of guard bits used by this quantizer in the given
 tile-component.

getNumImages() - Method in class com.sun.media.imageio.stream.RawImageInputStream

Retrieves the number of images in the ImageInputStream.

getNumImages(boolean) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

Overrides the method defined in the superclass.

getNumImages(boolean) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

Overrides the method defined in the superclass.

getNumImages(boolean) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
getNumImages(boolean) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

Overrides the method defined in the superclass.

getNumImages(boolean) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader

Overrides the method defined in the superclass.

getNumImages(boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getNumImages(boolean) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader

Overrides the method defined in the superclass.

getNumLayers() - Method in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

Returns the number of layers that are actually generated.

getNumPrecinct(int, int) - Method in class jj2000.j2k.codestream.reader.PktDecoder

Gets the number of precincts in a given component and resolution level.

getNumSeries() - Method in class loci.formats.in.LegacyND2Reader
 
getNumThumbnails(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getNumTIFFFields() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Returns the number of TIFFFields in this directory.

getNumTileParts(int) - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Returns the number of tile-part found for a given tile

getNumTiles() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets the number of tiles

getNumTiles(Point) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the number of tiles in the horizontal and vertical
 directions.

getNumTiles() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the total number of tiles in the image.

getNumTiles() - Method in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
getNumTiles(Point) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the number of tiles in the horizontal and vertical directions.

getNumTiles() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the total number of tiles in the image.

getNumTiles() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Return the number of tiles in the image

getNumTiles(Point) - Method in interface jj2000.j2k.image.ImgData

Returns the number of tiles in the horizontal and vertical directions.

getNumTiles() - Method in interface jj2000.j2k.image.ImgData

Returns the total number of tiles in the image.

getNumTiles(Point) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the number of tiles in the horizontal and vertical directions.

getNumTiles() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the total number of tiles in the image.

getNumTiles(Point) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the number of tiles in the horizontal and vertical
 directions.

getNumTiles() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the total number of tiles in the image.

getNumTiles(Point) - Method in class jj2000.j2k.image.input.ImgReader

Returns the number of tiles in the horizontal and vertical
 directions.

getNumTiles() - Method in class jj2000.j2k.image.input.ImgReader

Returns the total number of tiles in the image.

getNumTiles(Point) - Method in class jj2000.j2k.image.Tiler

Returns the number of tiles in the horizontal and vertical directions.

getNumTiles() - Method in class jj2000.j2k.image.Tiler

Returns the total number of tiles in the image.

getNumTiles(Point) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the number of tiles in the horizontal and vertical directions.

getNumTiles() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the total number of tiles in the image.

getNumTiles(Point) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the number of tiles in the horizontal and vertical directions.

getNumTiles() - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the total number of tiles in the image.

getNumTiles(Point) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the number of tiles in the horizontal and vertical directions.

getNumTiles() - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the total number of tiles in the image.

getNumXTiles() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the number of tiles along the tile grid in the
 horizontal direction.

getNumXTiles() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getNumXTiles() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getNumYTiles() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the number of tiles along the tile grid in the vertical
 direction.

getNumYTiles() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getNumYTiles() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getObject(int) - Method in class loci.formats.cache.ByteArraySource
 
getObject(int[]) - Method in class loci.formats.cache.Cache

Gets the cached object at the given dimensional position.

getObject(int) - Method in class loci.formats.cache.CacheSource
 
getObject(int) - Method in interface loci.formats.cache.ICacheSource

Get the object corresponding to the given index.

getObject(int) - Method in class loci.formats.gui.BufferedImageSource
 
getObject(int) - Method in class loci.plugins.util.ImageProcessorSource
 
getObjectArrayMaxLength(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectArrayMinLength(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectClass(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectCount() - Method in class loci.formats.cache.CacheSource
 
getObjectCount() - Method in interface loci.formats.cache.ICacheSource

Get the total number of objects that this source can retrieve.

getObjectCount() - Method in class loci.formats.gui.BufferedImageSource
 
getObjectCount() - Method in class loci.plugins.util.ImageProcessorSource
 
getObjectDefaultValue(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectEnumerations(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectiveLens() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the objective lens string for this Frame.

getObjectiveLensNA() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the numerical aperture of the lens for this Frame.

getObjectiveManufacturer() - Method in class loci.formats.in.PrairieMetadata.Frame

Extracts the objective manufacturer from the objective lens string.

getObjectiveModel() - Method in class loci.formats.in.ND2Handler
 
getObjectiveName(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getObjectMaxValue(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectMinValue(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectValue(Node) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getObjectValueType(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getOffLastROIPkt() - Method in class jj2000.j2k.codestream.writer.CodestreamWriter

Gives the offset of the end of last packet containing ROI information

getOffLastROIPkt() - Method in class jj2000.j2k.codestream.writer.FileCodestreamWriter

Gives the offset of the end of last packet containing ROI information

getOffset(int) - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the cth offset for this Frame.

getOMEMetadata(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService

Returns a OMEXMLMetadata object with the same
 contents as the given MetadataRetrieve, converting it if necessary.

getOMEMetadata(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getOMEMetadata() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getOMEXML(String) - Method in class loci.formats.out.OMETiffWriter
 
getOMEXML(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService

Extracts an OME-XML metadata string from the given metadata object,
 by converting to an OME-XML metadata object if necessary.

getOMEXML(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getOMEXML() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getOmeXmlMetadata() - Method in class loci.formats.in.FakeReader
 
getOmeXmlService() - Method in class loci.formats.in.FakeReader
 
getOMEXMLVersion(Object) - Method in interface loci.formats.services.OMEXMLService

Gets the schema version for the given OME-XML metadata or root object
 (e.g., "2007-06" or "2003-FC").

getOMEXMLVersion(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getOnDemandStripOffsets() - Method in class loci.formats.tiff.IFD
 
getOpenAllSeriesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getOpticalZoom() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the optical zoom associated with this Frame.

getOptimalTileHeight() - Method in class loci.formats.DelegateReader
 
getOptimalTileHeight() - Method in class loci.formats.FormatReader
 
getOptimalTileHeight() - Method in interface loci.formats.IFormatReader

Returns the optimal sub-image height for use with openBytes.

getOptimalTileHeight() - Method in class loci.formats.ImageReader
 
getOptimalTileHeight() - Method in class loci.formats.in.AFIReader
 
getOptimalTileHeight() - Method in class loci.formats.in.AmiraReader
 
getOptimalTileHeight() - Method in class loci.formats.in.APLReader
 
getOptimalTileHeight() - Method in class loci.formats.in.BaseZeissReader
 
getOptimalTileHeight() - Method in class loci.formats.in.BDReader
 
getOptimalTileHeight() - Method in class loci.formats.in.BioRadReader
 
getOptimalTileHeight() - Method in class loci.formats.in.CellH5Reader
 
getOptimalTileHeight() - Method in class loci.formats.in.CellSensReader
 
getOptimalTileHeight() - Method in class loci.formats.in.EPSReader
 
getOptimalTileHeight() - Method in class loci.formats.in.FilePatternReader
 
getOptimalTileHeight() - Method in class loci.formats.in.FlexReader
 
getOptimalTileHeight() - Method in class loci.formats.in.FV1000Reader
 
getOptimalTileHeight() - Method in class loci.formats.in.HamamatsuVMSReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ImageIOReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ImarisHDFReader
 
getOptimalTileHeight() - Method in class loci.formats.in.InCellReader
 
getOptimalTileHeight() - Method in class loci.formats.in.IPWReader
 
getOptimalTileHeight() - Method in class loci.formats.in.L2DReader
 
getOptimalTileHeight() - Method in class loci.formats.in.LeicaReader
 
getOptimalTileHeight() - Method in class loci.formats.in.LeicaSCNReader
 
getOptimalTileHeight() - Method in class loci.formats.in.LIFReader
 
getOptimalTileHeight() - Method in class loci.formats.in.MIASReader
 
getOptimalTileHeight() - Method in class loci.formats.in.MicromanagerReader
 
getOptimalTileHeight() - Method in class loci.formats.in.MinimalTiffReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ND2Reader
 
getOptimalTileHeight() - Method in class loci.formats.in.NDPIReader
 
getOptimalTileHeight() - Method in class loci.formats.in.NDPISReader
 
getOptimalTileHeight() - Method in class loci.formats.in.NRRDReader
 
getOptimalTileHeight() - Method in class loci.formats.in.OMETiffReader
 
getOptimalTileHeight() - Method in class loci.formats.in.OpenlabReader
 
getOptimalTileHeight() - Method in class loci.formats.in.PCIReader
 
getOptimalTileHeight() - Method in class loci.formats.in.PerkinElmerReader
 
getOptimalTileHeight() - Method in class loci.formats.in.PrairieReader
 
getOptimalTileHeight() - Method in class loci.formats.in.PyramidTiffReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ScanrReader
 
getOptimalTileHeight() - Method in class loci.formats.in.SVSReader
 
getOptimalTileHeight() - Method in class loci.formats.in.TrestleReader
 
getOptimalTileHeight() - Method in class loci.formats.in.VisitechReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ZeissCZIReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ZeissLSMReader
 
getOptimalTileHeight() - Method in class loci.formats.ReaderWrapper
 
getOptimalTileWidth() - Method in class loci.formats.DelegateReader
 
getOptimalTileWidth() - Method in class loci.formats.FormatReader
 
getOptimalTileWidth() - Method in interface loci.formats.IFormatReader

Returns the optimal sub-image width for use with openBytes.

getOptimalTileWidth() - Method in class loci.formats.ImageReader
 
getOptimalTileWidth() - Method in class loci.formats.in.AFIReader
 
getOptimalTileWidth() - Method in class loci.formats.in.APLReader
 
getOptimalTileWidth() - Method in class loci.formats.in.BDReader
 
getOptimalTileWidth() - Method in class loci.formats.in.CellSensReader
 
getOptimalTileWidth() - Method in class loci.formats.in.EPSReader
 
getOptimalTileWidth() - Method in class loci.formats.in.FilePatternReader
 
getOptimalTileWidth() - Method in class loci.formats.in.FlexReader
 
getOptimalTileWidth() - Method in class loci.formats.in.FV1000Reader
 
getOptimalTileWidth() - Method in class loci.formats.in.HamamatsuVMSReader
 
getOptimalTileWidth() - Method in class loci.formats.in.ImarisHDFReader
 
getOptimalTileWidth() - Method in class loci.formats.in.InCellReader
 
getOptimalTileWidth() - Method in class loci.formats.in.IPWReader
 
getOptimalTileWidth() - Method in class loci.formats.in.L2DReader
 
getOptimalTileWidth() - Method in class loci.formats.in.LeicaReader
 
getOptimalTileWidth() - Method in class loci.formats.in.LeicaSCNReader
 
getOptimalTileWidth() - Method in class loci.formats.in.MIASReader
 
getOptimalTileWidth() - Method in class loci.formats.in.MicromanagerReader
 
getOptimalTileWidth() - Method in class loci.formats.in.MinimalTiffReader
 
getOptimalTileWidth() - Method in class loci.formats.in.NDPIReader
 
getOptimalTileWidth() - Method in class loci.formats.in.NDPISReader
 
getOptimalTileWidth() - Method in class loci.formats.in.OMETiffReader
 
getOptimalTileWidth() - Method in class loci.formats.in.PCIReader
 
getOptimalTileWidth() - Method in class loci.formats.in.PerkinElmerReader
 
getOptimalTileWidth() - Method in class loci.formats.in.PrairieReader
 
getOptimalTileWidth() - Method in class loci.formats.in.PyramidTiffReader
 
getOptimalTileWidth() - Method in class loci.formats.in.ScanrReader
 
getOptimalTileWidth() - Method in class loci.formats.in.SVSReader
 
getOptimalTileWidth() - Method in class loci.formats.in.TrestleReader
 
getOptimalTileWidth() - Method in class loci.formats.in.ZeissCZIReader
 
getOptimalTileWidth() - Method in class loci.formats.ReaderWrapper
 
getOptimalWidth() - Method in class loci.formats.in.ZeissLSMReader
 
getOption(String) - Method in class loci.plugins.prefs.OptionsList

Gets the option with the given key.

getOptions() - Method in class loci.formats.ClassList

Gets the list of options as a map.

getOptions() - Method in class loci.plugins.in.ImportProcess
 
getOrder() - Method in class loci.formats.cache.CacheStrategy
 
getOrder() - Method in interface loci.formats.cache.ICacheStrategy

Retrieves the order in which objects should be loaded along each axis.

getOrgX() - Method in interface loci.formats.services.WlzService

Gets column origin.

getOrgX() - Method in class loci.formats.services.WlzServiceImpl
 
getOrgY() - Method in interface loci.formats.services.WlzService

Gets line origin.

getOrgY() - Method in class loci.formats.services.WlzServiceImpl
 
getOrgZ() - Method in interface loci.formats.services.WlzService

Gets plane origin.

getOrgZ() - Method in class loci.formats.services.WlzServiceImpl
 
getOrigBitDepth(int) - Method in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
getOriginalBitDepth(int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the original bitdepth of the specified component.

getOriginalIndex(int) - Method in class loci.formats.ChannelMerger

Returns the image number in the original dataset that corresponds to the
 given image number.

getOriginalIndex(int) - Method in class loci.formats.ChannelSeparator

Returns the image number in the original dataset that corresponds to the
 given image number.

getOriginalMetadata(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService

Parse any OriginalMetadata annotations from the given OME-XML metadata
 object and store them in a Hashtable.

getOriginalMetadata(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getOriginalMetadata() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.METADATA.

getOriginalOrder() - Method in class loci.formats.AxisGuesser

Gets the original dimension order.

getOriginalOrder() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getPackedBinaryData(Raster, Rectangle) - Static method in class com.sun.media.imageioimpl.common.ImageUtil

For the case of binary data (isBinary() returns
 true), return the binary data as a packed byte array.

getPackedPktHead(int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Return the packed packet headers for a given tile.

getPacketPerTilePart() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets packetPerTilePart

getPackPacketHeaderInMain() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets packPacketHeaderInMain

getPackPacketHeaderInTile() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets packPacketHeaderInTile

getParameterInfo() - Static method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the parameters that are used in this class and implementing
 classes.

getParameterInfo() - Static method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the parameters that are used in this class.

getParameterInfo() - Static method in class jj2000.j2k.codestream.writer.PktEncoder

Returns the parameters that are used in this class and implementing
 classes.

getParameterInfo() - Static method in class jj2000.j2k.entropy.decoder.EntropyDecoder

Returns the parameters that are used in this class and
 implementing classes.

getParameterInfo() - Static method in class jj2000.j2k.entropy.encoder.EntropyCoder

Returns the parameters that are used in this class and
 implementing classes.

getParameterInfo() - Static method in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

Returns the parameters that are used in this class and implementing
 classes.

getParameterInfo() - Static method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Returns the parameters that are used in this class and implementing
 classes.

getParameterInfo() - Static method in class jj2000.j2k.image.invcomptransf.InvCompTransf

Returns the parameters that are used in this class and implementing
 classes.

getParameterInfo() - Static method in class jj2000.j2k.quantization.dequantizer.Dequantizer

Returns the parameters that are used in this class and
 implementing classes.

getParameterInfo() - Static method in class jj2000.j2k.quantization.quantizer.Quantizer

Returns the parameters that are used in this class and implementing
 classes.

getParameterInfo() - Static method in class jj2000.j2k.roi.encoder.ROIScaler

Returns the parameters that are used in this class and
 implementing classes.

getParameterInfo() - Static method in class jj2000.j2k.roi.ROIDeScaler

Returns the parameters that are used in this class and implementing
 classes.

getParameterInfo() - Static method in class jj2000.j2k.wavelet.analysis.AnWTFilter

Returns the parameters that are used in this class and
 implementing classes.

getParameterInfo() - Static method in class jj2000.j2k.wavelet.analysis.ForwardWT

Returns the parameters that are used in this class and implementing
 classes.

getParent(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
getParent(String) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormat
 
getParent() - Method in class jj2000.j2k.wavelet.analysis.SubbandAn

Returns the parent of this subband.

getParent() - Method in class jj2000.j2k.wavelet.Subband

Returns the parent of this subband.

getParent() - Method in class jj2000.j2k.wavelet.synthesis.SubbandSyn

Returns the parent of this subband.

getParent(int) - Method in class loci.formats.in.LeicaSCNReader
 
getParentTag() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Returns the parent TIFFTag of this directory if one
 has been defined or null otherwise.

getParsingEnabled() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava

Gets parsingEnabled

getPath(PrairieMetadata.PFile) - Method in class loci.formats.in.PrairieReader

Gets the absolute path to the filename of the given PrairieMetadata.PFile.

getPath() - Method in class loci.plugins.util.BFVirtualStack
 
getPattern() - Method in class loci.formats.FilePattern

Gets the file pattern string.

getPhotometricInterpretation() - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam

Returns the current value that will be written to the
 Photometricinterpretation tag.

getPhotometricInterpretation() - Method in class loci.formats.tiff.IFD

Retrieves the image's photometric interpretation (TIFF tag
 PhotometricInterpretation) from this IFD.

getPhysicalSize(Double, String) - Static method in class loci.formats.FormatTools
 
getPhysicalSizes() - Method in class loci.formats.in.SVSReader
 
getPhysicalSizeX(Double) - Static method in class loci.formats.FormatTools

Formats the input value for the physical size in X into a length in
 microns

getPhysicalSizeX(Double, String) - Static method in class loci.formats.FormatTools

Formats the input value for the physical size in X into a length of the
 given unit.

getPhysicalSizeX(Double, Unit<Length>) - Static method in class loci.formats.FormatTools

Formats the input value for the physical size in X into a length of the
 given unit.

getPhysicalSizeY(Double) - Static method in class loci.formats.FormatTools

Formats the input value for the physical size in Y into a length in
 microns

getPhysicalSizeY(Double, String) - Static method in class loci.formats.FormatTools

Formats the input value for the physical size in Y into a length of the
 given unit.

getPhysicalSizeY(Double, Unit<Length>) - Static method in class loci.formats.FormatTools

Formats the input value for the physical size in Y into a length of the
 given unit.

getPhysicalSizeZ(Double) - Static method in class loci.formats.FormatTools

Formats the input value for the physical size in Z into a length in
 microns.

getPhysicalSizeZ(Double, String) - Static method in class loci.formats.FormatTools

Formats the input value for the physical size in Z into a length of the
 given unit.

getPhysicalSizeZ(Double, Unit<Length>) - Static method in class loci.formats.FormatTools

Formats the input value for the physical size in Z into a length of the
 given unit.

getPictDimensions(byte[]) - Method in class loci.formats.gui.LegacyQTTools

Gets width and height for the given PICT bytes.

getPinholeSize() - Method in class loci.formats.in.ND2Handler
 
getPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixelBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools

Return a 2D array of bytes representing the image.

getPixelBytes(WritableRaster, boolean) - Static method in class loci.formats.gui.AWTImageTools

Return a 2D array of bytes representing the image.

getPixelBytes(BufferedImage, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Return a 2D array of bytes representing the image.

getPixelBytes(WritableRaster, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Return a 2D array of bytes representing the image.

getPixelCount() - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixelInterpolated(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixels(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools

Gets the image's pixel data as arrays of primitives, one per channel.

getPixels(BufferedImage, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Gets the image's pixel data as arrays of primitives, one per channel.

getPixels(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools

Gets the raster's pixel data as arrays of primitives, one per channel.

getPixels(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Gets the raster's pixel data as arrays of primitives, one per channel.

getPixels() - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixelsCopy() - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixelSize(int) - Static method in class org.libjpegturbo.turbojpeg.TJ

Returns the pixel size (in bytes) of the given pixel format.

getPixelSizeX() - Method in class loci.formats.in.MetamorphHandler
 
getPixelSizeX() - Method in class loci.formats.in.ND2Handler
 
getPixelSizeY() - Method in class loci.formats.in.MetamorphHandler
 
getPixelSizeY() - Method in class loci.formats.in.ND2Handler
 
getPixelSizeZ() - Method in class loci.formats.in.ND2Handler
 
getPixelsPerLine() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the pixels per line for this Frame.

getPixelsPhysicalSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getPixelsPhysicalSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getPixelsPhysicalSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getPixelsTimeIncrement(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getPixelString(int) - Method in class loci.formats.in.DeltavisionReader

Get a descriptive string representing the pixel type.

getPixelType() - Method in class loci.formats.FileStitcher
 
getPixelType() - Method in class loci.formats.FormatReader
 
getPixelType(String) - Method in class loci.formats.FormatReader

Retrieves an PixelType enumeration
 value for the given String.

getPixelType(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools

Gets the pixel type of the given image.

getPixelType() - Method in interface loci.formats.IFormatReader

Gets the pixel type.

getPixelType() - Method in class loci.formats.ImageReader
 
getPixelType(int) - Method in class loci.formats.in.DeltavisionReader

Get the OME pixel type from the pixel type stored in the file.

getPixelType() - Method in class loci.formats.in.FilePatternReader
 
getPixelType(int) - Method in class loci.formats.in.OBFReader
 
getPixelType() - Method in class loci.formats.ReaderWrapper
 
getPixelType() - Method in interface loci.formats.services.WlzService

Gets the image pixel type.

getPixelType() - Method in class loci.formats.services.WlzServiceImpl
 
getPixelType() - Method in class loci.formats.tiff.IFD

Retrieves the image's pixel type based on the BitsPerSample tag.

getPixelType(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getPixelTypeFromString(String) - Method in class loci.formats.in.LiFlimReader
 
getPixelTypes() - Method in class loci.formats.FormatWriter
 
getPixelTypes(String) - Method in class loci.formats.FormatWriter
 
getPixelTypes() - Method in interface loci.formats.IFormatWriter

Gets the supported pixel types.

getPixelTypes(String) - Method in interface loci.formats.IFormatWriter

Gets the supported pixel types for the given codec.

getPixelTypes() - Method in class loci.formats.ImageWriter
 
getPixelTypes(String) - Method in class loci.formats.ImageWriter
 
getPixelTypes(String) - Method in class loci.formats.out.APNGWriter
 
getPixelTypes(String) - Method in class loci.formats.out.AVIWriter
 
getPixelTypes(String) - Method in class loci.formats.out.CellH5Writer
 
getPixelTypes(String) - Method in class loci.formats.out.EPSWriter
 
getPixelTypes(String) - Method in class loci.formats.out.ICSWriter
 
getPixelTypes(String) - Method in class loci.formats.out.ImageIOWriter
 
getPixelTypes(String) - Method in class loci.formats.out.JavaWriter
 
getPixelTypes(String) - Method in class loci.formats.out.JPEG2000Writer

Overridden to return the formats supported by the writer.

getPixelTypes(String) - Method in class loci.formats.out.JPEGWriter
 
getPixelTypes(String) - Method in class loci.formats.out.OMEXMLWriter
 
getPixelTypes(String) - Method in class loci.formats.out.QTWriter
 
getPixelTypes(String) - Method in class loci.formats.out.TiffWriter
 
getPixelTypes(String) - Method in class loci.formats.out.V3DrawWriter
 
getPixelTypes(String) - Method in class loci.formats.out.WlzWriter
 
getPixelTypes() - Method in class loci.formats.WriterWrapper
 
getPixelTypes(String) - Method in class loci.formats.WriterWrapper
 
getPixelTypeString(int) - Static method in class loci.formats.FormatTools

Takes a pixel type value and gets a corresponding string representation.

getPixelValue(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getPlanarConfiguration() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getPlanarConfiguration() - Method in class loci.formats.tiff.IFD

Retrieves the image's planar configuration (TIFF tag PlanarConfiguration)
 from this IFD.

getPlane(int, int) - Method in class loci.formats.in.FV1000Reader
 
getPlane(int[]) - Method in class loci.formats.in.OpenlabReader
 
getPlaneByteOffset(int, int, int) - Method in class loci.formats.in.DeltavisionReader

Given any specific Z, W, and T of a plane, determine the absolute
 byte offset of the plane in the file.

getPlaneCount() - Method in class loci.formats.FormatWriter

Retrieve the total number of planes in the current series.

getPlaneCount(int) - Method in class loci.formats.FormatWriter

Retrieve the total number of planes in given series.

getPlaneCount() - Method in class loci.formats.out.CellH5Writer
 
getPlaneCount() - Method in class loci.formats.out.TiffWriter
 
getPlaneCount(int) - Method in class loci.formats.out.TiffWriter
 
getPlaneIndex(IFormatReader, int) - Static method in class loci.plugins.macro.LociFunctions

Finds the Plane index corresponding to the given image plane number.

getPlaneMaximum(int) - Method in class loci.formats.MinMaxCalculator

Retrieves the maximum pixel value for the specified plane.

getPlaneMinimum(int) - Method in class loci.formats.MinMaxCalculator

Retrieves the minimum pixel value for the specified plane.

getPlanePositionX(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
 
getPlanePositionY(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
 
getPlanePositionZ(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
 
getPlanes() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlaneSize(IFormatReader) - Static method in class loci.formats.FormatTools

Returns the size in bytes of a single plane.

getPlaneSize(IFormatReader, int, int) - Static method in class loci.formats.FormatTools

Returns the size in bytes of a w * h tile.

getPlanesToLoad(int) - Method in class loci.plugins.in.ImagePlusReader
 
getPlaneTimingDeltaT(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
 
getPlaneTimingExposureTime(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
 
getPlateColumns() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getPlateColumns() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlateDescription() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlateIdentifier() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlateName(String) - Method in class loci.formats.in.CellomicsReader
 
getPlateName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getPlateName() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlateRows() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getPlateRows() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlateType() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getPoints() - Method in enum loci.formats.in.BaseZeissReader.FeatureType
 
getPoints(int) - Method in class loci.formats.in.FakeReader
 
getPos() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO

Returns the stream position clamped to a maximum of
 Integer.MAX_VALUE.

getPos() - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Returns the current offset in the file

getPos() - Method in interface jj2000.j2k.io.RandomAccessIO

Returns the current position in the stream, which is the position from
 where the next byte of data would be read.

getPos() - Method in class jj2000.j2k.util.ISRandomAccessIO

Returns the current position in the stream, which is the
 position from where the next byte of data would be read.

getPos(int) - Method in class loci.formats.in.FluoviewReader
 
getPosition(int) - Method in class loci.formats.in.ZeissLSMReader
 
getPositionFromFile(String) - Method in class loci.formats.in.MIASReader

Returns an array of length 5 that contains the well, time point,
 Z and channel indices corresponding to the given analysis file.

getPositionNames() - Method in class loci.formats.in.ND2Handler
 
getPositionX() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the X stage position associated with this Frame.

getPositionY() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the Y stage position associated with this Frame.

getPositionZ() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the Z stage position associated with this Frame.

getPossible(String) - Method in class loci.plugins.prefs.OptionsList

Gets the possible values for the string option with the given key.

getPossible() - Method in class loci.plugins.prefs.StringOption

Gets the list of possible values.

getPossibleDomains(String) - Method in class loci.formats.FormatReader
 
getPossibleDomains(String) - Method in interface loci.formats.IFormatReader

Returns a list of scientific domains in which this format is used.

getPossibleDomains(String) - Method in class loci.formats.ImageReader
 
getPossibleDomains(String) - Method in class loci.formats.in.FilePatternReader
 
getPossibleDomains(String) - Method in class loci.formats.ReaderWrapper
 
getPossiblePositions() - Method in class loci.formats.cache.CacheStrategy

Gets positions to consider for possible inclusion in the cache,
 assuming a current position at the origin (0).

getPossiblePositions() - Method in class loci.formats.cache.CrosshairStrategy
 
getPossiblePositions() - Method in class loci.formats.cache.RectangleStrategy
 
getPowers() - Method in class loci.formats.in.ND2Handler
 
getPPX(int, int, int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the precinct partition width for the specified tile-component
 and (tile-component) resolution level.

getPPX(int, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the precinct partition width for the specified tile-component
 and resolution level.

getPPX(int, int, int) - Method in class jj2000.j2k.codestream.reader.PktDecoder

Returns the precinct partition width for the specified component,
 resolution level and tile.

getPPX(int, int, int) - Method in interface jj2000.j2k.entropy.encoder.CodedCBlkDataSrcEnc

Returns the width of a packet for the specified tile-
 component and resolution level.

getPPX(int, int, int) - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Returns the precinct partition width for the specified
 component, tile and resolution level.

getPPX(int, int, int) - Method in class jj2000.j2k.entropy.PrecinctSizeSpec

Returns the precinct partition width in component 'n' and tile 't' at
 resolution level 'rl'.

getPPY(int, int, int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the precinct partition height for the specified tile-component
 and (tile-component) resolution level.

getPPY(int, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the precinct partition height for the specified component, tile
 and resolution level.

getPPY(int, int, int) - Method in class jj2000.j2k.codestream.reader.PktDecoder

Returns the precinct partition height for the specified component,
 resolution level and tile.

getPPY(int, int, int) - Method in interface jj2000.j2k.entropy.encoder.CodedCBlkDataSrcEnc

Returns the height of a packet for the specified tile-
 component and resolution level.

getPPY(int, int, int) - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Returns the precinct partition height for the specified
 component, tile and resolution level.

getPPY(int, int, int) - Method in class jj2000.j2k.entropy.PrecinctSizeSpec

Returns the precinct partition height in component 'n' and tile 't' at
 resolution level 'rl'.

getPrecedence() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox

Returns Precedence.

getPrecinctPartition() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets precinctPartition

getPrecInfo(int, int, int) - Method in class jj2000.j2k.codestream.reader.PktDecoder

Get PrecInfo instance of the specified resolution level, component and
 precinct.

getPrecInfo(int, int, int, int) - Method in class jj2000.j2k.codestream.writer.PktEncoder

Returns information about a given precinct

getPref(String, Class<? extends IFormatReader>, boolean) - Static method in class loci.plugins.util.LociPrefs
 
getPreferredCompressionType(ColorModel, SampleModel) - Static method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
getPreferredCompressionType(ImageTypeSpecifier) - Static method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
getPreferredSize() - Method in class loci.formats.gui.CacheIndicator
 
getPreferredSize() - Method in class loci.formats.gui.PreviewPane
 
getPrefix() - Method in class loci.formats.FilePattern

Gets the pattern's substring that comes before any block sections.

getPrefix(int) - Method in class loci.formats.FilePattern

Gets the pattern's substring between block i-1 (or the beginning
 of the pattern, if i is 0) and block i.

getPrefix(String) - Method in class loci.formats.in.ZeissTIFFReader
 
getPrefixes() - Method in class loci.formats.FilePattern

Gets all block prefixes.

getPrefixMetadataName(String) - Method in class loci.formats.in.MicromanagerReader
 
getPreviewNameIndex(String) - Method in class loci.formats.in.FV1000Reader
 
getPreviousSibling() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getPriorities() - Method in class loci.formats.cache.CacheStrategy
 
getPriorities() - Method in interface loci.formats.cache.ICacheStrategy

Retrieves the priority for caching each axis.

getProcessor(int) - Method in class loci.plugins.util.BFVirtualStack
 
getProgressionName() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets progressionType

getProgressionType() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Gets progressionType.

getProgressionType() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets progressionType

getProgressWatch() - Static method in class jj2000.j2k.util.FacilityManager

Returns the ProgressWatch instance registered with the current
 thread (the thread that calls this method).

getProperty(String) - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Gets a property from the property set of this image.

getProperty(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getPropertyNames() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns a list of the properties recognized by this image.

getPropertyNames(String) - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns an array of Strings recognized as names by
 this property source that begin with the supplied prefix.

getPropertyNames() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getPulse(String) - Method in class loci.formats.FormatReader

Retrieves an Pulse enumeration
 value for the given String.

getQTVersion() - Method in class loci.formats.gui.LegacyQTTools

Gets the QuickTime for Java version number.

getQuantizationStep() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets quantizationStep

getQuantizationType() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets quantizationType

getQuantType() - Method in class jj2000.j2k.codestream.HeaderInfo.QCC
 
getQuantType() - Method in class jj2000.j2k.codestream.HeaderInfo.QCD
 
getQuantTypeSpec() - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer

Returns the quantization type spec object associated to the quantizer.

getQuietInfo() - Method in class loci.plugins.in.ImporterOptions
 
getRange() - Method in class loci.formats.cache.CacheStrategy
 
getRange() - Method in interface loci.formats.cache.ICacheStrategy

Retrieves the number of objects to cache along each axis.

getRasterLength(int[]) - Static method in class loci.formats.FormatTools

Computes the number of raster values for a positional array
 with the given lengths.

getRaw() - Method in class com.sun.media.imageio.plugins.pnm.PNMImageWriteParam

Returns the value of the raw parameter.

getRawImageType() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Returns an ImageTypeSpecifier describing an image
 whose underlying data array has the same format as the raw
 source pixel data.

getRawImageTypeSpecifier(int, int, int, int[], int[], int[], char[]) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

A utility method that returns an
 ImageTypeSpecifier suitable for decoding an image
 with the given parameters.

getReader(int) - Method in class loci.formats.FileStitcher.ExternalSeries
 
getReader() - Method in class loci.formats.FileStitcher

Gets the wrapped reader prototype.

getReader(int) - Method in class loci.formats.FileStitcher

Gets the reader appropriate for use with the given image plane.

getReader(int, int) - Method in class loci.formats.FileStitcher

Gets the reader that should be used with the given series and image plane.

getReader(IFormatReader, Class<? extends IFormatReader>) - Static method in class loci.formats.FormatTools

Recursively look for the first underlying reader that is an
 instance of the given class.

getReader() - Method in class loci.formats.gui.FormatFileFilter

Returns the filter's reader.

getReader(String) - Method in class loci.formats.ImageReader

Gets the reader used to open the given file.

getReader() - Method in class loci.formats.ImageReader

Gets the reader used to open the current file.

getReader(Class<? extends IFormatReader>) - Method in class loci.formats.ImageReader

Gets the file format reader instance matching the given class.

getReader(String, boolean) - Method in class loci.formats.in.CellWorxReader
 
getReader() - Method in class loci.formats.ReaderWrapper

Gets the wrapped reader.

getReader() - Method in class loci.formats.services.JAIIIOServiceImpl

Set up the JPEG-2000 image reader.

getReader() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getReader() - Method in class loci.plugins.util.BFVirtualStack
 
getReaders() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getReaders() - Method in class loci.formats.ImageReader

Gets all constituent file format readers.

getReadOutRate() - Method in class loci.formats.in.MetamorphHandler
 
getRealSTKFile(Location) - Method in class loci.formats.in.MetamorphReader

Check that the given STK file exists.

getRecordedProcessor() - Method in class loci.plugins.util.BFVirtualStack
 
getRed(int) - Method in class loci.formats.gui.Index16ColorModel
 
getRed(int) - Method in class loci.formats.gui.SignedColorModel
 
getRed(Object) - Method in class loci.formats.gui.SignedColorModel
 
getRed(int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getRed(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getRedOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ

For the given pixel format, returns the number of bytes that the red
 component is offset from the start of the pixel.

getReds() - Method in class loci.formats.gui.Index16ColorModel

Return the array of red color components.

getReducedRect(Rectangle, int, int, int, int) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

Convert a rectangle provided in the coordinate system of the JPEG2000
 reference grid to coordinates at a lower resolution level where zero
 denotes the lowest resolution level.

getRefractiveIndex() - Method in class loci.formats.in.ND2Handler
 
getRelativeTime() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the relativeTime associated with this Frame.

getReorderedIndex(IFormatReader, String, int) - Static method in class loci.formats.FormatTools

Converts index from the given dimension order to the reader's native one.

getReorderedIndex(String, String, int, int, int, int, int) - Static method in class loci.formats.FormatTools

Converts index from one dimension order to another.

getRequiredDirectories(String[]) - Method in class loci.formats.FileStitcher
 
getRequiredDirectories(String[]) - Method in class loci.formats.FormatReader
 
getRequiredDirectories(String[]) - Method in interface loci.formats.IFormatReader

Returns the number of parent directories that are important when
 processing the given list of files.

getRequiredDirectories(String[]) - Method in class loci.formats.ImageReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.BrukerReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.CellVoyagerReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.ColumbusReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.DicomReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.MIASReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.OperettaReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.ReaderWrapper
 
getResetMQ() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets resetMQ

getResolution() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageReadParam

Gets resolution.

getResolution() - Method in class loci.formats.FormatReader
 
getResolution() - Method in interface loci.formats.IFormatReader

Get the current resolution level.

getResolution() - Method in class loci.formats.ImageReader
 
getResolution() - Method in class loci.formats.in.FilePatternReader
 
getResolution() - Method in class loci.formats.ReaderWrapper
 
getResolutionCount() - Method in class loci.formats.FormatReader
 
getResolutionCount() - Method in interface loci.formats.IFormatReader

Return the number of resolutions for the current series.

getResolutionCount() - Method in class loci.formats.ImageReader
 
getResolutionCount() - Method in class loci.formats.in.FilePatternReader
 
getResolutionCount() - Method in class loci.formats.ReaderWrapper
 
getResolutionLevels() - Method in class loci.formats.in.JPEG2000MetadataParser

Returns the number of resolution levels the file JPEG 2000 data has.

getResolutionMultiplier() - Method in class loci.formats.tiff.IFD

Retrieve the value by which to multiply the X and Y resolution so that
 the resolutions are in microns per pixel.

getResolutionUnitFromComment(IFD) - Method in class loci.formats.in.BaseTiffReader

Extracts the resolution unit symbol from the comment field

getResource(String, Locale) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getRestartMarkers() - Method in interface loci.formats.services.JPEGTurboService
 
getRestartMarkers() - Method in class loci.formats.services.JPEGTurboServiceImpl
 
getResULX(int, int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the horizontal coordinate of the upper-left corner of the
 specified resolution in the given component of the current tile.

getResULX(int, int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the horizontal coordinate of the upper-left corner of the
 specified resolution in the given component of the current tile.

getResULX(int, int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the horizontal coordinate of the upper-left corner of the
 specified resolution level in the given component of the current tile.

getResULY(int, int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the vertical coordinate of the upper-left corner of the
 specified component in the given component of the current tile.

getResULY(int, int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the vertical coordinate of the upper-left corner of the
 specified resolution in the given component of the current tile.

getResULY(int, int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the vertical coordinate of the upper-left corner of the
 specified resolution in the given component of the current tile.

getRevision(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getRGB() - Method in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
getRGBChannelCount() - Method in class loci.formats.FormatReader
 
getRGBChannelCount() - Method in interface loci.formats.IFormatReader

Gets the number of channels returned with each call to openBytes.

getRGBChannelCount() - Method in class loci.formats.ImageReader
 
getRGBChannelCount() - Method in class loci.formats.in.FilePatternReader
 
getRGBChannelCount() - Method in class loci.formats.ReaderWrapper
 
getRGBChannelCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getRoi() - Method in class loci.plugins.util.RecordedImageProcessor
 
getROILen() - Method in class jj2000.j2k.codestream.writer.PktEncoder

Gives the length to read in current packet body to get all ROI
 information

getROIMask(DataBlkInt, Subband, int, int) - Method in class jj2000.j2k.roi.encoder.ArbROIMaskGenerator

This functions gets a DataBlk the size of the current code-block an
 fills this block with the ROI mask.

getROIMask(DataBlkInt, Subband, int, int) - Method in class jj2000.j2k.roi.encoder.RectROIMaskGenerator

This functions gets a DataBlk the size of the current code-block and
 fills this block with the ROI mask.

getROIMask(DataBlkInt, Subband, int, int) - Method in class jj2000.j2k.roi.encoder.ROIMaskGenerator

This functions gets a DataBlk with the size of the current code-block
 and fills it with the ROI mask.

getROIMaskGenerator() - Method in class jj2000.j2k.roi.encoder.ROIScaler

This function returns the ROI mask generator.

getROIs() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets ROIs

getROIs() - Method in class jj2000.j2k.roi.encoder.ROIMaskGenerator

This function returns the ROIs in the image

getROIs() - Method in class loci.formats.in.ND2Handler
 
getROIs() - Method in class loci.formats.in.SPEReader.SpeHeader

Method used to read and return meta data for upto 10 rectangular ROI's stored in the SPE header table

getROIsMode() - Method in class loci.plugins.in.ImporterOptions
 
getROIsModeInfo() - Method in class loci.plugins.in.ImporterOptions
 
getROIsModes() - Method in class loci.plugins.in.ImporterOptions
 
getRootIFD() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getRootName() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getRotationTransform(double) - Method in class loci.formats.FormatReader

Construct an AffineTransform corresponding to
 the given angle.

getRow() - Method in class loci.formats.in.OMEXMLReader.BinData
 
getRow(String) - Method in class loci.formats.in.ScreenReader
 
getRow(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getRowAndColumn(int) - Method in class loci.formats.in.ScreenReader
 
getRowCount(int) - Method in interface loci.formats.services.MetakitService
 
getRowCount(String) - Method in interface loci.formats.services.MetakitService
 
getRowCount(int) - Method in class loci.formats.services.MetakitServiceImpl
 
getRowCount(String) - Method in class loci.formats.services.MetakitServiceImpl
 
getRowData(String[], double[]) - Method in class loci.formats.in.TextReader

Parses numerical row data from the given tokens.

getRowData(int, String) - Method in interface loci.formats.services.MetakitService
 
getRowData(int, int) - Method in interface loci.formats.services.MetakitService
 
getRowData(int, String) - Method in class loci.formats.services.MetakitServiceImpl
 
getRowData(int, int) - Method in class loci.formats.services.MetakitServiceImpl
 
getRowsPerStrip() - Method in class loci.formats.tiff.IFD

Retrieves the number of rows per strip for image (TIFF tag RowsPerStrip)
 from this IFD.

getSample(BitBuffer, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec

Deprecated.

getSample(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
 
getSampleModel() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the SampleModel of the image.

getSampleModel() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getSampleModel() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getSamples(IFD, byte[]) - Method in class loci.formats.tiff.TiffParser
 
getSamples(IFD, byte[], int, int, long, long) - Method in class loci.formats.tiff.TiffParser
 
getSamples(IFD, byte[], int, int, long, long, int, int) - Method in class loci.formats.tiff.TiffParser
 
getSamplesPerPixel() - Method in class loci.formats.FormatWriter

Retrieve the number of samples per pixel for the current series.

getSamplesPerPixel(int) - Method in class loci.formats.FormatWriter

Retrieve the number of samples per pixel for given series.

getSamplesPerPixel() - Method in class loci.formats.tiff.IFD

Retrieves the number of samples per pixel for the image (TIFF tag
 SamplesPerPixel) from this IFD.

getScaled(int) - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor

Returns the scaled value of dimension.

getScaledHeight(int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Returns the height of the largest scaled down image that the TurboJPEG
 decompressor can generate without exceeding the desired image width and
 height.

getScaledWidth(int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Returns the width of the largest scaled down image that the TurboJPEG
 decompressor can generate without exceeding the desired image width and
 height.

getScalingFactors() - Static method in class org.libjpegturbo.turbojpeg.TJ

Returns a list of fractional scaling factors that the JPEG decompressor in
 this implementation of TurboJPEG supports.

getScanline(int) - Method in class loci.formats.codec.JPEGTileDecoder
 
getScanlinePad() - Method in class loci.formats.in.NativeND2Reader
 
getScanNames() - Method in class loci.formats.in.L2DReader

Return a list of scan names.

getScreenName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getSegmentLength() - Method in class com.sun.media.imageio.stream.StreamSegment

Returns the length of the segment.

getSequence() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the <Sequence> containing this <Frame>.

getSequence(int) - Method in class loci.formats.in.PrairieMetadata

Gets the Sequence at the given cycle.

getSequences() - Method in class loci.formats.in.PrairieMetadata

Gets all Sequences, ordered by cycle.

getSeries() - Method in class loci.formats.FileStitcher
 
getSeries() - Method in class loci.formats.FormatReader
 
getSeries() - Method in class loci.formats.FormatWriter
 
getSeries() - Method in interface loci.formats.IFormatReader

Gets the currently active series.

getSeries() - Method in interface loci.formats.IFormatWriter

Returns the current series.

getSeries() - Method in class loci.formats.ImageReader
 
getSeries() - Method in class loci.formats.ImageWriter
 
getSeries() - Method in class loci.formats.in.FilePatternReader
 
getSeries() - Method in class loci.formats.ReaderWrapper
 
getSeries() - Method in class loci.formats.WriterWrapper
 
getSeries(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSeriesCount() - Method in class loci.formats.FileStitcher
 
getSeriesCount() - Method in class loci.formats.FormatReader
 
getSeriesCount() - Method in interface loci.formats.IFormatReader

Gets the number of series in this file.

getSeriesCount() - Method in class loci.formats.ImageReader
 
getSeriesCount() - Method in class loci.formats.in.FilePatternReader
 
getSeriesCount() - Method in class loci.formats.in.ND2Handler
 
getSeriesCount() - Method in class loci.formats.ReaderWrapper
 
getSeriesCount() - Method in class loci.formats.TileStitcher
 
getSeriesCount() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getSeriesCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSeriesHashtable(int) - Method in class loci.formats.in.LeicaHandler
 
getSeriesIndex(int, int, int) - Method in class loci.formats.in.MetamorphTiffReader
 
getSeriesIndex(int, int) - Method in class loci.formats.in.ScreenReader
 
getSeriesLabel(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getSeriesMeta(String) - Method in class loci.formats.FormatReader

Gets an entry from the metadata table for the current series.

getSeriesMetadata() - Method in class loci.formats.FileStitcher
 
getSeriesMetadata() - Method in class loci.formats.FormatReader
 
getSeriesMetadata() - Method in interface loci.formats.IFormatReader

Obtains the hashtable containing metadata field/value pairs from the
 current series in the current file.

getSeriesMetadata() - Method in class loci.formats.ImageReader
 
getSeriesMetadata() - Method in class loci.formats.in.FilePatternReader
 
getSeriesMetadata() - Method in class loci.formats.ReaderWrapper
 
getSeriesMetadataValue(String) - Method in class loci.formats.FormatReader
 
getSeriesMetadataValue(String) - Method in interface loci.formats.IFormatReader

Obtains the specified metadata field's value for the current series
 in the current file.

getSeriesMetadataValue(String) - Method in class loci.formats.ImageReader
 
getSeriesMetadataValue(String) - Method in class loci.formats.in.FilePatternReader
 
getSeriesMetadataValue(String) - Method in class loci.formats.ReaderWrapper
 
getSeriesMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
getSeriesName(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.DelegateReader
 
getSeriesUsedFiles() - Method in class loci.formats.FileStitcher
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
 
getSeriesUsedFiles() - Method in class loci.formats.FormatReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
 
getSeriesUsedFiles() - Method in interface loci.formats.IFormatReader

Returns an array of filenames needed to open the current series.

getSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader

Returns an array of filenames needed to open the current series.

getSeriesUsedFiles() - Method in class loci.formats.ImageReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.AFIReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.AnalyzeReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.APLReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BDReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BioRadReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BrukerReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellomicsReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellSensReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellVoyagerReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellWorxReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ColumbusReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DeltavisionReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DicomReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FakeReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FlexReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FujiReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FV1000Reader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HamamatsuVMSReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HitachiReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ICSReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImagicReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImprovisionTiffReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.InCellReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JEOLReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JPEGReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.L2DReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LeicaReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MetamorphReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MIASReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MicromanagerReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NativeQTReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NDPISReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NiftiReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NRRDReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OMETiffReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OperettaReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PCORAWReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PDSReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PerkinElmerReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PrairieReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ScanrReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ScreenReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SlidebookTiffReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SPCReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TCSReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TiffReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TillVisionReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TrestleReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VarianFDFReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VisitechReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VolocityReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissCZIReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissLSMReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissTIFFReader
 
getSeriesUsedFiles() - Method in class loci.formats.ReaderWrapper
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
 
getService() - Method in class loci.formats.Memoizer
 
getShallowClone() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD

Returns a TIFFIFD wherein all fields from the
 BaselineTIFFTagSet are copied by value and all other
 fields copied by reference.

getShallowClone() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata

Returns a TIFFImageMetadata wherein all fields in the
 root IFD from the BaselineTIFFTagSet are copied by value
 and all other fields copied by reference.

getShape(String) - Method in interface loci.formats.services.JHDFService

Retrieves the shape of a dataset.

getShape(String) - Method in class loci.formats.services.JHDFServiceImpl
 
getShort(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader

Method used to retrieve data values for Short entries into the SPE header table

getShort(int) - Method in class loci.formats.in.SPEReader.SpeHeader

Private method used to retrieve a Short value from the SPE header

getShortArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader

Method used to retrieve data values for Short Array entries into the SPE header table

getShortElementValue(Node) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Gets its short value from an IIOMetadataNode.

getShorts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of unsigned shorts, one per channel.

getShorts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of unsigned shorts, one per channel.

getShorts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Extracts pixel data as arrays of unsigned shorts, one per channel.

getShortValue(Node) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getShowMetadataInfo() - Method in class loci.plugins.in.ImporterOptions
 
getShowOMEXMLInfo() - Method in class loci.plugins.in.ImporterOptions
 
getShowROIsInfo() - Method in class loci.plugins.in.ImporterOptions
 
getSize(int) - Static method in class jj2000.j2k.image.DataBlk

Returns the size in bits, given the data type.

getSize() - Method in class jj2000.j2k.util.ThreadPool

Returns the size of the pool.

getSize(Image) - Static method in class loci.formats.gui.AWTImageTools

Gets the width and height of the given AWT image,
 waiting for it to finish loading if necessary.

getSize() - Method in class loci.plugins.util.BFVirtualStack
 
getSizeC() - Method in class loci.formats.ChannelFiller
 
getSizeC() - Method in class loci.formats.DimensionSwapper
 
getSizeC() - Method in class loci.formats.FileStitcher
 
getSizeC() - Method in class loci.formats.FormatReader
 
getSizeC() - Method in interface loci.formats.IFormatReader

Gets the size of the C dimension.

getSizeC() - Method in class loci.formats.ImageReader
 
getSizeC() - Method in class loci.formats.in.FilePatternReader
 
getSizeC() - Method in class loci.formats.ReaderWrapper
 
getSizeC() - Method in interface loci.formats.services.WlzService

Gets number of channels.

getSizeC() - Method in class loci.formats.services.WlzServiceImpl
 
getSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSizeOfType(int) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFTag

Returns the number of bytes used to store a value of the given
 data type.

getSizeT() - Method in class loci.formats.DimensionSwapper
 
getSizeT() - Method in class loci.formats.FileStitcher
 
getSizeT() - Method in class loci.formats.FormatReader
 
getSizeT() - Method in interface loci.formats.IFormatReader

Gets the size of the T dimension.

getSizeT() - Method in class loci.formats.ImageReader
 
getSizeT() - Method in class loci.formats.in.FilePatternReader
 
getSizeT() - Method in class loci.formats.ReaderWrapper
 
getSizeT() - Method in interface loci.formats.services.WlzService

Gets number of time samples.

getSizeT() - Method in class loci.formats.services.WlzServiceImpl
 
getSizeT(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSizeX() - Method in class loci.formats.DimensionSwapper
 
getSizeX() - Method in class loci.formats.FileStitcher
 
getSizeX() - Method in class loci.formats.FormatReader
 
getSizeX() - Method in interface loci.formats.IFormatReader

Gets the size of the X dimension.

getSizeX() - Method in class loci.formats.ImageReader
 
getSizeX() - Method in class loci.formats.in.FilePatternReader
 
getSizeX() - Method in class loci.formats.ReaderWrapper
 
getSizeX() - Method in interface loci.formats.services.WlzService

Gets width in pixels/voxels.

getSizeX() - Method in class loci.formats.services.WlzServiceImpl
 
getSizeX() - Method in class loci.formats.TileStitcher
 
getSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSizeY() - Method in class loci.formats.DimensionSwapper
 
getSizeY() - Method in class loci.formats.FileStitcher
 
getSizeY() - Method in class loci.formats.FormatReader
 
getSizeY() - Method in interface loci.formats.IFormatReader

Gets the size of the Y dimension.

getSizeY() - Method in class loci.formats.ImageReader
 
getSizeY() - Method in class loci.formats.in.FilePatternReader
 
getSizeY() - Method in class loci.formats.ReaderWrapper
 
getSizeY() - Method in interface loci.formats.services.WlzService

Gets height in pixels/voxels.

getSizeY() - Method in class loci.formats.services.WlzServiceImpl
 
getSizeY() - Method in class loci.formats.TileStitcher
 
getSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSizeZ() - Method in class loci.formats.DimensionSwapper
 
getSizeZ() - Method in class loci.formats.FileStitcher
 
getSizeZ() - Method in class loci.formats.FormatReader
 
getSizeZ() - Method in interface loci.formats.IFormatReader

Gets the size of the Z dimension.

getSizeZ() - Method in class loci.formats.ImageReader
 
getSizeZ() - Method in class loci.formats.in.FilePatternReader
 
getSizeZ() - Method in class loci.formats.ReaderWrapper
 
getSizeZ() - Method in interface loci.formats.services.WlzService

Gets depth (number of x-y planes) in voxels.

getSizeZ() - Method in class loci.formats.services.WlzServiceImpl
 
getSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getslice(int) - Method in class loci.formats.in.ZeissTIFFReader
 
getSlopeFromSIndex(int) - Static method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Returns the minimum slope value associated with a summary table
 index.

getSnapshotPixels() - Method in class loci.plugins.util.RecordedImageProcessor
 
getSOP() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Gets SOP.

getSOP() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets SOP

getSource() - Method in class loci.formats.cache.Cache

Gets the cache's caching source.

getSource() - Method in class loci.formats.cache.CacheEvent

Gets the source of the cache update.

getSources() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage
 
getSources() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getSpec(int, int) - Method in class jj2000.j2k.ModuleSpec

Gets value of specified tile-component without knowing if a
 specific tile-component value has been previously entered.

getSpecificationTitle() - Static method in class com.sun.media.imageioimpl.common.PackageUtil

Return the Specification Title string for the package.

getSpecified() - Method in class jj2000.j2k.roi.MaxShiftSpec
 
getSpecified() - Method in class jj2000.j2k.StringSpec
 
getSpecifyRangesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getSpectra() - Method in class loci.formats.in.IM3Reader

If a Nuance file is a spectral library set (.csl) file,
 there is a spectral library inside that contains a profile
 of spectral bin magnitudes for each of several measured
 fluorophores (or auto fluorescence).

getSpecValType(int, int) - Method in class jj2000.j2k.ModuleSpec

Return the spec type of the given tile-component.

getSpeeds() - Method in class loci.formats.in.ND2Handler
 
getSplitChannelsInfo() - Method in class loci.plugins.in.ImporterOptions
 
getSplitFocalPlanesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getSplitTimepointsInfo() - Method in class loci.plugins.in.ImporterOptions
 
getSPWIndexes(int) - Method in class loci.formats.in.ScreenReader
 
getSrcColor(int, int) - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
 
getStackFormat() - Method in class loci.plugins.in.ImporterOptions
 
getStackFormatInfo() - Method in class loci.plugins.in.ImporterOptions
 
getStackFormats() - Method in class loci.plugins.in.ImporterOptions
 
getStackOrder() - Method in class loci.plugins.in.ImporterOptions
 
getStackOrder() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getStackOrderInfo() - Method in class loci.plugins.in.ImporterOptions
 
getStackOrders() - Method in class loci.plugins.in.ImporterOptions
 
getStackSize() - Method in class loci.formats.in.SPEReader.SpeHeader

Method used to determined the stack size of the SPE file.

getStackType(String) - Method in class loci.formats.in.CellSensReader
 
getStageLabel() - Method in class loci.formats.in.MetamorphHandler
 
getStagePosition(Double, Unit<Length>) - Static method in class loci.formats.FormatTools

Formats the input value for the stage position into a length of the given
 unit.

getStagePosition(Double, String) - Static method in class loci.formats.FormatTools

Formats the input value for the stage position into a length of the given
 unit.

getStagePositionX() - Method in class loci.formats.in.MetamorphHandler
 
getStagePositionY() - Method in class loci.formats.in.MetamorphHandler
 
getStandardChromaNode() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardChromaNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardChromaNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardChromaNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardChromaNode() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getStandardChromaNode() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardChromaNode() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
getStandardCompressionNode() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardCompressionNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardCompressionNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardCompressionNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardCompressionNode() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardDataNode() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardDataNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardDataNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardDataNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardDataNode() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getStandardDataNode() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardDataNode() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
getStandardDimensionNode() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardDimensionNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardDimensionNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardDimensionNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardDimensionNode() - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
getStandardDimensionNode() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getStandardDimensionNode() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardDimensionNode() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
getStandardDocumentNode() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardDocumentNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardDocumentNode() - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
getStandardDocumentNode() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardTextNode() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardTextNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardTextNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardTextNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardTextNode() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getStandardTextNode() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardTransparencyNode() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardTransparencyNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardTransparencyNode() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardTransparencyNode() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardTransparencyNode() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStartLevelROI() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets startLevel

getStartPos() - Method in class com.sun.media.imageio.stream.StreamSegment

Returns the starting position of the segment.

getStartX() - Method in class loci.formats.in.SPEReader.SpeROI
 
getStartY() - Method in class loci.formats.in.SPEReader.SpeROI
 
getStatistics(int, int, double, double) - Method in class loci.plugins.util.VirtualImagePlus
 
getStep() - Method in class loci.formats.FilePattern

Gets the STEP element for all blocks.

getStep() - Method in class loci.formats.FilePatternBlock

Gets the difference between consecutive elements in a range block.

getStep(int) - Static method in enum loci.plugins.in.ImportStep
 
getStep() - Method in enum loci.plugins.in.ImportStep
 
getStepSize(Hashtable<String, Object>) - Method in class loci.formats.in.MINCReader
 
getStitchTilesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getStrategy() - Method in class loci.formats.cache.Cache

Gets the cache's caching strategy.

getStream() - Method in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Returns the ImageOutputStream that will be written.

getStream(int) - Method in class loci.formats.in.VolocityReader
 
getStream() - Method in class loci.formats.in.ZeissCZIReader.Segment
 
getStream() - Method in class loci.formats.tiff.OnDemandLongArray
 
getStream() - Method in class loci.formats.tiff.TiffParser

Gets the stream from which TIFF data is being parsed.

getStream() - Method in class loci.formats.tiff.TiffSaver

Gets the stream from which TIFF data is being saved.

getStreamMetadata() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
getStreamMetadata() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getStreamMetadata() - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
getStreamMetadata() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
getStreamMetadata() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
getStreamMetadata() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getStreamMetadata(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getStreamMetadata() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getStreamPosition() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
getStreams() - Method in class loci.formats.tools.AmiraParameters
 
getStreamSegment(long, int) - Method in class com.sun.media.imageio.stream.SectorStreamSegmentMapper
 
getStreamSegment(long, int, StreamSegment) - Method in class com.sun.media.imageio.stream.SectorStreamSegmentMapper
 
getStreamSegment(long, int) - Method in interface com.sun.media.imageio.stream.StreamSegmentMapper

Returns a StreamSegment object indicating the
 location of the initial portion of a desired segment in the
 source stream.

getStreamSegment(long, int, StreamSegment) - Method in interface com.sun.media.imageio.stream.StreamSegmentMapper

Sets the values of a StreamSegment object
 indicating the location of the initial portion of a desired
 segment in the source stream.

getStreamSegment(long, int) - Method in class com.sun.media.imageio.stream.StreamSegmentMapperImpl
 
getStreamSegment(long, int, StreamSegment) - Method in class com.sun.media.imageio.stream.StreamSegmentMapperImpl
 
getString(String) - Static method in class com.sun.media.imageio.plugins.bmp.I18N
 
getString(String) - Static method in class com.sun.media.imageio.stream.I18N
 
getString(String) - Static method in class com.sun.media.imageioimpl.common.I18N
 
getString(String, String) - Static method in class com.sun.media.imageioimpl.common.I18NImpl

Returns the message string with the specified key from the
 "properties" file in the package containing the class with
 the specified name.

getString(String) - Static method in class com.sun.media.imageioimpl.plugins.bmp.I18N
 
getString(String) - Static method in class com.sun.media.imageioimpl.plugins.clib.I18N
 
getString(String) - Static method in class com.sun.media.imageioimpl.plugins.jpeg.I18N
 
getString(String) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.I18N
 
getString(String) - Static method in class com.sun.media.imageioimpl.plugins.png.I18N
 
getString(String) - Static method in class com.sun.media.imageioimpl.plugins.pnm.I18N
 
getString(String) - Static method in class com.sun.media.imageioimpl.plugins.raw.I18N
 
getString(String) - Static method in class com.sun.media.imageioimpl.plugins.tiff.I18N
 
getString(String) - Static method in class com.sun.media.imageioimpl.plugins.wbmp.I18N
 
getString(String) - Static method in class com.sun.media.jai.imageioimpl.I18N
 
getString(String) - Static method in class com.sun.media.jai.operator.I18N
 
getString(int) - Method in class loci.formats.in.LeicaReader
 
getString(boolean) - Method in class loci.formats.in.LeicaReader
 
getString(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader

Method used to retrieve data values for String entries into the SPE header table

getString(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader

Private method used to retrieve a String value from the SPE header

getString(Integer) - Method in class loci.formats.in.VolocityReader
 
getStringAttribute(Node, String, String, boolean, String[]) - Static method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
getStringElementValue(Node) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Gets its String value from an IIOMetadataNode.

getStringOption(String) - Method in class loci.plugins.prefs.OptionsList

Gets the string option with the given key.

getStringValue(Node) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStringValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
getStringWidth(String) - Method in class loci.plugins.util.RecordedImageProcessor
 
getStripByteCounts() - Method in class loci.formats.tiff.IFD

Retrieves strip byte counts for the image (TIFF tag StripByteCounts) from
 this IFD.

getStripOffsets() - Method in class loci.formats.tiff.IFD

Retrieves the strip offsets for the image (TIFF tag StripOffsets) from
 this IFD.

getStripOrTileByteCountsPosition() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD
 
getStripOrTileOffsetsPosition() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD
 
getSubband(int, int) - Method in class jj2000.j2k.wavelet.Subband

Returns a reference to the Subband element to which the specified point
 belongs.

getSubbandByIdx(int, int) - Method in class jj2000.j2k.wavelet.Subband

Returns a subband element in the tree, given its resolution level and
 subband index.

getSubbandRectROIMask(int, int) - Method in class jj2000.j2k.roi.encoder.SubbandROIMask

Returns a reference to the Subband mask element to which the specified
 point belongs.

getSubimage(BufferedImage, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Returns a subimage of the specified image.

getSubimage(byte[], byte[], int, int, int, int, int, int, int, int, boolean) - Static method in class loci.formats.ImageTools
 
getSubsamp() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Returns the level of chrominance subsampling used in the JPEG image
 associated with this decompressor instance.

getSuffix() - Method in class loci.formats.FilePattern

Gets the pattern's substring that comes after all block sections.

getSuffixes() - Method in class loci.formats.FormatHandler
 
getSuffixes() - Method in interface loci.formats.IFormatHandler

Gets the default file suffixes for this file format.

getSuffixes() - Method in class loci.formats.ImageReader
 
getSuffixes() - Method in class loci.formats.ImageWriter
 
getSuffixes() - Method in class loci.formats.ReaderWrapper
 
getSuffixes() - Method in class loci.formats.WriterWrapper
 
getSupPixelTypes() - Method in interface loci.formats.services.WlzService

Gets supported pixel types.

getSupPixelTypes() - Method in class loci.formats.services.WlzServiceImpl
 
getSupportedMetadataLevels() - Method in class loci.formats.DelegateReader
 
getSupportedMetadataLevels() - Method in class loci.formats.FormatHandler
 
getSupportedMetadataLevels() - Method in class loci.formats.ImageReader
 
getSupportedMetadataLevels() - Method in class loci.formats.ImageWriter
 
getSupportedMetadataLevels() - Method in interface loci.formats.IMetadataConfigurable
 
getSupportedMetadataLevels() - Method in class loci.formats.ReaderWrapper
 
getSupportedMetadataLevels() - Method in class loci.formats.WriterWrapper
 
getSwapDimensionsInfo() - Method in class loci.plugins.in.ImporterOptions
 
getSynHighNegSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the negative support of the high-pass synthesis
 filter.

getSynHighNegSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the negative support of the high-pass synthesis filter.

getSynHighNegSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns the negative support of the high-pass synthesis filter.

getSynHighNegSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns the negative support of the high-pass synthesis filter.

getSynHighNegSupport() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the negative support of the high-pass synthesis
 filter.

getSynHighPosSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the positive support of the high-pass synthesis
 filter.

getSynHighPosSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the positive support of the high-pass synthesis filter.

getSynHighPosSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns the positive support of the high-pass synthesis filter.

getSynHighPosSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns the positive support of the high-pass synthesis filter.

getSynHighPosSupport() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the positive support of the high-pass synthesis
 filter.

getSynLowNegSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the negative support of the low-pass synthesis
 filter.

getSynLowNegSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the negative support of the low-pass synthesis filter.

getSynLowNegSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns the negative support of the low-pass synthesis filter.

getSynLowNegSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns the negative support of the low-pass synthesis filter.

getSynLowNegSupport() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the negative support of the low-pass synthesis
 filter.

getSynLowPosSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the positive support of the low-pass synthesis
 filter.

getSynLowPosSupport() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the positive support of the low-pass synthesis filter.

getSynLowPosSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns the positive support of the low-pass synthesis filter.

getSynLowPosSupport() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns the positive support of the low-pass synthesis filter.

getSynLowPosSupport() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the positive support of the low-pass synthesis
 filter.

getSynSubbandTree(int, int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the subband tree, for the specified tile-component.

getSynSubbandTree(int, int) - Method in class jj2000.j2k.entropy.decoder.EntropyDecoder

Returns the subband tree, for the specified tile-component.

getSynSubbandTree(int, int) - Method in class jj2000.j2k.quantization.dequantizer.Dequantizer

Returns the subband tree, for the specified tile-component.

getSynSubbandTree(int, int) - Method in class jj2000.j2k.roi.ROIDeScaler

Returns the subband tree, for the specified tile-component.

getSynSubbandTree(int, int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the specified synthesis subband tree

getSynSubbandTree(int, int) - Method in interface jj2000.j2k.wavelet.synthesis.InvWTData

Returns the subband tree, for the specified tile-component.

getSynSubbandTree(int, int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the specified synthesis subband tree

getT() - Method in class loci.formats.gui.ImageViewer

Gets the T value of the currently displayed image.

getTableCount() - Method in interface loci.formats.services.MetakitService
 
getTableCount() - Method in class loci.formats.services.MetakitServiceImpl
 
getTableData(String) - Method in interface loci.formats.services.MetakitService
 
getTableData(int) - Method in interface loci.formats.services.MetakitService
 
getTableData(String) - Method in class loci.formats.services.MetakitServiceImpl
 
getTableData(int) - Method in class loci.formats.services.MetakitServiceImpl
 
getTableNames() - Method in interface loci.formats.services.MetakitService
 
getTableNames() - Method in class loci.formats.services.MetakitServiceImpl
 
getTag(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Returns the TIFFTag which has tag number equal to
 tagNumber or null if no such tag
 exists in the TIFFTagSets associated with this
 directory.

getTag() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Retrieves the tag associated with this field.

getTag(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFTagSet

Returns the TIFFTag from this set that is
 associated with the given tag number, or null if
 no tag exists for that number.

getTag(String) - Method in class com.sun.media.imageio.plugins.tiff.TIFFTagSet

Returns the TIFFTag having the given tag name, or
 null if the named tag does not belong to this tag set.

getTag(int, List) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD
 
getTag(String, List) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD
 
getTag() - Method in class loci.formats.tiff.TiffIFDEntry

Retrieves the entry's Tag value.

getTagName(int) - Method in class loci.formats.in.CellSensReader
 
getTagNames() - Method in class com.sun.media.imageio.plugins.tiff.TIFFTagSet

Retrieves an unmodifiable lexicographically increasing set of tag names.

getTagNumber() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Retrieves the tag number in the range [0, 65535].

getTagNumbers() - Method in class com.sun.media.imageio.plugins.tiff.TIFFTagSet

Retrieves an unmodifiable numerically increasing set of tag numbers.

getTags() - Method in interface loci.formats.services.EXIFService
 
getTags() - Method in class loci.formats.services.EXIFServiceImpl
 
getTagSet() - Method in class com.sun.media.imageio.plugins.tiff.TIFFTag

Returns the TIFFTagSet of which this tag is a part.

getTagSetList() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD
 
getTagSets() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Returns the TIFFTagSets of which this directory is aware.

getTargetBitrate(int) - Method in class jj2000.j2k.entropy.encoder.LayersInfo

Returns the target bitrate of the optmimization point 'n'.

getTargetNbytes() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Return the target number of read bytes.

getTargetRate() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Return the target decoding rate in bits per pixel.

getTBegin(int) - Method in class loci.plugins.in.ImporterOptions
 
getTBegin(int) - Method in class loci.plugins.in.ImportProcess
 
getTCount(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.SERIES.

getTemperature() - Method in class loci.formats.in.MetamorphHandler
 
getTemperatures() - Method in class loci.formats.in.ND2Handler
 
getTEnd(int) - Method in class loci.plugins.in.ImporterOptions
 
getTEnd(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getTerminateOnByte() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Gets terminateOnByte

getTFrames(int) - Method in class loci.formats.in.LegacyND2Reader
 
getThreadConcurrency() - Static method in class jj2000.j2k.util.NativeServices

Returns the current concurrency level.

getThreadConcurrencyN() - Static method in class jj2000.j2k.util.NativeServices

Calls the POSIX threads 'pthread_getconcurrency', or equivalent,
 function and return the result.

getThumbnailIFDs() - Method in class loci.formats.in.MinimalTiffReader

Gets the list of IFDs associated with the current TIFF's thumbnails.

getThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser

Returns thumbnail IFDs.

getThumbSizeX() - Method in class loci.formats.FileStitcher
 
getThumbSizeX() - Method in class loci.formats.FormatReader
 
getThumbSizeX() - Method in interface loci.formats.IFormatReader

Get the size of the X dimension for the thumbnail.

getThumbSizeX() - Method in class loci.formats.ImageReader
 
getThumbSizeX() - Method in class loci.formats.in.FilePatternReader
 
getThumbSizeX() - Method in class loci.formats.in.LeicaSCNReader
 
getThumbSizeX() - Method in class loci.formats.in.MinimalTiffReader
 
getThumbSizeX() - Method in class loci.formats.ReaderWrapper
 
getThumbSizeY() - Method in class loci.formats.FileStitcher
 
getThumbSizeY() - Method in class loci.formats.FormatReader
 
getThumbSizeY() - Method in interface loci.formats.IFormatReader

Get the size of the Y dimension for the thumbnail.

getThumbSizeY() - Method in class loci.formats.ImageReader
 
getThumbSizeY() - Method in class loci.formats.in.FilePatternReader
 
getThumbSizeY() - Method in class loci.formats.in.LeicaSCNReader
 
getThumbSizeY() - Method in class loci.formats.in.MinimalTiffReader
 
getThumbSizeY() - Method in class loci.formats.ReaderWrapper
 
getTIFFCompressor() - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam

Returns the TIFFCompressor that is currently set
 to be used by the ImageWriter to encode each image
 strip or tile, or null if none has been set.

getTIFFDecompressor() - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam

Returns the TIFFDecompressor that is currently set
 to be used by the ImageReader to decode each image
 strip or tile, or null if none has been set.

getTIFFField(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Retrieves a TIFF field from the directory.

getTIFFField(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getTIFFFields() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Retrieves all TIFF fields from the directory.

getTiffFiles(String, char, int, int, int) - Method in class loci.formats.in.CellWorxReader
 
getTIFFList() - Method in class loci.formats.in.LeicaReader
 
getTiffs() - Method in class loci.formats.in.BDReader
 
getTile(int, int) - Method in class com.sun.media.imageioimpl.common.SingleTileRenderedImage

Returns the image's Raster as tile (0, 0).

getTile(int, int, WritableRaster) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getTile(int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
 
getTile(Point) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the coordinates of the current tile.

getTile(int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTile(int, int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
getTile(int, int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
getTile(int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.EmptyImage
 
getTile(int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getTile(Point) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the indexes of the current tile.

getTile(Point) - Method in interface jj2000.j2k.image.ImgData

Returns the indixes of the current tile.

getTile(Point) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the indexes of the current tile.

getTile(Point) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the coordinates of the current tile.

getTile(Point) - Method in class jj2000.j2k.image.input.ImgReader

Returns the coordinates of the current tile.

getTile(Point) - Method in class jj2000.j2k.image.Tiler

Returns the horizontal and vertical indexes of the current tile.

getTile(Point) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the indixes of the current tile.

getTile(Point) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the indexes of the current tile.

getTile(Point) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the indexes of the current tile.

getTile(int, int, int, int, Region) - Method in class loci.formats.in.MIASReader
 
getTile(byte[], Region, Region) - Method in class loci.formats.out.TiffWriter
 
getTile(byte[], int, int, int, int) - Method in interface loci.formats.services.JPEGTurboService
 
getTile(int, int) - Method in interface loci.formats.services.JPEGTurboService
 
getTile(byte[], int, int, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
 
getTile(int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
 
getTile(IFD, byte[], int, int) - Method in class loci.formats.tiff.TiffParser
 
getTile0Rect() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState

Returns the bounding rectangle of the upper left tile at
 the current resolution level.

getTileCompHeight(int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTileCompHeight(int, int, int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the height in pixels of the specified tile-component for the
 given (tile-component) resolution level.

getTileCompHeight(int, int) - Method in interface jj2000.j2k.image.ImgData

Returns the height in pixels of the specified tile-component.

getTileCompHeight(int, int) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the height in pixels of the specified tile-component.

getTileCompHeight(int, int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the height in pixels of the specified tile-component.

getTileCompHeight(int, int) - Method in class jj2000.j2k.image.input.ImgReader

Returns the height in pixels of the specified tile-component.

getTileCompHeight(int, int) - Method in class jj2000.j2k.image.Tiler

Returns the height in pixels of the specified tile-component.

getTileCompHeight(int, int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the height in pixels of the specified tile-component.

getTileCompHeight(int, int, int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the height in pixels of the specified tile-component for the
 given resolution level.

getTileCompHeight(int, int, int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the height in pixels of the specified tile-component for the
 given resolution level.

getTileCompVal(int, int) - Method in class jj2000.j2k.ModuleSpec

Gets value of specified tile-component.

getTileCompWidth(int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTileCompWidth(int, int, int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the width in pixels of the specified tile-component for the
 given (tile-component) resolution level.

getTileCompWidth(int, int) - Method in interface jj2000.j2k.image.ImgData

Returns the width in pixels of the specified tile-component

getTileCompWidth(int, int) - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the width in pixels of the specified tile-component
 tile.

getTileCompWidth(int, int) - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the width in pixels of the specified tile-component

getTileCompWidth(int, int) - Method in class jj2000.j2k.image.input.ImgReader

Returns the width in pixels of the specified tile-component.

getTileCompWidth(int, int) - Method in class jj2000.j2k.image.Tiler

Returns the width in pixels of the specified tile-component.

getTileCompWidth(int, int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the width in pixels of the specified tile-component

getTileCompWidth(int, int, int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the width in pixels of the specified tile-component for the
 given resolution level.

getTileCompWidth(int, int, int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the width in pixels of the specified tile-component for the
 given resolution level.

getTileDef(int) - Method in class jj2000.j2k.ModuleSpec

Gets default value of the specified tile.

getTileFilename(int, int, int, String) - Static method in class loci.formats.FormatTools
 
getTileGridXOffset() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the X coordinate of the upper-left pixel of tile (0, 0).

getTileGridXOffset(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getTileGridXOffset() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTileGridXOffset() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getTileGridYOffset() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the Y coordinate of the upper-left pixel of tile (0, 0).

getTileGridYOffset(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getTileGridYOffset() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTileGridYOffset() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getTileHeight() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the height of a tile.

getTileHeight(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getTileHeight() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the overall height of the current tile in pixels.

getTileHeight(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
getTileHeight(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getTileHeight() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getTileHeight(int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the overall height of the current tile in pixels, for the given
 resolution level.

getTileHeight() - Method in interface jj2000.j2k.image.ImgData

Returns the overall height of the current tile in pixels.

getTileHeight() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the overall height of the current tile in pixels.

getTileHeight() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the overall height of the current tile in pixels.

getTileHeight() - Method in class jj2000.j2k.image.input.ImgReader

Returns the overall height of the current tile in pixels, assuming
 there is no-tiling.

getTileHeight() - Method in class jj2000.j2k.image.Tiler

Returns the overall height of the current tile in pixels.

getTileHeight() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the overall height of the current tile in pixels.

getTileHeight(int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the overall height of the current tile in pixels, for the given
 resolution level.

getTileHeight(int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the overall height of the current tile in pixels, for the given
 resolution level.

getTileIdx() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the index of the current tile, relative to a standard scan-line
 order.

getTileIdx() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the index of the current tile, relative to a standard scan-line
 order.

getTileIdx() - Method in interface jj2000.j2k.image.ImgData

Returns the index of the current tile, relative to a standard scan-line
 order.

getTileIdx() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the index of the current tile, relative to a standard scan-line
 order.

getTileIdx() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the index of the current tile, relative to a standard scan-line
 order.

getTileIdx() - Method in class jj2000.j2k.image.input.ImgReader

Returns the index of the current tile, relative to a standard scan-line
 order.

getTileIdx() - Method in class jj2000.j2k.image.Tiler

Returns the index of the current tile, relative to a standard scan-line
 order.

getTileIdx() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the index of the current tile, relative to a standard scan-line
 order.

getTileIdx() - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the index of the current tile, relative to a standard scan-line
 order.

getTileIdx() - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the index of the current tile, relative to a standard scan-line
 order.

getTileIndex(int) - Method in class loci.formats.in.LIFReader
 
getTileLength() - Method in class loci.formats.tiff.IFD

Returns the length of an image tile.

getTileNum(int, int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
getTileOff(Point, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the horizontal and vertical offset of the upper-left corner of
 the current tile, in the specified component, relative to the canvas
 origin, in the component coordinates (not in the reference grid
 coordinates).

getTileOrStripByteCount(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getTileOrStripHeight() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getTileOrStripOffset(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getTileOrStripWidth() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getTilePartULX() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTilePartULX() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the horizontal offset of tile partition

getTilePartULX() - Method in interface jj2000.j2k.image.ImgData

Returns the horizontal tile partition offset in the reference grid

getTilePartULX() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the horizontal tile partition offset in the reference grid

getTilePartULX() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the horizontal tile partition offset in the reference grid

getTilePartULX() - Method in class jj2000.j2k.image.input.ImgReader

Returns the horizontal tile partition offset in the reference grid

getTilePartULX() - Method in class jj2000.j2k.image.Tiler

Returns the horizontal tile partition offset in the reference grid

getTilePartULX() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the horizontal tile partition offset in the reference grid

getTilePartULX() - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the horizontal tile partition offset in the reference grid

getTilePartULX() - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the horizontal tile partition offset in the reference grid

getTilePartULY() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTilePartULY() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the vertical offset of tile partition

getTilePartULY() - Method in interface jj2000.j2k.image.ImgData

Returns the vertical tile partition offset in the reference grid

getTilePartULY() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the vertical tile offset in the reference grid

getTilePartULY() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the vertical tile partition offset in the reference grid

getTilePartULY() - Method in class jj2000.j2k.image.input.ImgReader

Returns the vertical tile partition offset in the reference grid

getTilePartULY() - Method in class jj2000.j2k.image.Tiler

Returns the vertical tile partition offset in the reference grid

getTilePartULY() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the vertical tile partition offset in the reference grid

getTilePartULY() - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the vertical tile partition offset in the reference grid

getTilePartULY() - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the vertical tile partition offset in the reference grid

getTileSize(SampleModel) - Static method in class com.sun.media.imageioimpl.common.ImageUtil
 
getTileSize() - Method in class loci.formats.in.CellSensReader
 
getTileSizeX() - Method in class loci.formats.FormatWriter
 
getTileSizeX() - Method in interface loci.formats.IFormatWriter

Retrieves the current tile width
 Defaults to full image width if not supported

getTileSizeX() - Method in class loci.formats.ImageWriter
 
getTileSizeX() - Method in class loci.formats.out.TiffWriter
 
getTileSizeX() - Method in class loci.formats.WriterWrapper
 
getTileSizeY() - Method in class loci.formats.FormatWriter
 
getTileSizeY() - Method in interface loci.formats.IFormatWriter

Retrieves the current tile height
 Defaults to full image height if not supported

getTileSizeY() - Method in class loci.formats.ImageWriter
 
getTileSizeY() - Method in class loci.formats.out.TiffWriter
 
getTileSizeY() - Method in class loci.formats.WriterWrapper
 
getTilesPerColumn() - Method in class loci.formats.tiff.IFD

Returns the number of image tiles per column.

getTilesPerRow() - Method in class loci.formats.tiff.IFD

Returns the number of image tiles per row.

getTileWidth() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the width of a tile.

getTileWidth(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getTileWidth() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns the width of the current tile in pixels.

getTileWidth(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
getTileWidth(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getTileWidth() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getTileWidth(int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Returns the overall width of the current tile in pixels for the given
 (tile) resolution level.

getTileWidth() - Method in interface jj2000.j2k.image.ImgData

Returns the overall width of the current tile in pixels.

getTileWidth() - Method in class jj2000.j2k.image.ImgDataAdapter

Returns the overall width of the current tile in pixels.

getTileWidth() - Method in class jj2000.j2k.image.ImgDataJoiner

Returns the overall width of the current tile in pixels.

getTileWidth() - Method in class jj2000.j2k.image.input.ImgReader

Returns the width of the current tile in pixels, assuming there is
 no-tiling.

getTileWidth() - Method in class jj2000.j2k.image.Tiler

Returns the overall width of the current tile in pixels.

getTileWidth() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Returns the overall width of the current tile in pixels.

getTileWidth(int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Returns the overall width of the current tile in pixels for the given
 resolution level.

getTileWidth(int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Returns the overall width of the current tile in pixels, for the given
 resolution level.

getTileWidth() - Method in class loci.formats.tiff.IFD

Returns the width of an image tile.

getTilingOrigin(Point) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the tiling origin, referred to as '(Px,Py)' in the 'ImgData'
 interface.

getTilingOrigin(Point) - Method in class jj2000.j2k.image.Tiler

Returns the tiling origin, referred to as '(xt0siz,yt0siz)' in the
 codestream header (SIZ marker segment).

getTime(Double, String) - Static method in class loci.formats.FormatTools

Formats the input value for the time into a length of the
 given unit.

getTimeBinCount() - Method in class loci.formats.in.SDTReader

Gets the number of bins in the lifetime histogram.

getTimepoint(int) - Method in class loci.formats.in.ZeissTIFFReader
 
getTimepoints() - Method in class loci.formats.in.ND2Handler
 
getTimestamp(String) - Method in class loci.formats.in.BDReader
 
getTimestamp(String) - Method in class loci.formats.in.SlidebookTiffReader
 
getTimestampIndex(String) - Method in class loci.formats.in.PCIReader
 
getTimestamps() - Method in class loci.formats.in.MetamorphHandler
 
getTiming(int) - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor

Returns the wall time spent by this compressor for component 'c'
 since the last call to this method (or the creation of this
 compressor if not yet called).

getTotalOffset(int, int, int) - Method in class loci.formats.in.DeltavisionReader

Given any specific Z, W, and T of a plane, determine the totalOffset from
 the start of the extended header.

getTotBitrate() - Method in class jj2000.j2k.entropy.encoder.LayersInfo

Returns the overall target bitrate for the entire bit stream.

getTotNumLayers() - Method in class jj2000.j2k.entropy.encoder.LayersInfo

Returns the total number of layers, according to the layer
 specification of this object and the overall target bitrate.

getTransformedSizes() - Method in class org.libjpegturbo.turbojpeg.TJTransformer

Returns an array containing the sizes of the transformed JPEG images from
 the most recent call to transform().

getTransparency(String) - Static method in class com.sun.media.imageio.stream.RawImageInputStream
 
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class loci.formats.gui.XMLCellRenderer
 
getTStep(int) - Method in class loci.plugins.in.ImporterOptions
 
getTStep(int) - Method in class loci.plugins.in.ImportProcess
 
getType() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns the type of the data stored in the field.

getType(int) - Static method in class com.sun.media.imageioimpl.common.BogusColorSpace

Return the type given the number of components.

getType() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Returns the box type.

getType() - Method in class loci.formats.cache.CacheEvent

Gets the type of cache update.

getType() - Method in class loci.formats.gui.TwoChannelColorSpace
 
getType() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the type associated with this Sequence.

getType() - Method in class loci.formats.tiff.TiffIFDEntry

Retrieves the entry's Type value.

getTypeByName(String) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns the data type constant corresponding to the supplied data
 type name.

getTypeByName(String) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Returns the type String based on the provided name.

getTypeInt(String) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Converts the box type from integer to string.

getTypeName(int) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns the name of the supplied data type constant.

getTypes() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox

Returns the channel types.

getTypeString(int) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Converts the box type from integer to string.

getUnderlyingReaders() - Method in class loci.formats.FileStitcher
 
getUnderlyingReaders() - Method in class loci.formats.FormatReader
 
getUnderlyingReaders() - Method in interface loci.formats.IFormatReader

Retrieves all underlying readers.

getUnderlyingReaders() - Method in class loci.formats.ImageReader
 
getUnderlyingReaders() - Method in class loci.formats.in.FilePatternReader
 
getUnderlyingReaders() - Method in class loci.formats.ReaderWrapper
 
getUngroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getUniverse() - Method in class loci.formats.gui.LegacyQTTools

Gets QuickTime for Java reflected universe.

getUnknownColorspace() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Returns the UnknowColorspace flag.

getUnpackedBinaryData(Raster, Rectangle) - Static method in class com.sun.media.imageioimpl.common.ImageUtil

Returns the binary data unpacked into an array of bytes.

getUpgradeCheckInfo() - Method in class loci.plugins.in.ImporterOptions
 
getURL() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox

Returns the URL data element.

getUsedFile(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
 
getUsedFileCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getUsedFiles() - Method in class loci.formats.FileStitcher
 
getUsedFiles(boolean) - Method in class loci.formats.FileStitcher
 
getUsedFiles() - Method in class loci.formats.FormatReader
 
getUsedFiles(boolean) - Method in class loci.formats.FormatReader
 
getUsedFiles() - Method in interface loci.formats.IFormatReader

Returns an array of filenames needed to open this dataset.

getUsedFiles(boolean) - Method in interface loci.formats.IFormatReader

Returns an array of filenames needed to open this dataset.

getUsedFiles() - Method in class loci.formats.ImageReader
 
getUsedFiles(boolean) - Method in class loci.formats.ImageReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.InveonReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.MetamorphTiffReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.UnisokuReader
 
getUsedFiles() - Method in class loci.formats.ReaderWrapper
 
getUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
 
getUUID() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDBox

Returns the UUID of this box.

getUUID(String) - Method in class loci.formats.in.ImprovisionTiffReader
 
getUUID(String) - Method in class loci.formats.out.OMETiffWriter

Gets the UUID corresponding to the given filename.

getValue(int, int) - Method in class jj2000.j2k.codestream.reader.TagTreeDecoder

Returns the current value of the specified element in the tag
 tree.

getValue() - Method in enum loci.formats.in.BaseZeissReader.Charset
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.DrawStyle
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.FeatureType
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.FillStyle
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.LineEndPositions
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.LineEndStyle
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.PointStyle
 
getValue() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.TextAlignment
 
getValue(IRandomAccess) - Method in class loci.formats.in.IM3Reader.StringIM3Record

Return the string value for this record

getValue(String) - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the value of the given key, beneath this
 Frame, inferring the value from the parent <Sequence>
 or grandparent <PVScan> section as needed.

getValue(String) - Method in class loci.formats.in.PrairieMetadata

Gets the value of the given key, at the top-level
 <PVScan> element.

getValue(String) - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the value of the given key, beneath this
 Sequence, inferring the value from the parent <PVScan>
 section as needed.

getValue() - Method in class loci.plugins.prefs.BooleanOption

Gets the current value of the option.

getValue() - Method in class loci.plugins.prefs.DoubleOption

Gets the current value of the option.

getValue(String) - Method in class loci.plugins.prefs.OptionsList

Gets the value of the string option with the given key.

getValue() - Method in class loci.plugins.prefs.StringOption

Gets the current value of the option.

getValueAsString(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Returns a String containing a human-readable
 version of the data item.

getValueCount() - Method in class loci.formats.tiff.TiffIFDEntry

Retrieves the entry's ValueCount value.

getValueForKey() - Method in class loci.formats.meta.OriginalMetadataAnnotation

Return just the value (i.e.

getValueName(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFTag

Returns the mnemonic name associated with a particular value
 that this tag's data may take on, or null if
 no name is present.

getValueOffset() - Method in class loci.formats.tiff.TiffIFDEntry

Retrieves the entry's ValueOffset value.

getValues() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the table of Frame key/value pairs.

getValues() - Method in class loci.formats.in.PrairieMetadata

Gets the table of PVScan key/value pairs.

getValues() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the table of Frame key/value pairs.

getVariableAttributes(String) - Method in interface loci.formats.services.NetCDFService

Retrieves all of a variable's attributes.

getVariableAttributes(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getVariableList() - Method in interface loci.formats.services.NetCDFService

Retrieves an exhaustive list of the HDF paths for all variables in the
 HDF document.

getVariableList() - Method in class loci.formats.services.NetCDFServiceImpl
 
getVariableValue(String) - Method in interface loci.formats.services.NetCDFService

Retrieves a variable's value.

getVariableValue(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getVariant() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
getVariant() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
getVendor() - Static method in class com.sun.media.imageioimpl.common.PackageUtil

Return a vendor string for the package.

getVersion() - Method in class com.sun.media.imageio.plugins.bmp.BMPImageWriteParam

Deprecated. 

getVersion() - Static method in class com.sun.media.imageioimpl.common.PackageUtil

Return a version string for the package.

getVersion() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox

Returns the Version data element.

getVersionNumber(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getVertAnWaveletFilters(int, int) - Method in interface jj2000.j2k.wavelet.analysis.ForwWT

Returns the vertical analysis wavelet filters used in each
 level, for the specified tile-component.

getVertAnWaveletFilters(int, int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the vertical analysis wavelet filters used in each level, for
 the specified component and tile.

getVerticalResolution() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox

Return the vertical resolution.

getVerWFilter() - Method in class jj2000.j2k.wavelet.analysis.SubbandAn

This function returns the vertical wavelet filter relevant to this
 subband

getVerWFilter() - Method in class jj2000.j2k.wavelet.Subband

This function returns the vertical wavelet filter relevant to this
 subband

getVerWFilter() - Method in class jj2000.j2k.wavelet.synthesis.SubbandSyn

This function returns the vertical wavelet filter relevant to this
 subband

getVFilters(int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterSpec

Returns the vertical analysis filters to be used in component 'n' and
 tile 't'.

getVFilters(int, int) - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterSpec

Returns the vertical analysis filters to be used in component 'n' and
 tile 't'.

getVirtualInfo() - Method in class loci.plugins.in.ImporterOptions
 
getVirtualReader() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getVoltage() - Method in class loci.formats.in.ND2Handler
 
getVolumeName(int) - Method in class loci.formats.in.CellSensReader
 
getVoxSzX() - Method in interface loci.formats.services.WlzService

Gets voxel width.

getVoxSzX() - Method in class loci.formats.services.WlzServiceImpl
 
getVoxSzY() - Method in interface loci.formats.services.WlzService

Gets voxel height.

getVoxSzY() - Method in class loci.formats.services.WlzServiceImpl
 
getVoxSzZ() - Method in interface loci.formats.services.WlzService

Gets voxel depth.

getVoxSzZ() - Method in class loci.formats.services.WlzServiceImpl
 
getWaitTime() - Method in class loci.formats.in.PrairieMetadata

Gets the waitTime recorded in the configuration.

getWavelength(Double, String) - Static method in class loci.formats.FormatTools

Formats the input value for the wavelength into a length of the
 given unit.

getWavelength(Double) - Static method in class loci.formats.FormatTools
 
getWavelength(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getWavelengthMax() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the wavelengthMax associated with this File.

getWavelengthMin() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the wavelengthMin associated with this File.

getWavelengths() - Method in class loci.formats.in.IM3Reader.Spectrum
 
getWavelengths() - Method in class loci.formats.in.MetamorphHandler
 
getWell(int) - Method in class loci.formats.in.CellWorxReader

Retrieve the well index corresponding to the given series.

getWell(String) - Method in class loci.formats.in.FlexReader

Returns a two-element array containing the well row and well column
 corresponding to the given file.

getWell(int) - Method in class loci.formats.in.MetamorphTiffReader
 
getWellColumn(String) - Method in class loci.formats.in.CellomicsReader
 
getWellColumn(int) - Method in class loci.formats.in.CellWorxReader

Retrieve the well column corresponding to the given series.

getWellColumn(String) - Method in class loci.formats.in.MetamorphTiffReader
 
getWellFromSeries(int) - Method in class loci.formats.in.InCellReader
 
getWellName(String) - Method in class loci.formats.in.CellomicsReader
 
getWellRow(String) - Method in class loci.formats.in.CellomicsReader
 
getWellRow(int) - Method in class loci.formats.in.CellWorxReader

Retrieve the well row corresponding to the given series.

getWellRow(String) - Method in class loci.formats.in.MetamorphTiffReader
 
getWidgets() - Method in class loci.plugins.config.FlexWidgets
 
getWidgets() - Method in interface loci.plugins.config.IFormatWidgets
 
getWidgets() - Method in class loci.plugins.config.LIFWidgets
 
getWidgets() - Method in class loci.plugins.config.ND2Widgets
 
getWidgets() - Method in class loci.plugins.config.PictWidgets
 
getWidgets() - Method in class loci.plugins.config.QTWidgets
 
getWidgets() - Method in class loci.plugins.config.SDTWidgets
 
getWidgets() - Method in class loci.plugins.config.TiffDelegateWidgets
 
getWidgets() - Method in class loci.plugins.config.ZeissCZIWidgets
 
getWidth() - Method in class com.sun.media.imageioimpl.common.SimpleRenderedImage

Returns the width of the image.

getWidth(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
getWidth() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Returns the width of the image.

getWidth(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getWidth() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getWidth(int) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
getWidth(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
getWidth(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
getWidth() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
getWidth() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getWidth(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getWidth() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getWidth(int) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getWidth() - Method in class jj2000.j2k.codestream.reader.TagTreeDecoder

Returns the number of leafs along the horizontal direction.

getWidth() - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Returns the number of leafs along the horizontal direction.

getWidth() - Method in class loci.formats.codec.JPEGTileDecoder
 
getWidth() - Method in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
getWidth(int) - Method in class loci.formats.in.LegacyND2Reader
 
getWidth() - Method in interface loci.formats.services.LuraWaveService

Wraps lwfDecoder.getWidth()

getWidth() - Method in class loci.formats.services.LuraWaveServiceImpl
 
getWidth(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack
 
getWidth() - Method in class loci.plugins.util.BFVirtualStack
 
getWidth() - Method in class loci.plugins.util.RecordedImageProcessor
 
getWidth() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Returns the width of the JPEG image associated with this decompressor
 instance.

getWindowlessInfo() - Method in class loci.plugins.in.ImporterOptions
 
getWlzOrgLabelName() - Method in interface loci.formats.services.WlzService

Gets the text string used for the Woolz origin label.

getWlzOrgLabelName() - Method in class loci.formats.services.WlzServiceImpl
 
getWrappedStream() - Method in class com.sun.media.imageioimpl.plugins.clib.InputStreamAdapter
 
getWriteCodeStreamOnly() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Gets writeCodeStreamOnly.

getWriter() - Method in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Returns the current ImageWriter.

getWriter(String) - Method in class loci.formats.ImageWriter

Gets the writer used to save the given file.

getWriter() - Method in class loci.formats.ImageWriter

Gets the writer used to save the current file.

getWriter(Class<? extends IFormatWriter>) - Method in class loci.formats.ImageWriter

Gets the file format writer instance matching the given class.

getWriter() - Method in class loci.formats.WriterWrapper

Gets the wrapped writer.

getWriters() - Method in class loci.formats.ImageWriter

Gets all constituent file format writers.

getWTDataType(int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterSpec

Returns the data type used by the filters in this object, as defined in
 the 'DataBlk' interface for specified tile-component.

getWTDataType(int, int) - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterSpec

Returns the data type used by the filters in this object, as defined in
 the 'DataBlk' interface for specified tile-component.

getWTDataType() - Method in class jj2000.j2k.wavelet.WTFilterSpec

Returns the data type used by the filters in this object, as defined in 
 the 'DataBlk' interface.

getX(int) - Method in class loci.formats.in.FakeReader
 
getX(double[]) - Method in class loci.formats.in.TextReader
 
getXFields() - Method in class loci.formats.in.ND2Handler
 
getXML() - Method in class loci.formats.tools.EditTiffG
 
getXPositions() - Method in class loci.formats.in.ND2Handler
 
getXResolution() - Method in class loci.formats.tiff.IFD

Retrieve the X resolution (TIFF tag XResolution) from this IFD.

getY(int) - Method in class loci.formats.in.FakeReader
 
getY(double[]) - Method in class loci.formats.in.TextReader
 
getYPositions() - Method in class loci.formats.in.ND2Handler
 
getYResolution() - Method in class loci.formats.tiff.IFD

Retrieve the Y resolution (TIFF tag YResolution) from this IFD.

getZ() - Method in class loci.formats.gui.ImageViewer

Gets the Z value of the currently displayed image.

getZBegin(int) - Method in class loci.plugins.in.ImporterOptions
 
getZBegin(int) - Method in class loci.plugins.in.ImportProcess
 
getZCount(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.SERIES.

getZCTCoords(int) - Method in class loci.formats.ChannelMerger
 
getZCTCoords(int) - Method in class loci.formats.ChannelSeparator
 
getZCTCoords(int) - Method in class loci.formats.DimensionSwapper
 
getZCTCoords(int) - Method in class loci.formats.FileStitcher
 
getZCTCoords(int) - Method in class loci.formats.FormatReader
 
getZCTCoords(IFormatReader, int) - Static method in class loci.formats.FormatTools

Gets the Z, C and T coordinates corresponding
 to the given rasterized index value (real sizes).

getZCTCoords(String, int, int, int, int, int) - Static method in class loci.formats.FormatTools

Gets the Z, C and T coordinates corresponding to the given rasterized
 index value (real sizes).

getZCTCoords(String, int, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools

Gets the Z, C and T coordinates corresponding to the given
 rasterized index value.

getZCTCoords(int) - Method in interface loci.formats.IFormatReader

Gets the Z, C and T coordinates (real sizes) corresponding to the
 given rasterized index value.

getZCTCoords(int) - Method in class loci.formats.ImageReader
 
getZCTCoords(int) - Method in class loci.formats.in.FilePatternReader
 
getZCTCoords(int) - Method in class loci.formats.ReaderWrapper
 
getZCTCoords(Double, Double[], Double[], Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getZCTModuloCoords(int) - Method in class loci.formats.ChannelMerger
 
getZCTModuloCoords(int) - Method in class loci.formats.ChannelSeparator
 
getZCTModuloCoords(int) - Method in class loci.formats.DimensionSwapper
 
getZCTModuloCoords(int) - Method in class loci.formats.FileStitcher
 
getZCTModuloCoords(int) - Method in class loci.formats.FormatReader
 
getZCTModuloCoords(IFormatReader, int) - Static method in class loci.formats.FormatTools

Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates
 corresponding to the given rasterized index value (effective
 sizes).

getZCTModuloCoords(int) - Method in interface loci.formats.IFormatReader

Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates
 (effective sizes) corresponding to the given rasterized index
 value.

getZCTModuloCoords(int) - Method in class loci.formats.ImageReader
 
getZCTModuloCoords(int) - Method in class loci.formats.ReaderWrapper
 
getZEnd(int) - Method in class loci.plugins.in.ImporterOptions
 
getZEnd(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getZeroOffset(ImagePlus) - Static method in class loci.plugins.in.Colorizer
 
getZoom() - Method in class loci.formats.in.MetamorphHandler
 
getZPositions() - Method in class loci.formats.in.MetamorphHandler
 
getZPositions() - Method in class loci.formats.in.ND2Handler
 
getZSections() - Method in class loci.formats.in.ND2Handler
 
getZSlices(int) - Method in class loci.formats.in.LegacyND2Reader
 
getZStep(int) - Method in class loci.plugins.in.ImporterOptions
 
getZStep(int) - Method in class loci.plugins.in.ImportProcess
 
GIF_MAGIC_STRING - Static variable in class loci.formats.in.GIFReader
 
GIFImageMetadata - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFImageMetadata(boolean, String, String, String[], String[]) - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
GIFImageMetadata() - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
GIFImageMetadataFormat - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFImageMetadataFormat() - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadataFormat
 
GIFImageMetadataFormatResources - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFImageMetadataFormatResources() - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadataFormatResources
 
GIFImageWriteParam - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFImageWriteParam(Locale) - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFImageWriteParam
 
GIFImageWriter - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFImageWriter(GIFImageWriterSpi) - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
GIFImageWriterSpi - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFImageWriterSpi() - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
GIFMetadata - Class in com.sun.media.imageioimpl.plugins.gif

Class which adds utility DOM element attribute access methods to
 IIOMetadata for subclass use.

GIFMetadata(boolean, String, String, String[], String[]) - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
GIFReader - Class in loci.formats.in

GIFReader is the file format reader for Graphics Interchange Format
 (GIF) files.

GIFReader() - Constructor for class loci.formats.in.GIFReader

Constructs a new GIF reader.

GIFStreamMetadata - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFStreamMetadata(boolean, String, String, String[], String[]) - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
GIFStreamMetadata() - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
GIFStreamMetadataFormat - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFStreamMetadataFormat() - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadataFormat
 
GIFStreamMetadataFormatResources - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFStreamMetadataFormatResources() - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadataFormatResources
 
GIFWritableImageMetadata - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFWritableImageMetadata() - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFWritableImageMetadata
 
GIFWritableStreamMetadata - Class in com.sun.media.imageioimpl.plugins.gif
 
GIFWritableStreamMetadata() - Constructor for class com.sun.media.imageioimpl.plugins.gif.GIFWritableStreamMetadata
 
global - Variable in class loci.formats.in.BMPReader

Offset to image data.

globalColorTable - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
globalMetadata - Variable in class loci.formats.in.LeicaHandler
 
gotHeader - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

Indicates whether the header is read.

gotHeader - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

Indicates whether the header is read.

gotHeader - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
gotHeader - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

Indicates whether the header is read.

gotHeader - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
gotHeader - Variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader

Indicates whether the header is read.

gotxmin - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
gotymin - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
GPS_VERSION_2_2 - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

An array of bytes containing the values {'2', '2', '0',
 '0'} to be used with the "GPSVersionID" tag to indicate
 GPS version 2.2.

GPSAltitude() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSAltitude
 
GPSAltitudeRef() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSAltitudeRef
 
GPSAreaInformation() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSAreaInformation
 
GPSDateStamp() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDateStamp
 
GPSDestBearing() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDestBearing
 
GPSDestBearingRef() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDestBearingRef
 
GPSDestDistance() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDestDistance
 
GPSDestDistanceRef() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDestDistanceRef
 
GPSDestLatitude() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDestLatitude
 
GPSDestLatitudeRef() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDestLatitudeRef
 
GPSDestLongitude() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDestLongitude
 
GPSDestLongitudeRef() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDestLongitudeRef
 
GPSDifferential() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDifferential
 
GPSDOP() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSDOP
 
GPSImgDirection() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSImgDirection
 
GPSImgDirectionRef() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSImgDirectionRef
 
GPSInfoIFDPointer() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFParentTIFFTagSet.GPSInfoIFDPointer
 
GPSLatitude() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSLatitude
 
GPSLatitudeRef() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSLatitudeRef
 
GPSLongitude() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSLongitude
 
GPSLongitudeRef() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSLongitudeRef
 
GPSMapDatum() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSMapDatum
 
GPSMeasureMode() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSMeasureMode
 
GPSProcessingMethod() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSProcessingMethod
 
GPSSatellites() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSSatellites
 
GPSSpeed() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSSpeed
 
GPSSpeedRef() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSSpeedRef
 
GPSStatus() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSStatus
 
GPSTimeStamp() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSTimeStamp
 
GPSTrack() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSTrack
 
GPSTrackRef() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSTrackRef
 
GPSVersionID() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet.GPSVersionID
 
gradient(int, int, int) - Method in class loci.formats.tools.MakeTestOmeTiff
 
GRADIENT_LUT - Static variable in class loci.formats.in.CellSensReader
 
GRAPHICS - Static variable in class loci.formats.in.GIFReader
 
GRAPHICS_DOMAIN - Static variable in class loci.formats.FormatTools

Identifies the graphics domain.

GRAY16 - Static variable in class loci.formats.in.ZeissCZIReader
 
GRAY32 - Static variable in class loci.formats.in.ZeissCZIReader
 
GRAY8 - Static variable in class loci.formats.in.ZeissCZIReader

Pixel type constants.

GRAY_ALPHA - Static variable in class loci.formats.in.APNGReader
 
GRAY_DOUBLE - Static variable in class loci.formats.in.ZeissCZIReader
 
GRAY_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
 
GRAY_RESPONSE_CURVE - Static variable in class loci.formats.tiff.IFD
 
GRAY_RESPONSE_UNIT - Static variable in class loci.formats.tiff.IFD
 
GRAY_RESPONSE_UNIT_HUNDRED_THOUSANDTHS - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "GrayResponseUnit" tag.

GRAY_RESPONSE_UNIT_HUNDREDTHS - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "GrayResponseUnit" tag.

GRAY_RESPONSE_UNIT_TEN_THOUSANDTHS - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "GrayResponseUnit" tag.

GRAY_RESPONSE_UNIT_TENTHS - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "GrayResponseUnit" tag.

GRAY_RESPONSE_UNIT_THOUSANDTHS - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "GrayResponseUnit" tag.

GrayResponseCurve() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.GrayResponseCurve
 
GrayResponseUnit() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.GrayResponseUnit
 
GRAYSCALE - Static variable in class loci.formats.in.APNGReader

Color types.

green - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
green - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
GREEN_GAIN - Static variable in class loci.formats.in.CellSensReader
 
GREEN_OFFSET - Static variable in class loci.formats.in.CellSensReader
 
GREEN_TO_RED_MIN - Static variable in class loci.plugins.in.Colorizer
 
greenGain - Variable in class loci.formats.in.CellSensReader.Pyramid
 
greenMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
greenMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
greenOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
 
greenOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
greenShort - Variable in class loci.formats.gui.Index16ColorModel

Lookup tables.

greenX - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
greenY - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
greenZ - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
GREYSCALE_COMPRESSION - Static variable in class loci.formats.in.FlowSightReader
 
GRID - Static variable in class loci.formats.in.FV1000Reader
 
GRIDSIZE_OFFSET - Static variable in class loci.formats.in.MRCReader
 
group - Variable in class loci.formats.FileStitcher
 
group - Variable in class loci.formats.FormatReader

Whether or not to group multi-file formats.

GROUP - Static variable in class loci.formats.in.GatanReader

Tag types.

groupFiles(String[], MetadataStore) - Method in class loci.formats.in.FlexReader
 
groupFiles() - Method in class loci.formats.in.TCSReader
 
groupFilesBox - Variable in class loci.plugins.in.MainDialog
 
groupX - Variable in class loci.formats.in.SPEReader.SpeROI
 
groupY - Variable in class loci.formats.in.SPEReader.SpeROI
 
growBuffer() - Method in class jj2000.j2k.util.ISRandomAccessIO

Grows the cache buffer by 'inc', upto a maximum of 'maxsize'.

guardBits - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

The number of bits used for each tile-component in
  the quantizer to avoid overflow.

GuardBitsSpec - Class in jj2000.j2k.quantization

This class extends ModuleSpec class in order to hold specifications about
 number of guard bits in each tile-component.

GuardBitsSpec(int, int, byte) - Constructor for class jj2000.j2k.quantization.GuardBitsSpec

Constructs an empty 'GuardBitsSpec' with specified number of tile and
 components.

GuardBitsSpec(int, int, byte, J2KImageWriteParamJava, String) - Constructor for class jj2000.j2k.quantization.GuardBitsSpec

Constructs a new 'GuardBitsSpec' for the specified number of components
 and tiles and the arguments of "-Qguard_bits" option.

GUITools - Class in loci.formats.gui

A utility class for working with graphical user interfaces.

GUITools() - Constructor for class loci.formats.gui.GUITools
 
gz - Variable in class loci.formats.in.LiFlimReader

Stream to use for reading gzip-compressed pixel data.

gzip - Variable in class loci.formats.in.ICSReader

Whether or not the pixels are GZIP-compressed.

gzip - Variable in class loci.formats.in.LiFlimReader

True if gzip compression was used to deflate the pixels.

gzipStream - Variable in class loci.formats.in.ICSReader
 
gzPos - Variable in class loci.formats.in.LiFlimReader

Image number indicating position in gzip stream.

gzSeries - Variable in class loci.formats.in.LiFlimReader

Series number indicating position in gzip stream.





H

h - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
h - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

The height of the image

h - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
h - Variable in class jj2000.j2k.codestream.CoordInfo

Object's height

h - Variable in class jj2000.j2k.codestream.PrecInfo

Precinct height in the corresponding resolution level

h - Variable in class jj2000.j2k.codestream.reader.CBlkInfo

Height of the code-block

h - Variable in class jj2000.j2k.codestream.reader.TagTreeDecoder

The vertical dimensions of the base level

h - Variable in class jj2000.j2k.codestream.writer.TagTreeEncoder

The vertical dimensions of the base level

h - Variable in class jj2000.j2k.entropy.decoder.DecLyrdCBlk

The height of the code-block

h - Variable in class jj2000.j2k.image.DataBlk

The height of the block, in pixels.

h - Variable in class jj2000.j2k.image.ImgDataJoiner

The height of the image

h - Variable in class jj2000.j2k.image.input.ImgReader

The height of the image

h - Variable in class jj2000.j2k.roi.encoder.ROI

height of rectangular ROI

h - Variable in class jj2000.j2k.roi.encoder.SubbandROIMask

Height of the subband mask

h - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTData

The height of the code-block

h - Variable in class jj2000.j2k.wavelet.Subband

The height of the subband

HALFTONE_HINTS - Static variable in class loci.formats.tiff.IFD
 
HalftoneHints() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.HalftoneHints
 
HamamatsuVMSReader - Class in loci.formats.in

HamamatsuVMSReader is the file format reader for Hamamatsu VMS datasets.

HamamatsuVMSReader() - Constructor for class loci.formats.in.HamamatsuVMSReader

Constructs a new Hamamatsu VMS reader.

handle - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
handle - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
handleBitmap(int) - Method in class loci.formats.in.PictReader

Extract the image data in a PICT bitmap structure.

handleException(Throwable) - Static method in class jj2000.j2k.JJ2KExceptionHandler

Handles the exception.

handleExtension(String, Object[]) - Method in class loci.plugins.macro.MacroFunctions
 
handleMetadataStore(IFormatReader) - Method in class loci.formats.Memoizer

Return the IFormatReader instance that is passed in or null if
 it has been invalidated, which will include the instance being closed.

handlePixmap(int) - Method in class loci.formats.in.PictReader

Extracts the image data in a PICT pixmap structure.

handlePixmap(int, int) - Method in class loci.formats.in.PictReader

Handles the unpacking of the image data.

handler - Variable in class loci.formats.in.LeicaSCNReader
 
handler - Variable in class loci.formats.in.NikonElementsTiffReader
 
handler - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
handleSize - Variable in class loci.formats.in.BaseZeissReader.Shape
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.ColorDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.CropDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.FilePatternDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.IdDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.ImporterDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.LocationDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.MainDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.MemoryDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.RangeDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.SeriesDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.SwapDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog
 
HAS_EXTERNAL_FILE - Static variable in class loci.formats.in.CellSensReader
 
hasAbsoluteZ - Variable in class loci.formats.in.MetamorphReader
 
hasAbsoluteZValid - Variable in class loci.formats.in.MetamorphReader
 
hasChildNodes() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
hasChipOffsets - Variable in class loci.formats.in.MetamorphReader
 
hasCompanionFiles - Variable in class loci.formats.FormatReader

Whether this format supports multi-file datasets.

hasCompanionFiles() - Method in class loci.formats.FormatReader
 
hasCompanionFiles() - Method in interface loci.formats.IFormatReader

Returns true if this format supports multi-file datasets.

hasCompanionFiles() - Method in class loci.formats.ImageReader
 
hasCompanionFiles() - Method in class loci.formats.in.FilePatternReader
 
hasCompanionFiles() - Method in class loci.formats.ReaderWrapper
 
hasDetectorSettings - Variable in class loci.formats.in.ZeissCZIReader
 
hasDualCamera() - Method in class loci.formats.in.MetamorphHandler
 
hasExtendedMeasureInfo - Variable in class loci.formats.in.SDTInfo
 
hasFlattenedResolutions() - Method in class loci.formats.FormatReader
 
hasFlattenedResolutions() - Method in interface loci.formats.IFormatReader

Return whether or not resolution flattening is enabled.

hasFlattenedResolutions() - Method in class loci.formats.ImageReader
 
hasFlattenedResolutions() - Method in class loci.formats.in.FilePatternReader
 
hasFlattenedResolutions() - Method in class loci.formats.ReaderWrapper
 
Hash(short, byte) - Static method in class com.sun.media.imageioimpl.common.LZWStringTable
 
HASH_FREE - Static variable in class com.sun.media.imageioimpl.common.LZWStringTable
 
HASH_SIZE - Static variable in class loci.formats.codec.LZWCodec

Size of hash table.

HASH_STEP - Static variable in class loci.formats.codec.LZWCodec

Rehashing step.

hashCode() - Method in class loci.formats.in.MetamorphTiffReader.Well
 
hashCode() - Method in class loci.formats.in.ZeissCZIReader.Coordinate
 
hashCode() - Method in class loci.formats.tiff.TiffRational

Reasonable hash value for use with hashtables.

hashCode() - Method in class loci.plugins.config.FormatEntry
 
hashCode() - Method in class loci.plugins.prefs.OptionsList
 
HASHSIZE - Static variable in class com.sun.media.imageioimpl.common.LZWStringTable
 
HASHSTEP - Static variable in class com.sun.media.imageioimpl.common.LZWStringTable
 
hasInstrumentData - Variable in class loci.formats.in.ICSReader
 
hasJPEGTables - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
hasMeasFCSInfo - Variable in class loci.formats.in.SDTInfo
 
hasMeasHISTInfo - Variable in class loci.formats.in.SDTInfo
 
hasMeasStopInfo - Variable in class loci.formats.in.SDTInfo
 
hasMeasureInfo - Variable in class loci.formats.in.SDTInfo
 
hasPaddingByte - Variable in class loci.formats.in.IvisionReader
 
hasPlainTextExtension - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
hasPlaneReader - Variable in class loci.formats.in.AmiraReader
 
hasSPW - Variable in class loci.formats.in.OMETiffReader
 
hasSPW - Variable in class loci.formats.in.OMEXMLReader
 
hasStagePositions - Variable in class loci.formats.in.MetamorphReader
 
hasThumbnails(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
hasValidWells(Location) - Method in class loci.formats.in.ScreenReader
 
hasValueNames() - Method in class com.sun.media.imageio.plugins.tiff.TIFFTag

Returns true if there are mnemonic names associated with
 the set of legal values for the data associated with this tag.

hbuf - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

The DataOutputStream to store header data.

HCS_DOMAIN - Static variable in class loci.formats.FormatTools

Identifies the high content screening domain.

hd - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

The J2K HeaderDecoder defined in jj2000 packages.

hd - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
hd - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The decoded bit stream header

hd - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Reference to the HeaderDecoder

HDF_MAGIC_STRING - Static variable in class loci.formats.in.CellH5Reader
 
HDF_MAGIC_STRING - Static variable in class loci.formats.in.ImarisHDFReader
 
hdfReader - Variable in class loci.formats.services.JHDFServiceImpl

Root of the HDF5 file.

hdfWriter - Variable in class loci.formats.services.JHDFServiceImpl

Root of the HDF5 file.

hdpi - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
HDRI_EXPOSURE_RANGE - Static variable in class loci.formats.in.CellSensReader
 
HDRI_FRAMES - Static variable in class loci.formats.in.CellSensReader
 
HDRI_MAP_MODE - Static variable in class loci.formats.in.CellSensReader
 
HDRI_ON - Static variable in class loci.formats.in.CellSensReader
 
hdStr - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Current header information in a string

headEnc - Variable in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

The header encoder

HEADER - Static variable in class loci.formats.codec.MJPBCodec
 
HEADER - Static variable in class loci.formats.in.InveonReader
 
header - Variable in class loci.formats.in.SPEReader
 
header - Variable in class loci.formats.in.SPEReader.SpeHeader
 
header - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
HEADER_LENGTH - Static variable in class loci.formats.in.DeltavisionReader
 
HEADER_MARKER - Static variable in class loci.formats.in.VisitechReader
 
HEADER_SIZE - Static variable in class loci.formats.in.Ecat7Reader
 
HEADER_SIZE - Static variable in class loci.formats.in.GatanDM2Reader
 
HEADER_SIZE - Static variable in class loci.formats.in.I2IReader
 
HEADER_SIZE - Static variable in class loci.formats.in.INRReader
 
HEADER_SIZE - Static variable in class loci.formats.in.MRCReader
 
HEADER_SIZE - Static variable in class loci.formats.in.OpenlabRawReader
 
HEADER_SIZE - Static variable in class loci.formats.in.PovrayReader
 
HEADER_SIZE - Static variable in class loci.formats.in.PQBinReader
 
HEADER_SIZE - Static variable in class loci.formats.in.RHKReader
 
HEADER_SIZE - Static variable in class loci.formats.in.SBIGReader
 
HEADER_SIZE - Static variable in class loci.formats.in.SeikoReader
 
HEADER_SIZE - Static variable in class loci.formats.in.SMCameraReader
 
HEADER_SIZE - Static variable in class loci.formats.in.UBMReader
 
HEADER_SIZE - Static variable in class loci.formats.in.WATOPReader
 
HEADER_SIZE - Static variable in class loci.formats.in.ZeissCZIReader
 
HeaderBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000

This class is defined to represent an Image Header Box of JPEG JP2 file
  format.

HeaderBox(int, int, int, int, int, int, int) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Create an Image Header Box from the element values.

HeaderBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Create an Image Header Box using the content data.

HeaderBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Constructs an Image Header Box from a Node.

HeaderDecoder - Class in jj2000.j2k.codestream.reader

This class reads Main and Tile-part headers from the codestream.

HeaderDecoder(RandomAccessIO, J2KImageReadParamJava, HeaderInfo) - Constructor for class jj2000.j2k.codestream.reader.HeaderDecoder

Creates a HeaderDecoder instance and read in two passes the main header
 of the codestream.

HeaderEncoder - Class in jj2000.j2k.codestream.writer

This class writes almost of the markers and marker segments in main header
 and in tile-part headers.

HeaderEncoder(ImgData, boolean[], ForwardWT, Tiler, J2KImageWriteParamJava, ROIScaler, PostCompRateAllocator) - Constructor for class jj2000.j2k.codestream.writer.HeaderEncoder

Initializes the header writer with the references to the coding chain.

headerIFDs - Variable in class loci.formats.in.LeicaReader

Array of IFD-like structures containing metadata.

HeaderInfo - Class in jj2000.j2k.codestream

Classe that holds information found in the marker segments of the main and
 tile-part headers.

HeaderInfo() - Constructor for class jj2000.j2k.codestream.HeaderInfo
 
HeaderInfo.COC - Class in jj2000.j2k.codestream

Internal class holding information found in the COC marker segments

HeaderInfo.COD - Class in jj2000.j2k.codestream

Internal class holding information found in the COD marker segments

HeaderInfo.COM - Class in jj2000.j2k.codestream

Internal class holding information found in the COM marker segments

HeaderInfo.CRG - Class in jj2000.j2k.codestream

Internal class holding information found in the CRG marker segment

HeaderInfo.POC - Class in jj2000.j2k.codestream

Internal class holding information found in the POC marker segments

HeaderInfo.QCC - Class in jj2000.j2k.codestream

Internal class holding information found in the QCC marker segments

HeaderInfo.QCD - Class in jj2000.j2k.codestream

Internal class holding information found in the QCD marker segments

HeaderInfo.RGN - Class in jj2000.j2k.codestream

Internal class holding information found in the RGN marker segments

HeaderInfo.SIZ - Class in jj2000.j2k.codestream

Internal class holding information found in the SIZ marker segment

HeaderInfo.SOT - Class in jj2000.j2k.codestream

Internal class holding information found in the SOt marker segments

headerPixelType - Variable in class loci.formats.in.JPEG2000MetadataParser

Pixel type as specified in the header.

headerPosition - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
headerSize - Variable in class loci.formats.in.FEIReader
 
headerSize - Variable in class loci.formats.in.OxfordInstrumentsReader
 
headerSize - Static variable in class loci.formats.in.SPEReader.SpeHeader
 
headerSize - Variable in class loci.formats.in.SpiderReader
 
headerSizeC - Variable in class loci.formats.in.JPEG2000MetadataParser

Number of channels the image has as specified in the header.

headerSizeX - Variable in class loci.formats.in.JPEG2000MetadataParser

Width of the image as specified in the header.

headerSizeY - Variable in class loci.formats.in.JPEG2000MetadataParser

Height of the image as specified in the header.

headerValid - Variable in class loci.formats.in.SDTInfo
 
headLen - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Length of main and tile-parts headers

height - Variable in class com.sun.media.imageioimpl.common.SimpleRenderedImage

The image's height in pixels.

height - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

The original image height.

height - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
height - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox
 
height - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

The image height.

height - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
height - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
height - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

The original image height.

height - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata

The image height.

height - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
height - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
height - Variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader

The original image height.

height - Variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
height - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
 
height - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter

Image height

height - Variable in class loci.formats.codec.CodecOptions

Height, in pixels, of the image.

height - Variable in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
height - Variable in class loci.formats.in.BaseZeissReader.Shape
 
height - Variable in class loci.formats.in.CellSensReader.Pyramid
 
height - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
 
height - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
height - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
height - Variable in class loci.formats.in.SDTInfo
 
height - Variable in class loci.formats.out.LegacyQTWriter

Frame height.

height - Variable in class loci.formats.tools.AmiraParameters
 
HELIOS_TAG - Static variable in class loci.formats.in.FEITiffReader
 
HELP_MENU - Static variable in class loci.plugins.shortcut.ShortcutPanel

Name of the 'About Plugins' submenu.

helper - Variable in class loci.formats.gui.SignedColorModel
 
helper - Variable in class loci.formats.gui.SignedShortBuffer
 
helper - Variable in class loci.formats.gui.UnsignedIntColorModel
 
helper - Variable in class loci.formats.in.DicomReader
 
helper - Variable in class loci.formats.in.FilePatternReader
 
helper - Variable in class loci.formats.in.NRRDReader

Helper reader.

helperReader - Variable in class loci.formats.in.HitachiReader
 
hex2Rgb(String) - Static method in class loci.formats.in.CellH5Reader
 
hFilter - Variable in class jj2000.j2k.wavelet.analysis.SubbandAn

The horizontal analysis filter used to decompose this
        subband.

hFilter - Variable in class jj2000.j2k.wavelet.synthesis.SubbandSyn

The horizontal analysis filter used to recompose this subband,
        from its childs.

hh - Variable in class jj2000.j2k.roi.encoder.SubbandROIMask

The subband masks of the child HH

hh - Variable in class loci.formats.codec.JPEGTileDecoder.TileCache
 
hh - Variable in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
hi - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
hi - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Reference to the HeaderInfo instance (used when reading SOT marker
 segments)

hi - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

The reference to the HeaderInfo instance holding the information found
 in headers

HIDDEN_LAYER - Static variable in class loci.formats.in.CellSensReader
 
HIGH_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
 
highFields - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

A mapping of Integer tag numbers to TIFFFields
 for fields which are not low tag numbered.

HIS_MAGIC_STRING - Static variable in class loci.formats.in.HISReader
 
HISReader - Class in loci.formats.in

HISReader is the file format reader for Hamamatsu .his files.

HISReader() - Constructor for class loci.formats.in.HISReader

Constructs a new Hamamatsu .his reader.

HISTOLOGY_DOMAIN - Static variable in class loci.formats.FormatTools

Identifies the histology domain.

HISTORY_KEYS - Static variable in class loci.formats.in.ICSReader
 
HitachiReader - Class in loci.formats.in

HitachiReader is the file format reader for S-4800 files.

HitachiReader() - Constructor for class loci.formats.in.HitachiReader

Constructs a new Hitachi reader.

hl - Variable in class jj2000.j2k.roi.encoder.SubbandROIMask

The subband masks of the child HL

HORIZONTAL_FLIP - Static variable in class loci.formats.in.FluoviewReader
 
horz - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Black and white horizontal mode table.

horzMode - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Horizontal mode table.

HOST_COMPUTER - Static variable in class loci.formats.tiff.IFD
 
HostComputer() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.HostComputer
 
hostnames - Variable in class loci.formats.in.FlexReader.MeaHandler
 
HOT_PIXEL_CORRECTION - Static variable in class loci.formats.in.CellSensReader
 
HPSynthesisFilter - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

The high-pass synthesis filter of the 9x7 wavelet transform

HPSynthesisFilter - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

The high-pass synthesis filter of the 5x3 wavelet transform

HRDGDFReader - Class in loci.formats.in

HRDGDFReader is the file format reader for the Gridded Data Format used
 by NOAA's Hurricane Research Division.

HRDGDFReader() - Constructor for class loci.formats.in.HRDGDFReader

Constructs a new Gridded Data Format reader.

hRes - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox

The cached horizontal/vertical resolutions.

hsize - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
ht - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

HashTable used to store marker segment byte buffers

HTM_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
 
HTML_REGEX - Static variable in class loci.formats.in.PerkinElmerReader
 
HTML_SUFFIX - Static variable in class loci.formats.in.VisitechReader
 
HUE - Static variable in class loci.formats.in.NikonReader
 
HuffmanCodec - Class in loci.formats.codec

This class implements Huffman decoding.

HuffmanCodec() - Constructor for class loci.formats.codec.HuffmanCodec
 
HuffmanCodec.Decoder - Class in loci.formats.codec
 
HuffmanCodecOptions - Class in loci.formats.codec

Options for compressing and decompressing Huffman data.

HuffmanCodecOptions() - Constructor for class loci.formats.codec.HuffmanCodecOptions
 
humidity - Variable in class loci.formats.in.ZeissCZIReader
 
HxRLE(int, long) - Constructor for class loci.formats.in.AmiraReader.HxRLE
 
HxZip(long) - Constructor for class loci.formats.in.AmiraReader.HxZip
 




I

I - Variable in class jj2000.j2k.entropy.decoder.MQDecoder

The current index of each context

I - Variable in class jj2000.j2k.entropy.encoder.MQCoder

The current index of each context

i(String) - Method in class loci.formats.in.PrairieMetadata

Converts the given string to an Integer, or null if incompatible.

I18N - Class in com.sun.media.imageio.plugins.bmp
 
I18N() - Constructor for class com.sun.media.imageio.plugins.bmp.I18N
 
I18N - Class in com.sun.media.imageio.stream
 
I18N() - Constructor for class com.sun.media.imageio.stream.I18N
 
I18N - Class in com.sun.media.imageioimpl.common
 
I18N() - Constructor for class com.sun.media.imageioimpl.common.I18N
 
I18N - Class in com.sun.media.imageioimpl.plugins.bmp
 
I18N() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.I18N
 
I18N - Class in com.sun.media.imageioimpl.plugins.clib
 
I18N() - Constructor for class com.sun.media.imageioimpl.plugins.clib.I18N
 
I18N - Class in com.sun.media.imageioimpl.plugins.jpeg
 
I18N() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg.I18N
 
I18N - Class in com.sun.media.imageioimpl.plugins.jpeg2000
 
I18N() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.I18N
 
I18N - Class in com.sun.media.imageioimpl.plugins.png
 
I18N() - Constructor for class com.sun.media.imageioimpl.plugins.png.I18N
 
I18N - Class in com.sun.media.imageioimpl.plugins.pnm
 
I18N() - Constructor for class com.sun.media.imageioimpl.plugins.pnm.I18N
 
I18N - Class in com.sun.media.imageioimpl.plugins.raw
 
I18N() - Constructor for class com.sun.media.imageioimpl.plugins.raw.I18N
 
I18N - Class in com.sun.media.imageioimpl.plugins.tiff
 
I18N() - Constructor for class com.sun.media.imageioimpl.plugins.tiff.I18N
 
I18N - Class in com.sun.media.imageioimpl.plugins.wbmp
 
I18N() - Constructor for class com.sun.media.imageioimpl.plugins.wbmp.I18N
 
I18N - Class in com.sun.media.jai.imageioimpl
 
I18N() - Constructor for class com.sun.media.jai.imageioimpl.I18N
 
I18N - Class in com.sun.media.jai.operator
 
I18N() - Constructor for class com.sun.media.jai.operator.I18N
 
I18NImpl - Class in com.sun.media.imageioimpl.common

Class to simplify use of internationalization message strings.

I18NImpl() - Constructor for class com.sun.media.imageioimpl.common.I18NImpl
 
I2IReader - Class in loci.formats.in

I2IReader is the file format reader for I2I files.

I2IReader() - Constructor for class loci.formats.in.I2IReader

Constructs a new I2I reader.

ICacheSource - Interface in loci.formats.cache

Interface for cache sources.

ICacheStrategy - Interface in loci.formats.cache

Interface for cache strategies.

iCbTab - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
ICC_ENABLED - Static variable in class loci.formats.in.CellSensReader
 
ICCProfile() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ICCProfile
 
iccs - Variable in class jj2000.j2k.decoder.DecoderSpecs

ICC Profiling specifications

iceil(int, int) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
icon - Variable in class loci.formats.gui.ImageViewer
 
icon - Variable in class loci.formats.gui.PreviewPane
 
ICON_IMAGE_SEQUENCE - Static variable in class loci.formats.in.DicomReader
 
iconLabel - Variable in class loci.formats.gui.ImageViewer
 
iconLabel - Variable in class loci.formats.gui.PreviewPane

Labels containing thumbnail and dimensional information.

iconText - Variable in class loci.formats.gui.PreviewPane
 
iconTip - Variable in class loci.formats.gui.PreviewPane
 
iCrTab - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
ICSReader - Class in loci.formats.in

ICSReader is the file format reader for ICS (Image Cytometry Standard)
 files.

ICSReader() - Constructor for class loci.formats.in.ICSReader

Constructs a new ICSReader.

ICSWriter - Class in loci.formats.out

ICSWriter is the file format writer for ICS files.

ICSWriter() - Constructor for class loci.formats.out.ICSWriter
 
ictransf - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
id - Variable in class loci.formats.gui.CacheComponent

File name that the cache is working with (debugging only).

id - Variable in class loci.formats.in.BaseZeissReader.Shape
 
id - Variable in class loci.formats.in.FlexReader.FilterGroup
 
id - Variable in class loci.formats.in.LeicaHandler.Laser
 
id - Variable in class loci.formats.in.LeicaReader.Detector
 
id - Variable in class loci.formats.in.OIRReader.Channel
 
id - Variable in class loci.formats.in.OIRReader.Detector
 
id - Variable in class loci.formats.in.OIRReader.Laser
 
id - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane

File containing this plane.

id - Variable in class loci.formats.in.ZeissCZIReader.Segment
 
id - Variable in class loci.formats.in.ZeissTIFFReader.Channel
 
id - Variable in class loci.formats.in.ZeissTIFFReader.Slice
 
id - Variable in class loci.formats.in.ZeissTIFFReader.Timepoint
 
id - Variable in class loci.plugins.util.BFVirtualStack
 
idatCount - Variable in class loci.formats.in.APNGReader
 
IdDialog - Class in loci.plugins.in

Bio-Formats Importer id chooser dialog box.

IdDialog(ImportProcess) - Constructor for class loci.plugins.in.IdDialog

Creates an id chooser dialog for the Bio-Formats Importer.

idle - Variable in class jj2000.j2k.util.ThreadPool

The array of idle threads and the lock for the manipulation of the
 idle thread list.

idleComps - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The queue of idle compressors.

idLoc - Variable in class loci.plugins.in.ImportProcess
 
idName - Variable in class loci.plugins.in.ImportProcess
 
idx - Variable in class jj2000.j2k.codestream.CBlkCoordInfo

The code-block horizontal and vertical indexes

idx - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor

The index of this compressor.

idx1Pos - Variable in class loci.formats.out.AVIWriter
 
ifd - Variable in class loci.formats.in.LeicaSCNReader.Dimension
 
ifd - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane

IFD number of this plane.

IFD - Class in loci.formats.tiff

Data structure for working with TIFF Image File Directories (IFDs).

IFD() - Constructor for class loci.formats.tiff.IFD
 
IFD(IFD) - Constructor for class loci.formats.tiff.IFD
 
ifdCounts - Variable in class loci.formats.out.OMETiffWriter
 
IFDList - Class in loci.formats.tiff

Data structure for working with a list of TIFF IFDs.

IFDList() - Constructor for class loci.formats.tiff.IFDList
 
ifdList - Variable in class loci.formats.tiff.TiffParser

Cached list of IFDs in the current file.

IFDMap - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
ifdmap - Variable in class loci.formats.in.SVSReader
 
ifdOffsets - Variable in class loci.formats.in.FlowSightReader
 
ifds - Variable in class loci.formats.in.APLReader
 
ifds - Variable in class loci.formats.in.CellSensReader
 
ifds - Variable in class loci.formats.in.EPSReader
 
ifds - Variable in class loci.formats.in.FlexReader.FlexFile
 
ifds - Variable in class loci.formats.in.FV1000Reader
 
ifds - Variable in class loci.formats.in.LeicaReader
 
ifds - Variable in class loci.formats.in.MinimalTiffReader

List of IFDs for the current TIFF.

ifdsList - Variable in class loci.formats.in.ZeissLSMReader
 
IFDType - Enum in loci.formats.tiff

An enumeration of IFD types.

IFDType(int, int) - Constructor for enum loci.formats.tiff.IFDType

Default constructor.

ifloor(int, int) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
IFormatHandler - Interface in loci.formats

Interface for all biological file format readers and writers.

IFormatReader - Interface in loci.formats

Interface for all biological file format readers.

IFormatWidgets - Interface in loci.plugins.config

Interface for defining custom widgets for a specific file format reader.

IFormatWriter - Interface in loci.formats

Interface for all biological file format writers.

iGCbTab - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
iGCrTab - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
ignore - Variable in class loci.plugins.util.SearchableWindow.SearchBox
 
ignoreCase - Variable in class loci.plugins.util.SearchableWindow.SearchBox
 
iGYTab - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
ih - Variable in class loci.formats.in.GIFReader

Current image rectangle.

IHB_LENGTH - Static variable in class jj2000.j2k.fileformat.writer.FileFormatWriter

Length of Image Header Box

IIOByteArrayOutputStream() - Constructor for class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor.IIOByteArrayOutputStream
 
IIOByteArrayOutputStream(int) - Constructor for class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor.IIOByteArrayOutputStream
 
IIOWriteProgressAdapter() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter.IIOWriteProgressAdapter
 
iis - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

The input stream where reads from

iis - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO

The ImageInputStream that is wrapped

iis - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

The input stream where reads from

iis - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState

The input stream we read from

iis - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
iis - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

The input stream where reads from

iis - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageReader

The input stream where reads from

iis - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

The input stream we read from

iis - Variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader

The input stream where reads from

IISRandomAccessIO - Class in com.sun.media.imageioimpl.plugins.jpeg2000

A wrapper for converting an ImageInputStream into a
 RandomAccessIO.

IISRandomAccessIO(ImageInputStream) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO

Creates a RandomAccessIO instance from the supplied
 ImageInputStream.

IJStatusEchoer - Class in loci.plugins.util

Echoes status messages to the ImageJ status bar.

IJStatusEchoer() - Constructor for class loci.plugins.util.IJStatusEchoer
 
IllegalBlockException - Exception in loci.formats

Exception thrown when FilePatternBlock encounters an
 invalid pattern.

IllegalBlockException() - Constructor for exception loci.formats.IllegalBlockException
 
IllegalBlockException(String) - Constructor for exception loci.formats.IllegalBlockException
 
IllegalBlockException(String, Throwable) - Constructor for exception loci.formats.IllegalBlockException
 
IllegalBlockException(Throwable) - Constructor for exception loci.formats.IllegalBlockException
 
ILLUM_CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
 
ILLUM_CHANNEL_ATTENUATION - Static variable in class loci.formats.in.ZeissLSMReader
 
ILLUM_CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
 
ILLUM_CHANNEL_WAVELENGTH - Static variable in class loci.formats.in.ZeissLSMReader
 
ILLUMINATION - Static variable in class loci.formats.FormatTools

Identifies the Illumination dimensional type,
 representing a dimension consisting of illuminations.

illumination - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
IlluminationChannel() - Constructor for class loci.formats.in.ZeissLSMReader.IlluminationChannel
 
illuminationLabels - Variable in class loci.formats.in.ZeissCZIReader
 
illuminations - Variable in class loci.formats.in.FV1000Reader
 
illuminations - Variable in class loci.formats.in.ZeissCZIReader
 
illuminations - Variable in class loci.formats.in.ZeissLSMReader
 
illumNA - Variable in class loci.formats.in.LeicaSCNReader.Image
 
illumSource - Variable in class loci.formats.in.LeicaSCNReader.Image
 
IM3Reader - Class in loci.formats.in
 
IM3Reader() - Constructor for class loci.formats.in.IM3Reader

Construct an uninitialized reader of .im3 files.

IM3Reader.BooleanIM3Record - Class in loci.formats.in

A record containing boolean values

IM3Reader.ContainerRecord - Class in loci.formats.in
 
IM3Reader.FloatIM3Record - Class in loci.formats.in
 
IM3Reader.IM3Record - Class in loci.formats.in
 
IM3Reader.IntIM3Record - Class in loci.formats.in
 
IM3Reader.Spectrum - Class in loci.formats.in
 
IM3Reader.StringIM3Record - Class in loci.formats.in
 
IM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.IM3Record
 
ImaconHandler() - Constructor for class loci.formats.in.ImaconReader.ImaconHandler
 
ImaconReader - Class in loci.formats.in

ImaconReader is the file format reader for Imacon .fff (TIFF) files.

ImaconReader() - Constructor for class loci.formats.in.ImaconReader

Constructs a new Imacon reader.

ImaconReader.ImaconHandler - Class in loci.formats.in
 
image - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The final destination image.

image - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
IMAGE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
Image() - Constructor for class loci.formats.in.InCellReader.Image
 
image - Variable in class loci.formats.in.LegacyQTReader

Image containing current frame.

Image(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Image
 
image - Variable in class loci.formats.in.VeecoReader
 
IMAGE_BOUNDARY - Static variable in class loci.formats.in.CellSensReader
 
IMAGE_COLLECTION_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
IMAGE_DESCRIPTION - Static variable in class loci.formats.tiff.IFD
 
IMAGE_FRAME_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
IMAGE_HEADER_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes

JP2 Header boxes

IMAGE_LENGTH - Static variable in class loci.formats.tiff.IFD
 
IMAGE_METADATA_NAME - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
IMAGE_METADATA_NAME - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
IMAGE_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
IMAGE_PRO_TAG_1 - Static variable in class loci.formats.in.SEQReader

An array of shorts (length 12) with identical values in all of our
 samples; assuming this is some sort of format identifier.

IMAGE_PRO_TAG_2 - Static variable in class loci.formats.in.SEQReader

Frame rate.

IMAGE_PRO_TAG_3 - Static variable in class loci.formats.in.SEQReader
 
IMAGE_SEPARATOR - Static variable in class loci.formats.in.GIFReader
 
IMAGE_SOURCE_DATA - Static variable in class loci.formats.in.PhotoshopTiffReader
 
IMAGE_TYPE_1 - Static variable in class loci.formats.in.OpenlabReader

Tag types.

IMAGE_TYPE_2 - Static variable in class loci.formats.in.OpenlabReader
 
IMAGE_TYPES - Static variable in class loci.formats.in.DeltavisionReader
 
IMAGE_WIDTH - Static variable in class loci.formats.tiff.IFD
 
ImageCollection(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.ImageCollection
 
imageComplete(ImageReader) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader.EmbeddedProgressAdapter
 
imageComplete(ImageWriter) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter.IIOWriteProgressAdapter
 
imageComplete(int) - Method in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
imageCount - Variable in class loci.formats.CoreMetadata

Total number of images.

imageCount - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
 
imageCreationDate - Variable in class loci.formats.in.MetamorphReader

The TIFF's creation date

imageData - Variable in class jj2000.j2k.image.ImgDataJoiner

The list of input ImgData

imageDataOffset - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

The stream position where the image data starts.

imageDataOffset - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

The stream position where the image data starts.

imageDataOffset - Variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader

The stream position where the image data starts.

imageDepth - Variable in class loci.formats.in.FV1000Reader
 
ImageDescription() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ImageDescription
 
imageDescription - Variable in class loci.formats.in.BaseZeissReader
 
imageDescription - Variable in class loci.formats.in.FEITiffReader
 
imageDescriptions - Variable in class loci.formats.in.SlidebookReader
 
imageDimensions - Variable in class com.sun.media.imageio.stream.RawImageInputStream

The image sizes.

imageDimensions - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
imageFile - Variable in class loci.formats.in.PCORAWReader
 
imageFiles - Variable in class loci.formats.in.BaseZeissReader
 
imageFiles - Variable in class loci.formats.in.InCellReader
 
imageFiles - Variable in class loci.formats.in.IPWReader

List of embedded image file names (one per image plane).

imageFiles - Variable in class loci.formats.in.PCIReader
 
imageFolder - Variable in class loci.formats.in.CellVoyagerReader
 
imageHeight - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
imageHeight - Variable in class loci.formats.in.InCellReader
 
imageHeight - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
imageIFD(int) - Method in class loci.formats.in.LeicaSCNReader
 
imageIndex - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter

The index of the image being written.

imageIndex - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

The image index in this stream.

imageIndex - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
imageIndex - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
ImageInputStreamWrapper - Class in com.sun.media.imageioimpl.plugins.jpeg2000

This class is designed to wrap a ImageInputStream into
  a InputStream.


ImageInputStreamWrapper(ImageInputStream) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper

Constructs an ImageInputStreamWrapper from the provided
  ImageInputStream.

ImageIOReader - Class in loci.formats.in

ImageIOReader is the superclass for file format readers
 that use the javax.imageio package.

ImageIOReader(String, String) - Constructor for class loci.formats.in.ImageIOReader

Constructs a new ImageIOReader.

ImageIOReader(String, String[]) - Constructor for class loci.formats.in.ImageIOReader

Constructs a new ImageIOReader.

ImageIOWriter - Class in loci.formats.out

ImageIOWriter is the superclass for file format writers that use the
 javax.imageio library.

ImageIOWriter(String, String, String) - Constructor for class loci.formats.out.ImageIOWriter

Constructs an ImageIO-based writer with the given name, default suffix
 and output type (e.g., png, jpeg).

ImageIOWriter(String, String[], String) - Constructor for class loci.formats.out.ImageIOWriter

Constructs an ImageIO-based writer with the given name, default suffixes
 and output type (e.g., png, jpeg).

imageIsContiguous(RenderedImage) - Static method in class com.sun.media.imageioimpl.common.ImageUtil

Returns whether the image has contiguous data across rows.

IMAGEJ_MSG - Static variable in class loci.plugins.util.LibraryChecker

Message to be displayed if ImageJ is too old for Bio-Formats plugins.

IMAGEJ_TAG - Static variable in class loci.formats.in.TiffReader
 
IMAGEJ_VERSION - Static variable in class loci.plugins.util.LibraryChecker

Minimum version of ImageJ necessary for Bio-Formats plugins.

imageLeftPosition - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
ImageLength() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ImageLength
 
imageLocations - Variable in class loci.formats.out.OMETiffWriter
 
imageMap - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
imageMetadata - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

Image metadata, valid for the imageMetadataIndex only.

imageMetadata - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
imageMetadata - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
imageMetadataIndex - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

The image index for the cached metadata.

imageName - Variable in class loci.formats.in.BioRadSCNReader
 
imageName - Variable in class loci.formats.in.FEITiffReader
 
imageName - Variable in class loci.formats.in.ImaconReader
 
imageName - Variable in class loci.formats.in.MetamorphHandler
 
imageName - Variable in class loci.formats.in.MetamorphReader

The TIFF's name

imageName - Variable in class loci.formats.in.SISReader
 
imageName - Variable in class loci.formats.in.ZeissCZIReader
 
imageNames - Variable in class loci.formats.in.LIFReader
 
imageNames - Variable in class loci.formats.in.TillVisionReader
 
imageNames - Variable in class loci.formats.in.ZeissLSMReader
 
imageNumber - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
imageNumEnd - Variable in class loci.formats.in.LeicaSCNReader.Image
 
imageNumStart - Variable in class loci.formats.in.LeicaSCNReader.Image
 
imageOffset - Variable in class loci.formats.in.IvisionReader
 
imageOffsets - Variable in class com.sun.media.imageio.stream.RawImageInputStream

The position of the first sample for each image.

ImagePlusReader - Class in loci.plugins.in

A high-level reader for ImagePlus objects.

ImagePlusReader() - Constructor for class loci.plugins.in.ImagePlusReader

Constructs an ImagePlusReader with the default options.

ImagePlusReader(ImportProcess) - Constructor for class loci.plugins.in.ImagePlusReader

Constructs an ImagePlusReader with the
 given complete import preparation process.

ImageProcessorReader - Class in loci.plugins.util

A low-level reader for ImageProcessor objects.

ImageProcessorReader() - Constructor for class loci.plugins.util.ImageProcessorReader

Constructs an ImageProcessorReader around a new image reader.

ImageProcessorReader(IFormatReader) - Constructor for class loci.plugins.util.ImageProcessorReader

Constructs an ImageProcessorReader with the given reader.

ImageProcessorSource - Class in loci.plugins.util

Retrieves ImageJ image processors from an image reader.

ImageProcessorSource(IFormatReader) - Constructor for class loci.plugins.util.ImageProcessorSource
 
imageProgress(ImageReader, float) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader.EmbeddedProgressAdapter
 
imageProgress(ImageWriter, float) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter.IIOWriteProgressAdapter
 
ImageReader - Class in loci.formats

ImageReader is the master file format reader for all supported formats.

ImageReader() - Constructor for class loci.formats.ImageReader

Constructs a new ImageReader with the default
 list of reader classes from readers.txt.

ImageReader(ClassList<IFormatReader>) - Constructor for class loci.formats.ImageReader

Constructs a new ImageReader from the given list of reader classes.

imageReader - Variable in class loci.plugins.in.ImportProcess
 
imageReadParam - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
imageROIs - Variable in class loci.formats.in.LIFReader
 
imageRX - Variable in class loci.formats.in.SDTInfo
 
imageRY - Variable in class loci.formats.in.SDTInfo
 
images - Variable in class loci.formats.gui.ImageViewer
 
images - Variable in class loci.formats.in.GIFReader
 
IMAGES - Static variable in class loci.formats.in.LeicaReader
 
images - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
imageSize - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
imageSize - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
imagesPerFile - Variable in class loci.formats.FileStitcher.ExternalSeries
 
imagesPerFile - Variable in class loci.formats.in.DicomReader
 
imageStarted(ImageReader, int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader.EmbeddedProgressAdapter
 
imageStarted(ImageWriter, int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter.IIOWriteProgressAdapter
 
imageStartPosition - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
imageThumbnail - Variable in class loci.formats.in.LeicaSCNReader.Image
 
ImageTools - Class in loci.formats

A utility class with convenience methods for manipulating images
 in primitive array form.

ImageTools() - Constructor for class loci.formats.ImageTools
 
imageTopPosition - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
imageType - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
imageType - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
imageType - Variable in class loci.formats.in.DicomReader
 
imageTypeMap - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
ImageUniqueID() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ImageUniqueID
 
ImageUtil - Class in com.sun.media.imageioimpl.common
 
ImageUtil() - Constructor for class com.sun.media.imageioimpl.common.ImageUtil
 
ImageViewer - Class in loci.formats.gui

ImageViewer is a simple viewer/converter
 for the Bio-Formats image formats.

ImageViewer() - Constructor for class loci.formats.gui.ImageViewer

Constructs an image viewer.

ImageViewer(boolean) - Constructor for class loci.formats.gui.ImageViewer

Constructs an image viewer.

ImageWidth() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ImageWidth
 
imageWidth - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
imageWidth - Variable in class loci.formats.in.InCellReader
 
imageWidth - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
ImageWriter - Class in loci.formats

ImageWriter is the master file format writer for all supported formats.

ImageWriter() - Constructor for class loci.formats.ImageWriter

Constructs a new ImageWriter with the default
 list of writer classes from writers.txt.

ImageWriter(ClassList<IFormatWriter>) - Constructor for class loci.formats.ImageWriter

Constructs a new ImageWriter from the given list of writer classes.

imageX - Variable in class loci.formats.in.SDTInfo

4 subsequent fields valid only for Camera mode
 or FIFO_IMAGE mode.

imageY - Variable in class loci.formats.in.SDTInfo
 
ImagicReader - Class in loci.formats.in

ImagicReader is the file format reader for IMAGIC files.

ImagicReader() - Constructor for class loci.formats.in.ImagicReader

Constructs a new IMAGIC reader.

IMARIS_MAGIC_BYTES - Static variable in class loci.formats.in.ImarisReader

Magic number; present in all files.

ImarisHDFReader - Class in loci.formats.in

Reader for Bitplane Imaris 5.5 (HDF) files.

ImarisHDFReader() - Constructor for class loci.formats.in.ImarisHDFReader

Constructs a new Imaris HDF reader.

ImarisReader - Class in loci.formats.in

ImarisReader is the file format reader for Bitplane Imaris files.

ImarisReader() - Constructor for class loci.formats.in.ImarisReader

Constructs a new Imaris reader.

ImarisTiffReader - Class in loci.formats.in

ImarisTiffReader is the file format reader for
 Bitplane Imaris 3 files (TIFF variant).

ImarisTiffReader() - Constructor for class loci.formats.in.ImarisTiffReader

Constructs a new Imaris TIFF reader.

IMB_C - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
IMB_IPR - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
IMB_UnkC - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
IMB_VERS - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes

Image Header Box Fields

IMetadata - Interface in loci.formats.meta
 
IMetadataConfigurable - Interface in loci.formats
 
img - Variable in class loci.formats.in.ImageIOReader

Transient reference to a BufferedImage for this
 FormatHandler.currentId.

img - Variable in class loci.formats.tools.AsciiImage
 
ImgData - Interface in jj2000.j2k.image

This interface defines methods to access image attributes (width, height,
 number of components, etc.).

ImgDataAdapter - Class in jj2000.j2k.image

This class provides a default implementation of the methods in the
 'ImgData' interface.

ImgDataAdapter(ImgData) - Constructor for class jj2000.j2k.image.ImgDataAdapter

Instantiates the ImgDataAdapter object specifying the ImgData source.

ImgDataConverter - Class in jj2000.j2k.image

This class is responsible of all data type conversions.

ImgDataConverter(BlkImgDataSrc, int) - Constructor for class jj2000.j2k.image.ImgDataConverter

Constructs a new ImgDataConverter object that operates on the specified
 source of image data.

ImgDataConverter(BlkImgDataSrc) - Constructor for class jj2000.j2k.image.ImgDataConverter

Constructs a new ImgDataConverter object that operates on the specified
 source of image data.

ImgDataJoiner - Class in jj2000.j2k.image

This class implements the ImgData interface and allows to obtain data from
 different sources.

ImgDataJoiner(BlkImgDataSrc[], int[]) - Constructor for class jj2000.j2k.image.ImgDataJoiner

Class constructor.

imgdatasrc - Variable in class jj2000.j2k.image.ImgDataAdapter

The ImgData source

imgH - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The image width on the hi-res reference grid

ImgReader - Class in jj2000.j2k.image.input

This is the generic interface to be implemented by all image file (or other
 resource) readers for different image file formats.

ImgReader() - Constructor for class jj2000.j2k.image.input.ImgReader
 
ImgReaderPGM - Class in jj2000.j2k.image.input

This class implements the ImgData interface for reading 8 bit unsigned data
 from a binary PGM file.

ImgReaderPGM(File) - Constructor for class jj2000.j2k.image.input.ImgReaderPGM

Creates a new PGM file reader from the specified file.

ImgReaderPGM(String) - Constructor for class jj2000.j2k.image.input.ImgReaderPGM

Creates a new PGM file reader from the specified file name.

ImgReaderPGM(RandomAccessFile) - Constructor for class jj2000.j2k.image.input.ImgReaderPGM

Creates a new PGM file reader from the specified RandomAccessFile
 object.

imgsrc - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
 
imgW - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The image width on the hi-res reference grid

IMinMaxStore - Interface in loci.formats.meta

Interface for consumers of minima and maxima pixel intensities across a
 given wavelength.

immersion - Variable in class loci.formats.in.ND2Handler
 
immersion - Variable in class loci.formats.in.NikonTiffReader
 
immersion - Variable in class loci.formats.in.OIRReader.Objective
 
immersion - Variable in class loci.formats.in.SimplePCITiffReader
 
immersion - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
immersions - Variable in class loci.formats.in.LIFReader
 
IMODReader - Class in loci.formats.in

Reader for IMOD binary files.

IMODReader() - Constructor for class loci.formats.in.IMODReader

Constructs a new IMOD reader.

IMODSTAMP_OFFSET - Static variable in class loci.formats.in.MRCReader
 
imp - Variable in class loci.plugins.out.Exporter

Current stack.

imp - Variable in class loci.plugins.Slicer

Current image stack.

IMPLICIT_VR - Static variable in class loci.formats.in.DicomReader
 
importData(JComponent, Transferable) - Method in class loci.plugins.shortcut.ShortcutTransferHandler
 
Importer - Class in loci.plugins.in

Core logic for the Bio-Formats Importer ImageJ plugin.

Importer(LociImporter) - Constructor for class loci.plugins.in.Importer
 
ImporterDialog - Class in loci.plugins.in

Abstract superclass of importer dialogs.

ImporterDialog(ImportProcess) - Constructor for class loci.plugins.in.ImporterDialog
 
ImporterMetadata - Class in loci.plugins.in

Helper class for storing original metadata key/value pairs.

ImporterMetadata(IFormatReader, ImportProcess, boolean) - Constructor for class loci.plugins.in.ImporterMetadata
 
ImporterOptions - Class in loci.plugins.in

Helper class for managing Bio-Formats Importer options.

ImporterOptions() - Constructor for class loci.plugins.in.ImporterOptions
 
ImporterPrompter - Class in loci.plugins.in

Helper class for presenting the user with dialog boxes
 for configuring importer options.

ImporterPrompter(ImportProcess) - Constructor for class loci.plugins.in.ImporterPrompter
 
ImportProcess - Class in loci.plugins.in

Manages the import preparation process.

ImportProcess() - Constructor for class loci.plugins.in.ImportProcess
 
ImportProcess(ImporterOptions) - Constructor for class loci.plugins.in.ImportProcess
 
ImportStep - Enum in loci.plugins.in

An enumeration of the steps in the import preparation process.

ImportStep(int, String) - Constructor for enum loci.plugins.in.ImportStep
 
IMPROVISION_MAGIC_STRING - Static variable in class loci.formats.in.ImprovisionTiffReader
 
ImprovisionTiffReader - Class in loci.formats.in

ImprovisionTiffReader is the file format reader for
 Improvision TIFF files.

ImprovisionTiffReader() - Constructor for class loci.formats.in.ImprovisionTiffReader
 
ImspectorReader - Class in loci.formats.in

ImspectorReader is the file format reader for Imspector .msr files.

ImspectorReader() - Constructor for class loci.formats.in.ImspectorReader

Constructs a new Imspector reader.

in - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
in - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

The RandomAccessIO where to get data from

in - Variable in class jj2000.j2k.codestream.reader.PktHeaderBitReader

The byte based source of data

in - Variable in class jj2000.j2k.entropy.decoder.ByteToBitInput

The byte based input

in - Variable in class jj2000.j2k.entropy.decoder.MQDecoder

The ByteInputBuffer used to read the compressed bit stream.

in - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader

The random access from which the file format boxes are read

in - Variable in class jj2000.j2k.image.input.ImgReaderPGM

Where to read the data from

in - Variable in class loci.formats.codec.JPEGTileDecoder
 
in - Variable in class loci.formats.FormatReader

Current file.

in - Variable in class loci.formats.gui.ImageViewer
 
in - Variable in class loci.formats.in.JPEG2000MetadataParser

Stream that we're parsing metadata from.

in - Variable in class loci.formats.in.ZeissTIFFReader.Plane
 
in - Variable in class loci.formats.out.TiffWriter

Input stream to use when overwriting data.

in - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
in - Variable in class loci.formats.tiff.TiffParser

Input source from which to parse TIFF data.

in - Variable in class loci.formats.tools.AmiraParameters
 
inblk - Variable in class jj2000.j2k.quantization.dequantizer.StdDequantizer

The 'DataBlkInt' object used to request data, used when output data is
 not int

inc - Variable in class jj2000.j2k.util.ISRandomAccessIO
 
inCache - Variable in class loci.formats.cache.Cache

Whether each position is currently supposed to be cached.

incCompImageSize(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
InCell3000Reader - Class in loci.formats.in

InCell3000Reader is the file format reader for InCell 3000.

InCell3000Reader() - Constructor for class loci.formats.in.InCell3000Reader

Constructs a new InCell 3000 reader.

INCELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader
 
InCellHandler(MetadataStore) - Constructor for class loci.formats.in.InCellReader.InCellHandler
 
InCellReader - Class in loci.formats.in

InCellReader is the file format reader for InCell 1000/2000 datasets.

InCellReader() - Constructor for class loci.formats.in.InCellReader

Constructs a new InCell 1000/2000 reader.

InCellReader.Image - Class in loci.formats.in
 
InCellReader.InCellHandler - Class in loci.formats.in

SAX handler for parsing XML.

InCellReader.MinimalInCellHandler - Class in loci.formats.in
 
INCLUDE_ATTACHMENTS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
 
INCLUDE_ATTACHMENTS_KEY - Static variable in class loci.formats.in.ZeissCZIReader
 
includeC - Variable in class loci.formats.gui.DataConverter
 
includeCZIAttachments() - Static method in class loci.plugins.util.LociPrefs
 
includeT - Variable in class loci.formats.gui.DataConverter
 
includeZ - Variable in class loci.formats.gui.DataConverter
 
incr - Variable in class loci.formats.in.SDTInfo
 
index - Variable in class loci.formats.cache.CacheEvent

Relevant index to the event, if any.

index - Variable in class loci.formats.codec.BitWriter

Deprecated.
Byte index into the buffer.

index - Variable in class loci.formats.in.BaseZeissReader.Tag
 
index - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
 
index - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
 
index - Variable in class loci.formats.in.LeicaHandler.Laser
 
index - Variable in class loci.formats.in.LeicaReader.Detector
 
Index(int[]) - Constructor for class loci.formats.in.MicromanagerReader.Index
 
index - Variable in class loci.formats.in.PrairieMetadata.Frame

index of this <Frame>.

index - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
 
index - Variable in class loci.plugins.in.ThumbLoader.SeriesInfo
 
index - Variable in class loci.plugins.util.SearchableWindow
 
Index16ColorModel - Class in loci.formats.gui

ColorModel that handles 16 bits per channel lookup tables.

Index16ColorModel(int, int, short[][], boolean) - Constructor for class loci.formats.gui.Index16ColorModel
 
index_ - Variable in class com.sun.media.imageioimpl.common.BitFile
 
indexed - Variable in class loci.formats.CoreMetadata

Indicates whether or not the images are stored as indexed color.

INDEXED - Static variable in class loci.formats.in.APNGReader
 
indexedAsRGB - Variable in class loci.formats.FormatReader

Whether or not MetadataStore sets C = 3 for indexed color images.

indexedToRGB(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools

Converts an indexed color BufferedImage to an RGB BufferedImage.

indexedToRGB(byte[][], byte[]) - Static method in class loci.formats.ImageTools

Converts a LUT and an array of indices into an array of RGB tuples.

indexedToRGB(short[][], byte[], boolean) - Static method in class loci.formats.ImageTools

Converts a LUT and an array of indices into an array of RGB tuples.

indexIntoPlanes - Variable in class loci.formats.in.ZeissCZIReader
 
indexMax - Variable in class loci.formats.in.PrairieMetadata.Sequence

Maximum index value.

indexMin - Variable in class loci.formats.in.PrairieMetadata.Sequence

Minimum index value.

indexToValue - Variable in class loci.formats.in.FakeReader

For indexed color, mapping from indices to values and vice versa.

inDimensionProperties - Variable in class loci.formats.in.CellSensReader
 
INDIVIDUAL_JARS - Static variable in class loci.formats.UpgradeChecker

Names of the individual JARs.

infblk - Variable in class jj2000.j2k.quantization.quantizer.StdQuantizer

The 'CBlkWTDataFloat' object used to request data, used when
 quantizing floating-point data.

infFile - Variable in class loci.formats.in.FujiReader
 
infFiles - Variable in class loci.formats.in.TillVisionReader
 
inflater - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFDeflateDecompressor
 
inflater - Variable in class loci.formats.in.OBFReader
 
INFO - Static variable in interface jj2000.j2k.util.MsgLogger

Severity of message.

info - Variable in class loci.formats.in.GatanReader
 
info - Variable in class loci.formats.in.OMETiffReader

Mapping from series and plane numbers to files and IFD entries.

info - Variable in class loci.formats.in.SDTInfo
 
info - Variable in class loci.formats.in.SDTReader

Object containing SDT header information.

info - Variable in class loci.plugins.prefs.Option

Documentation about the option, in HTML.

INFO_DEFAULT - Static variable in class loci.plugins.in.MainDialog

Initial message to display in help text box.

INFO_TABLE - Static variable in class loci.formats.in.LiFlimReader
 
infoLength - Variable in class loci.formats.in.SDTInfo

Length of the info part.

infoOffs - Variable in class loci.formats.in.SDTInfo

Offset of the info part which contains general text
 information (Title, date, time, contents etc.).

infoPane - Variable in class loci.plugins.in.MainDialog
 
infoSrc - Variable in class jj2000.j2k.codestream.writer.PktEncoder

The source object

infoTable - Variable in class loci.plugins.in.MainDialog
 
ini - Variable in class loci.formats.in.LiFlimReader

Parsed configuration data.

INI_DEFAULT - Static variable in class loci.plugins.prefs.Option

INI key indicating option's default value.

INI_INFO - Static variable in class loci.plugins.prefs.Option

INI key indicating option's info.

INI_KEY - Static variable in class loci.plugins.prefs.Option

INI key indicating option's key.

INI_LABEL - Static variable in class loci.plugins.prefs.Option

INI key indicating option's label.

INI_POSSIBLE - Static variable in class loci.plugins.prefs.StringOption

INI key indicating option's possible values.

INI_SAVE - Static variable in class loci.plugins.prefs.Option

INI key indicating whether option should be saved to prefs file.

INI_TYPE - Static variable in class loci.plugins.prefs.OptionsList

INI key indicating option's type.

iniFile - Variable in class loci.formats.in.FakeReader

Properties companion file which can be associated with this fake file

init(int, int) - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Initializes the variables of this class, given the dimensions
 at the base level (leaf level).

init() - Method in class jj2000.j2k.entropy.decoder.MQDecoder

Initializes the state of the MQ coder, without modifying the current
 context states.

init() - Method in class loci.formats.services.NetCDFServiceImpl
 
init() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
init() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
init() - Method in class org.libjpegturbo.turbojpeg.TJTransformer
 
INIT_EL_COPYING - Static variable in class jj2000.j2k.util.ArrayUtil

The number of elements to copy initially in an optimized array copy

INIT_LBLOCK - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Initial value of the state variable associated with code-block
 length.

INIT_LBLOCK - Static variable in class jj2000.j2k.codestream.writer.PktEncoder

The initial value for the lblock

initAlternateMetadata() - Method in class loci.formats.in.FluoviewReader
 
initAlternateMetadataStore() - Method in class loci.formats.in.FluoviewReader
 
initBitBuf() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Initialize bit buffer machinery.

initBlack - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
initChilds() - Method in class jj2000.j2k.wavelet.Subband

Initializes the childs of this node with the correct values.

initClass() - Method in class loci.formats.gui.LegacyQTTools

Initializes the class.

initCoreMetadata(int, int) - Method in class loci.formats.in.LeicaSCNReader
 
initCoreMetadata() - Method in class loci.formats.in.LiFlimReader
 
initData(Node, int[], int[], Object[]) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFField
 
initDecompressor() - Method in class loci.formats.in.AmiraReader.HxZip
 
initExtraMetadata() - Method in class loci.formats.in.DeltavisionReader
 
initFile(String) - Method in class loci.formats.FileStitcher

Initializes the given file or file pattern.

initFile(String) - Method in class loci.formats.FormatReader

Initializes the given file (parsing header information, etc.).

initFile(String) - Method in class loci.formats.in.AFIReader
 
initFile(String) - Method in class loci.formats.in.AIMReader
 
initFile(String) - Method in class loci.formats.in.AliconaReader
 
initFile(String) - Method in class loci.formats.in.AmiraReader
 
initFile(String) - Method in class loci.formats.in.AnalyzeReader
 
initFile(String) - Method in class loci.formats.in.APLReader
 
initFile(String) - Method in class loci.formats.in.APNGReader
 
initFile(String) - Method in class loci.formats.in.ARFReader
 
initFile(String) - Method in class loci.formats.in.AVIReader
 
initFile(String) - Method in class loci.formats.in.BaseTiffReader
 
initFile(String) - Method in class loci.formats.in.BDReader
 
initFile(String) - Method in class loci.formats.in.BioRadGelReader
 
initFile(String) - Method in class loci.formats.in.BioRadReader
 
initFile(String) - Method in class loci.formats.in.BioRadSCNReader
 
initFile(String) - Method in class loci.formats.in.BMPReader
 
initFile(String) - Method in class loci.formats.in.BrukerReader
 
initFile(String) - Method in class loci.formats.in.BurleighReader
 
initFile(String) - Method in class loci.formats.in.CanonRawReader
 
initFile(String) - Method in class loci.formats.in.CellH5Reader
 
initFile(String) - Method in class loci.formats.in.CellomicsReader
 
initFile(String) - Method in class loci.formats.in.CellSensReader
 
initFile(String) - Method in class loci.formats.in.CellVoyagerReader
 
initFile(String) - Method in class loci.formats.in.CellWorxReader
 
initFile(String) - Method in class loci.formats.in.ColumbusReader
 
initFile(String) - Method in class loci.formats.in.DeltavisionReader
 
initFile(String) - Method in class loci.formats.in.DicomReader
 
initFile(String) - Method in class loci.formats.in.DNGReader
 
initFile(String) - Method in class loci.formats.in.Ecat7Reader
 
initFile(String) - Method in class loci.formats.in.EPSReader
 
initFile(String) - Method in class loci.formats.in.FakeReader
 
initFile(String) - Method in class loci.formats.in.FEIReader
 
initFile(String) - Method in class loci.formats.in.FilePatternReader
 
initFile(String) - Method in class loci.formats.in.FitsReader
 
initFile(String) - Method in class loci.formats.in.FlexReader
 
initFile(String) - Method in class loci.formats.in.FlowSightReader
 
initFile(String) - Method in class loci.formats.in.FujiReader
 
initFile(String) - Method in class loci.formats.in.FV1000Reader
 
initFile(String) - Method in class loci.formats.in.GatanDM2Reader
 
initFile(String) - Method in class loci.formats.in.GatanReader
 
initFile(String) - Method in class loci.formats.in.GIFReader
 
initFile(String) - Method in class loci.formats.in.HamamatsuVMSReader
 
initFile(String) - Method in class loci.formats.in.HISReader
 
initFile(String) - Method in class loci.formats.in.HitachiReader
 
initFile(String) - Method in class loci.formats.in.HRDGDFReader
 
initFile(String) - Method in class loci.formats.in.I2IReader
 
initFile(String) - Method in class loci.formats.in.ICSReader
 
initFile(String) - Method in class loci.formats.in.IM3Reader
 
initFile(String) - Method in class loci.formats.in.ImageIOReader
 
initFile(String) - Method in class loci.formats.in.ImagicReader
 
initFile(String) - Method in class loci.formats.in.ImarisHDFReader
 
initFile(String) - Method in class loci.formats.in.ImarisReader
 
initFile(String) - Method in class loci.formats.in.ImarisTiffReader
 
initFile(String) - Method in class loci.formats.in.IMODReader
 
initFile(String) - Method in class loci.formats.in.ImspectorReader
 
initFile(String) - Method in class loci.formats.in.InCell3000Reader
 
initFile(String) - Method in class loci.formats.in.InCellReader
 
initFile(String) - Method in class loci.formats.in.INRReader
 
initFile(String) - Method in class loci.formats.in.InveonReader
 
initFile(String) - Method in class loci.formats.in.IPLabReader
 
initFile(String) - Method in class loci.formats.in.IPWReader
 
initFile(String) - Method in class loci.formats.in.IvisionReader
 
initFile(String) - Method in class loci.formats.in.JEOLReader
 
initFile(String) - Method in class loci.formats.in.JPEG2000Reader
 
initFile(String) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
 
initFile(String) - Method in class loci.formats.in.JPXReader
 
initFile(String) - Method in class loci.formats.in.KhorosReader
 
initFile(String) - Method in class loci.formats.in.KodakReader
 
initFile(String) - Method in class loci.formats.in.L2DReader
 
initFile(String) - Method in class loci.formats.in.LegacyND2Reader
 
initFile(String) - Method in class loci.formats.in.LegacyQTReader
 
initFile(String) - Method in class loci.formats.in.LeicaReader
 
initFile(String) - Method in class loci.formats.in.LiFlimReader
 
initFile(String) - Method in class loci.formats.in.LIFReader
 
initFile(String) - Method in class loci.formats.in.LIMReader
 
initFile(String) - Method in class loci.formats.in.MetamorphReader
 
initFile(String) - Method in class loci.formats.in.MetamorphTiffReader
 
initFile(String) - Method in class loci.formats.in.MIASReader
 
initFile(String) - Method in class loci.formats.in.MicromanagerReader
 
initFile(String) - Method in class loci.formats.in.MINCReader
 
initFile(String) - Method in class loci.formats.in.MinimalTiffReader
 
initFile(String) - Method in class loci.formats.in.MNGReader
 
initFile(String) - Method in class loci.formats.in.MolecularImagingReader
 
initFile(String) - Method in class loci.formats.in.MRCReader
 
initFile(String) - Method in class loci.formats.in.MRWReader
 
initFile(String) - Method in class loci.formats.in.NAFReader
 
initFile(String) - Method in class loci.formats.in.NativeND2Reader
 
initFile(String) - Method in class loci.formats.in.NativeQTReader
 
initFile(String) - Method in class loci.formats.in.NDPIReader
 
initFile(String) - Method in class loci.formats.in.NDPISReader
 
initFile(String) - Method in class loci.formats.in.NiftiReader
 
initFile(String) - Method in class loci.formats.in.NikonReader
 
initFile(String) - Method in class loci.formats.in.NRRDReader
 
initFile(String) - Method in class loci.formats.in.OBFReader
 
initFile(String) - Method in class loci.formats.in.OIRReader
 
initFile(String) - Method in class loci.formats.in.OMETiffReader
 
initFile(String) - Method in class loci.formats.in.OMEXMLReader
 
initFile(String) - Method in class loci.formats.in.OpenlabRawReader
 
initFile(String) - Method in class loci.formats.in.OpenlabReader
 
initFile(String) - Method in class loci.formats.in.OperettaReader
 
initFile(String) - Method in class loci.formats.in.OxfordInstrumentsReader
 
initFile(String) - Method in class loci.formats.in.PCIReader
 
initFile(String) - Method in class loci.formats.in.PCORAWReader
 
initFile(String) - Method in class loci.formats.in.PCXReader
 
initFile(String) - Method in class loci.formats.in.PDSReader
 
initFile(String) - Method in class loci.formats.in.PerkinElmerReader
 
initFile(String) - Method in class loci.formats.in.PGMReader
 
initFile(String) - Method in class loci.formats.in.PhotoshopTiffReader
 
initFile(String) - Method in class loci.formats.in.PictReader
 
initFile(String) - Method in class loci.formats.in.PovrayReader
 
initFile(String) - Method in class loci.formats.in.PQBinReader
 
initFile(String) - Method in class loci.formats.in.PrairieReader
 
initFile(String) - Method in class loci.formats.in.PSDReader
 
initFile(String) - Method in class loci.formats.in.QuesantReader
 
initFile(String) - Method in class loci.formats.in.RHKReader
 
initFile(String) - Method in class loci.formats.in.SBIGReader
 
initFile(String) - Method in class loci.formats.in.ScanrReader
 
initFile(String) - Method in class loci.formats.in.ScreenReader
 
initFile(String) - Method in class loci.formats.in.SDTReader
 
initFile(String) - Method in class loci.formats.in.SeikoReader
 
initFile(String) - Method in class loci.formats.in.SIFReader
 
initFile(String) - Method in class loci.formats.in.SlidebookReader
 
initFile(String) - Method in class loci.formats.in.SMCameraReader
 
initFile(String) - Method in class loci.formats.in.SPCReader
 
initFile(String) - Method in class loci.formats.in.SPEReader
 
initFile(String) - Method in class loci.formats.in.SpiderReader
 
initFile(String) - Method in class loci.formats.in.TargaReader
 
initFile(String) - Method in class loci.formats.in.TCSReader
 
initFile(String) - Method in class loci.formats.in.TextReader
 
initFile(String) - Method in class loci.formats.in.TiffJAIReader
 
initFile(String) - Method in class loci.formats.in.TileJPEGReader
 
initFile(String) - Method in class loci.formats.in.TillVisionReader
 
initFile(String) - Method in class loci.formats.in.TopometrixReader
 
initFile(String) - Method in class loci.formats.in.TrestleReader
 
initFile(String) - Method in class loci.formats.in.UBMReader
 
initFile(String) - Method in class loci.formats.in.UnisokuReader
 
initFile(String) - Method in class loci.formats.in.VarianFDFReader
 
initFile(String) - Method in class loci.formats.in.VeecoReader
 
initFile(String) - Method in class loci.formats.in.VGSAMReader
 
initFile(String) - Method in class loci.formats.in.VisitechReader
 
initFile(String) - Method in class loci.formats.in.VolocityClippingReader
 
initFile(String) - Method in class loci.formats.in.VolocityReader
 
initFile(String) - Method in class loci.formats.in.WATOPReader
 
initFile(String) - Method in class loci.formats.in.WlzReader
 
initFile(String) - Method in class loci.formats.in.ZeissCZIReader
 
initFile(String) - Method in class loci.formats.in.ZeissLMSReader
 
initFile(String) - Method in class loci.formats.in.ZeissLSMReader
 
initFile(String) - Method in class loci.formats.in.ZeissTIFFReader
 
initFile(String) - Method in class loci.formats.in.ZeissZVIReader
 
initFile(String) - Method in class loci.formats.in.ZipReader
 
initFileMain(String) - Method in class loci.formats.in.BaseZeissReader
 
initFlexFile(String) - Method in class loci.formats.in.FlexReader
 
initForwICT() - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Initialize some variables used with ICT.

initForwRCT() - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Initialize some variables used with RCT.

initialize(ColorModel, SampleModel, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
initialize(ImageTypeSpecifier, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
initialize() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
initialize(ImageInputStream, boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD
 
initialize() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
initialize() - Method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Initializes the layers array.

initialize() - Method in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

Initializes the rate allocation points, taking into account header
 overhead and such.

initialize() - Method in class loci.formats.codec.JPEG2000Codec

Initializes the JAI ImageIO dependency service.

initialize(String, int) - Method in class loci.formats.codec.JPEGTileDecoder
 
initialize(RandomAccessInputStream, int) - Method in class loci.formats.codec.JPEGTileDecoder
 
initialize(RandomAccessInputStream, int, int, int) - Method in class loci.formats.codec.JPEGTileDecoder
 
initialize() - Method in class loci.formats.codec.JPEGXRCodec

Initializes the JPEG-XR dependency service.

initialize() - Method in class loci.formats.codec.LuraWaveCodec

Initializes the LuraWave dependency service.

initialize(String) - Method in interface loci.formats.services.EXIFService
 
initialize(String) - Method in class loci.formats.services.EXIFServiceImpl
 
initialize(RandomAccessInputStream, int, int) - Method in interface loci.formats.services.JPEGTurboService
 
initialize(RandomAccessInputStream, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
 
initialize(InputStream) - Method in interface loci.formats.services.LuraWaveService

Wraps lwfDecoder.lwfDecoder(InputStream, String, String).

initialize(InputStream) - Method in class loci.formats.services.LuraWaveServiceImpl
 
initialize(String) - Method in interface loci.formats.services.MDBService

Prepare the given .mdb file for reading.

initialize(String) - Method in class loci.formats.services.MDBServiceImpl
 
initialize(String) - Method in interface loci.formats.services.MetakitService
 
initialize(RandomAccessInputStream) - Method in interface loci.formats.services.MetakitService
 
initialize(String) - Method in class loci.formats.services.MetakitServiceImpl
 
initialize(RandomAccessInputStream) - Method in class loci.formats.services.MetakitServiceImpl
 
initialize(String) - Method in interface loci.formats.services.POIService

Construct a new POI filesystem around the given file.

initialize(RandomAccessInputStream) - Method in interface loci.formats.services.POIService

Construct a new POI filesystem around the given stream.

initialize(String) - Method in class loci.formats.services.POIServiceImpl
 
initialize(RandomAccessInputStream) - Method in class loci.formats.services.POIServiceImpl
 
initializeColors() - Method in class loci.plugins.in.ImportProcess

Performed following ImportStep.COLORS notification.

initializeCrop() - Method in class loci.plugins.in.ImportProcess

Performed following ImportStep.CROP notification.

initialized - Variable in class loci.formats.FormatWriter

Whether each plane in each series of the current file has been
 prepped for writing.

initialized - Variable in class loci.formats.gui.LegacyQTTools

Flag indicating this class has been initialized.

initializedFile - Variable in class loci.formats.in.HamamatsuVMSReader
 
initializeDimOrder() - Method in class loci.plugins.in.ImportProcess

Performed following ImportStep.DIM_ORDER notification.

initializedPlane - Variable in class loci.formats.in.HamamatsuVMSReader
 
initializedPlane - Variable in class loci.formats.in.NDPIReader
 
initializedSeries - Variable in class loci.formats.in.HamamatsuVMSReader
 
initializedSeries - Variable in class loci.formats.in.NDPIReader
 
initializeFile() - Method in class loci.plugins.in.ImportProcess

Performed following ImportStep.FILE notification.

initializeFromMetadata() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader

Initializes these instance variables from the image metadata:

initializeFromStream(ImageInputStream, boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
initializeHelper - Variable in class loci.formats.in.NRRDReader
 
initializeJHDFService(String) - Method in class loci.formats.in.CellH5Reader
 
initializeMetadata() - Method in class loci.plugins.in.ImportProcess

Performed following ImportStep.METADATA notification.

initializeRange() - Method in class loci.plugins.in.ImportProcess

Performed following ImportStep.RANGE notification.

initializeRead(int, J2KImageReadParamJava, J2KMetadata) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
initializeReader() - Method in class loci.plugins.in.ImportProcess

Performed following ImportStep.READER notification.

initializeScaleTables(int[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
initializeSeries() - Method in class loci.plugins.in.ImportProcess

Performed following ImportStep.SERIES notification.

initializeStack() - Method in class loci.plugins.in.ImportProcess

Performed following ImportStep.STACK notification.

initializeStringTable() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor

Initialize the string table.

initializeStringTable() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil

Initialize the string table.

initImage() - Method in class loci.formats.in.ImageIOReader
 
initIntArray(String, long[], long) - Method in interface loci.formats.services.JHDFService

Creates an HDF5 dataset in path consisting of integers specified 
 by bytes per pixel bpp.

initIntArray(String, long[], long) - Method in class loci.formats.services.JHDFServiceImpl
 
initJPEGWriter(boolean, boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor

Initializes the JPEGWriter and JPEGParam instance variables.

initLicense() - Method in class loci.formats.services.LuraWaveServiceImpl
 
initLicenseCode() - Static method in class loci.plugins.util.LuraWave

Reads LuraWave license code from ImageJ preferences, if available.

initMeaFile(String) - Method in class loci.formats.in.FlexReader

Initialize the dataset from a .mea file.

initMetadata() - Method in class loci.formats.in.BaseTiffReader

Populates the metadata hashtable and metadata store.

initMetadata() - Method in class loci.formats.in.GelReader
 
initMetadata(String) - Method in class loci.formats.in.LIFReader

Parses a string of XML and puts the values in a Hashtable.

initMetadata(int) - Method in class loci.formats.in.ZeissLSMReader
 
initMetadataStore() - Method in class loci.formats.in.BaseTiffReader

Populates the metadata store using the data parsed in
 BaseTiffReader.initStandardMetadata() along with some further parsing done in
 the method itself.

initMetadataStore() - Method in class loci.formats.in.FEITiffReader
 
initMetadataStore() - Method in class loci.formats.in.FluoviewReader
 
initMetadataStore() - Method in class loci.formats.in.ImaconReader
 
initMetadataStore() - Method in class loci.formats.in.ImprovisionTiffReader
 
initMetadataStore() - Method in class loci.formats.in.JPKReader
 
initMetadataStore() - Method in class loci.formats.in.LeicaSCNReader
 
initMetadataStore() - Method in class loci.formats.in.LEOReader
 
initMetadataStore() - Method in class loci.formats.in.NDPIReader
 
initMetadataStore() - Method in class loci.formats.in.NikonElementsTiffReader
 
initMetadataStore() - Method in class loci.formats.in.NikonTiffReader
 
initMetadataStore() - Method in class loci.formats.in.PyramidTiffReader
 
initMetadataStore() - Method in class loci.formats.in.SimplePCITiffReader
 
initMetadataStore() - Method in class loci.formats.in.SISReader
 
initMetadataStore() - Method in class loci.formats.in.SlidebookTiffReader
 
initMetadataStore() - Method in class loci.formats.in.SVSReader
 
initMetadataStore() - Method in class loci.formats.in.TiffReader
 
initMetadataStore() - Method in class loci.formats.in.TrestleReader
 
initMinMax() - Method in class loci.formats.MinMaxCalculator

Ensures internal min/max variables are initialized properly.

initOMEMetadata() - Method in class loci.formats.in.LiFlimReader
 
initOriginalMetadata() - Method in class loci.formats.in.LiFlimReader
 
initPixels() - Method in class loci.formats.in.DeltavisionReader
 
initPlaneReader() - Method in class loci.formats.in.AmiraReader
 
initPOIService() - Method in class loci.formats.in.FV1000Reader
 
initPOIService() - Method in class loci.formats.in.IPWReader
 
initPOIService() - Method in class loci.formats.in.PCIReader
 
initPOIService() - Method in class loci.formats.in.ZeissZVIReader
 
initProgressWatch(int, int, String) - Method in interface jj2000.j2k.util.ProgressWatch

Initialize the progress watching process

initReader(int, int) - Method in class loci.formats.FileStitcher
 
initResFile(String) - Method in class loci.formats.in.FlexReader

Initialize the dataset from a .res file.

initSOP_EPHArrays() - Method in class jj2000.j2k.codestream.writer.FileCodestreamWriter

Performs the initialisation of the arrays that are used to store the
 values used to write SOP and EPH markers

initStack(long, int) - Method in class loci.formats.in.OBFReader
 
initStandardMetadata() - Method in class loci.formats.in.BaseTiffReader

Parses standard metadata.

initStandardMetadata() - Method in class loci.formats.in.DNGReader
 
initStandardMetadata() - Method in class loci.formats.in.FEITiffReader
 
initStandardMetadata() - Method in class loci.formats.in.FluoviewReader
 
initStandardMetadata() - Method in class loci.formats.in.ImaconReader
 
initStandardMetadata() - Method in class loci.formats.in.ImprovisionTiffReader
 
initStandardMetadata() - Method in class loci.formats.in.JPKReader
 
initStandardMetadata() - Method in class loci.formats.in.LeicaSCNReader
 
initStandardMetadata() - Method in class loci.formats.in.LEOReader
 
initStandardMetadata() - Method in class loci.formats.in.MetamorphReader
 
initStandardMetadata() - Method in class loci.formats.in.NDPIReader
 
initStandardMetadata() - Method in class loci.formats.in.NikonElementsTiffReader
 
initStandardMetadata() - Method in class loci.formats.in.NikonReader
 
initStandardMetadata() - Method in class loci.formats.in.NikonTiffReader
 
initStandardMetadata() - Method in class loci.formats.in.PyramidTiffReader
 
initStandardMetadata() - Method in class loci.formats.in.SEQReader
 
initStandardMetadata() - Method in class loci.formats.in.SimplePCITiffReader
 
initStandardMetadata() - Method in class loci.formats.in.SISReader
 
initStandardMetadata() - Method in class loci.formats.in.SlidebookTiffReader
 
initStandardMetadata() - Method in class loci.formats.in.SVSReader
 
initStandardMetadata() - Method in class loci.formats.in.TiffReader
 
initStandardMetadata() - Method in class loci.formats.in.TrestleReader
 
initStates - Variable in class jj2000.j2k.entropy.decoder.MQDecoder

The initial state of each context

initStates - Variable in class jj2000.j2k.entropy.encoder.MQCoder

The initial state of each context

initSubbandsFields(int, SubbandSyn) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Initialises subbands fields, such as code-blocks dimension and number
 of magnitude bits, in the subband tree.

initSubbandsFields(int, int, Subband) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Initialises subbands fields, such as number of code-blocks and
 code-blocks dimension, in the subband tree.

initTags() - Static method in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet
 
initTags() - Static method in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet
 
initTags() - Static method in class com.sun.media.imageio.plugins.tiff.EXIFInteroperabilityTagSet
 
initTags() - Static method in class com.sun.media.imageio.plugins.tiff.EXIFParentTIFFTagSet
 
initTags() - Static method in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet
 
initTags() - Static method in class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet
 
initTags() - Static method in class com.sun.media.imageio.plugins.tiff.GeoTIFFTagSet
 
initTiffParser() - Method in class loci.formats.in.MinimalTiffReader

Reinitialize the underlying TiffParser.

initTile(int) - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Read all tile-part headers of the requested tile.

initTileComp(int, int) - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Load options, length calculation type and termination type for
 each tile-component.

initTime - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

The wall time for the initialization.

initTLM() - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
 
initVars(String) - Method in class loci.formats.in.BaseZeissReader
 
initVars(String) - Method in class loci.formats.in.ZeissTIFFReader
 
initVars(String) - Method in class loci.formats.in.ZeissZVIReader
 
INK_NAMES - Static variable in class loci.formats.tiff.IFD
 
INK_SET - Static variable in class loci.formats.tiff.IFD
 
INK_SET_CMYK - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "InkSet" tag.

INK_SET_NOT_CMYK - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "InkSet" tag.

InkNames() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.InkNames
 
InkSet() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.InkSet
 
inPixels - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
input - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

The source raster if write raster.

input - Variable in class loci.formats.gui.DataConverter
 
input - Variable in class loci.formats.Memoizer.KryoDeser
 
inputIsRaster - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Indicates a raster rather than a RenderedImage
  to be encoded.

inputOrder - Variable in class loci.formats.SwappableMetadata

Order in which dimensions are stored.

inputOrder - Variable in class loci.plugins.in.ImporterOptions
 
inputRaster - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
inputRaster - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

The input source raster.

InputStreamAdapter - Class in com.sun.media.imageioimpl.plugins.clib
 
InputStreamAdapter(ImageInputStream) - Constructor for class com.sun.media.imageioimpl.plugins.clib.InputStreamAdapter
 
INR_MAGIC - Static variable in class loci.formats.in.INRReader
 
inReplacePixelsNest - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
INRReader - Class in loci.formats.in

INRReader is the file format reader for INR files.

INRReader() - Constructor for class loci.formats.in.INRReader

Constructs a new INR reader.

inSequence - Variable in class loci.formats.in.DicomReader
 
insert(int, IIOImage, ImageWriteParam, boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
insert(ImageProcessor, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
insertBefore(Node, Node) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
insertNode(PaletteBuilder.ColorNode, Color, int) - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
 
insertNodeIntoTree(IIOMetadataNode, IIOMetadataNode) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
insertUpdate(DocumentEvent) - Method in class loci.plugins.config.FlexWidgets
 
insertWarningComment(String) - Method in class loci.formats.out.OMETiffWriter
 
install(String, String) - Method in class loci.formats.UpgradeChecker

Download and install a JAR file from the given URL.

install(String) - Static method in class loci.plugins.Updater

Install the tools bundle which can be retrieved from the specified path.

installIndividualJars(String, String) - Method in class loci.formats.UpgradeChecker

Download and install all of the individual JAR files into the given
 directory.

InstallWizard - Class in loci.plugins.config

A wizard for walking users through installation of third party
 libraries and plugins used by the Bio-Formats plugins.

InstallWizard() - Constructor for class loci.plugins.config.InstallWizard
 
instance - Static variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadataFormat
 
instance - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadataFormat
 
instance - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadataFormat
 
instance - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
instance - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormat
 
instance - Static variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadataFormat
 
instrumentModel - Variable in class loci.formats.in.NDPIReader
 
INT - Static variable in class loci.formats.in.CellSensReader
 
INT - Static variable in class loci.formats.in.GatanReader
 
INT16 - Static variable in class loci.formats.FormatTools

Identifies the INT16 data type used to store pixel values.

INT16 - Static variable in class loci.formats.in.SPEReader
 
INT32 - Static variable in class loci.formats.FormatTools

Identifies the INT32 data type used to store pixel values.

INT32 - Static variable in class loci.formats.in.SPEReader
 
INT8 - Static variable in class loci.formats.FormatTools

Identifies the INT8 data type used to store pixel values.

INT_2 - Static variable in class loci.formats.in.CellSensReader
 
INT_3 - Static variable in class loci.formats.in.CellSensReader
 
INT_4 - Static variable in class loci.formats.in.CellSensReader
 
INT_ARRAY_2 - Static variable in class loci.formats.in.CellSensReader
 
INT_ARRAY_3 - Static variable in class loci.formats.in.CellSensReader
 
INT_ARRAY_4 - Static variable in class loci.formats.in.CellSensReader
 
INT_ARRAY_5 - Static variable in class loci.formats.in.CellSensReader
 
INT_INTERVAL - Static variable in class loci.formats.in.CellSensReader
 
INT_RECT - Static variable in class loci.formats.in.CellSensReader
 
INT_SIGN_BIT - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The sign bit for int data

INT_SIGN_BIT - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The sign bit for int data

intArraySet(int[], int) - Static method in class jj2000.j2k.util.ArrayUtil

Reinitializes an int array to the given value in an optimized way.

intBlk - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Temporary DataBlkInt object (needed when encoder uses floating-point
        filters).

intBlk - Variable in class jj2000.j2k.image.input.ImgReaderPGM

Temporary DataBlkInt object (needed when encoder uses floating-point
        filters).

intData - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull

Boolean to know if one are currently dealing with int or float
        data.

IntegerSpec - Class in jj2000.j2k

This class extends ModuleSpec and is responsible of Integer
 specifications for each tile-component.

IntegerSpec(int, int, byte) - Constructor for class jj2000.j2k.IntegerSpec

Constructs a new 'IntegerSpec' for the specified number of
 tiles and components and with allowed type of
 specifications.

IntegerSpec(int, int, byte, J2KImageWriteParamJava, String, String) - Constructor for class jj2000.j2k.IntegerSpec

Constructs a new 'IntegerSpec' for the specified number of
 tiles and components, the allowed specifications type
 instance.

INTELLECTUAL_PROPERTY_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
intelProp - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox
 
intelProp - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
 
intenScaling - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Intensity scaling factor.

intensity - Variable in class loci.formats.in.LeicaHandler.Laser
 
intensity - Variable in class loci.formats.in.SDTReader

Whether to combine lifetime bins into single intensity image planes.

intent - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
interlace - Variable in class loci.formats.in.APNGReader
 
interlace - Variable in class loci.formats.in.GIFReader

Interlace flag.

interlaced - Variable in class loci.formats.codec.MJPBCodecOptions

Indicates whether or not channels are interlaced.

interlaced - Variable in class loci.formats.in.NativeQTReader

Set to true if the scanlines in a plane are interlaced (mjpb only).

interlaceFlag - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
interleaved - Variable in class loci.formats.codec.CodecOptions

Indicates whether or not channels are interleaved.

interleaved - Variable in class loci.formats.CoreMetadata

True if channels are stored RGBRGBRGB...; false if channels are stored
 RRR...GGG...BBB...

interleaved - Variable in class loci.formats.FormatWriter

Whether the channels in an RGB image are interleaved.

internalOffsets - Variable in class loci.formats.in.AmiraReader.HxRLE
 
internalStamps - Variable in class loci.formats.in.MetamorphReader
 
INTEROPERABILITY_INDEX_R98 - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFInteroperabilityTagSet

A value to be used with the "InteroperabilityIndex" tag.

INTEROPERABILITY_INDEX_THM - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFInteroperabilityTagSet

A value to be used with the "InteroperabilityIndex" tag.

InteroperabilityIFD() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.InteroperabilityIFD
 
InteroperabilityIndex() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFInteroperabilityTagSet.InteroperabilityIndex
 
interpolate(short[], byte[], int[], int, int, boolean) - Static method in class loci.formats.ImageTools
 
intFormat(int, int) - Static method in class loci.formats.in.MetamorphReader

Formats an integer value with leading 0s if needed.

intFormatMax(int, int) - Static method in class loci.formats.in.MetamorphReader

Formats an integer with leading 0 using maximum sequence number.

IntIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.IntIM3Record
 
intToMultiByte(int) - Static method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
intValue() - Method in class loci.formats.tiff.TiffRational

Returns the value of the specified number as an int.

INV_ICT - Static variable in class jj2000.j2k.image.invcomptransf.InvCompTransf

Identifier for the Inverse Irreversible Component
        Transformation (INV_ICT).

INV_RCT - Static variable in class jj2000.j2k.image.invcomptransf.InvCompTransf

Identifier for the Inverse Reversible Component Transformation
        (INV_RCT).

INVALID_LICENSE_MSG - Static variable in class loci.formats.services.LuraWaveServiceImpl

Message to display if an invalid LuraWave license code is given.

INVALID_PIXELS - Static variable in class loci.formats.in.FEIReader
 
invalidAndMark(int) - Method in class loci.formats.in.SPCReader
 
invalidAndMarkInit(int) - Method in class loci.formats.in.SPCReader
 
InvCompTransf - Class in jj2000.j2k.image.invcomptransf

This class apply inverse component transformations to the tiles depending
 on specification read from the codestream header.

InvCompTransf(BlkImgDataSrc, DecoderSpecs, int[]) - Constructor for class jj2000.j2k.image.invcomptransf.InvCompTransf

Constructs a new ForwCompTransf object that operates on the
 specified source of image data.

InveonReader - Class in loci.formats.in

InveonReader is the file format reader for Inveon files.

InveonReader() - Constructor for class loci.formats.in.InveonReader

Constructs a new Inveon reader.

inverseFill - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Whether bits are inserted in reverse order (TIFF FillOrder 2).

InverseWT - Class in jj2000.j2k.wavelet.synthesis

This abstract class extends the WaveletTransform one with the specifics of
 inverse wavelet transforms.

InverseWT(MultiResImgData, DecoderSpecs) - Constructor for class jj2000.j2k.wavelet.synthesis.InverseWT

Initializes this object with the given source of wavelet
 coefficients.

invert() - Method in class loci.plugins.util.RecordedImageProcessor
 
inverted - Variable in class loci.formats.in.DicomReader
 
InvertedCMYKColorSpace - Class in com.sun.media.imageioimpl.common

Singleton class representing a simple, mathematically defined
 inverted CMYK color space.

InvertedCMYKColorSpace() - Constructor for class com.sun.media.imageioimpl.common.InvertedCMYKColorSpace
 
invertLut() - Method in class loci.plugins.util.RecordedImageProcessor
 
invertX - Variable in class loci.formats.in.RHKReader
 
invertY - Variable in class loci.formats.in.BMPReader
 
invertY - Variable in class loci.formats.in.ICSReader

Whether or not the image is inverted along the Y axis.

invertY - Variable in class loci.formats.in.RHKReader
 
invICT(DataBlk, int) - Method in class jj2000.j2k.image.invcomptransf.InvCompTransf

Apply inverse irreversible component transformation to obtain requested
 component from specified block of data.

invokeMethod(String, String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
 
invRCT(DataBlk, int) - Method in class jj2000.j2k.image.invcomptransf.InvCompTransf

Apply inverse component transformation to obtain requested component
 from specified block of data.

invWT - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
InvWT - Interface in jj2000.j2k.wavelet.synthesis

This interface extends the WaveletTransform with the
 specifics of inverse wavelet transforms.

InvWTAdapter - Class in jj2000.j2k.wavelet.synthesis

This class provides default implementation of the methods in the 'InvWT'
 interface.

InvWTAdapter(MultiResImgData, DecoderSpecs) - Constructor for class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Instantiates the 'InvWTAdapter' object using the specified
 'MultiResImgData' source.

InvWTData - Interface in jj2000.j2k.wavelet.synthesis

This interface extends the MultiResImgData interface with the methods that
 are necessary for inverse wavelet data (i.e.

InvWTFull - Class in jj2000.j2k.wavelet.synthesis

This class implements the InverseWT with the full-page approach for int and
 float data.

InvWTFull(CBlkWTDataSrcDec, DecoderSpecs) - Constructor for class jj2000.j2k.wavelet.synthesis.InvWTFull

Initializes this object with the given source of wavelet
 coefficients.

ios - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
ipixels - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
IPLabReader - Class in loci.formats.in

IPLabReader is the file format reader for IPLab (.IPL) files.

IPLabReader() - Constructor for class loci.formats.in.IPLabReader

Constructs a new IPLab reader.

IPW_MAGIC_BYTES - Static variable in class loci.formats.in.IPWReader
 
IPWReader - Class in loci.formats.in

IPWReader is the file format reader for Image-Pro Workspace (IPW) files.

IPWReader() - Constructor for class loci.formats.in.IPWReader

Constructs a new IPW reader.

ir - Variable in class loci.plugins.in.ThumbLoader
 
iris - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
is - Variable in class jj2000.j2k.util.ISRandomAccessIO

The InputStream that is wrapped

IS - Static variable in class loci.formats.in.DicomReader
 
is1DMode - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFT4Compressor
 
IS_EOS - Static variable in class jj2000.j2k.util.MsgPrinter

Signals that the end-of-string was reached

IS_GLITCHED - Static variable in class loci.plugins.prefs.OptionsDialog

Flag indicating whether to invoke workaround for AWT refresh bug.

IS_LITTLE - Static variable in class loci.formats.in.ImarisReader

Specifies endianness.

IS_NEWLINE - Static variable in class jj2000.j2k.util.MsgPrinter

Signals that a newline was found

IS_TRANSMISSION - Static variable in class loci.formats.in.CellSensReader
 
isAttributeRequired(String, String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
isAutoscale() - Method in class loci.plugins.in.ImporterOptions
 
isBigTiff - Variable in class loci.formats.out.TiffWriter

Whether or not the output file is a BigTIFF file.

isBigTiff() - Method in class loci.formats.tiff.IFD

Gets whether this is a BigTIFF IFD.

isBigTiff() - Method in class loci.formats.tiff.TiffParser

Returns whether or not the current TIFF file contains BigTIFF data.

isBigTiff() - Method in class loci.formats.tiff.TiffSaver

Returns whether or not we are writing BigTIFF data.

isBilevel - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
isBilevel - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
isBinary(SampleModel) - Static method in class com.sun.media.imageioimpl.common.ImageUtil
 
isBinary - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
isBitOnByteBoundary() - Method in class loci.formats.codec.BitBuffer

Deprecated.
Checks if the current position is on a byte boundary, that is the next
 bit in the byte array is the first bit in a byte.

isBottomUp - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
isCached() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
isCachedFile() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
isCachedMemory() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
isCertain() - Method in class loci.formats.AxisGuesser

Gets whether the guesser is confident that all axes are correct.

isColorLut() - Method in class loci.plugins.util.RecordedImageProcessor
 
isColorModeColorized() - Method in class loci.plugins.in.ImporterOptions
 
isColorModeComposite() - Method in class loci.plugins.in.ImporterOptions
 
isColorModeCustom() - Method in class loci.plugins.in.ImporterOptions
 
isColorModeDefault() - Method in class loci.plugins.in.ImporterOptions
 
isColorModeGrayscale() - Method in class loci.plugins.in.ImporterOptions
 
isCompatibleRaster(Raster) - Method in class loci.formats.gui.Index16ColorModel
 
isCompatibleRaster(Raster) - Method in class loci.formats.gui.SignedColorModel
 
isCompatibleRaster(Raster) - Method in class loci.formats.gui.UnsignedIntColorModel
 
isCompressed - Variable in class loci.formats.in.LIMReader
 
isCompressionLossless - Variable in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Whether the compression is lossless.

isCompressionLossless() - Method in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Retrieves a value indicating whether the compression is lossless.

isCompressionLossless() - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam
 
isCompressionLossless - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter

Lossless flag for known compression types.

isCompSpecified(int) - Method in class jj2000.j2k.ModuleSpec

Whether or not specifications have been entered for the given
 component.

isCompTransfUsed() - Method in class jj2000.j2k.image.CompTransfSpec

Check if component transformation is used in any of the tiles.

isConcatenate() - Method in class loci.plugins.in.ImporterOptions
 
isContainer(String) - Method in class loci.formats.in.NativeQTReader

Checks if the given String is a container atom type.

isContiguous - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
isCS_sRGB() - Method in class loci.formats.gui.TwoChannelColorSpace
 
isDataBufferBitContiguous(SampleModel) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Determines whether the DataBuffer is filled without
 any interspersed padding bits.

isDataTypeOK(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFTag

Returns true if the given data type
 may be used for the data associated with this tag.

isDeflate - Variable in class loci.formats.in.DicomReader
 
isDerived(int, int) - Method in class jj2000.j2k.quantization.quantizer.Quantizer

Returns true if the quantizer of given tile-component uses derived
 quantization step sizes.

isDerived(int, int) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer

Returns true if given tile-component uses derived quantization step
 sizes.

isDerived(int, int) - Method in class jj2000.j2k.quantization.QuantTypeSpec

Returns true if given tile-component uses derived quantization step
 size.

isDimensions(String) - Method in class loci.formats.in.ND2Handler

Returns whether or not the specified key is denotes dimensions.

isEnabled - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
isEncodingEmpty() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
isEOCFound - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Whether or not a EOC marker has been found instead of a SOT

isEOFInBuffer - Variable in class jj2000.j2k.io.BufferedRandomAccessFile

Whether the end of the file is in the current buffer or not

isEOLAligned - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFT4Compressor
 
isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService

Determine whether or not two OMEXMLMetadata objects are equal.

isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
 
isEven(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
isFalseColor() - Method in class loci.formats.FileStitcher
 
isFalseColor() - Method in class loci.formats.FormatReader
 
isFalseColor() - Method in interface loci.formats.IFormatReader

Returns false if IFormatReader.isIndexed() is false, or if IFormatReader.isIndexed()
 is true and the lookup table represents "real" color data.

isFalseColor() - Method in class loci.formats.ImageReader
 
isFalseColor() - Method in class loci.formats.in.FilePatternReader
 
isFalseColor() - Method in class loci.formats.ReaderWrapper
 
isFiji() - Static method in class loci.plugins.Updater

Returns true if the current ImageJ instance is actually a Fiji instance.

isFilled() - Method in class loci.formats.ChannelFiller

Returns true if the indices are being factored out.

isFirstBitDepthTable - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
isFirstTime() - Method in class loci.plugins.in.ImporterOptions
 
isFixed() - Method in class loci.formats.FilePatternBlock

Whether or not this is a fixed-width block.

isFLIM - Variable in class loci.formats.in.ImspectorReader

Whether or not this file contains FLIM data.

isFloatingPoint(IFormatReader) - Static method in class loci.formats.FormatTools

Determines whether the given reader represents any floating point data.

isFloatingPoint(int) - Static method in class loci.formats.FormatTools

Determines whether the given pixel type is floating point or integer.

isForceThumbnails() - Method in class loci.plugins.in.ImporterOptions
 
isFullPlane(int, int, int, int) - Method in class loci.formats.FormatWriter

Returns true if the given rectangle coordinates correspond to a full
 image in the given series.

isFullyNonReversible() - Method in class jj2000.j2k.quantization.QuantTypeSpec

Check the irreversibility of the whole image.

isFullyReversible() - Method in class jj2000.j2k.quantization.QuantTypeSpec

Check the reversibility of the whole image.

isGrayscaleMapping(IndexColorModel) - Static method in class com.sun.media.imageioimpl.common.ImageUtil

Tests whether the color indices represent a gray-scale image with
 the indicated number of bits over the color component range [0,255].

isGreaterThanEpsilon(double) - Method in class loci.formats.in.SlidebookReader

Returns true if the given double is greater than epsilon (defined here as
 0.000001), i.e.

isGroupFiles() - Method in class loci.formats.FileStitcher
 
isGroupFiles() - Method in class loci.formats.FormatReader
 
isGroupFiles() - Method in interface loci.formats.IFormatReader

Returns true if we should group files in multi-file formats.

isGroupFiles() - Method in class loci.formats.ImageReader
 
isGroupFiles() - Method in class loci.formats.in.FilePatternReader
 
isGroupFiles() - Method in class loci.formats.ReaderWrapper
 
isGroupFiles() - Method in class loci.plugins.in.ImporterOptions
 
isGroupFiles(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isHTTP() - Method in class loci.plugins.in.ImporterOptions
 
isIFD - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
isIFDPointer() - Method in class com.sun.media.imageio.plugins.tiff.TIFFTag

Returns true if this tag is used to point to an IFD
 structure containing additional tags.

isImageSimple - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
isImageSimple - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
isImageTiled(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
isImageTiled(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
isInCache(int[]) - Method in class loci.formats.cache.Cache

Returns true if the object at the given dimensional position is
 in the cache.

isInCache(int) - Method in class loci.formats.cache.Cache

Returns true if the object at the given index is in the cache.

isIndexed - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter

Indicates that the colorModel is a
  IndexColorModel

isIndexed() - Method in class loci.formats.ChannelFiller
 
isIndexed() - Method in class loci.formats.ChannelMerger
 
isIndexed() - Method in class loci.formats.FileStitcher
 
isIndexed() - Method in class loci.formats.FormatReader
 
isIndexed() - Method in interface loci.formats.IFormatReader

Gets whether the image planes are indexed color.

isIndexed() - Method in class loci.formats.ImageReader
 
isIndexed() - Method in class loci.formats.in.FilePatternReader
 
isIndexed() - Method in class loci.formats.ReaderWrapper
 
isIndexed(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isIndicesForGrayscale(byte[], byte[], byte[]) - Static method in class com.sun.media.imageioimpl.common.ImageUtil

Tests whether the color indices represent a gray-scale image.

isInitialized - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode

Initialization flag.

isInitialized - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
isInsertingEmpty - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
isIntegral - Static variable in class com.sun.media.imageio.plugins.tiff.TIFFField
 
isIntegral() - Method in class com.sun.media.imageio.plugins.tiff.TIFFField

Indicates whether the value associated with the field is of
 integral data type.

isIntensity() - Method in class loci.formats.in.SDTReader

Gets whether the reader is combining each lifetime
 histogram into a summed intensity image plane.

isInterleaved() - Method in class loci.formats.ChannelMerger
 
isInterleaved() - Method in class loci.formats.FileStitcher
 
isInterleaved(int) - Method in class loci.formats.FileStitcher
 
isInterleaved() - Method in class loci.formats.FormatReader
 
isInterleaved(int) - Method in class loci.formats.FormatReader
 
isInterleaved() - Method in class loci.formats.FormatWriter
 
isInterleaved() - Method in interface loci.formats.IFormatReader

Gets whether or not the channels are interleaved.

isInterleaved(int) - Method in interface loci.formats.IFormatReader

Gets whether or not the given sub-channel is interleaved.

isInterleaved() - Method in interface loci.formats.IFormatWriter

Gets whether or not the channels in an image are interleaved.

isInterleaved() - Method in class loci.formats.ImageReader
 
isInterleaved(int) - Method in class loci.formats.ImageReader
 
isInterleaved() - Method in class loci.formats.ImageWriter
 
isInterleaved() - Method in class loci.formats.in.FilePatternReader
 
isInterleaved(int) - Method in class loci.formats.in.FilePatternReader
 
isInterleaved(int) - Method in class loci.formats.in.ICSReader
 
isInterleaved(int) - Method in class loci.formats.in.SDTReader
 
isInterleaved() - Method in class loci.formats.ReaderWrapper
 
isInterleaved(int) - Method in class loci.formats.ReaderWrapper
 
isInterleaved() - Method in class loci.formats.WriterWrapper
 
isInterleaved(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isInterleavedSubC(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
 
isInverted - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
isInvertedLut() - Method in class loci.plugins.util.RecordedImageProcessor
 
isInvertX() - Method in class loci.formats.in.PrairieMetadata

Gets whether the stage position X coordinates are inverted (i.e.,
 left-to-right).

isInvertY() - Method in class loci.formats.in.PrairieMetadata

Gets whether the stage position Y coordinates are inverted (i.e.,
 bottom-to-top).

isJNG - Variable in class loci.formats.in.MNGReader
 
isJP2K - Variable in class loci.formats.in.DicomReader
 
isJPEG - Variable in class loci.formats.in.BaseZeissReader
 
isJPEG - Variable in class loci.formats.in.DicomReader
 
isJPEG - Variable in class loci.formats.in.NativeND2Reader

Whether or not the pixel data is compressed using JPEG 2000.

isJVM64Bit() - Method in class loci.formats.gui.LegacyQTTools

Whether this JVM is 64-bit.

isLeaf - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
isLeaf(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
isLegacy() - Method in class loci.formats.DelegateReader

Gets whether to use the legacy reader by default.

isLeicaLIFPhysicalSizeBackwardsCompatible() - Static method in class loci.plugins.util.LociPrefs
 
isLicenseCodeException(FormatException) - Static method in class loci.plugins.util.LuraWave

Returns true if the given exception was cause
 by a missing or invalid LuraWave license code.

isLittleEndian() - Method in class loci.formats.FileStitcher
 
isLittleEndian() - Method in class loci.formats.FormatReader
 
isLittleEndian() - Method in interface loci.formats.IFormatReader

Gets whether the data is in little-endian format.

isLittleEndian() - Method in class loci.formats.ImageReader
 
isLittleEndian() - Method in class loci.formats.in.FilePatternReader
 
isLittleEndian() - Method in class loci.formats.ReaderWrapper
 
isLittleEndian() - Method in class loci.formats.tiff.IFD

Gets whether the TIFF information in this IFD is little-endian.

isLittleEndian() - Method in class loci.formats.tiff.TiffSaver

Returns whether or not we are writing little-endian data.

isLittleEndian(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isLoadedFromMemo() - Method in class loci.formats.Memoizer

Returns whether the ReaderWrapper.reader instance currently active was loaded
  from the memo file during Memoizer.setId(String).

isLocal() - Method in class loci.plugins.in.ImporterOptions
 
isLossless - Variable in class loci.formats.in.NativeND2Reader

Whether or not the pixel data is losslessly compressed.

isLossless - Variable in class loci.formats.in.ND2Handler
 
isLossless() - Method in class loci.formats.in.ND2Handler
 
isMetadataComplete() - Method in class loci.formats.FormatReader
 
isMetadataComplete() - Method in interface loci.formats.IFormatReader

Returns true if this format's metadata is completely parsed.

isMetadataComplete() - Method in class loci.formats.ImageReader
 
isMetadataComplete() - Method in class loci.formats.in.FilePatternReader
 
isMetadataComplete() - Method in class loci.formats.ReaderWrapper
 
isMetadataComplete(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isMetadataFiltered() - Method in class loci.formats.FormatReader
 
isMetadataFiltered() - Method in interface loci.formats.IFormatReader

Returns true if ugly metadata (entries with unprintable characters,
 and extremely large entries) are discarded from the metadata table.

isMetadataFiltered() - Method in class loci.formats.ImageReader
 
isMetadataFiltered() - Method in class loci.formats.in.FilePatternReader
 
isMetadataFiltered() - Method in class loci.formats.ReaderWrapper
 
isMetadataFiltered(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isMINC2 - Variable in class loci.formats.in.MINCReader
 
isMinimumMetadata() - Method in class loci.formats.in.PrairieReader

Gets whether to populate only the minimum required metadata.

isMinMaxPopulated() - Method in class loci.formats.MinMaxCalculator

Returns true if the values returned by
 getChannelGlobalMinimum/Maximum can be trusted.

isModulo - Variable in class loci.formats.tools.MakeTestOmeTiff
 
isND2Nikon() - Static method in class loci.plugins.util.LociPrefs
 
isNode - Variable in class jj2000.j2k.roi.encoder.SubbandROIMask

Flag indicating whether this subband mask is a node or not

isNode - Variable in class jj2000.j2k.wavelet.Subband

True if it is a node in the tree, false if it is a leaf.

isNonStandardICCColorSpace(ColorSpace) - Static method in class com.sun.media.imageioimpl.common.ImageUtil

Returns true if the given ColorSpace object
 is an instance of ICC_ColorSpace but is not one of the
 standard ColorSpaces returned by
 ColorSpace.getInstance().

isNormalized() - Method in class loci.formats.FormatReader
 
isNormalized() - Method in interface loci.formats.IFormatReader

Returns true if we should normalize float data.

isNormalized() - Method in class loci.formats.ImageReader
 
isNormalized() - Method in class loci.formats.in.FilePatternReader
 
isNormalized() - Method in class loci.formats.ReaderWrapper
 
isNormalized(Boolean[]) - Method in class loci.plugins.macro.LociFunctions
 
isNumeric() - Method in class loci.formats.FilePatternBlock

Whether or not this is a numeric block.

ISO - Static variable in class loci.formats.in.NikonReader
 
ISO_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
 
ISO_SPEED_RATINGS - Static variable in class loci.formats.tiff.IFD
 
isOIB - Variable in class loci.formats.in.FV1000Reader

Flag indicating this is an OIB dataset.

isOMERO() - Method in class loci.plugins.in.ImporterOptions
 
isOMEXMLMetadata(Object) - Method in interface loci.formats.services.OMEXMLService

Checks whether the given object is an OME-XML metadata object.

isOMEXMLMetadata(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
 
isOMEXMLRoot(Object) - Method in interface loci.formats.services.OMEXMLService

Checks whether the given object is an OME-XML root object.

isOMEXMLRoot(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
 
isOne() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor

Returns true or false, depending on whether this instance is equal to
 1/1.

isOrderCertain() - Method in class loci.formats.FileStitcher
 
isOrderCertain() - Method in class loci.formats.FormatReader
 
isOrderCertain() - Method in interface loci.formats.IFormatReader

Gets whether the dimension order and sizes are known, or merely guesses.

isOrderCertain() - Method in class loci.formats.ImageReader
 
isOrderCertain() - Method in class loci.formats.in.FilePatternReader
 
isOrderCertain() - Method in class loci.formats.ReaderWrapper
 
isOrderCertain(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isOriginalMetadataPopulated() - Method in class loci.formats.FormatReader
 
isOriginalMetadataPopulated() - Method in interface loci.formats.IFormatReader

Returns true if we should save proprietary metadata
 in the MetadataStore.

isOriginalMetadataPopulated() - Method in class loci.formats.ImageReader
 
isOriginalMetadataPopulated() - Method in class loci.formats.in.FilePatternReader
 
isOriginalMetadataPopulated() - Method in class loci.formats.ReaderWrapper
 
isOriginalMetadataPopulated(Boolean[]) - Method in class loci.plugins.macro.LociFunctions
 
isOriginalSigned(SampleModel) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
isOriginalSigned(int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns true if the original data of the specified component was
 signed.

isOrigSig - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

An array specifying, for each component,if the data was signed
        or not

isOrigSigned(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Returns true if the data read was originally signed in the specified
 component, false if not.

isOrigSigned(int) - Method in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
isOrigSigned(int) - Method in class jj2000.j2k.image.input.ImgReader

Returns true if the data read was originally signed in the specified
 component, false if not.

isOrigSigned(int) - Method in class jj2000.j2k.image.input.ImgReaderPGM

Returns true if the data read was originally signed in the specified
 component, false if not.

ISOSpeedRatings() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ISOSpeedRatings
 
isot - Variable in class jj2000.j2k.codestream.HeaderInfo.SOT
 
isPacketWritable() - Method in class jj2000.j2k.codestream.writer.PktEncoder

Returns true if the current packet is writable i.e.

isPictQTJava() - Static method in class loci.plugins.util.LociPrefs
 
isPositiveValue(Double) - Static method in class loci.formats.FormatTools
 
isPossible(String, String) - Method in class loci.plugins.prefs.OptionsList

Gets whether the specified value is a possible one
 for the string option with the given key.

isPredTerm - Variable in class jj2000.j2k.entropy.encoder.BitToByteOutput

Whether or not predictable termination is requested.

isPreviewName(String) - Method in class loci.formats.in.FV1000Reader
 
isPseudoColorLut() - Method in class loci.plugins.util.RecordedImageProcessor
 
isPsotEqualsZero - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Whether or not the last read Psot value was zero.

isQTExpired() - Method in class loci.formats.gui.LegacyQTTools

Whether QuickTime for Java has expired.

isQTQTJava() - Static method in class loci.plugins.util.LociPrefs
 
isQuiet() - Method in class loci.plugins.in.ImporterOptions
 
isRandomAccessEasy(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
isRandomAccessEasy(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
isRandomAccessEasy(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
isRandomAccessEasy(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
isRandomAccessEasy(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
isRandomAccessEasy(int) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
ISRandomAccessIO - Class in jj2000.j2k.util

This class implements a wrapper to turn an InputStream into a
 RandomAccessIO.

ISRandomAccessIO(InputStream, int, int, int) - Constructor for class jj2000.j2k.util.ISRandomAccessIO

Creates a new RandomAccessIO wrapper for the given InputStream
 'is'.

ISRandomAccessIO(InputStream) - Constructor for class jj2000.j2k.util.ISRandomAccessIO

Creates a new RandomAccessIO wrapper for the given InputStream
 'is'.

isRaw(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

Returns true if file variant is raw format, false if ASCII.

isRaw(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter

Returns true if file variant is raw format, false if ASCII.

isRaw() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
isRawCodestream - Variable in class loci.formats.in.JPEG2000MetadataParser

Whether or not the codestream is raw and not JP2 boxed.

isRawCodestream() - Method in class loci.formats.in.JPEG2000MetadataParser

Whether or not the codestream is raw and not JP2 boxed.

isReadActiveOnly - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullDecompressor

Whether to read the active source region only.

isReaderEnabled(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
 
isReaderEnabled(Class<? extends IFormatReader>) - Static method in class loci.plugins.util.LociPrefs
 
isReaderPref(String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
 
isReaderWindowless(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableImageMetadata
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableStreamMetadata
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
isReadOnly() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
isReadOnly - Variable in class jj2000.j2k.io.BufferedRandomAccessFile

Whether the opened file is read only or not (defined by the constructor
 arguments)

isRegex - Variable in class loci.formats.FilePattern

Whether or not this FilePattern represents a regular expression.

isRegex() - Method in class loci.formats.FilePattern

Returns whether or not this pattern is a regular expression.

isRequired - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFAttrInfo
 
isRescaling - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
isReversible(int, int) - Method in class jj2000.j2k.entropy.encoder.EntropyCoder

Returns the reversibility of the tile-component data that is provided
 by the object.

isReversible() - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Returns true if this transform is reversible in current
 tile.

isReversible() - Method in class jj2000.j2k.image.invcomptransf.InvCompTransf

Returns true if this transform is reversible in current
 tile.

isReversible(int, int) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer

Returns true if the quantized data is reversible, for the specified
 tile-component.

isReversible(int, int) - Method in class jj2000.j2k.quantization.QuantTypeSpec

Check the reversibility of the given tile-component.

isReversible(int, int) - Method in class jj2000.j2k.roi.encoder.ROIScaler

Since ROI scaling is always a reversible operation, it calls
 isReversible() method of it source (the quantizer module).

isReversible() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns the reversibility of the filter.

isReversible() - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns the reversibility of the filter.

isReversible(int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterSpec

Check the reversibility of filters contained is the given
 tile-component.

isReversible(int, int) - Method in interface jj2000.j2k.wavelet.analysis.ForwWTDataProps

Returns the reversibility of the given tile-component.

isReversible(int, int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Returns the reversibility of the wavelet transform for the specified
 component and tile.

isReversible(int, int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTFull

Returns the reversibility of the wavelet transform for the specified
 component, in the current tile.

isReversible() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns the reversibility of the filter.

isReversible() - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns the reversibility of the filter.

isReversible(int, int) - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterSpec

Check the reversibility of filters contained is the given
 tile-component.

isReversible() - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns the reversibility of the filter.

isReversible(int, int) - Method in interface jj2000.j2k.wavelet.WaveletTransform

Returns the reversibility of the wavelet transform for the
 specified component and tile.

isRGB() - Method in class loci.formats.ChannelFiller
 
isRGB() - Method in class loci.formats.ChannelMerger
 
isRGB() - Method in class loci.formats.ChannelSeparator
 
isRGB() - Method in class loci.formats.FileStitcher
 
isRGB() - Method in class loci.formats.FormatReader
 
isRGB() - Method in interface loci.formats.IFormatReader

Checks if the image planes in the file have more than one channel per
 IFormatReader.openBytes(int) call.

isRGB() - Method in class loci.formats.ImageReader
 
isRGB() - Method in class loci.formats.in.FilePatternReader
 
isRGB() - Method in class loci.formats.ReaderWrapper
 
isRGB() - Method in interface loci.formats.services.WlzService

Gets boolean for whether image is colour or not.

isRGB() - Method in class loci.formats.services.WlzServiceImpl
 
isRLE - Variable in class loci.formats.in.DicomReader
 
isROIinPkt() - Method in class jj2000.j2k.codestream.writer.PktEncoder

Tells if there was ROI information in the last written packet

isSameAsFullWT(int, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

Returns true if the wavelet filter computes or uses the
 same "inner" subband coefficient as the full frame wavelet transform,
 and false otherwise.

isSameAsFullWT(int, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

Returns true if the wavelet filter computes or uses the same "inner"
 subband coefficient as the full frame wavelet transform, and false
 otherwise.

isSameAsFullWT(int, int, int) - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

Returns true if the wavelet filter computes or uses the
 same "inner" subband coefficient as the full frame wavelet transform,
 and false otherwise.

isSameAsFullWT(int, int, int) - Method in class jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3

Returns true if the wavelet filter computes or uses the same "inner"
 subband coefficient as the full frame wavelet transform, and false
 otherwise.

isSameAsFullWT(int, int, int) - Method in interface jj2000.j2k.wavelet.WaveletFilter

Returns true if the wavelet filter computes or uses the
 same "inner" subband coefficient as the full frame wavelet transform,
 and false otherwise.

isSaved() - Method in class loci.plugins.prefs.Option

Gets whether option should be saved to ImageJ preferences file.

isSaved(String) - Method in class loci.plugins.prefs.OptionsList

Gets whether the option with the given key
 is saved to the ImageJ preferences file.

isSavedToMemo() - Method in class loci.formats.Memoizer

Returns whether the ReaderWrapper.reader instance currently active was saved
  to the memo file during Memoizer.setId(String).

isSDTIntensity() - Static method in class loci.plugins.util.LociPrefs
 
isSeriesOn(int) - Method in class loci.plugins.in.ImporterOptions
 
isSet(String) - Method in class loci.plugins.prefs.OptionsList

Gets the value of the boolean option with the given key.

isSetByDefault(String) - Method in class loci.plugins.prefs.OptionsList

Gets the default value of the boolean option with the given key.

isShowMetadata() - Method in class loci.plugins.in.ImporterOptions
 
isShowOMEXML() - Method in class loci.plugins.in.ImporterOptions
 
isSigned - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
isSigned(int) - Static method in class loci.formats.FormatTools

Determines whether the given pixel type is signed or unsigned.

isSingleFile(String) - Method in class loci.formats.FormatReader
 
isSingleFile(String) - Method in interface loci.formats.IFormatReader

Returns true if this is a single-file format.

isSingleFile(String) - Method in class loci.formats.ImageReader
 
isSingleFile(String) - Method in class loci.formats.in.AFIReader
 
isSingleFile(String) - Method in class loci.formats.in.AnalyzeReader
 
isSingleFile(String) - Method in class loci.formats.in.APLReader
 
isSingleFile(String) - Method in class loci.formats.in.BDReader
 
isSingleFile(String) - Method in class loci.formats.in.BioRadReader
 
isSingleFile(String) - Method in class loci.formats.in.BrukerReader
 
isSingleFile(String) - Method in class loci.formats.in.CellSensReader
 
isSingleFile(String) - Method in class loci.formats.in.CellVoyagerReader
 
isSingleFile(String) - Method in class loci.formats.in.ColumbusReader
 
isSingleFile(String) - Method in class loci.formats.in.DeltavisionReader
 
isSingleFile(String) - Method in class loci.formats.in.FakeReader
 
isSingleFile(String) - Method in class loci.formats.in.FilePatternReader
 
isSingleFile(String) - Method in class loci.formats.in.FlexReader
 
isSingleFile(String) - Method in class loci.formats.in.FujiReader
 
isSingleFile(String) - Method in class loci.formats.in.FV1000Reader
 
isSingleFile(String) - Method in class loci.formats.in.HitachiReader
 
isSingleFile(String) - Method in class loci.formats.in.ICSReader
 
isSingleFile(String) - Method in class loci.formats.in.ImagicReader
 
isSingleFile(String) - Method in class loci.formats.in.InCellReader
 
isSingleFile(String) - Method in class loci.formats.in.L2DReader
 
isSingleFile(String) - Method in class loci.formats.in.LeicaReader
 
isSingleFile(String) - Method in class loci.formats.in.MetamorphReader
 
isSingleFile(String) - Method in class loci.formats.in.MIASReader
 
isSingleFile(String) - Method in class loci.formats.in.MicromanagerReader
 
isSingleFile(String) - Method in class loci.formats.in.NDPISReader
 
isSingleFile(String) - Method in class loci.formats.in.NiftiReader
 
isSingleFile(String) - Method in class loci.formats.in.NRRDReader
 
isSingleFile(String) - Method in class loci.formats.in.OMETiffReader
 
isSingleFile(String) - Method in class loci.formats.in.OperettaReader
 
isSingleFile(String) - Method in class loci.formats.in.PerkinElmerReader
 
isSingleFile(String) - Method in class loci.formats.in.PrairieReader
 
isSingleFile(String) - Method in class loci.formats.in.ScanrReader
 
isSingleFile(String) - Method in class loci.formats.in.ScreenReader
 
isSingleFile(String) - Method in class loci.formats.in.SPCReader
 
isSingleFile(String) - Method in class loci.formats.in.TCSReader
 
isSingleFile(String) - Method in class loci.formats.in.TillVisionReader
 
isSingleFile(String) - Method in class loci.formats.in.VisitechReader
 
isSingleFile(String) - Method in class loci.formats.in.ZeissLSMReader
 
isSingleFile(String) - Method in class loci.formats.in.ZeissTIFFReader
 
isSingleFile(String) - Method in class loci.formats.ReaderWrapper
 
isSpecifyRanges() - Method in class loci.plugins.in.ImporterOptions
 
isSpectralMode() - Method in class loci.formats.in.PrairieMetadata.Sequence
 
isSplitChannels() - Method in class loci.plugins.in.ImporterOptions
 
isSplitFocalPlanes() - Method in class loci.plugins.in.ImporterOptions
 
isSplitTimepoints() - Method in class loci.plugins.in.ImporterOptions
 
isSpool - Variable in class loci.formats.in.SlidebookReader
 
isSPWStructure(String) - Method in class loci.formats.in.FakeReader
 
isSubbandReversible(Subband) - Method in class jj2000.j2k.wavelet.synthesis.InvWTFull

Returns the reversibility of the current subband.

isSubsampling - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
isSupportedType(int) - Method in class loci.formats.FormatWriter
 
isSupportedType(int) - Method in interface loci.formats.IFormatWriter

Checks if the given pixel type is supported.

isSupportedType(int) - Method in class loci.formats.ImageWriter
 
isSupportedType(int) - Method in class loci.formats.WriterWrapper
 
isSwapDimensions() - Method in class loci.plugins.in.ImporterOptions
 
isTable() - Method in interface loci.formats.in.PrairieMetadata.Value
 
isTable() - Method in class loci.formats.in.PrairieMetadata.ValueItem
 
isTable() - Method in class loci.formats.in.PrairieMetadata.ValueTable
 
istermbufT - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The buffer for indicating terminated passes (avoids reallocation for
 each code-block), for each thread.

isTermPass - Variable in class jj2000.j2k.entropy.encoder.CBlkRateDistStats

Array of flags indicating terminated passes (valid or non-valid
 truncation points).

isThisType(String, boolean) - Method in class loci.formats.DelegateReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.DelegateReader
 
isThisType(String) - Method in class loci.formats.FormatHandler

Checks if a file matches the type of this format handler.

isThisType(String, boolean) - Method in class loci.formats.FormatReader

Checks if a file matches the type of this format reader.

isThisType(byte[]) - Method in class loci.formats.FormatReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.FormatReader
 
isThisType(String) - Method in class loci.formats.FormatReader
 
isThisType(String) - Method in interface loci.formats.IFormatHandler

Checks if the given string is a valid filename for this file format.

isThisType(String, boolean) - Method in interface loci.formats.IFormatReader

Checks if the given file is a valid instance of this file format.

isThisType(byte[]) - Method in interface loci.formats.IFormatReader

Checks if the given block is a valid header for this file format.

isThisType(RandomAccessInputStream) - Method in interface loci.formats.IFormatReader

Checks if the given stream is a valid stream for this file format.

isThisType(String, boolean) - Method in class loci.formats.ImageReader
 
isThisType(byte[]) - Method in class loci.formats.ImageReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.ImageReader
 
isThisType(String) - Method in class loci.formats.ImageReader
 
isThisType(String) - Method in class loci.formats.ImageWriter
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AFIReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AliconaReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AmiraReader
 
isThisType(String, boolean) - Method in class loci.formats.in.AnalyzeReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AnalyzeReader
 
isThisType(String, boolean) - Method in class loci.formats.in.APLReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.APNGReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ARFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AVIReader
 
isThisType(String, boolean) - Method in class loci.formats.in.BDReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BDReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadGelReader
 
isThisType(String, boolean) - Method in class loci.formats.in.BioRadReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadSCNReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BMPReader
 
isThisType(String, boolean) - Method in class loci.formats.in.BrukerReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BrukerReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BurleighReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CanonRawReader
 
isThisType(String, boolean) - Method in class loci.formats.in.CellH5Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CellH5Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CellomicsReader
 
isThisType(String, boolean) - Method in class loci.formats.in.CellVoyagerReader
 
isThisType(String, boolean) - Method in class loci.formats.in.CellWorxReader
 
isThisType(String, boolean) - Method in class loci.formats.in.ColumbusReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ColumbusReader
 
isThisType(String, boolean) - Method in class loci.formats.in.DeltavisionReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DeltavisionReader
 
isThisType(String, boolean) - Method in class loci.formats.in.DicomReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DicomReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DNGReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.Ecat7Reader
 
isThisType(String, boolean) - Method in class loci.formats.in.FakeReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FEIReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FEITiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FlowSightReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FluoviewReader
 
isThisType(String, boolean) - Method in class loci.formats.in.FujiReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FujiReader
 
isThisType(String, boolean) - Method in class loci.formats.in.FV1000Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FV1000Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GatanDM2Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GatanReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GelReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GIFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HISReader
 
isThisType(String, boolean) - Method in class loci.formats.in.HitachiReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HitachiReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HRDGDFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.I2IReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IM3Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImaconReader
 
isThisType(String, boolean) - Method in class loci.formats.in.ImagicReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImarisHDFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImarisReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IMODReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImprovisionTiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImspectorReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InCell3000Reader
 
isThisType(String, boolean) - Method in class loci.formats.in.InCellReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InCellReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.INRReader
 
isThisType(String, boolean) - Method in class loci.formats.in.InveonReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InveonReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IPLabReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IPWReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IvisionReader
 
isThisType(String, boolean) - Method in class loci.formats.in.JEOLReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JEOLReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPEG2000Reader
 
isThisType(String, boolean) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
 
isThisType(String, boolean) - Method in class loci.formats.in.JPKReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPXReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.KhorosReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.KodakReader
 
isThisType(String, boolean) - Method in class loci.formats.in.L2DReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.L2DReader
 
isThisType(String, boolean) - Method in class loci.formats.in.LegacyND2Reader
 
isThisType(String, boolean) - Method in class loci.formats.in.LeicaReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LeicaReader
 
isThisType(String, boolean) - Method in class loci.formats.in.LeicaSCNReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LEOReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LIFReader
 
isThisType(String, boolean) - Method in class loci.formats.in.MetamorphReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphTiffReader
 
isThisType(String, boolean) - Method in class loci.formats.in.MIASReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MIASReader
 
isThisType(String, boolean) - Method in class loci.formats.in.MicromanagerReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MicromanagerReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MinimalTiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MNGReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MolecularImagingReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MRCReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MRWReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NativeND2Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NativeQTReader
 
isThisType(String, boolean) - Method in class loci.formats.in.NDPIReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NDPISReader
 
isThisType(String, boolean) - Method in class loci.formats.in.NiftiReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NiftiReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonElementsTiffReader
 
isThisType(String, boolean) - Method in class loci.formats.in.NikonReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonTiffReader
 
isThisType(String, boolean) - Method in class loci.formats.in.NRRDReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NRRDReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
 
isThisType(String, boolean) - Method in class loci.formats.in.OMETiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OMETiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OMEXMLReader
 
isThisType(String, boolean) - Method in class loci.formats.in.OMEXMLReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OpenlabRawReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OpenlabReader
 
isThisType(String, boolean) - Method in class loci.formats.in.OperettaReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OperettaReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OxfordInstrumentsReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCIReader
 
isThisType(String, boolean) - Method in class loci.formats.in.PCORAWReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCORAWReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCXReader
 
isThisType(String, boolean) - Method in class loci.formats.in.PDSReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PDSReader
 
isThisType(String, boolean) - Method in class loci.formats.in.PerkinElmerReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PGMReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PhotoshopTiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PQBinReader
 
isThisType(String, boolean) - Method in class loci.formats.in.PrairieReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PrairieReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PSDReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PyramidTiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SBIGReader
 
isThisType(String, boolean) - Method in class loci.formats.in.ScanrReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ScanrReader
 
isThisType(String, boolean) - Method in class loci.formats.in.ScreenReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ScreenReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SEQReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SIFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SimplePCITiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SISReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookTiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SMCameraReader
 
isThisType(String, boolean) - Method in class loci.formats.in.SPCReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SPEReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SpiderReader
 
isThisType(String, boolean) - Method in class loci.formats.in.SVSReader
 
isThisType(String, boolean) - Method in class loci.formats.in.TCSReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TCSReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TextReader
 
isThisType(String, boolean) - Method in class loci.formats.in.TillVisionReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TopometrixReader
 
isThisType(String, boolean) - Method in class loci.formats.in.TrestleReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TrestleReader
 
isThisType(String, boolean) - Method in class loci.formats.in.UnisokuReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.UnisokuReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VarianFDFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VGSAMReader
 
isThisType(String, boolean) - Method in class loci.formats.in.VisitechReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VolocityClippingReader
 
isThisType(String, boolean) - Method in class loci.formats.in.VolocityReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VolocityReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.WATOPReader
 
isThisType(String, boolean) - Method in class loci.formats.in.WlzReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissLMSReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissLSMReader
 
isThisType(String, boolean) - Method in class loci.formats.in.ZeissTIFFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
 
isThisType(String, boolean) - Method in class loci.formats.ReaderWrapper
 
isThisType(byte[]) - Method in class loci.formats.ReaderWrapper
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.ReaderWrapper
 
isThisType(String) - Method in class loci.formats.ReaderWrapper
 
isThisType(String) - Method in class loci.formats.WriterWrapper
 
isThisType(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
isThisTypeFast(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
isThumbnailSeries() - Method in class loci.formats.FileStitcher
 
isThumbnailSeries() - Method in class loci.formats.FormatReader
 
isThumbnailSeries() - Method in interface loci.formats.IFormatReader

Gets whether the current series is a lower resolution copy of a different
 series.

isThumbnailSeries() - Method in class loci.formats.ImageReader
 
isThumbnailSeries() - Method in class loci.formats.in.FilePatternReader
 
isThumbnailSeries() - Method in class loci.formats.ReaderWrapper
 
isTiff - Variable in class loci.formats.in.EPSReader
 
isTiff - Variable in class loci.formats.in.InCellReader.Image
 
isTiff - Variable in class loci.formats.in.PerkinElmerReader

Flag indicating that the image data is in TIFF format.

isTiffImageIO() - Static method in class loci.plugins.util.LociPrefs
 
isTileCompSpecified(int, int) - Method in class jj2000.j2k.ModuleSpec

Whether or not a tile-component specification has been defined

isTiled - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
isTiled() - Method in class loci.formats.tiff.IFD
 
isTileSpecified(int) - Method in class jj2000.j2k.ModuleSpec

Whether or not specifications have been entered for the given
 tile.

isTimeSeries() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets whether this Sequence should be considered a time series.

isTopDown() - Method in class com.sun.media.imageio.plugins.bmp.BMPImageWriteParam

Returns the value of the topDown parameter.

isTopDown - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
isTruncMode - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

True if truncation mode is used.

isTruncMode - Variable in class jj2000.j2k.codestream.reader.PktDecoder

True if truncation mode is used.

isUngroupFiles() - Method in class loci.plugins.in.ImporterOptions
 
isUsedFile(String) - Method in class loci.formats.FormatReader

Returns true if the given file name is in the used files list.

isUsingPatternIds() - Method in class loci.formats.FileStitcher

Gets whether the reader is using file patterns for IDs.

isValid() - Method in class loci.formats.FilePattern

Returns whether or not the file pattern is valid.

isValidate() - Method in class loci.formats.in.DefaultMetadataOptions
 
isValidate() - Method in class loci.formats.in.DynamicMetadataOptions
 
isValidate() - Method in interface loci.formats.in.MetadataOptions

Checks whether file validation has been set.

isValidHeader() - Method in class loci.formats.tiff.TiffParser

Tests this stream to see if it represents a TIFF file.

isValidPlateName(String) - Method in class loci.formats.in.ScreenReader
 
isValidRange(int, int, int) - Static method in class loci.formats.tools.FakeImage
 
isValidWbmpType(int) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
isValidWellName(String) - Method in class loci.formats.in.ScreenReader
 
isVersionChecking() - Method in class loci.formats.Memoizer

Returns whether or not version checking is done based upon major/minor
 version numbers.

isViewBrowser() - Method in class loci.plugins.in.ImporterOptions
 
isViewHyperstack() - Method in class loci.plugins.in.ImporterOptions
 
isViewImage5D() - Method in class loci.plugins.in.ImporterOptions
 
isViewNone() - Method in class loci.plugins.in.ImporterOptions
 
isViewStandard() - Method in class loci.plugins.in.ImporterOptions
 
isViewView5D() - Method in class loci.plugins.in.ImporterOptions
 
isVirtual() - Method in class loci.plugins.in.ImporterOptions
 
isWhitelistedKey(String) - Method in class loci.formats.ClassList

Returns whether a given key is a whitelisted option.

isWindowless() - Method in class loci.plugins.in.ImporterOptions
 
isWindowless() - Method in class loci.plugins.in.ImportProcess
 
isWindowless(IFormatReader) - Static method in class loci.plugins.util.LociPrefs

Gets whether windowless mode should be used when
 opening this reader's currently initialized dataset.

isWritingEmpty - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
isWritingSequence - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter

Whether a sequence is being written.

isWritingSequence - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
isZlib - Variable in class loci.formats.in.BaseZeissReader
 
italic - Variable in class loci.formats.in.BaseZeissReader.Shape
 
ITEM - Static variable in class loci.formats.in.DicomReader
 
ITEM_DELIMINATION - Static variable in class loci.formats.in.DicomReader
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ConfigWindow
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.LIFWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ND2Widgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.PictWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.QTWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.SDTWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.TiffDelegateWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ZeissCZIWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.in.MainDialog

Handles toggling of mutually exclusive options.

itemStateChanged(ItemEvent) - Method in class loci.plugins.in.SwapDialog
 
iterateIn(RandomAccessInputStream, Long) - Method in class loci.formats.in.NativeND2Reader

Function for iterating through ND2 metaAttributes

iterator() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD

Returns an Iterator over the TIFF fields.

its - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
IvisionHandler() - Constructor for class loci.formats.in.IvisionReader.IvisionHandler
 
IvisionReader - Class in loci.formats.in

IvisionReader is the file format reader for IVision (.IPM) files.

IvisionReader() - Constructor for class loci.formats.in.IvisionReader

Constructs a new Ivision reader.

IvisionReader.IvisionHandler - Class in loci.formats.in
 
iw - Variable in class loci.formats.in.GIFReader

Current image rectangle.

ix - Variable in class loci.formats.in.GIFReader

Current image rectangle.

iy - Variable in class loci.formats.in.GIFReader

Current image rectangle.

iYTab - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 




J

j2kCodecOptions - Variable in class loci.formats.in.MinimalTiffReader

Codec options to use when decoding JPEG 2000 data.

J2KImageReader - Class in com.sun.media.imageioimpl.plugins.jpeg2000

This class is the Java Image IO plugin reader for JPEG 2000 JP2 image file
  format.

J2KImageReader(ImageReaderSpi) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

Constructs J2KImageReader from the provided
  ImageReaderSpi.

J2KImageReaderResources - Class in com.sun.media.imageioimpl.plugins.jpeg2000
 
J2KImageReaderResources() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderResources
 
J2KImageReaderSpi - Class in com.sun.media.imageioimpl.plugins.jpeg2000
 
J2KImageReaderSpi() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
J2KImageReadParam - Class in com.sun.media.imageio.plugins.jpeg2000

A subclass of ImageReadParam for reading images in
 the JPEG 2000 format.

J2KImageReadParam() - Constructor for class com.sun.media.imageio.plugins.jpeg2000.J2KImageReadParam

Constructs a default instance of J2KImageReadParam.

J2KImageReadParamJava - Class in com.sun.media.imageioimpl.plugins.jpeg2000

A subclass of ImageReadParam for reading images in
 the JPEG 2000 format.

J2KImageReadParamJava() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava

Constructs a default instance of J2KImageReadParamJava.

J2KImageReadParamJava(ImageReadParam) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava
 
J2KImageWriteParam - Class in com.sun.media.imageio.plugins.jpeg2000

A subclass of ImageWriteParam for writing images in
 the JPEG 2000 format.

J2KImageWriteParam(Locale) - Constructor for class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Constructor which sets the Locale.

J2KImageWriteParam() - Constructor for class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Constructs a J2KImageWriteParam object with default
 values for all parameters.

J2KImageWriteParamJava - Class in com.sun.media.imageioimpl.plugins.jpeg2000

A subclass of ImageWriteParam for writing images in
 the JPEG 2000 format.

J2KImageWriteParamJava(RenderedImage, Locale) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Constructor to set locales.

J2KImageWriteParamJava(IIOImage, ImageWriteParam) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Constructor to set locales.

J2KImageWriteParamJava() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Constructs a J2KImageWriteParamJava object with default
 values for all parameters.

J2KImageWriteParamJava(RenderedImage) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Constructs a J2KImageWriteParamJava object with default
 values for all parameters.

J2KImageWriteParamJava(Raster) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Constructs a J2KImageWriteParamJava object with default
 values for all parameters.

J2KImageWriter - Class in com.sun.media.imageioimpl.plugins.jpeg2000

The Java Image IO plugin writer for encoding a RenderedImage into
 a JPEG 2000 part 1 file (JP2) format.

J2KImageWriter(ImageWriterSpi) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter

Constructs J2KImageWriter based on the provided
  ImageWriterSpi.

J2KImageWriterResources - Class in com.sun.media.imageioimpl.plugins.jpeg2000
 
J2KImageWriterResources() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterResources
 
J2KImageWriterSpi - Class in com.sun.media.imageioimpl.plugins.jpeg2000
 
J2KImageWriterSpi() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
J2KMetadata - Class in com.sun.media.imageioimpl.plugins.jpeg2000

Metadata for the J2K plug-in.

J2KMetadata() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata

Constructor containing code shared by other constructors.

J2KMetadata(ImageInputStream, J2KImageReader) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
J2KMetadata(ImageWriteParam, ImageWriter) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata

Constructs a default stream J2KMetadata object appropriate
 for the given write parameters.

J2KMetadata(ImageTypeSpecifier, ImageWriteParam, ImageWriter) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata

Constructs a default image J2KMetadata object appropriate
 for the given image type and write parameters.

J2KMetadata(ColorModel, SampleModel, int, int, ImageWriteParam, ImageWriter) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata

Constructs a default image J2KMetadata object appropriate
 for the given image type and write parameters.

J2KMetadataFormat - Class in com.sun.media.imageioimpl.plugins.jpeg2000
 
J2KMetadataFormat() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat

Constructs J2KMetadataFormat.

J2KMetadataFormatResources - Class in com.sun.media.imageioimpl.plugins.jpeg2000
 
J2KMetadataFormatResources() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormatResources
 
J2KReadState - Class in com.sun.media.imageioimpl.plugins.jpeg2000
 
J2KReadState(ImageInputStream, J2KImageReadParamJava, J2KMetadata, J2KImageReader) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState

Constructs J2KReadState.

J2KReadState(ImageInputStream, J2KImageReadParamJava, J2KImageReader) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState

Constructs J2KReadState.

J2KRenderedImage - Class in com.sun.media.imageioimpl.plugins.jpeg2000
 
J2KRenderedImage(ImageInputStream, J2KImageReadParamJava, J2KMetadata, J2KImageReader) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
 
J2KRenderedImage(ImageInputStream, J2KImageReadParamJava, J2KImageReader) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
 
J2KRenderedImage(J2KReadState) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
 
j2krparam - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
j2krparam - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Reference to the J2KImageReadParamJava instance

j2krparam - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

The J2KImageReadParamJava instance of the decoder

JAIIIOService - Interface in loci.formats.services

Interface defining methods for reading data using JAI Image I/O.

JAIIIOServiceImpl - Class in loci.formats.services

Implementation of JAIIIOService for reading and writing JPEG-2000 data.

JAIIIOServiceImpl() - Constructor for class loci.formats.services.JAIIIOServiceImpl

Default constructor.

JavaWriter - Class in loci.formats.out

JavaWriter is the file format writer for Java source code.

JavaWriter() - Constructor for class loci.formats.out.JavaWriter
 
JEOLReader - Class in loci.formats.in

JEOLReader is the file format reader for JEOL files.

JEOLReader() - Constructor for class loci.formats.in.JEOLReader

Constructs a new JEOL reader.

jhdf - Variable in class loci.formats.in.CellH5Reader
 
jhdf - Variable in class loci.formats.out.CellH5Writer
 
JHDFService - Interface in loci.formats.services

Utility class for working with NetCDF/HDF files.

JHDFServiceImpl - Class in loci.formats.services

Utility class for working with HDF files.

JHDFServiceImpl() - Constructor for class loci.formats.services.JHDFServiceImpl

Default constructor.

jj2000.j2k - package jj2000.j2k
 
jj2000.j2k.codestream - package jj2000.j2k.codestream
 
jj2000.j2k.codestream.reader - package jj2000.j2k.codestream.reader
 
jj2000.j2k.codestream.writer - package jj2000.j2k.codestream.writer
 
jj2000.j2k.decoder - package jj2000.j2k.decoder
 
jj2000.j2k.entropy - package jj2000.j2k.entropy
 
jj2000.j2k.entropy.decoder - package jj2000.j2k.entropy.decoder
 
jj2000.j2k.entropy.encoder - package jj2000.j2k.entropy.encoder
 
jj2000.j2k.fileformat - package jj2000.j2k.fileformat
 
jj2000.j2k.fileformat.reader - package jj2000.j2k.fileformat.reader
 
jj2000.j2k.fileformat.writer - package jj2000.j2k.fileformat.writer
 
jj2000.j2k.image - package jj2000.j2k.image
 
jj2000.j2k.image.forwcomptransf - package jj2000.j2k.image.forwcomptransf
 
jj2000.j2k.image.input - package jj2000.j2k.image.input
 
jj2000.j2k.image.invcomptransf - package jj2000.j2k.image.invcomptransf
 
jj2000.j2k.io - package jj2000.j2k.io
 
jj2000.j2k.quantization - package jj2000.j2k.quantization
 
jj2000.j2k.quantization.dequantizer - package jj2000.j2k.quantization.dequantizer
 
jj2000.j2k.quantization.quantizer - package jj2000.j2k.quantization.quantizer
 
jj2000.j2k.roi - package jj2000.j2k.roi
 
jj2000.j2k.roi.encoder - package jj2000.j2k.roi.encoder
 
jj2000.j2k.util - package jj2000.j2k.util
 
jj2000.j2k.wavelet - package jj2000.j2k.wavelet
 
jj2000.j2k.wavelet.analysis - package jj2000.j2k.wavelet.analysis
 
jj2000.j2k.wavelet.synthesis - package jj2000.j2k.wavelet.synthesis
 
JJ2KExceptionHandler - Class in jj2000.j2k

This class handles exceptions.

JJ2KExceptionHandler() - Constructor for class jj2000.j2k.JJ2KExceptionHandler
 
JJ2KInfo - Class in jj2000.j2k

This class holds general JJ2000 information, such as the version number,
 copyright, contact address, etc.

JJ2KInfo() - Constructor for class jj2000.j2k.JJ2KInfo
 
JP2_HEADER_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
JP2_SIGNATURE_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes

Main boxes

JPEG - Static variable in class loci.formats.in.AVIReader
 
JPEG - Static variable in class loci.formats.in.CellSensReader
 
jpeg - Variable in class loci.formats.in.CellSensReader
 
JPEG - Static variable in class loci.formats.in.ZeissCZIReader
 
JPEG2000BoxType - Enum in loci.formats.codec

An enumeration of JPEG 2000 box types.

JPEG2000BoxType(int, String) - Constructor for enum loci.formats.codec.JPEG2000BoxType

Default constructor.

JPEG2000Codec - Class in loci.formats.codec

This class implements JPEG 2000 compression and decompression.

JPEG2000Codec() - Constructor for class loci.formats.codec.JPEG2000Codec
 
JPEG2000CodecOptions - Class in loci.formats.codec

Options for compressing and decompressing JPEG-2000 data.

JPEG2000CodecOptions() - Constructor for class loci.formats.codec.JPEG2000CodecOptions

Creates a new instance.

JPEG2000CodecOptions(CodecOptions) - Constructor for class loci.formats.codec.JPEG2000CodecOptions

Creates a new instance with options.

JPEG2000MetadataParser - Class in loci.formats.in

A parser for JPEG 2000 metadata.

JPEG2000MetadataParser(RandomAccessInputStream) - Constructor for class loci.formats.in.JPEG2000MetadataParser

Constructs a new JPEG2000MetadataParser.

JPEG2000MetadataParser(RandomAccessInputStream, long) - Constructor for class loci.formats.in.JPEG2000MetadataParser

Constructs a new JPEG2000MetadataParser.

JPEG2000Reader - Class in loci.formats.in

JPEG2000Reader is the file format reader for JPEG-2000 images.

JPEG2000Reader() - Constructor for class loci.formats.in.JPEG2000Reader

Constructs a new JPEG2000Reader.

JPEG2000SegmentMarker - Enum in loci.formats.codec

An enumeration of JPEG 2000 segment markers.

JPEG2000SegmentMarker(int, String) - Constructor for enum loci.formats.codec.JPEG2000SegmentMarker

Default constructor.

JPEG2000Writer - Class in loci.formats.out

JPEG2000Writer is the file format writer for JPEG2000 files.

JPEG2000Writer() - Constructor for class loci.formats.out.JPEG2000Writer

Creates a new instance.

JPEG_2000 - Static variable in class loci.formats.in.CellSensReader
 
JPEG_AC_TABLES - Static variable in class loci.formats.tiff.IFD
 
JPEG_DC_TABLES - Static variable in class loci.formats.tiff.IFD
 
JPEG_INTERCHANGE_FORMAT - Static variable in class loci.formats.tiff.IFD
 
JPEG_INTERCHANGE_FORMAT_LENGTH - Static variable in class loci.formats.tiff.IFD
 
JPEG_LOSSLESS_PREDICTORS - Static variable in class loci.formats.tiff.IFD
 
JPEG_POINT_TRANSFORMS - Static variable in class loci.formats.tiff.IFD
 
JPEG_PROC - Static variable in class loci.formats.tiff.IFD
 
JPEG_PROC_BASELINE - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "JPEGProc" tag.

JPEG_PROC_LOSSLESS - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "JPEGProc" tag.

JPEG_Q_TABLES - Static variable in class loci.formats.tiff.IFD
 
JPEG_RESTART_INTERVAL - Static variable in class loci.formats.tiff.IFD
 
JPEG_TABLES - Static variable in class loci.formats.tiff.IFD
 
JPEGACTables() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGACTables
 
jpegBuf - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
jpegBufSize - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
JPEGCodec - Class in loci.formats.codec

This class implements JPEG compression and decompression.

JPEGCodec() - Constructor for class loci.formats.codec.JPEGCodec
 
JPEGDCTables() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGDCTables
 
jpegHeight - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
JPEGImageMetadata - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
JPEGInterchangeFormat() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGInterchangeFormat
 
JPEGInterchangeFormatLength() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGInterchangeFormatLength
 
JPEGLosslessPredictors() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGLosslessPredictors
 
jpegOffsets - Variable in class loci.formats.in.PictReader
 
JPEGParam - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor

ImageWriteParam for JPEG writer.

JPEGParam - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
JPEGPointTransforms() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGPointTransforms
 
JPEGProc() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGProc
 
JPEGQTables() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGQTables
 
jpegQuality - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
JPEGReader - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
JPEGReader - Class in loci.formats.in

JPEGReader is the file format reader for JPEG images.

JPEGReader() - Constructor for class loci.formats.in.JPEGReader

Constructs a new JPEGReader.

JPEGReader.DefaultJPEGReader - Class in loci.formats.in
 
JPEGRestartInterval() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGRestartInterval
 
JPEGSPIFilter() - Constructor for class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGCompressor.JPEGSPIFilter
 
JPEGStreamMetadata - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor

Stream metadata equivalent to a tables-only stream such as in
 the JPEGTables.

JPEGStreamOffset - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
jpegSubsamp - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
JPEGTables() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGTables
 
JPEGTileDecoder - Class in loci.formats.codec
 
JPEGTileDecoder() - Constructor for class loci.formats.codec.JPEGTileDecoder
 
JPEGTileDecoder.TileCache - Class in loci.formats.codec
 
JPEGTileDecoder.TileConsumer - Class in loci.formats.codec
 
JPEGTurboService - Interface in loci.formats.services
 
JPEGTurboServiceImpl - Class in loci.formats.services

Based upon the NDPI to OME-TIFF converter by Matthias Baldauf:

 http://matthias-baldauf.at/software/ndpi_converter/

JPEGTurboServiceImpl() - Constructor for class loci.formats.services.JPEGTurboServiceImpl
 
jpegWidth - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
JPEGWriter - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor

The JPEG writer.

JPEGWriter - Class in loci.formats.out

JPEGWriter is the file format writer for JPEG files.

JPEGWriter() - Constructor for class loci.formats.out.JPEGWriter
 
JPEGXR - Static variable in class loci.formats.in.ZeissCZIReader
 
JPEGXRCodec - Class in loci.formats.codec
 
JPEGXRCodec() - Constructor for class loci.formats.codec.JPEGXRCodec
 
JPEGXRService - Interface in loci.formats.services

Interface defining methods for working with JPEG-XR data

JPEGXRServiceImpl - Class in loci.formats.services

Interface defining methods for working with JPEG-XR data

JPEGXRServiceImpl() - Constructor for class loci.formats.services.JPEGXRServiceImpl
 
JPG - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
JPKReader - Class in loci.formats.in

JPKReader is the file format reader for JPK Instruments files.

JPKReader() - Constructor for class loci.formats.in.JPKReader

Constructs a new JPK reader.

JPXReader - Class in loci.formats.in

JPXReader is the file format reader for JPX (3D JPEG-2000) images.

JPXReader() - Constructor for class loci.formats.in.JPXReader

Constructs a new JPX Reader.

JSON_TAG - Static variable in class loci.formats.in.MicromanagerReader
 
jvm64Bit - Variable in class loci.formats.gui.LegacyQTTools

Flag indicating 64-bit JVM (does not support QTJava).

JVM_64BIT_MSG - Static variable in class loci.formats.gui.LegacyQTTools
 




K

key - Variable in class loci.formats.in.BaseZeissReader.Layer
 
key - Variable in class loci.formats.in.BioRadSCNReader.SCNHandler
 
key - Variable in class loci.formats.in.FEITiffReader.FEIHandler
 
key - Variable in class loci.formats.in.ImaconReader.ImaconHandler
 
key - Variable in class loci.formats.in.IvisionReader.IvisionHandler
 
key - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
key - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
 
key - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
 
key - Variable in class loci.formats.meta.OriginalMetadataAnnotation
 
key - Variable in class loci.plugins.prefs.Option

Key name for ImageJ preferences file.

KEY_AUTOSCALE - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_COLOR_MODE - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_CONCATENATE - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_CROP - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_FIRST - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_FORCE_THUMBS - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_GROUP_FILES - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_ID - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_LOCATION - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_MUST_GROUP - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_OPEN_ALL_SERIES - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_PREFIX - Static variable in class loci.plugins.prefs.Option

Prefix to use for all plugins preferences.

KEY_QUIET - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_ROIS_MODE - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SHOW_METADATA - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SHOW_OME_XML - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SHOW_ROIS - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SPECIFY_RANGES - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SPLIT_C - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SPLIT_T - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SPLIT_Z - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_STACK_FORMAT - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_STACK_ORDER - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_STITCH_TILES - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SWAP_DIMS - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_UNGROUP_FILES - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_UPGRADE_CHECK - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_VIRTUAL - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_WINDOWLESS - Static variable in class loci.plugins.in.ImporterOptions
 
keyid - Variable in class loci.formats.in.BaseZeissReader.Tag
 
keyPressed(KeyEvent) - Method in class loci.formats.gui.ImageViewer

Handles key presses.

keyReleased(KeyEvent) - Method in class loci.formats.gui.ImageViewer
 
KEYS - Static variable in class loci.formats.ClassList
 
keys(Hashtable<String, Object>) - Static method in class loci.formats.MetadataTools

Gets a sorted list of keys from the given hashtable.

keyTyped(KeyEvent) - Method in class loci.formats.gui.ImageViewer
 
KH - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

The value of the high-pass subband normalization factor

KH - Static variable in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

The value of the high-pass subband normalization factor

KHOROS_MAGIC_BYTES - Static variable in class loci.formats.in.KhorosReader
 
KhorosReader - Class in loci.formats.in

Reader for Khoros XV files.

KhorosReader() - Constructor for class loci.formats.in.KhorosReader

Constructs a new Khoros reader.

kind - Variable in class loci.formats.out.ImageIOWriter
 
KINETIC_CYCLE_TIME - Static variable in class loci.formats.in.FluoviewReader
 
KL - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

The value of the low-pass subband normalization factor

KL - Static variable in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7

The value of the low-pass subband normalization factor

KNOWN_VERSIONS - Static variable in class loci.formats.in.LiFlimReader
 
KodakReader - Class in loci.formats.in

KodakReader is the file format reader for Kodak Molecular Imaging .bip files.

KodakReader() - Constructor for class loci.formats.in.KodakReader

Constructs a new Kodak reader.

kryo - Variable in class loci.formats.Memoizer.KryoDeser
 
KryoDeser() - Constructor for class loci.formats.Memoizer.KryoDeser
 




L

L2DReader - Class in loci.formats.in

L2DReader is the file format reader for Li-Cor L2D datasets.

L2DReader() - Constructor for class loci.formats.in.L2DReader

Construct a new L2D reader.

l2Norm - Variable in class jj2000.j2k.wavelet.analysis.SubbandAn

The L2-norm of the synthesis basis waveform of this subband,
 applicable to "leafs" only.

label - Variable in class loci.plugins.prefs.Option

Label describing the option, for use with ImageJ dialogs.

LABEL_X - Static variable in class loci.formats.in.TextReader
 
LABEL_Y - Static variable in class loci.formats.in.TextReader
 
labels - Variable in class loci.formats.in.FakeReader
 
labels - Variable in class loci.formats.in.ICSReader

Dimensional reordering for lifetime data

labels - Variable in class loci.formats.Modulo
 
labels - Variable in class loci.plugins.config.FlexWidgets
 
labels - Variable in class loci.plugins.config.FormatEntry
 
labels - Variable in class loci.plugins.config.LIFWidgets
 
labels - Variable in class loci.plugins.config.ND2Widgets
 
labels - Variable in class loci.plugins.config.PictWidgets
 
labels - Variable in class loci.plugins.config.QTWidgets
 
labels - Variable in class loci.plugins.config.SDTWidgets
 
labels - Variable in class loci.plugins.config.TiffDelegateWidgets
 
labels - Variable in class loci.plugins.config.ZeissCZIWidgets
 
LAMBDA - Static variable in class loci.formats.in.CellSensReader
 
LAMBDA_INCREMENT - Static variable in class loci.formats.in.CellSensReader
 
LAMBDA_START - Static variable in class loci.formats.in.CellSensReader
 
LAMBDA_VALUE - Static variable in class loci.formats.in.CellSensReader
 
largePalette - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
Laser() - Constructor for class loci.formats.in.LeicaHandler.Laser
 
Laser() - Constructor for class loci.formats.in.OIRReader.Laser
 
Laser() - Constructor for class loci.formats.in.ZeissLSMReader.Laser
 
LASER_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
 
LASER_NAME - Static variable in class loci.formats.in.ZeissLSMReader
 
LASER_POWER - Static variable in class loci.formats.in.ZeissLSMReader
 
LASER_SCAN_CONFOCAL - Static variable in class loci.formats.in.LegacyND2Reader
 
laserActive - Variable in class loci.formats.in.LIFReader
 
laserCount - Variable in class loci.formats.in.LeicaHandler
 
laserFrap - Variable in class loci.formats.in.LIFReader
 
laserIDs - Variable in class loci.formats.in.NikonTiffReader
 
laserIndex - Variable in class loci.formats.in.OIRReader.Channel
 
laserIntensity - Variable in class loci.formats.in.LIFReader
 
lasers - Variable in class loci.formats.in.LeicaHandler
 
lasers - Variable in class loci.formats.in.OIRReader
 
laserWavelength - Variable in class loci.formats.in.LIFReader
 
lastChangingElement - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
lastChannel - Variable in class loci.formats.in.BioRadReader
 
lastChannel - Variable in class loci.formats.in.CellH5Reader
 
lastChannel - Variable in class loci.formats.in.FV1000Reader
 
lastChannel - Variable in class loci.formats.in.ImarisHDFReader
 
lastChannel - Variable in class loci.formats.in.LIFReader
 
lastChannel - Variable in class loci.formats.in.NativeND2Reader
 
lastChannel - Variable in class loci.formats.in.OIRReader
 
lastCodeOffset - Variable in class loci.formats.in.AmiraReader.HxRLE
 
lastDispose - Variable in class loci.formats.in.GIFReader
 
lastFile - Variable in class loci.formats.in.CellWorxReader
 
lastFile - Variable in class loci.formats.in.ImprovisionTiffReader
 
lastFile - Variable in class loci.formats.in.SlidebookTiffReader
 
lastId - Variable in class loci.formats.gui.PreviewPane

Last ID loaded.

lastIFD - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
lastImage - Variable in class loci.formats.ChannelSeparator

Last image opened.

lastImage - Variable in class loci.formats.in.APNGReader
 
lastImage - Variable in class loci.formats.in.AVIReader
 
lastImageHeight - Variable in class loci.formats.ChannelSeparator

Height of last image opened.

lastImageIndex - Variable in class loci.formats.ChannelSeparator

Index of last image opened.

lastImageIndex - Variable in class loci.formats.in.APNGReader
 
lastImageNo - Variable in class loci.formats.in.AVIReader
 
lastImageRow - Variable in class loci.formats.in.APNGReader
 
lastImageSeries - Variable in class loci.formats.ChannelSeparator

Series of last image opened.

lastImageWidth - Variable in class loci.formats.ChannelSeparator

Width of last image opened.

lastImageX - Variable in class loci.formats.ChannelSeparator

X index of last image opened.

lastImageY - Variable in class loci.formats.ChannelSeparator

Y index of last image opened.

lastIndex - Variable in class loci.formats.in.DNGReader
 
lastIndex - Variable in class loci.formats.in.NikonReader
 
lastm - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull

The vertical index of the last code-block "sent" in the current subband
 in each component.

lastn - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull

The horizontal index of the last code-block "sent" in the current
 subband in each component.

lastPlane - Variable in class loci.formats.in.BaseZeissReader
 
lastPlane - Variable in class loci.formats.in.DNGReader
 
lastPlane - Variable in class loci.formats.in.JPXReader
 
lastPlane - Variable in class loci.formats.in.LeicaReader
 
lastPlane - Variable in class loci.formats.in.MinimalTiffReader
 
lastPlane - Variable in class loci.formats.in.NikonReader
 
lastPlane - Variable in class loci.formats.in.OMETiffReader
 
lastPlane - Variable in class loci.formats.in.OpenlabReader
 
lastPlane - Variable in class loci.formats.in.TCSReader
 
lastPlane - Variable in class loci.formats.out.ICSWriter
 
lastPlane - Variable in class loci.formats.out.V3DrawWriter
 
lastPos - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
 
lastPosition - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD
 
lastReader - Variable in class loci.formats.in.CellWorxReader
 
lastRegion - Variable in class loci.formats.codec.JPEGTileDecoder.TileCache
 
lastSegmentLength - Variable in class com.sun.media.imageio.stream.SectorStreamSegmentMapper
 
lastSeries - Variable in class loci.formats.in.BrukerReader
 
lastSeries - Variable in class loci.formats.in.JPEG2000Reader
 
lastSeries - Variable in class loci.formats.in.JPXReader
 
lastSeriesPlane - Variable in class loci.formats.in.JPEG2000Reader
 
lastSeriesPlane - Variable in class loci.formats.in.JPXReader
 
lastTile - Variable in class loci.formats.codec.JPEGTileDecoder.TileCache
 
LATEST_VERSION - Static variable in class loci.formats.services.OMEXMLServiceImpl

Latest OME-XML version namespace.

LATITUDE_REF_NORTH - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSLatitudeRef" and
 "GPSDestLatitudeRef" tags.

LATITUDE_REF_SOUTH - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSLatitudeRef" and
 "GPSDestLatitudeRef" tags.

Layer() - Constructor for class loci.formats.in.BaseZeissReader.Layer
 
layer_count - Variable in class loci.formats.in.ZeissTIFFHandler
 
LAYER_INFO_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
LAYER_SELECTION - Static variable in class loci.formats.in.CellSensReader
 
LAYER_SELECTION_INDEX - Static variable in class loci.formats.in.CellSensReader
 
LAYER_XY_FIXED - Static variable in class loci.formats.in.CellSensReader
 
layerIdx - Variable in class jj2000.j2k.codestream.reader.PktInfo

The layer associated with the current code-block in this packet.

layerNames - Variable in class loci.formats.in.PhotoshopTiffReader
 
layerOffset - Variable in class loci.formats.in.PhotoshopTiffReader
 
layers - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Explicitly specifies the codestream layer formation parameters.

layers - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Array containing the layers information.

layers - Variable in class loci.formats.in.BaseZeissReader
 
layers - Variable in class loci.formats.in.ZeissTIFFHandler
 
LayersInfo - Class in jj2000.j2k.entropy.encoder

This class stores the specification of a layer distribution in the
 bit stream.

LayersInfo(float) - Constructor for class jj2000.j2k.entropy.encoder.LayersInfo

Creates a new LayersInfo object.

LAYOUT_KEYS - Static variable in class loci.formats.in.ICSReader
 
LAYOUT_TABLE - Static variable in class loci.formats.in.LiFlimReader
 
lbbuf - Variable in class jj2000.j2k.codestream.writer.PktEncoder

The body buffer of the last encoded packet

lblen - Variable in class jj2000.j2k.codestream.writer.PktEncoder

The body length of the last encoded packet

lblock - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Lblock value used to read code size information in each packet head:

 
  1st dim: component index.
  2nd dim: resolution level index.
  3rd dim: subband index.
  4th/5th dim: code-block index (vert.

lblock - Variable in class jj2000.j2k.codestream.writer.PktEncoder

The base number of bits for sending code-block length information
 (referred as Lblock in the JPEG 2000 standard).

lblockNo - Variable in class loci.formats.in.SDTInfo

Long blockNo - see remarks below.

lcm(int, int) - Static method in class jj2000.j2k.util.MathUtil

Method that calculates the Least Common Multiple (LCM) of two strictly
 positive integer numbers.

lcm(int[]) - Static method in class jj2000.j2k.util.MathUtil

Method that calculates the Least Common Multiple (LCM) of several
 positive integer numbers.

lcoc - Variable in class jj2000.j2k.codestream.HeaderInfo.COC
 
lcod - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
lcom - Variable in class jj2000.j2k.codestream.HeaderInfo.COM
 
lcrg - Variable in class jj2000.j2k.codestream.HeaderInfo.CRG
 
lcs - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The length calculation specifications

LCS_CALIBRATED_RGB - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
LCS_sRGB - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
LCS_WINDOWS_COLOR_SPACE - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
lcType - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor

The length calculation type to use in compression

leafCounter - Variable in class loci.formats.codec.HuffmanCodec
 
leafValue - Variable in class loci.formats.codec.HuffmanCodec.Decoder
 
LEAVES_OFFSET - Static variable in class loci.formats.codec.HuffmanCodec
 
legacy - Variable in class loci.formats.in.PictReader
 
legacy - Variable in class loci.formats.out.QTWriter

Legacy QuickTime writer.

LegacyND2Reader - Class in loci.formats.in

LegacyND2Reader is a file format reader for Nikon ND2 files that uses
 the Nikon ND2 SDK - it is only usable on Windows machines.

LegacyND2Reader() - Constructor for class loci.formats.in.LegacyND2Reader
 
LegacyQTReader - Class in loci.formats.in

LegacyQTReader is a file format reader for QuickTime movie files.

LegacyQTReader() - Constructor for class loci.formats.in.LegacyQTReader

Constructs a new QT reader.

LegacyQTTools - Class in loci.formats.gui

Utility class for working with QuickTime for Java.

LegacyQTTools() - Constructor for class loci.formats.gui.LegacyQTTools
 
LegacyQTWriter - Class in loci.formats.out

LegacyQTWriter is a file format writer for QuickTime movies.

LegacyQTWriter() - Constructor for class loci.formats.out.LegacyQTWriter
 
legacyReader - Variable in class loci.formats.DelegateReader

Legacy reader.

legacyReaderInitialized - Variable in class loci.formats.DelegateReader

Flag indicating that the legacy reader was successfully initialized.

LEI_SUFFIX - Static variable in class loci.formats.in.LeicaReader
 
LEICA_MAGIC_TAG - Static variable in class loci.formats.in.LeicaReader

All Leica TIFFs have this tag.

LeicaHandler - Class in loci.formats.in

SAX handler for parsing XML in Leica LIF and Leica TCS files.

LeicaHandler(MetadataStore, MetadataLevel) - Constructor for class loci.formats.in.LeicaHandler
 
LeicaHandler.Channel - Class in loci.formats.in
 
LeicaHandler.Detector - Class in loci.formats.in
 
LeicaHandler.Laser - Class in loci.formats.in
 
LeicaHandler.MultiBand - Class in loci.formats.in
 
LeicaHandler.ROI - Class in loci.formats.in
 
LeicaReader - Class in loci.formats.in

LeicaReader is the file format reader for Leica files.

LeicaReader() - Constructor for class loci.formats.in.LeicaReader

Constructs a new Leica reader.

LeicaReader.Detector - Class in loci.formats.in
 
LeicaSCNHandler() - Constructor for class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
LeicaSCNReader - Class in loci.formats.in

LeicaSCNReader is the file format reader for Leica SCN TIFF files.

LeicaSCNReader() - Constructor for class loci.formats.in.LeicaSCNReader

Constructs a new LeicaSCN reader.

LeicaSCNReader.Dimension - Class in loci.formats.in
 
LeicaSCNReader.Image - Class in loci.formats.in
 
LeicaSCNReader.ImageCollection - Class in loci.formats.in
 
LeicaSCNReader.LeicaSCNHandler - Class in loci.formats.in

SAX handler for parsing XML in Leica SCN files.

LeicaSCNReader.Pixels - Class in loci.formats.in
 
leiFilename - Variable in class loci.formats.in.LeicaReader

Name of current LEI file

len - Variable in class jj2000.j2k.codestream.reader.CBlkInfo

Length of each piece of code-block's codewords

len - Variable in class jj2000.j2k.util.ISRandomAccessIO
 
len - Variable in class loci.plugins.util.BFVirtualStack
 
lenC - Variable in class loci.formats.FileStitcher

Component lengths for each axis type.

lenCalc - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The length calculation type for each tile-component

length() - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream

Returns the number of bytes currently in the FileChannel.

length() - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream

Returns the number of bytes currently in the FileChannel.

length() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
length() - Method in class com.sun.media.imageio.stream.SectorStreamSegmentMapper
 
length() - Method in class com.sun.media.imageio.stream.SegmentedImageInputStream
 
length() - Method in class com.sun.media.imageio.stream.StreamSegmentMapperImpl
 
length - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Box length, extra length, type and content data array

length() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO

Returns the length of the data stream.

length() - Method in class jj2000.j2k.entropy.encoder.BitToByteOutput

Returns the length, in bytes, of the output bit stream as written by
 this object.

length() - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Returns the current length of the stream, in bytes, taking into
 account any buffering.

length() - Method in interface jj2000.j2k.io.RandomAccessIO

Returns the current length of the stream, in bytes, taking into account
 any buffering.

length() - Method in class jj2000.j2k.util.ISRandomAccessIO

Returns the length of the stream.

length() - Method in class loci.formats.cache.CacheStrategy

Shortcut for computing total number of positions.

length - Variable in class loci.formats.in.APNGReader.PNGBlock
 
length - Variable in class loci.formats.in.IM3Reader.IM3Record
 
length - Variable in class loci.formats.in.NativeND2Reader.ChunkMapEntry
 
length - Variable in class loci.formats.in.OBFReader.Stack
 
length - Variable in class loci.formats.in.OIRReader.PixelBlock
 
length() - Method in class loci.formats.Modulo
 
LENGTH_LAZY - Static variable in class jj2000.j2k.entropy.encoder.MQCoder

Identifier for the lazy length calculation.

LENGTH_LAZY_GOOD - Static variable in class jj2000.j2k.entropy.encoder.MQCoder

Identifier for a very simple length calculation.

LENGTH_NEAR_OPT - Static variable in class jj2000.j2k.entropy.encoder.MQCoder

Identifier for the near optimal length calculation.

lengths - Variable in class loci.formats.cache.CacheStrategy

Length of each dimensional axis.

lengths - Variable in class loci.formats.gui.CacheComponent

Length of each dimensional axis, obtained from cache strategy.

lengths - Variable in class loci.formats.in.AVIReader

Number of bytes in each plane.

lengths - Variable in class loci.formats.in.DeltavisionReader
 
lengths - Variable in class loci.formats.in.MNGReader.SeriesInfo
 
lenLastNoROI - Variable in class jj2000.j2k.codestream.writer.FileCodestreamWriter

Length of last packets containing no ROI information

LENS - Static variable in class loci.formats.in.NikonReader
 
lens - Variable in class loci.formats.in.PSDReader
 
LENS_TYPE - Static variable in class loci.formats.in.NikonReader
 
lensNA - Variable in class loci.formats.in.FluoviewReader
 
lensNA - Variable in class loci.formats.in.FV1000Reader
 
lensNA - Variable in class loci.formats.in.IvisionReader
 
lensNA - Variable in class loci.formats.in.LIFReader
 
lensNA - Variable in class loci.formats.in.MetamorphHandler
 
lensNA - Variable in class loci.formats.in.NikonTiffReader
 
lensNA - Variable in class loci.formats.in.OperettaReader.Plane
 
lensNA - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
lensRI - Variable in class loci.formats.in.MetamorphHandler
 
lenT - Variable in class loci.formats.FileStitcher

Component lengths for each axis type.

lenZ - Variable in class loci.formats.FileStitcher

Component lengths for each axis type.

LEO_TAG - Static variable in class loci.formats.in.LEOReader
 
LEOReader - Class in loci.formats.in

LEOReader is the file format reader for LEO EM files.

LEOReader() - Constructor for class loci.formats.in.LEOReader

Constructs a new LEO reader.

letter - Variable in class loci.formats.ResourceNamer
 
level - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
level - Variable in class jj2000.j2k.wavelet.Subband

The level in the tree to which this subband belongs, which is the
 number of wavelet decompositions performed to produce this subband.

level - Variable in class loci.formats.in.BioRadReader.Note
 
level - Variable in class loci.formats.in.FlexReader.FlexHandler
 
level - Variable in class loci.formats.in.LeicaHandler
 
levelShift - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
lh - Variable in class jj2000.j2k.roi.encoder.SubbandROIMask

The subband masks of the child LH

LIB_STATE_LOADED - Static variable in class jj2000.j2k.util.NativeServices

Library load state ID indicating that the library was successfully
 loaded.

LIB_STATE_NOT_FOUND - Static variable in class jj2000.j2k.util.NativeServices

Library load state ID indicating that an attempt to load the library
 was done and that it could not be found.

LIB_STATE_NOT_LOADED - Static variable in class jj2000.j2k.util.NativeServices

Library load state ID indicating that no attept to load the library has
 been done yet.

libClass - Variable in class loci.plugins.config.LibraryEntry
 
Library() - Constructor for enum loci.plugins.util.LibraryChecker.Library
 
LibraryChecker - Class in loci.plugins.util

Utility methods for verifying that classes
 are present and versions are correct.

LibraryChecker() - Constructor for class loci.plugins.util.LibraryChecker
 
LibraryChecker.Library - Enum in loci.plugins.util

List of possible libraries for which to check.

LibraryEntry - Class in loci.plugins.config

A list entry for the configuration window's Libraries tab.

LibraryEntry(PrintWriter, HashMap<String, String>) - Constructor for class loci.plugins.config.LibraryEntry
 
LibraryEntry(PrintWriter, String, String, String, String, String, String, String) - Constructor for class loci.plugins.config.LibraryEntry
 
libraryFound - Static variable in class loci.formats.in.LegacyND2Reader
 
libraryLoaded - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
libsList - Variable in class loci.plugins.config.ConfigWindow
 
libsListModel - Variable in class loci.plugins.config.ConfigWindow
 
libState - Static variable in class jj2000.j2k.util.NativeServices

The state of the library loading

license - Variable in class loci.formats.services.LuraWaveServiceImpl

License code.

license - Variable in class loci.plugins.config.ConfigWindow
 
license - Variable in class loci.plugins.config.LibraryEntry
 
LICENSE_PROPERTY - Static variable in class loci.formats.services.LuraWaveServiceImpl

System property to check for the LuraWave license code.

licenseBox - Variable in class loci.plugins.config.FlexWidgets
 
LICOR_MAGIC_STRING - Static variable in class loci.formats.in.L2DReader
 
LIF_MAGIC_BYTE - Static variable in class loci.formats.in.LIFReader
 
LIF_MEMORY_BYTE - Static variable in class loci.formats.in.LIFReader
 
LIFETIME - Static variable in class loci.formats.FormatTools

Identifies the Lifetime dimensional type,
 representing a dimension consisting of a lifetime histogram.

lifetime - Variable in class loci.formats.in.ICSReader

Whether or not the channels represent lifetime histogram bins.

LIFF_MAGIC_BYTES - Static variable in class loci.formats.in.OpenlabReader
 
LiFlimReader - Class in loci.formats.in

LiFlimReader is the file format reader for LI-FLIM files.

LiFlimReader() - Constructor for class loci.formats.in.LiFlimReader

Constructs a new LI-FLIM reader.

LiFlimReader.ROI - Class in loci.formats.in
 
LIFReader - Class in loci.formats.in

LIFReader is the file format reader for Leica LIF files.

LIFReader() - Constructor for class loci.formats.in.LIFReader

Constructs a new Leica LIF reader.

LIFReader.ROI - Class in loci.formats.in
 
LIFWidgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats Leica LIF support.

LIFWidgets() - Constructor for class loci.plugins.config.LIFWidgets
 
LIGHT_SOURCE - Static variable in class loci.formats.tiff.IFD
 
LIGHT_SOURCE_CLOUDY_WEATHER - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_COOL_WHITE_FLUORESCENT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_D50 - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_D55 - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_D65 - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_D75 - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_DAY_WHITE_FLUORESCENT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_DAYLIGHT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_DAYLIGHT_FLUORESCENT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_FINE_WEATHER - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_FLASH - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_FLUORESCENT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_ISO_STUDIO_TUNGSTEN - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_OTHER - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_SHADE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_STANDARD_LIGHT_A - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_STANDARD_LIGHT_B - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_STANDARD_LIGHT_C - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_TUNGSTEN - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_UNKNOWN - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_SOURCE_WHITE_FLUORESCENT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "LightSource" tag.

LIGHT_TYPE - Static variable in class loci.formats.in.NikonReader
 
LightSource() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.LightSource
 
lightSourceCombinationIDs - Variable in class loci.formats.in.FlexReader
 
lightSourceCombinationRefs - Variable in class loci.formats.in.FlexReader
 
lightSourceID - Variable in class loci.formats.in.FlexReader.FlexHandler
 
lightSourceIDs - Variable in class loci.formats.in.FlexReader
 
limit_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor

limit at which current number of bits code size has to be increased

limitHeight(JComponent) - Method in class loci.formats.gui.DataConverter
 
LIMReader - Class in loci.formats.in

LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.

LIMReader() - Constructor for class loci.formats.in.LIMReader

Constructs a new LIM reader.

LINE - Static variable in class loci.formats.in.FV1000Reader
 
line - Variable in class loci.formats.in.FV1000Reader
 
LINE - Static variable in class loci.formats.in.LeicaHandler.ROI
 
LINE - Static variable in class loci.formats.in.LIFReader.ROI
 
LINE - Static variable in class loci.formats.in.ZeissLSMReader
 
line - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
 
LINE_FEED - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
LINE_LENGTH - Static variable in class loci.formats.in.FitsReader
 
LINEAR - Static variable in class loci.formats.in.GelReader
 
lineBitNum - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
linediv - Variable in class loci.formats.in.SDTInfo

Line predivider = 2 ** (linediv).

LineEndPositions(int) - Constructor for enum loci.formats.in.BaseZeissReader.LineEndPositions
 
lineEndPositions - Variable in class loci.formats.in.BaseZeissReader.Shape
 
lineEndSize - Variable in class loci.formats.in.BaseZeissReader.Shape
 
LineEndStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.LineEndStyle
 
lineEndStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
 
lineMode - Variable in class loci.formats.in.SPCReader
 
lines - Variable in class loci.formats.in.FakeReader
 
lineSeparator - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
lineSeparator - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
lineStride - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

The strides for pixel, band, and scanline.

lineTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
lineWidth - Variable in class loci.formats.in.BaseZeissReader.Shape
 
linewidth - Variable in class loci.formats.in.LeicaHandler.ROI
 
linewidth - Variable in class loci.formats.in.LIFReader.ROI
 
linkedInstruments - Variable in class loci.formats.in.LeicaHandler
 
listeners - Variable in class loci.formats.cache.Cache

List of cache event listeners.

listeners - Variable in class loci.formats.cache.CacheStrategy

List of cache event listeners.

listeners - Variable in class loci.plugins.in.ImagePlusReader
 
listeners - Variable in class loci.plugins.in.ImportProcess
 
listFakeSeries(String) - Method in class loci.formats.in.FakeReader

Traverses a fake file folder structure indicated by traversedDirectory

listMaxLength - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFAttrInfo
 
listMinLength - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFAttrInfo
 
listString - Variable in class loci.formats.in.AVIReader
 
listToCharArray(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
listToIntArray(String) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
LITTLE - Static variable in class loci.formats.tiff.TiffConstants
 
LITTLE_ENDIAN - Static variable in interface jj2000.j2k.io.EndianType

Identifier for little-endian byte ordering (i.e.

LITTLE_ENDIAN - Static variable in class loci.formats.in.BioRadReader

Always little endian.

LITTLE_ENDIAN - Static variable in class loci.formats.in.DeltavisionReader
 
LITTLE_ENDIAN - Static variable in class loci.formats.in.OBFReader
 
LITTLE_ENDIAN - Static variable in class loci.formats.in.TextReader
 
LITTLE_ENDIAN - Static variable in class loci.formats.tiff.IFD
 
littleEndian - Variable in class loci.formats.codec.CodecOptions

Indicates endianness of pixel data.

littleEndian - Variable in class loci.formats.CoreMetadata

Indicates whether or not each pixel's bytes are in little endian order.

littleEndian - Variable in class loci.formats.out.APNGWriter
 
littleEndian - Variable in class loci.formats.tools.AmiraParameters
 
littleEndianString - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
LIVE_OVERFLOW - Static variable in class loci.formats.in.CellSensReader
 
ll - Variable in class jj2000.j2k.roi.encoder.SubbandROIMask

The subband masks of the child LL

LM_DOMAIN - Static variable in class loci.formats.FormatTools

Identifies the light microscopy domain.

LO - Static variable in class loci.formats.in.DicomReader
 
load(String, File, boolean) - Static method in class loci.formats.Memoizer
 
load() - Static method in class org.libjpegturbo.turbojpeg.TJLoader
 
loadedFromMemo - Variable in class loci.formats.Memoizer

Whether the ReaderWrapper.reader instance currently active was loaded from
 the memo file during Memoizer.setId(String).

LOADER - Static variable in class loci.formats.gui.LegacyQTTools

This custom class loader searches additional paths for the QTJava.zip
 library.

loader - Variable in class loci.formats.gui.PreviewPane

Thumbnail loading thread.

loader - Variable in class loci.plugins.in.ThumbLoader
 
loaderAlive - Variable in class loci.formats.gui.PreviewPane

Flag indicating whether loader thread should keep running.

loadId - Variable in class loci.formats.gui.PreviewPane

Current ID to load.

loadImage(Image) - Static method in class loci.formats.gui.AWTImageTools

Ensures the given AWT image is fully loaded.

loadLibrary() - Static method in class jj2000.j2k.util.NativeServices

Loads the shared library implementing the native methods of this
 class and returns true on success.

loadManifest() - Static method in class loci.formats.FormatTools
 
loadMemo() - Method in class loci.formats.Memoizer

Load a memo file if possible, returning a null if not.

loadOption() - Method in class loci.plugins.prefs.BooleanOption
 
loadOption() - Method in class loci.plugins.prefs.DoubleOption
 
loadOption() - Method in class loci.plugins.prefs.Option

Loads the option's value from the ImageJ preferences file.

loadOption() - Method in class loci.plugins.prefs.StringOption
 
loadOptions() - Method in class loci.plugins.prefs.OptionsList

Loads option values from the ImageJ preferences file.

loadProperties() - Static method in class loci.formats.FormatTools

Deprecated.
This method should no longer be used.  The properties
 are now obtained from the jar manifest.


loadReader() - Method in interface loci.formats.Memoizer.Deser
 
loadReader() - Method in class loci.formats.Memoizer.KryoDeser
 
loadReader() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
loadReleaseVersion() - Method in interface loci.formats.Memoizer.Deser
 
loadReleaseVersion() - Method in class loci.formats.Memoizer.KryoDeser
 
loadReleaseVersion() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
loadRevision() - Method in interface loci.formats.Memoizer.Deser
 
loadRevision() - Method in class loci.formats.Memoizer.KryoDeser
 
loadRevision() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
loadStart(File) - Method in interface loci.formats.Memoizer.Deser
 
loadStart(File) - Method in class loci.formats.Memoizer.KryoDeser
 
loadStart(File) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
loadStop() - Method in interface loci.formats.Memoizer.Deser
 
loadStop() - Method in class loci.formats.Memoizer.KryoDeser
 
loadStop() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
loadStream - Variable in class loci.formats.Memoizer.RandomAccessDeser
 
loadThumb(BufferedImageReader, int, Panel, boolean) - Static method in class loci.plugins.in.ThumbLoader
 
loadVersion() - Method in interface loci.formats.Memoizer.Deser
 
loadVersion() - Method in class loci.formats.Memoizer.KryoDeser
 
loadVersion() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
localColorTable - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
locateExperimentFile(String) - Method in class loci.formats.in.BDReader
 
locateFirstValidFile() - Method in class loci.formats.in.MetamorphReader

Locates the first valid file in the STK arrays.

locateIFD(int, long[], long[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
locateImage(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
location - Variable in class loci.formats.in.DicomReader
 
LOCATION_HTTP - Static variable in class loci.plugins.in.ImporterOptions
 
LOCATION_LOCAL - Static variable in class loci.plugins.in.ImporterOptions
 
LOCATION_OMERO - Static variable in class loci.plugins.in.ImporterOptions
 
LocationDialog - Class in loci.plugins.in

Bio-Formats Importer location chooser dialog box.

LocationDialog(ImportProcess) - Constructor for class loci.plugins.in.LocationDialog

Creates a location chooser dialog for the Bio-Formats Importer.

locator - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
loci.formats - package loci.formats

Bio-Formats: a library for reading and writing popular microscopy file
formats.

loci.formats.cache - package loci.formats.cache

Package containing Bio-Formats caching logic, for managing
subsets of large collections of image planes in memory.

loci.formats.codec - package loci.formats.codec

Package containing Bio-Formats compression and decompression logic.

loci.formats.gui - package loci.formats.gui

Package containing Bio-Formats graphical user interface code.

loci.formats.in - package loci.formats.in

Package containing Bio-Formats file format readers.

loci.formats.meta - package loci.formats.meta

Package containing core Bio-Formats metadata interfaces for the OME data model.

loci.formats.ome - package loci.formats.ome

Package containing Bio-Formats OME-related logic for
OME-XML metadata, and database import, upload and download.

loci.formats.out - package loci.formats.out

Package containing Bio-Formats file format writers.

loci.formats.services - package loci.formats.services
 
loci.formats.tiff - package loci.formats.tiff

Package containing Bio-Formats TIFF code of general utility.

loci.formats.tools - package loci.formats.tools

Package containing utility methods corresponding
to the Bio-Formats command line tools.

loci.plugins - package loci.plugins

Bio-Formats Plugins: a collection of plugins for ImageJ, including the
Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions,
Data Browser and Stack Slicer.

loci.plugins.config - package loci.plugins.config

Bio-Formats Plugins Configuration plugin for ImageJ.

loci.plugins.in - package loci.plugins.in

Bio-Formats Importer plugin for ImageJ.

loci.plugins.macro - package loci.plugins.macro

Bio-Formats Macro Extensions plugin for ImageJ.

loci.plugins.out - package loci.plugins.out

Bio-Formats Exporter plugin for ImageJ.

loci.plugins.prefs - package loci.plugins.prefs

Classes for managing Bio-Formats plugins preferences.

loci.plugins.shortcut - package loci.plugins.shortcut

Bio-Formats Plugins Shortcut Window plugin for ImageJ.

loci.plugins.util - package loci.plugins.util

Utility classes and methods for the Bio-Formats plugins for ImageJ.

LociConfig - Class in loci.plugins.config

An ImageJ plugin for displaying the Bio-Formats plugins configuration dialog.

LociConfig() - Constructor for class loci.plugins.config.LociConfig
 
LociExporter - Class in loci.plugins

ImageJ plugin for writing files using the OME Bio-Formats package.

LociExporter() - Constructor for class loci.plugins.LociExporter
 
LociFunctions - Class in loci.plugins.macro

This class provides macro extensions in ImageJ for Bio-Formats.

LociFunctions() - Constructor for class loci.plugins.macro.LociFunctions
 
LociImporter - Class in loci.plugins

ImageJ plugin for reading files using the OME Bio-Formats package.

LociImporter() - Constructor for class loci.plugins.LociImporter
 
LociInstaller - Class in loci.plugins.config

An ImageJ plugin for installing and upgrading libraries
 related to the Bio-Formats plugins.

LociInstaller() - Constructor for class loci.plugins.config.LociInstaller
 
LociPrefs - Class in loci.plugins.util

Utility methods for ImageJ preferences for Bio-Formats plugins.

LociPrefs() - Constructor for class loci.plugins.util.LociPrefs
 
lock - Variable in class jj2000.j2k.util.ThreadPool.ThreadPoolThread
 
LOG - Static variable in interface jj2000.j2k.util.MsgLogger

Severity of message.

log - Variable in class loci.plugins.config.ConfigWindow
 
log() - Method in class loci.plugins.util.RecordedImageProcessor
 
LOG2 - Static variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

The log of 2, natural base

log2 - Static variable in class jj2000.j2k.quantization.quantizer.StdQuantizer

Natural log of 2, used as a convenience variable

log2(int) - Static method in class jj2000.j2k.util.MathUtil

Method that calculates the floor of the log, base 2,
 of 'x'.

logFile - Variable in class loci.formats.in.DeltavisionReader
 
logFiles - Variable in class loci.formats.in.CellWorxReader
 
LOGGER - Static variable in class loci.formats.cache.CacheUpdater
 
LOGGER - Static variable in class loci.formats.ClassList
 
LOGGER - Static variable in class loci.formats.codec.BaseCodec
 
LOGGER - Static variable in class loci.formats.codec.BitBuffer

Deprecated.
 
LOGGER - Static variable in class loci.formats.codec.BitWriter

Deprecated.
 
LOGGER - Static variable in class loci.formats.codec.JPEGTileDecoder
 
LOGGER - Static variable in class loci.formats.FileStitcher
 
LOGGER - Static variable in class loci.formats.FormatHandler
 
LOGGER - Static variable in class loci.formats.FormatTools
 
LOGGER - Static variable in class loci.formats.gui.AWTImageTools
 
LOGGER - Static variable in class loci.formats.gui.CacheComponent
 
LOGGER - Static variable in class loci.formats.gui.DataConverter
 
LOGGER - Static variable in class loci.formats.gui.ImageViewer
 
LOGGER - Static variable in class loci.formats.gui.LegacyQTTools
 
LOGGER - Static variable in class loci.formats.gui.PreviewPane
 
LOGGER - Static variable in class loci.formats.ImageReader
 
LOGGER - Static variable in class loci.formats.ImageWriter
 
LOGGER - Static variable in class loci.formats.in.BaseTiffReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.DNGReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.IM3Reader

Logger for outputting summary diagnostics.

LOGGER - Static variable in class loci.formats.in.ImarisTiffReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.JPEG2000MetadataParser

Logger for this class.

LOGGER - Static variable in class loci.formats.in.JPEG2000Reader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.JPXReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.LeicaHandler

Logger for this class.

LOGGER - Static variable in class loci.formats.in.LeicaReader
 
LOGGER - Static variable in class loci.formats.in.LeicaSCNReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.MetamorphReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.MinimalTiffReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.ND2Handler
 
LOGGER - Static variable in class loci.formats.in.NikonReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.PyramidTiffReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.SVSReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.TiffReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.TrestleReader

Logger for this class.

LOGGER - Static variable in class loci.formats.in.ZeissTIFFHandler
 
LOGGER - Static variable in class loci.formats.Memoizer

Default Logger for the memoizer class

LOGGER - Static variable in class loci.formats.MetadataTools
 
logger - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
LOGGER - Static variable in class loci.formats.services.JPEGXRServiceImpl
 
LOGGER - Static variable in class loci.formats.services.OMEXMLServiceImpl

Logger for this class.

LOGGER - Static variable in class loci.formats.tiff.IFD
 
LOGGER - Static variable in enum loci.formats.tiff.TiffCompression
 
LOGGER - Static variable in class loci.formats.tiff.TiffParser
 
LOGGER - Static variable in class loci.formats.tiff.TiffSaver
 
LOGGER - Static variable in class loci.formats.TileStitcher
 
LOGGER - Static variable in class loci.formats.tools.EditTiffG
 
LOGGER - Static variable in class loci.formats.tools.FakeImage
 
LOGGER - Static variable in class loci.formats.UpgradeChecker
 
loggerList - Static variable in class jj2000.j2k.util.FacilityManager

The loggers associated to different threads

logicalScreenHeight - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
logicalScreenWidth - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
logJJ2000Msg - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

Whether to log JJ2000 messages.

LONG - Static variable in class loci.formats.in.CellSensReader
 
LONG_DATE_FORMAT - Static variable in class loci.formats.in.MetamorphReader
 
LONGITUDE_REF_EAST - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSLongitudeRef" and
 "GPSDestLongitudeRef" tags.

LONGITUDE_REF_WEST - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSLongitudeRef" and
 "GPSDestLongitudeRef" tags.

longValue() - Method in class loci.formats.tiff.TiffRational

Returns the value of the specified number as a long.

lookup - Static variable in enum loci.formats.codec.CompressionType

Map used to retrieve the compression type corresponding to the code.

lookup - Static variable in enum loci.formats.codec.JPEG2000BoxType

Map used to retrieve the box type corresponding to the code.

lookup - Static variable in enum loci.formats.codec.JPEG2000SegmentMarker

Map used to retrieve the segment marker corresponding to the code.

lookup - Static variable in enum loci.formats.in.BaseZeissReader.Charset
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.DrawStyle
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.FeatureType
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.FillStyle
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.LineEndPositions
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.LineEndStyle
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.PointStyle
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.TextAlignment
 
lookup - Variable in class loci.formats.in.PictReader

Color lookup table for palette color images.

lookup - Static variable in enum loci.formats.tiff.IFDType
 
lookup - Static variable in enum loci.formats.tiff.PhotoInterp
 
lookup - Static variable in enum loci.formats.tiff.TiffCompression

Reverse lookup of code to TIFF compression enumerate value.

lookupBase64Alphabet - Static variable in class loci.formats.codec.Base64Codec
 
lookupDimension(int, int, int) - Method in class loci.formats.in.LeicaSCNReader.Pixels
 
lookupFile(int, int, int) - Method in class loci.formats.in.FlexReader
 
lookupFile(int) - Method in class loci.formats.in.FlexReader
 
lookupFile(int) - Method in class loci.formats.in.PerkinElmerReader
 
lookupPlane(int, int, int, int, int) - Method in class loci.formats.in.ColumbusReader
 
lossless - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Indicates using the lossless scheme or not.

lossless - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Indicates using the loseless scheme or not.

lossless - Variable in class loci.formats.codec.CodecOptions

Used with codecs allowing lossy and lossless compression.

LOSSLESS_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
 
LOSSLESS_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
 
LosslessJPEGCodec - Class in loci.formats.codec

Decompresses lossless JPEG images.

LosslessJPEGCodec() - Constructor for class loci.formats.codec.LosslessJPEGCodec
 
LOSSY_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
 
LOSSY_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
 
lossyCompression - Variable in class loci.formats.in.NikonReader
 
LOW_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
 
lowFields - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

The fields in this directory which have a low tag number.

lPad - Variable in class loci.formats.gui.CacheIndicator
 
lpoc - Variable in class jj2000.j2k.codestream.HeaderInfo.POC
 
LPSynthesisFilter - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7

The low-pass synthesis filter of the 9x7 wavelet transform

LPSynthesisFilter - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3

The low-pass synthesis filter of the 5x3 wavelet transform

lqcc - Variable in class jj2000.j2k.codestream.HeaderInfo.QCC
 
lqcd - Variable in class jj2000.j2k.codestream.HeaderInfo.QCD
 
lQuit - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

The maximum number of layers to decode for any code-block

lrgn - Variable in class jj2000.j2k.codestream.HeaderInfo.RGN
 
lrxs - Variable in class jj2000.j2k.roi.encoder.RectROIMaskGenerator

The lower right xs of the ROIs

lrxs - Variable in class jj2000.j2k.roi.encoder.SubbandRectROIMask

The lower right x coordinates of the applicable ROIs

lrys - Variable in class jj2000.j2k.roi.encoder.RectROIMaskGenerator

The lower right ys of the ROIs

lrys - Variable in class jj2000.j2k.roi.encoder.SubbandRectROIMask

The lower right y coordinates of the applicable ROIs

lsiz - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
lsmFilenames - Variable in class loci.formats.in.ZeissLSMReader
 
lsot - Variable in class jj2000.j2k.codestream.HeaderInfo.SOT
 
LT - Static variable in class loci.formats.in.DicomReader
 
ltype - Variable in class jj2000.j2k.entropy.encoder.MQCoder

The length calculation type to use.

LUMA_BLUE - Static variable in enum loci.formats.tiff.PhotoInterp
 
LUMA_GREEN - Static variable in enum loci.formats.tiff.PhotoInterp
 
LUMA_RED - Static variable in enum loci.formats.tiff.PhotoInterp

Default luminance values for YCbCr data.

LumaBlue - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
LumaBlue - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
LumaGreen - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
LumaGreen - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
LumaRed - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
LumaRed - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
LuraWave - Class in loci.plugins.util

Utility methods for dealing with proprietary LuraWave licensing.

LuraWave() - Constructor for class loci.plugins.util.LuraWave
 
LuraWaveCodec - Class in loci.formats.codec

This class provides LuraWave decompression, using LuraWave's Java decoding
 library.

LuraWaveCodec() - Constructor for class loci.formats.codec.LuraWaveCodec
 
LuraWaveService - Interface in loci.formats.services
 
LuraWaveServiceImpl - Class in loci.formats.services
 
LuraWaveServiceImpl() - Constructor for class loci.formats.services.LuraWaveServiceImpl

Default constructor.

lut - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox
 
lut - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader

The lut in the palette box

lut - Variable in class loci.formats.in.AmiraReader
 
lut - Variable in class loci.formats.in.APNGReader
 
lut - Variable in class loci.formats.in.AVIReader
 
lut - Variable in class loci.formats.in.BioRadReader
 
lut - Variable in class loci.formats.in.DicomReader
 
lut - Variable in class loci.formats.in.FV1000Reader
 
lut - Variable in class loci.formats.in.IvisionReader
 
lut - Variable in class loci.formats.in.JPEG2000MetadataParser

Color lookup table stored in the file.

lut - Variable in class loci.formats.in.JPEG2000Reader

The color lookup table associated with this file.

lut - Variable in class loci.formats.in.JPXReader

The color lookup table associated with this file.

lut - Variable in class loci.formats.in.KhorosReader

Global lookup table.

lut - Variable in class loci.formats.in.OIRReader.Channel
 
lut - Variable in class loci.formats.in.PCXReader
 
lut - Variable in class loci.formats.in.PSDReader

Lookup table.

lut - Variable in class loci.formats.in.ZeissLMSReader
 
lut - Variable in class loci.formats.in.ZeissLSMReader
 
lut16 - Variable in class loci.formats.in.FakeReader

16-bit lookup table, if indexed color, one per channel.

lut8 - Variable in class loci.formats.in.FakeReader

8-bit lookup table, if indexed color, one per channel.

LUT_LENGTH - Static variable in class loci.formats.in.BioRadReader
 
LUT_SIZE - Static variable in class loci.formats.in.NAFReader
 
LUTDESC - Static variable in class loci.formats.in.LeicaReader
 
lutIndex - Variable in class loci.formats.in.PDSReader
 
lutLength - Variable in class loci.formats.ChannelFiller

Number of LUT components.

lutNames - Variable in class loci.formats.in.FV1000Reader
 
lutNames - Variable in class loci.formats.in.LeicaHandler
 
lutNames - Variable in class loci.formats.in.LIFReader
 
luts - Variable in class loci.formats.in.OpenlabReader
 
luts - Variable in class loci.plugins.util.VirtualImagePlus
 
lvls - Variable in class jj2000.j2k.codestream.reader.TagTreeDecoder

The number of levels in the tag tree

lvls - Variable in class jj2000.j2k.codestream.writer.TagTreeEncoder

The number of levels in the tag tree

lw - Variable in class jj2000.j2k.util.MsgPrinter

The line width to use

LY_RES_COMP_POS_PROG - Static variable in interface jj2000.j2k.codestream.ProgressionType

The bit stream is Layer/Resolution/Component/Position progressive : 0

lye - Variable in class jj2000.j2k.entropy.Progression

The index of the last layer.

lyepoc - Variable in class jj2000.j2k.codestream.HeaderInfo.POC
 
lyrSpec - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

The layer specifications

LZO_OVERRUN - Static variable in class loci.formats.codec.LZOCodec
 
LZOCodec - Class in loci.formats.codec

This class implements LZO decompression.

LZOCodec() - Constructor for class loci.formats.codec.LZOCodec
 
lzss_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor

general purpose LZW string table

LZW - Static variable in class loci.formats.in.ZeissCZIReader
 
LZWCodec - Class in loci.formats.codec

This is an optimized LZW codec for use with TIFF files.

LZWCodec() - Constructor for class loci.formats.codec.LZWCodec
 
LZWCompressor - Class in com.sun.media.imageioimpl.common

Modified from original LZWCompressor to change interface to passing a
 buffer of data to be compressed.

LZWCompressor(ImageOutputStream, int, boolean) - Constructor for class com.sun.media.imageioimpl.common.LZWCompressor
 
LZWStringTable - Class in com.sun.media.imageioimpl.common

General purpose LZW String Table.

LZWStringTable() - Constructor for class com.sun.media.imageioimpl.common.LZWStringTable

Constructor allocate memory for string store data





M

m - Variable in class jj2000.j2k.entropy.CodedCBlk

The vertical index of the code-block, within the subband.

m - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTData

The vertical index of the code-block, within the subband

MAC_16_BIT_COLOR - Static variable in class loci.formats.in.OpenlabReader
 
MAC_16_COLORS - Static variable in class loci.formats.in.OpenlabReader
 
MAC_16_GREYS - Static variable in class loci.formats.in.OpenlabReader
 
MAC_1_BIT - Static variable in class loci.formats.in.OpenlabReader

Image types.

MAC_24_BIT_COLOR - Static variable in class loci.formats.in.OpenlabReader
 
MAC_256_COLORS - Static variable in class loci.formats.in.OpenlabReader
 
MAC_256_GREYS - Static variable in class loci.formats.in.OpenlabReader
 
MAC_4_GREYS - Static variable in class loci.formats.in.OpenlabReader
 
MAC_OS_X - Static variable in class loci.formats.gui.LegacyQTTools
 
MACRO_IMAGE - Static variable in class loci.formats.in.CellSensReader
 
macroFile - Variable in class loci.formats.in.HamamatsuVMSReader
 
MacroFunctions - Class in loci.plugins.macro

Convenience class that simplifies implemention of ImageJ macro extensions.

MacroFunctions() - Constructor for class loci.plugins.macro.MacroFunctions
 
mag - Variable in class loci.formats.in.FluoviewReader
 
mag - Variable in class loci.formats.in.GatanReader
 
mag - Variable in class loci.formats.in.ND2Handler
 
MAG_MULTIPLIER - Static variable in class loci.formats.in.FEITiffReader
 
magbits - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTData

The number of magnitude bits in the integer representation.

magbits - Variable in class jj2000.j2k.wavelet.synthesis.SubbandSyn

The number of magnitude bits

MAGIC - Static variable in class loci.formats.in.AnalyzeReader
 
MAGIC - Static variable in class loci.formats.in.BioRadSCNReader
 
MAGIC - Static variable in class loci.formats.in.ColumbusReader
 
MAGIC - Static variable in class loci.formats.in.HitachiReader
 
MAGIC_BYTES - Static variable in class loci.formats.in.BioRadGelReader
 
MAGIC_NUMBER - Static variable in class loci.formats.in.OBFReader
 
MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
 
MAGIC_STRING - Static variable in class loci.formats.in.HRDGDFReader
 
MAGIC_STRING - Static variable in class loci.formats.in.IMODReader
 
MAGIC_STRING - Static variable in class loci.formats.in.ImspectorReader

The header for each file contains this string.

MAGIC_STRING - Static variable in class loci.formats.in.KodakReader
 
MAGIC_STRING - Static variable in class loci.formats.in.MolecularImagingReader
 
MAGIC_STRING - Static variable in class loci.formats.in.SIFReader
 
MAGIC_STRING - Static variable in class loci.formats.in.SimplePCITiffReader
 
MAGNIFICATION - Static variable in class loci.formats.in.CellSensReader
 
magnification - Variable in class loci.formats.in.CellSensReader.Pyramid
 
magnification - Variable in class loci.formats.in.FEITiffReader
 
magnification - Variable in class loci.formats.in.FV1000Reader
 
magnification - Variable in class loci.formats.in.IvisionReader
 
magnification - Variable in class loci.formats.in.LIFReader
 
magnification - Variable in class loci.formats.in.NDPIReader
 
magnification - Variable in class loci.formats.in.NikonTiffReader
 
magnification - Variable in class loci.formats.in.OIRReader.Objective
 
magnification - Variable in class loci.formats.in.OperettaReader.Plane
 
magnification - Variable in class loci.formats.in.SimplePCITiffReader
 
magnification - Variable in class loci.formats.in.SISReader
 
magnification - Variable in class loci.formats.in.SVSReader
 
magnification - Variable in class loci.formats.in.VolocityReader.Stack
 
magnification - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
MAGNIFICATION_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
 
magnitudes - Variable in class loci.formats.in.IM3Reader.Spectrum
 
magRefPass(DataBlk, MQDecoder, int, int[], boolean) - Method in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Performs the magnitude refinement pass on the specified data and
 bit-plane.

magRefPass(CBlkWTData, MQCoder, boolean, int, int[], int[], int[], int[], int[], int, int, int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Performs the magnitude refinement pass on the specified data and
 bit-plane.

main(String[]) - Static method in class loci.formats.codec.BitBuffer

Deprecated.
Testing method.

main(String[]) - Static method in class loci.formats.codec.BitWriter

Deprecated.
Tests the BitWriter class.

main(String[]) - Static method in class loci.formats.gui.DataConverter
 
main(String[]) - Static method in class loci.formats.gui.ImageViewer
 
main(String[]) - Static method in class loci.formats.gui.XMLWindow
 
main(String[]) - Static method in class loci.formats.in.IM3Reader

Write a summary of each record to STDOUT

main(String[]) - Static method in class loci.formats.Memoizer
 
main(String[]) - Static method in class loci.formats.tools.AmiraParameters
 
main(String[]) - Static method in class loci.formats.tools.BioFormatsExtensionPrinter
 
main(String[]) - Static method in class loci.formats.tools.CacheConsole

Interactive interpreter for testing Bio-Formats caching implementation.

main(String[]) - Static method in class loci.formats.tools.EditTiffG
 
main(String[]) - Static method in class loci.formats.tools.MakeTestOmeTiff
 
main(String[]) - Static method in class loci.formats.tools.UpgradeCheck
 
main(String[]) - Static method in class loci.plugins.About
 
main(String[]) - Static method in class loci.plugins.config.LociConfig
 
main(String[]) - Static method in class loci.plugins.in.Importer

Main method, for testing.

main_tagset - Variable in class loci.formats.in.ZeissTIFFHandler
 
mainDefDecompType - Variable in class jj2000.j2k.wavelet.WTDecompSpec

The main default decomposition

mainDefLevels - Variable in class jj2000.j2k.wavelet.WTDecompSpec

The main default number of decomposition levels

MainDialog - Class in loci.plugins.in

Bio-Formats Importer general options dialog box.

MainDialog(ImportProcess) - Constructor for class loci.plugins.in.MainDialog

Creates a general options dialog for the Bio-Formats Importer.

mainHeader - Variable in class jj2000.j2k.util.CodestreamManipulator

The main header

mainHeadLen - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Length of main header

mainHeadOff - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

The offset of the main header in the input stream

majorVersion - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
Make() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Make
 
MAKE - Static variable in class loci.formats.tiff.IFD
 
make24Bits(Object, int, int, boolean, boolean) - Static method in class loci.formats.ImageTools

Convert an arbitrary primitive type array with 3 samples per pixel to
 a 3 x (width * height) byte array.

make24Bits(Object, int, int, boolean, boolean, Double, Double) - Static method in class loci.formats.ImageTools

Convert an arbitrary primitive type array with 3 samples per pixel to
 a 3 x (width * height) byte array.

make24Bits(Object, int, int, boolean) - Static method in class loci.formats.ImageTools

Convert an arbitrary primitive type array with 3 samples per pixel to
 an int array, i.e.

make24Bits(Object, int, int, boolean, Double, Double) - Static method in class loci.formats.ImageTools

Convert an arbitrary primitive type array with 3 samples per pixel to
 an int array, i.e.

makeBitArray(int, int) - Static method in class loci.formats.gui.SignedColorModel
 
makeBitArray(int, int) - Static method in class loci.formats.gui.UnsignedIntColorModel
 
makeBuffered(Image) - Static method in class loci.formats.gui.AWTImageTools

Creates a buffered image from the given AWT image object.

makeBuffered(Image, ColorModel) - Static method in class loci.formats.gui.AWTImageTools

Creates a buffered image possessing the given color model,
 from the specified AWT image object.

makeBufferedImageReader(IFormatReader) - Static method in class loci.formats.gui.BufferedImageReader

Converts the given reader into a BufferedImageReader, wrapping if needed.

makeBufferedImageWriter(IFormatWriter) - Static method in class loci.formats.gui.BufferedImageWriter

Converts the given writer into a BufferedImageWriter, wrapping if needed.

makeChannelFiller(IFormatReader) - Static method in class loci.formats.ChannelFiller

Converts the given reader into a ChannelFiller, wrapping if needed.

makeChannelMerger(IFormatReader) - Static method in class loci.formats.ChannelMerger

Converts the given reader into a ChannelMerger, wrapping if needed.

makeChannelSeparator(IFormatReader) - Static method in class loci.formats.ChannelSeparator

Converts the given reader into a ChannelSeparator, wrapping if needed.

makeColorModel(int, int) - Static method in class loci.formats.gui.AWTImageTools

Gets a color model for the given number of color components.

makeColorSpace(int) - Static method in class loci.formats.gui.AWTImageTools

Gets a color space for the given number of color components.

makeComboFilter(FileFilter[]) - Static method in class loci.formats.gui.GUITools

Creates an "All supported file types" combo filter
 encompassing all of the given filters.

makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities

Aligns the first rows * cols
 components of parent in
 a grid.

makeCompatible(BufferedImage, GraphicsConfiguration) - Static method in class loci.formats.gui.AWTImageTools

Creates a buffered image compatible with the given graphics
 configuration, using the given buffered image as a source.

makeDimensionSwapper(IFormatReader) - Static method in class loci.formats.DimensionSwapper

Converts the given reader into a DimensionSwapper, wrapping if needed.

makeDimensionTable() - Static method in class loci.formats.in.LeicaReader
 
makeDummySlider() - Static method in class loci.plugins.util.DataBrowser
 
makeFileList() - Method in class loci.formats.in.DicomReader
 
makeFilterMetadata() - Method in class loci.formats.FormatReader

Return a properly configured loci.formats.meta.FilterMetadata.

makeGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities

Aligns the first rows * cols
 components of parent in
 a grid.

makeHeavyPanel(Component) - Static method in class loci.plugins.util.DataBrowser

Makes AWT play nicely with Swing components.

makeImage(byte[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given single-channel byte data.

makeImage(short[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given single-channel short data.

makeImage(int[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given single-channel int data.

makeImage(float[], int, int) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given single-channel float data.

makeImage(double[], int, int) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given single-channel double data.

makeImage(byte[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given byte data.

makeImage(short[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given short data.

makeImage(int[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given int data.

makeImage(float[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given float data.

makeImage(double[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given double data.

makeImage(byte[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given byte data.

makeImage(short[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given short data.

makeImage(int[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given int data.

makeImage(float[][], int, int) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given single-precision floating point data.

makeImage(double[][], int, int) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given double-precision floating point data.

makeImage(byte[], boolean, MetadataRetrieve, int) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given raw byte array, obtaining the
 dimensional parameters from the specified metadata object.

makeImage(byte[], int, int, int, boolean, int, boolean, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given raw byte array,
 performing any necessary type conversions.

makeImage(byte[][], int, int, int, boolean, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given raw byte array,
 performing any necessary type conversions.

makeImage(String) - Method in class loci.formats.gui.PreviewPane

Creates a blank image with the given message painted on top (e.g.,
 a loading or error message), matching the size of the active reader's
 thumbnails.

makeImageName(int) - Method in class loci.formats.in.MetamorphReader

Create an appropriate name for the given series.

makeImageProcessorReader(IFormatReader) - Static method in class loci.plugins.util.ImageProcessorReader

Converts the given reader into a ImageProcessorReader, wrapping if needed.

makeImageReader() - Static method in class loci.plugins.util.LociPrefs

Creates an image reader according to the current configuration settings,
 including which format readers are currently enabled, as well as
 format-specific configuration settings.

makeJTree(Document) - Static method in class loci.formats.gui.XMLCellRenderer

Constructs a Swing JTree that displays the given XML DOM document.

makeLabel(String, boolean) - Method in class loci.plugins.config.ConfigWindow
 
makeLabel(String, int, int) - Method in class loci.plugins.in.ColorDialog
 
makeList(DefaultListModel) - Method in class loci.plugins.config.ConfigWindow
 
makeLUT(int, int) - Method in class loci.plugins.in.Colorizer
 
makeLUT(Color) - Method in class loci.plugins.in.Colorizer
 
makeLUTs(ColorModel[], boolean) - Method in class loci.plugins.in.Colorizer
 
makeLUTs(int) - Method in class loci.plugins.in.Colorizer
 
makeMask(Subband, int, int) - Method in class jj2000.j2k.roi.encoder.ArbROIMaskGenerator

This function generates the ROI mask for one tile-component.

makeMask(Subband, int, int) - Method in class jj2000.j2k.roi.encoder.RectROIMaskGenerator

This function generates the ROI mask for the entire tile.

makeMask(Subband, int, int) - Method in class jj2000.j2k.roi.encoder.ROIMaskGenerator

This function generates the ROI mask for the entire tile.

makeMinMaxCalculator(IFormatReader) - Static method in class loci.formats.MinMaxCalculator

Converts the given reader into a MinMaxCalculator, wrapping if needed.

makeModuloElement(Document) - Method in class loci.formats.meta.ModuloAnnotation

Construct a DOM element for this annotation using
 the given Document as the root.

makeOmeTiff(String...) - Method in class loci.formats.tools.MakeTestOmeTiff
 
makeOmeTiff(String, CoreMetadata) - Method in class loci.formats.tools.MakeTestOmeTiff
 
makeOmeTiffExtensions(String...) - Method in class loci.formats.tools.MakeTestOmeTiff
 
makeOriginalMetadata(Document) - Method in class loci.formats.meta.OriginalMetadataAnnotation

Create a DOM element for this annotation with the given document
 as the parent.

makePixelTypes() - Static method in class loci.formats.FormatTools
 
MAKER_NOTE - Static variable in class loci.formats.tiff.IFD
 
MAKER_WHITE_BALANCE - Static variable in class loci.formats.in.NikonReader
 
makeRGBImage(byte[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
 
makeRGBImage(byte[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
 
MakerNote() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.MakerNote
 
makerNoteOffset - Variable in class loci.formats.in.NikonReader

Offset to the Nikon Maker Note.

makeSamples() - Method in class loci.formats.tools.MakeTestOmeTiff
 
makeSaneDimensionOrder(String) - Static method in class loci.formats.MetadataTools

Adjusts the given dimension order as needed so that it contains exactly
 one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.

makeSplitPane(JList, JPanel) - Method in class loci.plugins.config.ConfigWindow
 
makeStack(ImageStack) - Method in class loci.plugins.Slicer

Returns a new ImageStack using the given ImageStack as a template.

MakeTestOmeTiff - Class in loci.formats.tools

Creates sample OME-TIFF datasets according to the given parameters.

MakeTestOmeTiff() - Constructor for class loci.formats.tools.MakeTestOmeTiff
 
MakeTestOmeTiff.TextLine - Class in loci.formats.tools
 
makeTextField() - Static method in class loci.plugins.config.ConfigWindow
 
makeTileStitcher(IFormatReader) - Static method in class loci.formats.TileStitcher

Converts the given reader into a TileStitcher, wrapping if needed.

makeTreeNode(Node) - Static method in class loci.formats.gui.XMLCellRenderer

Recursively builds JTree node structure from DOM node structure.

makeUnsigned(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools

Converts the given BufferedImage into an image with unsigned pixel data.

makeupCodes - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Black and white make-up code table.

makeupCodesBlack - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Make-up codes for black runs.

makeupCodesWhite - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Make-up codes for white runs.

makeValidIFD(IFD, int, int) - Method in class loci.formats.tiff.TiffSaver

Makes a valid IFD.

MANUFACTURER - Static variable in interface com.sun.media.imageioimpl.plugins.pcx.PCXConstants
 
manufacturer - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
map - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
 
map - Variable in class loci.formats.in.EPSReader
 
map - Variable in class loci.formats.tools.AmiraParameters
 
mapFile - Variable in class loci.formats.in.HamamatsuVMSReader
 
mapOIBFiles() - Method in class loci.formats.in.FV1000Reader
 
mappedBuffer - Variable in class com.sun.media.imageio.stream.FileChannelImageInputStream

A memory mapping of all or part of the channel.

mappedFiles - Variable in class loci.formats.in.ZipReader
 
mappedPos - Variable in class com.sun.media.imageio.stream.FileChannelImageInputStream

The stream position of the mapping.

mappedUpperBound - Variable in class com.sun.media.imageio.stream.FileChannelImageInputStream

The stream position least upper bound of the mapping.

mapper - Variable in class com.sun.media.imageio.stream.SegmentedImageInputStream
 
maps - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
 
mapServer(String, String) - Static method in class loci.formats.in.FlexReader

Map the server named 'alias' to the path 'realName'.

mapServer(String, String[]) - Static method in class loci.formats.in.FlexReader

Map the server named 'alias' to the paths in 'realNames'.

mapServersFromConfigurationFile(String) - Static method in class loci.formats.in.FlexReader

Read a configuration file with lines of the form:

 <server alias>=<real server name>

 and call mapServer(String, String) accordingly.

mapToSourceX(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
mapToSourceX(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
mapToSourceY(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
mapToSourceY(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
mark() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
mark(int) - Method in class com.sun.media.imageioimpl.plugins.clib.InputStreamAdapter
 
mark(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
MARKER - Static variable in class loci.formats.in.ZeissLMSReader
 
Marker() - Constructor for class loci.formats.in.ZeissLSMReader.Marker
 
MARKER_0 - Static variable in class loci.formats.in.TillVisionReader
 
MARKER_1 - Static variable in class loci.formats.in.TillVisionReader
 
MARKER_2 - Static variable in class loci.formats.in.TillVisionReader
 
MARKER_3 - Static variable in class loci.formats.in.TillVisionReader
 
MARKER_TAG - Static variable in class loci.formats.in.NDPIReader
 
markerFound - Variable in class jj2000.j2k.entropy.decoder.MQDecoder

Flag indicating if a marker has been found

Markers - Interface in jj2000.j2k.codestream

This interface defines the values of the different markers in the JPEG 2000
 codestream.

markSupported() - Method in class com.sun.media.imageioimpl.plugins.clib.InputStreamAdapter
 
markSupported() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
maskLineHigh - Variable in class jj2000.j2k.roi.encoder.ArbROIMaskGenerator

The High frequency part of a mask line

maskLineLow - Variable in class jj2000.j2k.roi.encoder.ArbROIMaskGenerator

The low frequency part of a mask line

maskPGM - Variable in class jj2000.j2k.roi.encoder.ROI

ImgReaderPGM object with the arbrtrary ROI

masks - Variable in class loci.formats.in.FakeReader
 
masterClock - Variable in class loci.formats.in.SDTInfo

Use or not  Master Clock (SPC140 multi-module).

matchFilename(String) - Method in class loci.formats.in.CellomicsReader
 
matchFiles(String[], NumberFilter) - Static method in class loci.formats.FilePattern
 
MathUtil - Class in jj2000.j2k.util

This class contains a collection of utility methods fro mathematical
 operations.

MathUtil() - Constructor for class jj2000.j2k.util.MathUtil
 
matrix - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
 
max - Variable in class loci.formats.gui.SignedColorModel
 
max(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
MAX_APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
 
MAX_BLOCK_SIZE - Static variable in class loci.formats.services.POIServiceImpl
 
MAX_CB_AREA - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The maximum code-block area (width x height).

MAX_CB_DIM - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The maximum code-block dimension.

MAX_COMP_BITDEPTH - Static variable in interface jj2000.j2k.codestream.Markers

The maximum number of component bitdepth

MAX_COMPONENTS - Static variable in class loci.plugins.in.SeriesDialog
 
MAX_DATATYPE - Static variable in class com.sun.media.imageio.plugins.tiff.TIFFTag

The numerically largest constant representing a TIFF data type.

MAX_EL_COPYING - Static variable in class jj2000.j2k.util.ArrayUtil

The maximum array size to do element by element copying, larger
 arrays are copyied in a n optimized way.

MAX_HEADER_SIZE - Static variable in class loci.formats.in.QuesantReader
 
MAX_INT - Static variable in class jj2000.j2k.IntegerSpec

The largest value of type int

MAX_JPEG_SIZE - Static variable in class loci.formats.in.HamamatsuVMSReader
 
MAX_LOW_FIELD_TAG_NUM - Static variable in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

The largest low-valued tag number in the TIFF 6.0 specification.

MAX_LPPM - Static variable in interface jj2000.j2k.codestream.Markers

Maximum length of PPM marker segment

MAX_LPPT - Static variable in interface jj2000.j2k.codestream.Markers

Maximum length of PPT marker segment

MAX_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
 
MAX_READERS - Static variable in class loci.formats.FileStitcher
 
MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
 
MAX_SERIES_THUMBS - Static variable in class loci.plugins.in.SeriesDialog
 
MAX_SERIES_TOGGLES - Static variable in class loci.plugins.in.SeriesDialog
 
MAX_SIZE - Static variable in class loci.formats.in.HamamatsuVMSReader
 
MAX_SIZE - Static variable in class loci.formats.in.JPEGReader
 
MAX_SIZE - Static variable in class loci.formats.in.NDPIReader
 
MAX_STACK_SIZE - Static variable in class loci.formats.in.GIFReader

Maximum buffer size.

MAX_TPSOT - Static variable in class jj2000.j2k.util.CodestreamManipulator

The maximum number of a tile part index (TPsot)

MAX_TRIES - Static variable in class loci.plugins.util.LuraWave
 
maxAdcRate - Variable in class loci.formats.in.SDTInfo
 
MaxApertureValue() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.MaxApertureValue
 
MAXBITS - Static variable in class com.sun.media.imageioimpl.common.LZWStringTable
 
maxByte - Variable in class jj2000.j2k.io.BufferedRandomAccessFile

The maximum number of bytes that can be read from the buffer

maxBytes - Variable in class jj2000.j2k.codestream.writer.CodestreamWriter

The maximum number of bytes that can be written to the
 bit stream

maxBytes - Variable in class jj2000.j2k.entropy.encoder.EBCOTLayer

This is the maximum number of bytes that should be allocated for
 this and previous layers.

maxBytes - Variable in class loci.formats.codec.CodecOptions

If compressing, this is the maximum number of raw bytes to compress.

maxCB - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Maximum number of codeblocks to read before ncb quit condition is
 reached

maxCBlkHeight - Variable in class jj2000.j2k.entropy.CBlkSizeSpec

The maximum code-block height

maxCBlkWidth - Variable in class jj2000.j2k.entropy.CBlkSizeSpec

The maximum code-block width

maxCfdRate - Variable in class loci.formats.in.SDTInfo

(-1.0 - not set).

maxChildren - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
maxCompHeight - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ

Maximum height among all components

maxCompWidth - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ

Maximum width among all components

maxDepth - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
MAXIMAL_NUMBER_OF_DIMENSIONS - Static variable in class loci.formats.in.OBFReader
 
maxImgRes - Variable in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

The maximum available image resolution level

maximumReadOffset - Variable in class loci.formats.in.JPEG2000MetadataParser

Maximum read offset within in the stream.

maxInten - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Maxiumum intensity.

MAXLEVEL - Static variable in class com.sun.media.imageioimpl.common.PaletteBuilder

maximum of tree depth

maxMagBits - Variable in class jj2000.j2k.roi.encoder.ROIScaler

The maximum number of magnitude bit-planes in any subband.

maxNodes - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
 
maxOffsetIndex - Variable in class loci.formats.in.AmiraReader.HxRLE
 
maxPixelRange - Variable in class loci.formats.in.DicomReader
 
maxPos - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
 
maxResolution - Variable in class loci.formats.in.ZeissCZIReader
 
maxSample - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata

The max value for the encoded/decoded image.

maxSampleSize - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata

Maximum number of bits per sample (not in metadata).

MaxSampleValue() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.MaxSampleValue
 
MaxShiftSpec - Class in jj2000.j2k.roi

This class contains the maxshift scaling value for each tile-component.

MaxShiftSpec(int, int, byte, String) - Constructor for class jj2000.j2k.roi.MaxShiftSpec

Constructs a 'ModuleSpec' object, initializing all the components and
 tiles to the 'SPEC_DEF' spec type, for the specified number of
 components and tiles.

maxsize - Variable in class jj2000.j2k.util.ISRandomAccessIO
 
maxSlope - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

The maximum slope accross all code-blocks and truncation points.

MAXSTR - Static variable in class com.sun.media.imageioimpl.common.LZWStringTable
 
maxSyncRate - Variable in class loci.formats.in.SDTInfo

Maximum rates during the measurement.

maxTacRate - Variable in class loci.formats.in.SDTInfo
 
maxTP - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
 
maxtp - Variable in class jj2000.j2k.util.CodestreamManipulator

The maximum number of tile parts in any tile

maxValue - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

Maximum pixel value.

maxValue - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
maxValue - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFAttrInfo
 
maxValue() - Method in class loci.plugins.util.RecordedImageProcessor
 
maxValues - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
maxX - Variable in class loci.formats.in.ImarisHDFReader
 
maxXTile - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
maxY - Variable in class loci.formats.in.ImarisHDFReader
 
maxYTile - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
maxZ - Variable in class loci.formats.in.ImarisHDFReader
 
mcsPoints - Variable in class loci.formats.in.SDTInfo

No of MCS values.

mcstaPoints - Variable in class loci.formats.in.SDTInfo

Number of MCS_TA points.

mcsTime - Variable in class loci.formats.in.SDTInfo

Interval time [ms] for MCS histogram.

mcuHeight - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
mcuWidth - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
MD_FILE_UNITS - Static variable in class loci.formats.in.GelReader
 
MD_FILETAG - Static variable in class loci.formats.in.GelReader
 
MD_LAB_NAME - Static variable in class loci.formats.in.GelReader
 
MD_PREP_DATE - Static variable in class loci.formats.in.GelReader
 
MD_PREP_TIME - Static variable in class loci.formats.in.GelReader
 
MD_SAMPLE_INFO - Static variable in class loci.formats.in.GelReader
 
MD_SCALE_PIXEL - Static variable in class loci.formats.in.GelReader
 
mdb - Variable in class loci.formats.services.MDBServiceImpl
 
MDB_SUFFIX - Static variable in class loci.formats.in.ZeissLSMReader
 
MDBService - Interface in loci.formats.services

Interface defining methods for parsing MDB database files.

MDBServiceImpl - Class in loci.formats.services

Implementation of MDBService for parsing MDB database files.

MDBServiceImpl() - Constructor for class loci.formats.services.MDBServiceImpl

Default constructor.

mdl - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The maximum number of decompostion levels for each component of the
 current tile.

MEA_SUFFIX - Static variable in class loci.formats.in.FlexReader
 
MeaHandler() - Constructor for class loci.formats.in.FlexReader.MeaHandler
 
measDescBlockLength - Variable in class loci.formats.in.SDTInfo
 
measDescBlockNo - Variable in class loci.formats.in.SDTInfo

Number of the measurement description block
 corresponding to this data block.

measDescBlockOffs - Variable in class loci.formats.in.SDTInfo
 
measMode - Variable in class loci.formats.in.SDTInfo
 
MEASURE_MODE_2D - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSMeasureMode" tag.

MEASURE_MODE_3D - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSMeasureMode" tag.

MEASUREMENT_SUFFIXES - Static variable in class loci.formats.in.FlexReader
 
measurementFiles - Variable in class loci.formats.in.FlexReader
 
measurementFolder - Variable in class loci.formats.in.CellVoyagerReader
 
MeasurementHandler() - Constructor for class loci.formats.in.ColumbusReader.MeasurementHandler
 
measurementID - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
measurementName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
measurementResultFile - Variable in class loci.formats.in.CellVoyagerReader
 
measurementTime - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
medianFilter() - Method in class loci.plugins.util.RecordedImageProcessor
 
MEDICAL_DOMAIN - Static variable in class loci.formats.FormatTools

Identifies the medical imaging domain.

medium - Variable in class loci.formats.in.ZeissCZIReader
 
medium - Variable in class loci.formats.in.ZeissLSMReader.Laser
 
MEM_MODEL - Static variable in class loci.formats.in.CellSensReader
 
memBank - Variable in class loci.formats.in.SDTInfo
 
memoFile - Variable in class loci.formats.Memoizer
 
Memoizer - Class in loci.formats

ReaderWrapper implementation which caches the state of the
 delegate (including and other ReaderWrapper instances)
 after Memoizer.setId(String) has been called.

Memoizer() - Constructor for class loci.formats.Memoizer

Constructs a memoizer around a new ImageReader creating memo
  files under the same directory as the original file only if the call to
  Memoizer.setId(java.lang.String) takes longer than 100L in
  milliseconds.

Memoizer(long) - Constructor for class loci.formats.Memoizer

Constructs a memoizer around a new ImageReader creating memo
  files under the same directory as the original file only if the call to
  Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.

Memoizer(long, File) - Constructor for class loci.formats.Memoizer

Constructs a memoizer around a new ImageReader creating memo file
  files under the directory argument including the full path of the
  original file only if the call to Memoizer.setId(java.lang.String) takes longer than
  minimumElapsed in milliseconds.

Memoizer(IFormatReader) - Constructor for class loci.formats.Memoizer

Constructs a memoizer around the given IFormatReader creating
  memo files under the same directory as the original file only if the
  call to Memoizer.setId(java.lang.String) takes longer than
  100L in milliseconds.

Memoizer(IFormatReader, long) - Constructor for class loci.formats.Memoizer

Constructs a memoizer around the given IFormatReader creating
  memo files under the same directory as the original file only if the
  call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in
  milliseconds.

Memoizer(IFormatReader, long, File) - Constructor for class loci.formats.Memoizer

Constructs a memoizer around the given IFormatReader creating
  memo files under the directory argument including the full path
  of the original file only if the call to Memoizer.setId(java.lang.String) takes longer than
  minimumElapsed in milliseconds.

Memoizer.Deser - Interface in loci.formats
 
Memoizer.KryoDeser - Class in loci.formats
 
Memoizer.RandomAccessDeser - Class in loci.formats

Helper implementation that can be used to implement Memoizer.Deser
 classes for libraries working solely with byte arrays.

MemoryDialog - Class in loci.plugins.in

Bio-Formats Importer memory usage confirmation dialog box.

MemoryDialog(ImportProcess) - Constructor for class loci.plugins.in.MemoryDialog

Creates a memory confirmation dialog for the Bio-Formats Importer.

merge(Map<String, Object>, Map<String, Object>, String) - Static method in class loci.formats.MetadataTools

Merges the given lists of metadata, prepending the
 specified prefix for the destination keys.

merge - Variable in class loci.plugins.util.BFVirtualStack
 
MERGE_NAMES - Static variable in class loci.formats.in.BioRadReader

List of merge types.

mergeChannels(BufferedImage[]) - Static method in class loci.formats.gui.AWTImageTools

Merges the given images into a single multi-channel image.

mergeNativeTree(Node) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
mergeNativeTree(Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
mergeNativeTree(Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
mergeNativeTree(Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
mergeNativeTree(Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableImageMetadata
 
mergeNativeTree(Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableStreamMetadata
 
mergeNativeTree(Node) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
mergeNativeTree(Node) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
mergeNativeTree(Node) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
mergeNativeTree(Node) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
mergeStandardTree(Node) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
mergeStandardTree(Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
mergeStandardTree(Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
mergeStandardTree(Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
mergeStandardTree(Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableImageMetadata
 
mergeStandardTree(Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableStreamMetadata
 
mergeStandardTree(Node) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
mergeStandardTree(Node) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
mergeStandardTree(Node) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
mergeStandardTree(Node) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
mergeTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
mergeTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFMetadata
 
mergeTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableStreamMetadata
 
mergeTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
mergeTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
mergeTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
mergeTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
mergeTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
mergeTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
message - Variable in enum loci.plugins.in.ImportStep
 
meta - Variable in class loci.formats.in.OMETiffReader
 
meta - Variable in class loci.formats.in.PrairieReader

Format-specific metadata.

meta - Variable in class loci.plugins.in.ImportProcess
 
META_EXT - Static variable in class loci.formats.in.BDReader
 
metadata - Variable in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

The IIOMetadata object containing metadata for the
 current image.

metadata - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The IIOMetadata object containing metadata for the
 current image.

metadata - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

The metadata from the stream.

metadata - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
metadata - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
metadata - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
metadata - Variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
metadata - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader

The meta data

metadata - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter

The sample model of the image to be compressed.

metadata - Variable in class loci.formats.FormatReader

Hashtable containing metadata key/value pairs.

metadata - Variable in class loci.formats.in.MetamorphHandler
 
METADATA - Static variable in class loci.formats.in.MicromanagerReader

File containing extra metadata.

metadata - Variable in class loci.formats.in.ND2Handler
 
Metadata() - Constructor for class loci.formats.in.ZeissCZIReader.Metadata
 
metadata - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
metadata - Variable in class loci.plugins.in.ImportProcess
 
metadata - Variable in class loci.plugins.util.DataBrowser
 
METADATA_KEYS - Static variable in class loci.formats.in.ZeissLSMReader
 
METADATA_LEVEL_DEFAULT - Static variable in class loci.formats.in.DynamicMetadataOptions
 
METADATA_LEVEL_KEY - Static variable in class loci.formats.in.DynamicMetadataOptions
 
METADATA_SUFFIXES - Static variable in class loci.formats.in.APLReader
 
METADATA_SUFFIXES - Static variable in class loci.formats.in.InCellReader
 
METADATA_SUFFIXES - Static variable in class loci.formats.in.ScanrReader
 
METADATA_TAG - Static variable in class loci.formats.in.NDPIReader
 
METADATA_XML_TAG - Static variable in class loci.formats.in.FlowSightReader
 
metadataComplete - Variable in class loci.formats.CoreMetadata

Indicates whether or not we are confident that all of the metadata stored
 within the file has been parsed.

MetadataConverter - Class in loci.formats.meta

Deprecated.
Use ome.xml.meta.MetadataConverter.


MetadataConverter() - Constructor for class loci.formats.meta.MetadataConverter

Deprecated.
Private constructor; all methods in MetadataConverter
 are static, so this should not be called.

metadataFile - Variable in class loci.formats.in.MicromanagerReader.Position
 
metadataFile - Variable in class loci.formats.in.OMETiffReader
 
metadataFiles - Variable in class loci.formats.in.BDReader
 
metadataFiles - Variable in class loci.formats.in.ColumbusReader
 
metadataFiles - Variable in class loci.formats.in.InCellReader
 
metadataFiles - Variable in class loci.formats.in.L2DReader

List of all metadata files in the dataset.

metadataFiles - Variable in class loci.formats.in.ScanrReader
 
metadataIndex - Variable in class loci.formats.in.CellSensReader
 
metadataInPlanes - Variable in class loci.formats.in.SlidebookReader
 
metadataLevel - Variable in class loci.formats.in.DefaultMetadataOptions
 
MetadataLevel - Enum in loci.formats.in
 
MetadataLevel() - Constructor for enum loci.formats.in.MetadataLevel
 
metadataOffsets - Variable in class loci.formats.in.SlidebookReader
 
metadataOptions - Variable in class loci.formats.FormatHandler

Metadata parsing options.

MetadataOptions - Interface in loci.formats.in

Holds metadata-related options.

metadataPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
metadataRetrieve - Variable in class loci.formats.FormatWriter

Current metadata retrieval object.

MetadataRetrieve - Interface in loci.formats.meta
 
metadataSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
metadataStore - Variable in class loci.formats.FormatReader

Current metadata store.

MetadataStore - Interface in loci.formats.meta
 
MetadataTools - Class in loci.formats

A utility class for working with metadata objects,
 including MetadataStore, MetadataRetrieve,
 and OME-XML strings.

MetadataTools() - Constructor for class loci.formats.MetadataTools
 
metadataType - Variable in enum loci.formats.tiff.PhotoInterp

Metadata type of the photometric interpretation.

metaFile - Variable in class loci.formats.in.OMETiffReader
 
MetakitService - Interface in loci.formats.services

Interface defining methods for interacting with the OME Metakit library.

MetakitServiceImpl - Class in loci.formats.services

Implementation of MetakitService for interacting with the
 OME Metakit library.

MetakitServiceImpl() - Constructor for class loci.formats.services.MetakitServiceImpl
 
METAMORPH_ID - Static variable in class loci.formats.in.MetamorphReader
 
MetamorphHandler - Class in loci.formats.in

MetamorphTiffReader is the file format reader for TIFF files produced by
 Metamorph software version 7.5 and above.

MetamorphHandler() - Constructor for class loci.formats.in.MetamorphHandler
 
MetamorphHandler(Hashtable) - Constructor for class loci.formats.in.MetamorphHandler
 
MetamorphReader - Class in loci.formats.in

Reader is the file format reader for Metamorph STK files.

MetamorphReader() - Constructor for class loci.formats.in.MetamorphReader

Constructs a new Metamorph reader.

MetamorphTiffReader - Class in loci.formats.in

MetamorphTiffReader is the file format reader for TIFF files produced by
 Metamorph software version 7.5 and above.

MetamorphTiffReader() - Constructor for class loci.formats.in.MetamorphTiffReader

Constructs a new Metamorph TIFF reader.

MetamorphTiffReader.NumericComparator - Class in loci.formats.in
 
MetamorphTiffReader.Well - Class in loci.formats.in
 
metaWindow - Variable in class loci.plugins.util.DataBrowser
 
METERING_MODE - Static variable in class loci.formats.tiff.IFD
 
METERING_MODE_AVERAGE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "MeteringMode" tag.

METERING_MODE_CENTER_WEIGHTED_AVERAGE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "MeteringMode" tag.

METERING_MODE_MAX_RESERVED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "MeteringMode" tag.

METERING_MODE_MIN_RESERVED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "MeteringMode" tag.

METERING_MODE_MULTI_SPOT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "MeteringMode" tag.

METERING_MODE_OTHER - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "MeteringMode" tag.

METERING_MODE_PARTIAL - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "MeteringMode" tag.

METERING_MODE_PATTERN - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "MeteringMode" tag.

METERING_MODE_SPOT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "MeteringMode" tag.

METERING_MODE_UNKNOWN - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "MeteringMode" tag.

MeteringMode() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.MeteringMode
 
method - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox

The elements' values.

method - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
 
MethodEntry() - Constructor for class loci.plugins.util.RecordedImageProcessor.MethodEntry
 
methodForMQLengthCalc - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies the algorithm to use in calculating the necessary MQ
  length for each decoding pass.

methodForMQTermination - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies the algorithm used to terminate the MQ codeword.

methodStack - Variable in class loci.plugins.util.RecordedImageProcessor
 
methodStacks - Variable in class loci.plugins.util.BFVirtualStack
 
mg - Variable in class jj2000.j2k.roi.encoder.ROIScaler

The class generating the ROI mask

MIASReader - Class in loci.formats.in

MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.

MIASReader() - Constructor for class loci.formats.in.MIASReader

Constructs a new MIAS reader.

MIASReader.AnalysisFile - Class in loci.formats.in
 
MicromanagerHandler() - Constructor for class loci.formats.in.MicromanagerReader.MicromanagerHandler
 
MicromanagerReader - Class in loci.formats.in

MicromanagerReader is the file format reader for Micro-Manager files.

MicromanagerReader() - Constructor for class loci.formats.in.MicromanagerReader

Constructs a new Micromanager reader.

MicromanagerReader.Index - Class in loci.formats.in
 
MicromanagerReader.MicromanagerHandler - Class in loci.formats.in

SAX handler for parsing Acqusition.xml.

MicromanagerReader.Position - Class in loci.formats.in
 
microscopeModel - Variable in class loci.formats.in.FEITiffReader
 
microscopeModels - Variable in class loci.formats.in.LIFReader
 
microscopyMode - Variable in class loci.formats.in.ImarisHDFReader
 
microSecPerFrame - Variable in class loci.formats.out.AVIWriter
 
mimeType - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
mimeType - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
mimeType - Static variable in class com.sun.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
mimeType - Static variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
mimeType - Static variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
mimeType - Static variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
mimeTypes - Static variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
mimeTypes - Static variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
MIMETypes - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
mimeTypes - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
mimeTypes - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
mimeTypes - Static variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
mimeTypes - Static variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
MIMETypes - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
MIMETypes - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
min(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
MIN_AVG_PACKET_SZ - Static variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Minimum average size of a packet.

MIN_BROWSER_WIDTH - Static variable in class loci.plugins.util.DataBrowser
 
MIN_CB_DIM - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The minimum code-block dimension.

MIN_DATATYPE - Static variable in class com.sun.media.imageio.plugins.tiff.TIFFTag

The numerically smallest constant representing a TIFF data type.

MIN_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
 
MIN_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
 
minAdcRate - Variable in class loci.formats.in.SDTInfo
 
minCfdRate - Variable in class loci.formats.in.SDTInfo

(-1.0 - not set).

minChildren - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
MINCReader - Class in loci.formats.in

MINCReader is the file format reader for MINC MRI files.

MINCReader() - Constructor for class loci.formats.in.MINCReader

Constructs a new MINC reader.

MINIMAL_TAGS - Static variable in class loci.formats.in.FlowSightReader

The tags that must be present for this reader
 to function properly

MinimalInCellHandler() - Constructor for class loci.formats.in.InCellReader.MinimalInCellHandler
 
MinimalTiffReader - Class in loci.formats.in

MinimalTiffReader is the superclass for file format readers compatible with
 or derived from the TIFF 6.0 file format.

MinimalTiffReader() - Constructor for class loci.formats.in.MinimalTiffReader

Constructs a new MinimalTiffReader.

MinimalTiffReader(String, String) - Constructor for class loci.formats.in.MinimalTiffReader

Constructs a new MinimalTiffReader.

MinimalTiffReader(String, String[]) - Constructor for class loci.formats.in.MinimalTiffReader

Constructs a new MinimalTiffReader.

MINIMUM_MEMORY_PADDING - Static variable in class loci.plugins.in.MemoryDialog

Minimum amount of wiggle room for available memory, in bytes.

minimumElapsed - Variable in class loci.formats.Memoizer

Minimum number of milliseconds which must elapse during the call to
 Memoizer.setId(java.lang.String) before a memo file will be created.

minInten - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Minimum intensity

MinMaxCalculator - Class in loci.formats

Logic to compute minimum and maximum values for each channel.

MinMaxCalculator() - Constructor for class loci.formats.MinMaxCalculator

Constructs a MinMaxCalculator around a new image reader.

MinMaxCalculator(IFormatReader) - Constructor for class loci.formats.MinMaxCalculator

Constructs a MinMaxCalculator with the given reader.

minMaxCalculator - Variable in class loci.plugins.in.ImportProcess
 
minMaxDone - Variable in class loci.formats.MinMaxCalculator

Number of planes for which min/max computations have been completed.

minMaxStore - Variable in class loci.formats.MinMaxCalculator

Consumer of channel global minima and maxima

minorVersion - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox
 
minorVersion - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
MinSampleValue() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.MinSampleValue
 
minSlope - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

The minimum slope accross all code-blocks and truncation points.

minSyncRate - Variable in class loci.formats.in.SDTInfo

Minimum rates during the measurement.

minTacRate - Variable in class loci.formats.in.SDTInfo
 
minValue - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFAttrInfo
 
minValue() - Method in class loci.plugins.util.RecordedImageProcessor
 
minValues - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
minX - Variable in class com.sun.media.imageioimpl.common.SimpleRenderedImage

The X coordinate of the image's upper-left pixel.

minX - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
 
minX - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

The destination upper-left corner

minX - Variable in class loci.formats.in.ImarisHDFReader
 
minY - Variable in class com.sun.media.imageioimpl.common.SimpleRenderedImage

The Y coordinate of the image's upper-left pixel.

minY - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
 
minY - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

The destination upper-left corner

minY - Variable in class loci.formats.in.ImarisHDFReader
 
minZ - Variable in class loci.formats.in.ImarisHDFReader
 
MIRROR_H - Static variable in class loci.formats.in.CellSensReader
 
MIRROR_V - Static variable in class loci.formats.in.CellSensReader
 
MISSING - Static variable in class loci.plugins.config.LibraryEntry

HTML markup for missing library.

MISSING_VERSION_CODE - Static variable in class loci.plugins.config.LibraryEntry

Version code to indicate a missing library.

MissingLibraryException - Exception in loci.formats

MissingLibraryException is the exception thrown when a particular data
 stream or filename requires a library that is not present on the system.

MissingLibraryException() - Constructor for exception loci.formats.MissingLibraryException
 
MissingLibraryException(String) - Constructor for exception loci.formats.MissingLibraryException
 
MissingLibraryException(String, Throwable) - Constructor for exception loci.formats.MissingLibraryException
 
MissingLibraryException(Throwable) - Constructor for exception loci.formats.MissingLibraryException
 
MJPBCodec - Class in loci.formats.codec

Methods for compressing and decompressing QuickTime Motion JPEG-B data.

MJPBCodec() - Constructor for class loci.formats.codec.MJPBCodec
 
MJPBCodecOptions - Class in loci.formats.codec

Options for compressing and decompressing MJPB data.

MJPBCodecOptions() - Constructor for class loci.formats.codec.MJPBCodecOptions
 
MJPEG_HUFFMAN_TABLE - Static variable in class loci.formats.in.AVIReader

Huffman table for MJPEG data.

MM_JSON_TAG - Static variable in class loci.formats.in.MicromanagerReader
 
MMHEADER - Static variable in class loci.formats.in.FluoviewReader

Private TIFF tags

mmPlanes - Variable in class loci.formats.in.MetamorphReader
 
MMSTAMP - Static variable in class loci.formats.in.FluoviewReader
 
MNG_MAGIC_BYTES - Static variable in class loci.formats.in.MNGReader
 
MNGReader - Class in loci.formats.in

MNGReader is the file format reader for Multiple-image Network Graphics
 (MNG) files.

MNGReader() - Constructor for class loci.formats.in.MNGReader

Constructs a new MNG reader.

MNGReader.SeriesInfo - Class in loci.formats.in
 
mod - Variable in class loci.formats.in.SDTInfo

Module number.

modality - Variable in class loci.formats.in.ND2Handler
 
Model() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Model
 
model - Variable in class loci.formats.in.BioRadSCNReader
 
MODEL - Static variable in class loci.formats.in.FluoviewReader
 
model - Variable in class loci.formats.in.FluoviewReader
 
model - Variable in class loci.formats.in.LeicaHandler.Detector
 
model - Variable in class loci.formats.in.ZeissLSMReader.Laser
 
MODEL - Static variable in class loci.formats.tiff.IFD
 
ModelPixelScale() - Constructor for class com.sun.media.imageio.plugins.tiff.GeoTIFFTagSet.ModelPixelScale
 
ModelTiePoint() - Constructor for class com.sun.media.imageio.plugins.tiff.GeoTIFFTagSet.ModelTiePoint
 
ModelTransformation() - Constructor for class com.sun.media.imageio.plugins.tiff.GeoTIFFTagSet.ModelTransformation
 
modFpgaVer - Variable in class loci.formats.in.SDTInfo

New in v.8.4.

modSerNo - Variable in class loci.formats.in.SDTInfo

Serial number of the module.

modType - Variable in class loci.formats.in.SDTInfo

Module type.

modTypeCode - Variable in class loci.formats.in.SDTInfo
 
ModuleSpec - Class in jj2000.j2k

This generic class is used to handle values to be used by a module for each
 tile and component.

ModuleSpec(int, int, byte) - Constructor for class jj2000.j2k.ModuleSpec

Constructs a 'ModuleSpec' object, initializing all the components and
 tiles to the 'SPEC_DEF' spec val type, for the specified number of
 components and tiles.

modulo - Variable in class loci.formats.meta.ModuloAnnotation
 
Modulo - Class in loci.formats

Represents a subdimension of Z, C, or T as needed for supporting Modulo
 annotations.

Modulo(String) - Constructor for class loci.formats.Modulo
 
Modulo(Modulo) - Constructor for class loci.formats.Modulo
 
MODULO_NS - Static variable in class loci.formats.meta.ModuloAnnotation
 
ModuloAnnotation - Class in loci.formats.meta
 
ModuloAnnotation() - Constructor for class loci.formats.meta.ModuloAnnotation
 
moduloC - Variable in class loci.formats.CoreMetadata
 
moduloT - Variable in class loci.formats.CoreMetadata
 
moduloZ - Variable in class loci.formats.CoreMetadata
 
MolecularImagingReader - Class in loci.formats.in

MolecularImagingReader is the file format reader for Molecular Imaging files.

MolecularImagingReader() - Constructor for class loci.formats.in.MolecularImagingReader

Constructs a new Molecular Imaging reader.

montageIndex - Variable in class loci.formats.in.FluoviewReader
 
montageOffsets - Variable in class loci.formats.in.FluoviewReader
 
mosaics - Variable in class loci.formats.in.ZeissCZIReader
 
mouseClicked(MouseEvent) - Method in class loci.plugins.in.MainDialog
 
mouseDragged(MouseEvent) - Method in class loci.formats.gui.ImageViewer

Handles cursor probes.

mouseEntered(MouseEvent) - Method in class loci.plugins.in.MainDialog

Focuses the component upon mouseover.

mouseExited(MouseEvent) - Method in class loci.plugins.in.MainDialog
 
mouseMoved(MouseEvent) - Method in class loci.formats.gui.ImageViewer

Handles cursor probes.

mousePressed(MouseEvent) - Method in class loci.plugins.in.MainDialog
 
mouseReleased(MouseEvent) - Method in class loci.plugins.in.MainDialog
 
mouseWheelMoved(MouseWheelEvent) - Method in class loci.plugins.util.DataBrowser
 
moveTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
mp - Variable in class jj2000.j2k.util.StreamMsgLogger

The printer that formats the text

mPS - Variable in class jj2000.j2k.entropy.decoder.MQDecoder

The current most probable signal for each context

mPS - Variable in class jj2000.j2k.entropy.encoder.MQCoder

The current most probable signal for each context

mq - Variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The MQ decoder to use.

MQ_INIT - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The initial states for the MQ coder

MQ_INIT - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The initial states for the MQ coder

MQCoder - Class in jj2000.j2k.entropy.encoder

This class implements the MQ arithmetic coder.

MQCoder(ByteOutputBuffer, int, int[]) - Constructor for class jj2000.j2k.entropy.encoder.MQCoder

Instantiates a new MQ-coder, with the specified number of contexts and
 initial states.

MQDecoder - Class in jj2000.j2k.entropy.decoder

This class implements the MQ arithmetic decoder.

MQDecoder(ByteInputBuffer, int, int[]) - Constructor for class jj2000.j2k.entropy.decoder.MQDecoder

Instantiates a new MQ-decoder, with the specified number of contexts and
 initial states.

mqrs - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

MQ reset specifications

mqT - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The MQ coder used, for each thread

mQuit - Variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The maximum number of bit planes to decode for any code-block

MR_LUT - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Magnitude Refinement context lookup table

MR_LUT - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Magnitude Refinement context lookup table

MR_LUT_BITS - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The number of bits used for the Magnitude Refinement lookup table

MR_LUT_BITS - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The number of bits used for the Magnitude Refinement lookup table

MR_MASK - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The mask to obtain the MR index to 'MR_LUT' from the 'state'
 information.

MR_MASK - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The mask to obtain the MR index to 'MR_LUT' from the 'state'
 information.

MRC_SUFFIXES - Static variable in class loci.formats.in.MRCReader
 
MRCReader - Class in loci.formats.in

MRCReader is the file format reader for MRC files.

MRCReader() - Constructor for class loci.formats.in.MRCReader

Constructs a new MRC reader.

mReserved1 - Variable in class loci.formats.in.SDTInfo
 
mReserved2 - Variable in class loci.formats.in.SDTInfo
 
mressrc - Variable in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

The 'MultiResImgData' source

mressrc - Variable in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

The MultiResImgData source

MRW_MAGIC_STRING - Static variable in class loci.formats.in.MRWReader
 
MRWReader - Class in loci.formats.in

MRWReader is the file format reader for Minolta MRW files.

MRWReader() - Constructor for class loci.formats.in.MRWReader

Constructs a new MRW reader.

MS_VIDEO - Static variable in class loci.formats.in.AVIReader
 
msbSkipped - Variable in class jj2000.j2k.codestream.reader.CBlkInfo

The number of most significant bits which are skipped for this
 code-block (= Mb-1-bitDepth).

MSE_LKP_BITS - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The number of bits used to index in the 'fm' lookup table, 7.

MSE_LKP_FRAC_BITS - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The number of fractional bits used to store data in the 'fm' and 'fs'
 lookup tables.

msg - Variable in class loci.formats.FilePattern

Error message generated during file pattern construction.

msg(String) - Method in class loci.formats.gui.DataConverter
 
MsgLogger - Interface in jj2000.j2k.util

This class provides a simple common abstraction of a facility that logs
 and/or displays messages or simple strings.

MsgPrinter - Class in jj2000.j2k.util

This utility class formats messages to the specified line width, by
 inserting line-breaks between words, and printing the resulting
 lines.

MsgPrinter(int) - Constructor for class jj2000.j2k.util.MsgPrinter

Creates a new message printer with the specified line width and
 with the default locale.

MSRLE - Static variable in class loci.formats.in.AVIReader

Supported compression types.

MSRLECodec - Class in loci.formats.codec

Methods for compressing and decompressing data using Microsoft RLE.

MSRLECodec() - Constructor for class loci.formats.codec.MSRLECodec
 
mss - Variable in class jj2000.j2k.roi.ROIDeScaler

The MaxShiftSpec containing the scaling values for all tile-components

MSVideoCodec - Class in loci.formats.codec

Methods for compressing and decompressing data using Microsoft Video 1.

MSVideoCodec() - Constructor for class loci.formats.codec.MSVideoCodec
 
mtResol - Variable in class loci.formats.in.SDTInfo

Macro time clock in 0.1 ns units.

MULTI_PHOTON - Static variable in class loci.formats.in.LegacyND2Reader
 
MultiBand() - Constructor for class loci.formats.in.LeicaHandler.MultiBand
 
multiBands - Variable in class loci.formats.in.LeicaHandler
 
MULTIDIM_IMAGE_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
MULTIDIM_STACK_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
multifile - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
multiply(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
MultiResImgData - Interface in jj2000.j2k.wavelet.synthesis

This interface defines methods to access image attributes (width, height,
 number of components, etc.) of multiresolution images, such as those
 resulting from an inverse wavelet transform.

MultiResImgDataAdapter - Class in jj2000.j2k.wavelet.synthesis

This class provides a default implementation for the methods of the
 'MultiResImgData' interface.

MultiResImgDataAdapter(MultiResImgData) - Constructor for class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Instantiates the MultiResImgDataAdapter object specifying the
 MultiResImgData source.

MUST_GROUP - Static variable in class loci.formats.FormatTools

File grouping options.

MUST_GROUP - Static variable in interface loci.formats.IFormatReader

File grouping options.

myReader - Variable in class loci.formats.gui.ImageViewer

Current format reader.

myWriter - Variable in class loci.formats.gui.ImageViewer

Current format writer.





N

n - Variable in class jj2000.j2k.entropy.CodedCBlk

The horizontal index of the code-block, within the subband.

n - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTData

The horizontal index of the code-block, within the subband

N_ACCUMULATIONS - Static variable in class loci.formats.in.FluoviewReader
 
N_FRAMES - Static variable in class loci.formats.in.FluoviewReader
 
na - Variable in class loci.formats.in.ND2Handler
 
na - Variable in class loci.formats.in.OIRReader.Objective
 
NAFReader - Class in loci.formats.in

NAFReader is the file format reader for Hamamatsu Aquacosmos NAF files.

NAFReader() - Constructor for class loci.formats.in.NAFReader

Constructs a new NAF reader.

name - Variable in class com.sun.media.imageio.plugins.tiff.TIFFTag
 
name - Variable in enum loci.formats.codec.JPEG2000BoxType

The name of the box type.

name - Variable in enum loci.formats.codec.JPEG2000SegmentMarker

The name of the segment marker.

name - Variable in enum loci.formats.in.BaseZeissReader.Charset
 
name - Variable in class loci.formats.in.BaseZeissReader.Layer
 
name - Variable in class loci.formats.in.BaseZeissReader.Shape
 
name - Variable in class loci.formats.in.CellSensReader.Pyramid
 
name - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
name - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
name - Variable in class loci.formats.in.IM3Reader.IM3Record
 
name - Variable in class loci.formats.in.IM3Reader.Spectrum
 
name - Variable in class loci.formats.in.LeicaHandler.Channel
 
name - Variable in class loci.formats.in.LeicaHandler.ROI
 
name - Variable in class loci.formats.in.LeicaReader.Detector
 
name - Variable in class loci.formats.in.LeicaSCNReader.Image
 
name - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
name - Variable in class loci.formats.in.LiFlimReader.ROI
 
name - Variable in class loci.formats.in.LIFReader.ROI
 
name - Variable in class loci.formats.in.NativeND2Reader.ChunkMapEntry
 
name - Variable in class loci.formats.in.OIRReader.Channel
 
name - Variable in class loci.formats.in.OIRReader.Laser
 
name - Variable in class loci.formats.in.OIRReader.Objective
 
name - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
name - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
name - Variable in class loci.formats.in.ZeissLSMReader.DataChannel
 
name - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
 
name - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
name - Variable in enum loci.formats.tiff.PhotoInterp

Given name of the photometric interpretation.

name - Variable in class loci.plugins.config.LibraryEntry
 
name - Variable in class loci.plugins.in.IdDialog
 
name - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
 
nameLength - Variable in class loci.formats.in.LeicaReader
 
names - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
names - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

The table to link tag names for all the JP2 boxes.

names - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
names - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
names - Variable in class loci.formats.in.FlexReader.FlexHandler
 
names - Static variable in class loci.plugins.shortcut.ShortcutPanel

Details for installed plugins.

nameStack - Variable in class loci.formats.in.LeicaHandler
 
nameStack - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
nameStack - Variable in class loci.formats.in.ZeissTIFFHandler
 
NATIVE_FORMAT_NAME - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFWritableImageMetadata
 
NATIVE_FORMAT_NAME - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFWritableStreamMetadata
 
NATIVE_LIB_CLASS - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
nativeMetadataFormatClassName - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
nativeMetadataFormatClassName - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
nativeMetadataFormatName - Static variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
nativeMetadataFormatName - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
nativeMetadataFormatName - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
nativeMetadataFormatName - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
nativeMetadataFormatName - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
nativeMetadataFormatName - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
nativeMetadataFormatName - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
nativeMetadataFormatName - Static variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
NativeND2Reader - Class in loci.formats.in

NativeND2Reader is the file format reader for Nikon ND2 files.

NativeND2Reader() - Constructor for class loci.formats.in.NativeND2Reader

Constructs a new ND2 reader.

NativeND2Reader.ChunkMapEntry - Class in loci.formats.in
 
nativePhotometricInterpretation - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
NativeQTReader - Class in loci.formats.in

NativeQTReader is the file format reader for QuickTime movie files.

NativeQTReader() - Constructor for class loci.formats.in.NativeQTReader

Constructs a new QuickTime reader.

nativeReader - Variable in class loci.formats.DelegateReader

Native reader.

nativeReaderInitialized - Variable in class loci.formats.DelegateReader

Flag indicating that the native reader was successfully initialized.

NativeServices - Class in jj2000.j2k.util

This class presents a collection of static methods that allow access to
 some native methods.

NativeServices() - Constructor for class jj2000.j2k.util.NativeServices

Private and only constructor, so that no class instance might be
 created.

nb - Variable in class jj2000.j2k.entropy.encoder.BitToByteOutput

The number of written bytes (excluding the bit buffer)

nblk - Variable in class jj2000.j2k.codestream.PrecInfo

Number of code-blocks in each subband belonging to this precinct

nBuffers - Variable in class loci.formats.in.SPCReader
 
nBusyComps - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The number of busy compressors, for each component.

nBytes - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Number of bytes allocated to each tile.

nc - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

The number of components in the image

nc - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The number of components

nc - Variable in class jj2000.j2k.codestream.reader.PktDecoder

The number of components

nc - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter

Number of components

nc - Variable in class jj2000.j2k.image.ImgDataJoiner

The number of components in the image

nc - Variable in class jj2000.j2k.image.input.ImgReader

The number of components in the image

ncb - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Number of codeblocks encountered.

ncblks - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull

Cache object to avoid excessive allocation/deallocation.

ncbQuit - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Flag indicating whether ncb quit condition has been reached

nChannels - Variable in class loci.formats.gui.SignedColorModel
 
nChannels - Variable in class loci.formats.gui.UnsignedIntColorModel
 
nChannels - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
nChannels - Variable in class loci.formats.in.SPCReader

Number of spectral nChannels.

nCOCMarkSeg - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Counts number of COC markers found in the header

nColorPlanes - Variable in class loci.formats.in.PCXReader
 
nCols - Variable in class loci.formats.in.FlexReader
 
nCols - Variable in class loci.formats.in.HamamatsuVMSReader
 
ncom - Variable in class jj2000.j2k.codestream.HeaderInfo

Number of found COM marker segment

nCOMMarkSeg - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Counts number of COM markers found in the header

nComp - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
nComp - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
nComp - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

The number of components in the image

nComp - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

The number of components in the image

nComp - Variable in class jj2000.j2k.ModuleSpec

The number of components

ncx - Variable in class loci.formats.in.SDTInfo
 
ncy - Variable in class loci.formats.in.SDTInfo
 
ND2_MAGIC_BYTES_1 - Static variable in class loci.formats.in.NativeND2Reader
 
ND2_MAGIC_BYTES_2 - Static variable in class loci.formats.in.NativeND2Reader
 
ND2Handler - Class in loci.formats.in

DefaultHandler implementation for handling XML produced by Nikon Elements.

ND2Handler(List<CoreMetadata>, int) - Constructor for class loci.formats.in.ND2Handler
 
ND2Handler(List<CoreMetadata>, boolean, int) - Constructor for class loci.formats.in.ND2Handler
 
ND2Reader - Class in loci.formats.in

ND2Reader is the file format reader for Nikon ND2 files.

ND2Reader() - Constructor for class loci.formats.in.ND2Reader

Constructs a new ND2 reader.

ND2Widgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats ND2 support.

ND2Widgets() - Constructor for class loci.plugins.config.ND2Widgets
 
ND_SUFFIX - Static variable in class loci.formats.in.MetamorphReader
 
ndata - Variable in class jj2000.j2k.codestream.writer.CodestreamWriter

The number of bytes already written to the bit stream

ndata - Variable in class jj2000.j2k.codestream.writer.FileCodestreamWriter

The number of bytes already written to the bit stream, excluding the
 header length, magic number and header length info.

nDecCblk - Variable in class jj2000.j2k.wavelet.synthesis.InvWTFull

The number of already decoded code-blocks

ndex - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Number of bits in the output bit buffer.

ndFilename - Variable in class loci.formats.in.MetamorphReader
 
ndFilter - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Neutral density value.

ndFilters - Variable in class loci.formats.in.DeltavisionReader
 
ndFilters - Variable in class loci.formats.in.SlidebookReader
 
nDimensions - Variable in class loci.formats.in.CellSensReader
 
nDimensions - Variable in class loci.formats.in.NiftiReader
 
ndl - Variable in class jj2000.j2k.wavelet.synthesis.InvWTFull

Number of decomposition levels in each component

ndpiFiles - Variable in class loci.formats.in.NDPISReader
 
NDPIReader - Class in loci.formats.in

NDPIReader is the file format reader for Hamamatsu .ndpi files.

NDPIReader() - Constructor for class loci.formats.in.NDPIReader

Constructs a new NDPI reader.

NDPISReader - Class in loci.formats.in

NDPISReader is the file format reader for Hamamatsu .ndpis files.

NDPISReader() - Constructor for class loci.formats.in.NDPISReader

Constructs a new NDPIS reader.

needLegacy - Variable in class loci.formats.out.QTWriter

Whether we need the legacy writer.

needMem - Variable in class loci.plugins.in.MemoryDialog

Required memory for the dataset, in bytes.

needPrompt() - Method in class loci.plugins.in.ColorDialog
 
needPrompt() - Method in class loci.plugins.in.CropDialog
 
needPrompt() - Method in class loci.plugins.in.FilePatternDialog
 
needPrompt() - Method in class loci.plugins.in.IdDialog
 
needPrompt() - Method in class loci.plugins.in.ImporterDialog
 
needPrompt() - Method in class loci.plugins.in.LocationDialog
 
needPrompt() - Method in class loci.plugins.in.MainDialog
 
needPrompt() - Method in class loci.plugins.in.MemoryDialog
 
needPrompt() - Method in class loci.plugins.in.RangeDialog
 
needPrompt() - Method in class loci.plugins.in.SeriesDialog
 
needPrompt() - Method in class loci.plugins.in.SwapDialog
 
needPrompt() - Method in class loci.plugins.in.UpgradeDialog
 
needToCreateIndex(RenderedImage) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
NEF_SUFFIX - Static variable in class loci.formats.in.NikonReader
 
netcdf - Variable in class loci.formats.in.ImarisHDFReader
 
netcdf - Variable in class loci.formats.in.MINCReader
 
netcdf - Variable in class loci.formats.in.VeecoReader
 
netCDFFile - Variable in class loci.formats.services.NetCDFServiceImpl

NetCDF file instance.

NetCDFService - Interface in loci.formats.services

Utility class for working with NetCDF/HDF files.

NetCDFServiceImpl - Class in loci.formats.services

Utility class for working with NetCDF/HDF files.

NetCDFServiceImpl() - Constructor for class loci.formats.services.NetCDFServiceImpl

Default constructor.

NEW_MDIM_VOLUME_HEADER - Static variable in class loci.formats.in.CellSensReader
 
NEW_SUBFILE_TYPE - Static variable in class loci.formats.tiff.IFD
 
NEW_SUBFILE_TYPE_REDUCED_RESOLUTION - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A mask to be used with the "NewSubfileType" tag.

NEW_SUBFILE_TYPE_SINGLE_PAGE - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A mask to be used with the "NewSubfileType" tag.

NEW_SUBFILE_TYPE_TRANSPARENCY - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A mask to be used with the "NewSubfileType" tag.

NEW_VOLUME_HEADER - Static variable in class loci.formats.in.CellSensReader
 
newOrder - Variable in class loci.formats.AxisGuesser

Adjusted ordering of internal dimensional axes.

NewSubfileType() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.NewSubfileType
 
newVersionAvailable(String) - Method in class loci.formats.UpgradeChecker

Contact the OME registry and return true if a new version is available.

newVersionAvailable(String, String) - Method in class loci.formats.UpgradeChecker

Contact the OME registry and return true if a new version is available.

NEXT_FIRST - Static variable in class com.sun.media.imageioimpl.common.LZWStringTable
 
nextbbuf - Variable in class jj2000.j2k.codestream.reader.PktHeaderBitReader

The next bit buffer, if bit stuffing occurred (i.e.

nextBits - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
nextBits - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
nextBlockOffs - Variable in class loci.formats.in.SDTInfo

Offset to the data block header of the next data block.

nextCamera - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextChannel - Variable in class loci.formats.in.LeicaHandler
 
nextChannel - Variable in class loci.formats.in.LeicaReader
 
nextChName - Variable in class loci.formats.in.BaseZeissReader
 
nextData - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
nextData - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
nextDetectChannel - Variable in class loci.formats.in.ZeissLSMReader
 
nextDetector - Variable in class loci.formats.in.LeicaReader
 
nextDetector - Variable in class loci.formats.in.ZeissLSMReader
 
nextDichroic - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextDichroic - Variable in class loci.formats.in.ZeissLSMReader
 
nextDichroicChannel - Variable in class loci.formats.in.ZeissLSMReader
 
nextEmWave - Variable in class loci.formats.in.BaseZeissReader
 
nextExWave - Variable in class loci.formats.in.BaseZeissReader
 
nextFilter - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextFilter - Variable in class loci.formats.in.LeicaHandler
 
nextFilter - Variable in class loci.formats.in.ZeissLSMReader
 
nextFilterSet - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextIFDPointerPos - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
nextIllumChannel - Variable in class loci.formats.in.ZeissLSMReader
 
nextImage - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextLaser - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextLaser - Variable in class loci.formats.in.ZeissLSMReader
 
nextLesserThan8Bits(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
nextLetter() - Method in class loci.formats.ResourceNamer

Increments the internal alphabet pointer to the next element of the
 alphabet.

nextLineEnd(String, int) - Method in class jj2000.j2k.util.MsgPrinter

Returns the index of the last character of the next word, plus 1, or
 IS_NEWLINE if a newline character is encountered before the next word,
 or IS_EOS if the end of the string is ecnounterd before the next
 word.

nextNBits(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
nextObjective - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextPlate - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextPlate - Variable in class loci.formats.in.InCellReader.InCellHandler
 
nextReducible - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
nextROI - Variable in class loci.formats.in.LeicaHandler
 
nextSegment(byte[], int, int) - Method in class jj2000.j2k.entropy.decoder.MQDecoder

Resets the MQ decoder to start a new segment.

nextSequenceNumber - Variable in class loci.formats.out.APNGWriter
 
nextSliderRef - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextSpace - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
nextState(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Return min of maxOffset or offset of first pixel
 different from pixel at bitOffset.

nextSubband() - Method in class jj2000.j2k.wavelet.Subband

Returns the next subband in the same resolution level, following the
 subband index order.

nextTag - Variable in class loci.formats.in.OpenlabReader
 
nextTile() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Advances to the next tile, in standard scan-line order (by rows
 then columns).

nextTile() - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Advances to the next tile, in standard scan-line order (by rows
 then columns).

nextTile() - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in interface jj2000.j2k.image.ImgData

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.image.ImgDataAdapter

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.image.ImgDataJoiner

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.image.input.ImgReader

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.image.invcomptransf.InvCompTransf

Advances to the next tile, in standard scan-line order (by rows
 then columns).

nextTile() - Method in class jj2000.j2k.image.Tiler

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.quantization.dequantizer.Dequantizer

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.roi.encoder.ROIScaler

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.wavelet.synthesis.InvWTFull

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextTile() - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Advances to the next tile, in standard scan-line order (by rows then
 columns).

nextWord(String, int) - Method in class jj2000.j2k.util.MsgPrinter

Returns the position of the first character in the next word, starting
 from 'from', if a newline is encountered first then the index of the
 newline character plus 1 is returned.

nextXPos - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
nextYPos - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
nFields - Variable in class loci.formats.in.ColumbusReader
 
nFiles - Variable in class loci.formats.in.FlexReader
 
nfMarkSeg - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Used to store which markers have been already read, by using flag
 bits.

nFrames - Variable in class loci.formats.in.SPCReader
 
nidle - Variable in class jj2000.j2k.util.ThreadPool

The number of idle threads

NiftiReader - Class in loci.formats.in

NiftiReader is the file format reader for NIfTI files.

NiftiReader() - Constructor for class loci.formats.in.NiftiReader

Constructs a new NIfTI reader.

NIKON_XML_TAG - Static variable in class loci.formats.in.NikonElementsTiffReader
 
NIKON_XML_TAG_2 - Static variable in class loci.formats.in.NikonElementsTiffReader
 
NikonCodec - Class in loci.formats.codec

This class implements Nikon decompression.

NikonCodec() - Constructor for class loci.formats.codec.NikonCodec
 
NikonCodecOptions - Class in loci.formats.codec

Options for compressing and decompressing Nikon NEF data.

NikonCodecOptions() - Constructor for class loci.formats.codec.NikonCodecOptions
 
NikonElementsTiffReader - Class in loci.formats.in

NikonElementsTiffReader is the file format reader for TIFF files produced
 by Nikon Elements.

NikonElementsTiffReader() - Constructor for class loci.formats.in.NikonElementsTiffReader
 
NikonReader - Class in loci.formats.in

NikonReader is the file format reader for Nikon NEF (TIFF) files.

NikonReader() - Constructor for class loci.formats.in.NikonReader

Constructs a new Nikon reader.

NikonTiffReader - Class in loci.formats.in

NikonTiffReader is the file format reader for Nikon TIFF files.

NikonTiffReader() - Constructor for class loci.formats.in.NikonTiffReader
 
nImages - Variable in class loci.formats.in.ND2Handler
 
nl - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Number of layers in t he current tile

nl - Variable in class jj2000.j2k.entropy.decoder.DecLyrdCBlk

The number of layers in the coded data.

NL - Static variable in class loci.formats.in.ICSReader

Newline characters.

NL - Static variable in class loci.formats.tools.AsciiImage
 
nLines - Variable in class loci.formats.in.SPCReader
 
nLPS - Static variable in class jj2000.j2k.entropy.decoder.MQDecoder

The indexes of the next LPS

nLPS - Static variable in class jj2000.j2k.entropy.encoder.MQCoder

The indexes of the next LPS

nls - Variable in class jj2000.j2k.decoder.DecoderSpecs

Number of layers specifications

nMPS - Static variable in class jj2000.j2k.entropy.decoder.MQDecoder

The indexes of the next MPS

nMPS - Static variable in class jj2000.j2k.entropy.encoder.MQCoder

The indexes of the next MPS

NO_ASSOC_ERROR - Static variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
NO_ASSOC_ERROR - Static variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
NO_J2K_MSG - Static variable in class loci.formats.services.JAIIIOServiceImpl
 
NO_JAI_MSG - Static variable in class loci.formats.in.TiffJAIReader
 
NO_JHDF_MSG - Static variable in class loci.formats.services.JHDFServiceImpl
 
NO_LICENSE_MSG - Static variable in class loci.formats.services.LuraWaveServiceImpl

Message to display if no LuraWave license code is given.

NO_LURAWAVE_MSG - Static variable in class loci.formats.services.LuraWaveServiceImpl

Message displayed if the LuraWave LWF decoder library is not found.

NO_NETCDF_MSG - Static variable in class loci.formats.services.NetCDFServiceImpl
 
NO_NIKON_MSG - Static variable in class loci.formats.in.LegacyND2Reader
 
NO_OME_XML_MSG - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
NO_QT_MSG - Static variable in class loci.formats.gui.LegacyQTTools
 
NO_WLZ_MSG - Static variable in class loci.formats.in.WlzReader
 
NO_WLZ_MSG - Static variable in class loci.formats.out.WlzWriter
 
NO_WLZ_MSG - Static variable in class loci.formats.services.WlzServiceImpl
 
noCompTransf - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf

Flag indicating whether the decoder should skip the component 
 transform

node - Variable in class loci.formats.gui.XMLCellRenderer.XMLItem
 
NoExtensionFileFilter - Class in loci.formats.gui

A file filter that selects files with no extension,
 for use with a JFileChooser.

NoExtensionFileFilter() - Constructor for class loci.formats.gui.NoExtensionFileFilter
 
noise(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
NOISE_REDUCTION - Static variable in class loci.formats.in.CellSensReader
 
nomCBlkH - Variable in class jj2000.j2k.wavelet.Subband

The nominal code-block height

nomCBlkW - Variable in class jj2000.j2k.wavelet.Subband

The nominal code-block width

NON_GRAPHICS_DOMAINS - Static variable in class loci.formats.FormatTools

List of non-graphics domains.

NON_HCS_DOMAINS - Static variable in class loci.formats.FormatTools

List of non-HCS domains.

NON_REV_FILTER_STR - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterSpec

The non-reversible default filter

NON_SPECIAL_DOMAINS - Static variable in class loci.formats.FormatTools

List of domains that do not require special handling.

NONE - Static variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Identifier for no component transformation.

NONE - Static variable in class jj2000.j2k.image.invcomptransf.InvCompTransf

Identifier for no component transformation.

NONE - Static variable in class loci.formats.in.APNGReader

Filter types.

NoNextElementException - Exception in jj2000.j2k

This exception is thrown whenever a next???? method is called and
 there is no next element to return.

NoNextElementException() - Constructor for exception jj2000.j2k.NoNextElementException

Constructs a new NoNextElementException exception with no
 detail message.

NoNextElementException(String) - Constructor for exception jj2000.j2k.NoNextElementException

Constructs a new NoNextElementException exception with
 the specified detail message.

noOfDataBlocks - Variable in class loci.formats.in.SDTInfo

no_of_data_blocks valid only when in 0 ..

noOfMeasDescBlocks - Variable in class loci.formats.in.SDTInfo
 
nopt - Variable in class jj2000.j2k.entropy.encoder.LayersInfo

The number of optimized layers, or optimization points, without
 counting the extra one coming from the overall target bitrate

noQT - Variable in class loci.formats.gui.LegacyQTTools

Flag indicating QuickTime for Java is not installed.

NORMAL_MENU - Static variable in class loci.plugins.shortcut.ShortcutPanel

Name of the 'Bio-Formats' submenu.

NORMAL_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
 
normalize() - Method in class loci.formats.in.LeicaHandler.ROI

Vertices and transformation values are not stored in pixel coordinates.

normalize() - Method in class loci.formats.in.LIFReader.ROI

Vertices and transformation values are not stored in pixel coordinates.

normalized - Variable in class loci.formats.in.LeicaHandler.ROI
 
normalized - Variable in class loci.formats.in.LIFReader.ROI
 
normalizeData - Variable in class loci.formats.FormatReader

Whether or not to normalize float data.

normalizeFilename(String, String) - Method in class loci.formats.in.OMETiffReader
 
noROIDescaling - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava

Ensures that no ROI de-scaling is performed.

noStitch - Variable in class loci.formats.FileStitcher
 
noSubband - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
noSubband - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
noSubresolutions - Variable in class loci.formats.in.MinimalTiffReader
 
Note() - Constructor for class loci.formats.in.BioRadReader.Note
 
NOTE_NAMES - Static variable in class loci.formats.in.BioRadReader

List of note types.

NOTE_TYPE_4D_SERIES - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_ARROW - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_COLLECT - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_FILE1 - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_FILE2 - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_LINE - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_LIVE - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_MERGE - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_NUMBER - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_SCALEBAR - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_STRUCTURE - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_THRUVIEW - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_USER - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_VARIABLE - Static variable in class loci.formats.in.BioRadReader
 
notes - Variable in class loci.plugins.config.ConfigWindow
 
notes - Variable in class loci.plugins.config.LibraryEntry
 
noteStrings - Variable in class loci.formats.in.BioRadReader
 
notifyListeners(CacheEvent) - Method in class loci.formats.cache.Cache

Informs listeners of a cache update.

notifyListeners(CacheEvent) - Method in class loci.formats.cache.CacheStrategy

Informs listeners of a cache update.

notifyListeners(StatusEvent) - Method in class loci.plugins.in.ImagePlusReader
 
notifyListeners(StatusEvent) - Method in class loci.plugins.in.ImportProcess
 
NotImplementedError - Error in jj2000.j2k

This exception is thrown whenever a feature or functionality that
 has not been implemented is calle.

NotImplementedError() - Constructor for error jj2000.j2k.NotImplementedError

Constructs a new NotImplementedError exception with
 the default detail message.

NotImplementedError(String) - Constructor for error jj2000.j2k.NotImplementedError

Constructs a new NotImplementedError exception with
 the specified detail message m.

noTransform - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

Indicates whether subsampled, subregion is required, and offset is
  defined

noTransform - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
noTransform - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
noTransform - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader

Indicates whether subsampled, subregion is required, and offset is
  defined

noTransform - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

Coordinate transform or sub selection is needed before encoding.

noTransform - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

Coordinate transform is not needed from the source (image stream)
  to the destination.

nPixels - Variable in class loci.formats.in.SPCReader
 
nPPMMarkSeg - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Counts number of PPM markers found in the header

nPPTMarkSeg - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Counts number of PPT markers found in the header

nQCCMarkSeg - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Counts number of QCC markers found in the header

nrc - Variable in class jj2000.j2k.roi.encoder.ROIMaskGenerator

Number of components

nRGNMarkSeg - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Counts number of RGN markers found in the header

nrOfWrittenBytes - Variable in class jj2000.j2k.entropy.encoder.MQCoder

The number of written bytes so far, excluding any delayed 0xFF
 bytes.

nROIbp - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTData

Number of ROI magnitude bit-planes

nROIcoeff - Variable in class jj2000.j2k.entropy.encoder.CBlkRateDistStats

The number of ROI coefficients in the code-block

nROIcoeff - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTData

Number of ROI coefficients in the code-block

nROIcp - Variable in class jj2000.j2k.entropy.encoder.CBlkRateDistStats

Number of ROI coding passes

nRows - Variable in class loci.formats.in.FlexReader
 
nRows - Variable in class loci.formats.in.HamamatsuVMSReader
 
NRRD_MAGIC_STRING - Static variable in class loci.formats.in.NRRDReader
 
NRRDReader - Class in loci.formats.in

File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.

NRRDReader() - Constructor for class loci.formats.in.NRRDReader

Constructs a new NRRD reader.

nrROIs - Variable in class jj2000.j2k.roi.encoder.RectROIMaskGenerator

Number of ROIs

nSaved - Variable in class jj2000.j2k.entropy.encoder.MQCoder

Number of saved states.

nSlider - Variable in class loci.formats.gui.ImageViewer
 
nStep - Variable in class jj2000.j2k.quantization.dequantizer.StdDequantizerParams

The quantization step for non-reversible systems, normalized to a
 dynamic range of 1, for each resolution level and subband, as derived
 from the exponent-mantissa representation in the codestream.

nStreams - Variable in class loci.formats.tools.AmiraParameters
 
nt - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The total number of tiles.

nt - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

The number of tiles in the image

nt - Variable in class jj2000.j2k.util.CodestreamManipulator

The number of tiles in the image

ntH - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The nominal tile height, in the hi-res reference grid

nTileParts - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

The number of tile parts per tile

nTiles - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

The number of tiles within the image

nTiles - Variable in class jj2000.j2k.ModuleSpec

The number of tiles

nTimebins - Variable in class loci.formats.in.SPCReader

Number of time bins in lifetime histogram.

nTotTrunc - Variable in class jj2000.j2k.entropy.encoder.CBlkRateDistStats

The total number of truncation points

ntp - Variable in class jj2000.j2k.codestream.reader.CBlkInfo

The number of truncation point for each layer

nTrunc - Variable in class jj2000.j2k.entropy.decoder.DecLyrdCBlk

The total number of truncation points from layer 1 to the last one in
 this object.

ntW - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The nominal tile width, in the hi-res reference grid

ntX - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The number of tile in the horizontal direction

ntX - Variable in class jj2000.j2k.image.Tiler

The number of tiles in the horizontal direction.

ntY - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The number of tiles in the vertical direction

ntY - Variable in class jj2000.j2k.image.Tiler

The number of tiles in the vertical direction.

num - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox

The cached data elements.

num - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDListBox

The data elements of this box.

num - Variable in class loci.formats.in.BioRadReader.Note
 
num - Variable in class org.libjpegturbo.turbojpeg.TJScalingFactor

Numerator

NUM_COMPONENTS - Static variable in class loci.formats.gui.TwoChannelColorSpace
 
NUM_CTXTS - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The number of contexts used

NUM_CTXTS - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The number of contexts used

NUM_DIMENSIONS - Static variable in class loci.formats.in.FV1000Reader
 
NUM_EMPTY_PASSES_IN_MS_BP - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The number of empty passes in the most significant bit-plane.

NUM_NON_BYPASS_MS_BP - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The number of most significant bit-planes where bypass mode is not to
 be used, even if bypass mode is on: 4.

NUM_PASSES - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The number of coding passes per bit-plane.

numBands - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
numBands - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

The number of components in the image

numBands - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
numBands - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
number - Variable in class com.sun.media.imageio.plugins.tiff.TIFFTag
 
number - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
number - Variable in class loci.formats.in.OBFReader.Frame
 
NUMBER_OF_FRAMES - Static variable in class loci.formats.in.DicomReader
 
NUMBER_OF_INKS - Static variable in class loci.formats.tiff.IFD
 
numberBuffer - Variable in class loci.formats.in.AmiraReader.ASCII
 
NumberFilter - Class in loci.formats

NumberFilter is a helper filter for FilePattern.findPattern().

NumberFilter(String, String) - Constructor for class loci.formats.NumberFilter

Creates a filter for files containing a numerical block,
 sandwiched between the given strings.

NumberOfInks() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.NumberOfInks
 
numBits_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor

current number bits output for each code

numBytes - Variable in class loci.formats.in.AliconaReader

Number of bytes per pixel (either 1 or 2).

numBytes - Variable in class loci.formats.out.QTWriter

Total number of pixel bytes.

numCb - Variable in class jj2000.j2k.wavelet.Subband

The number of code-blocks (in both directions) contained in this
 subband.

numChannels - Variable in class loci.formats.in.LeicaHandler
 
numComp - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox
 
numComp - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
 
numComponents - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
 
numComps - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox
 
numDatasets - Variable in class loci.formats.in.LeicaHandler
 
numDecompositionLevels - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

The number of decomposition levels.

numDecompositionLevels - Variable in class loci.formats.codec.JPEG2000CodecOptions

The number of decomposition levels as would be provided to:
 J2KImageWriteParam.setNumDecompositionLevels(int)
 (WRITE).

numEntries - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

The value of the data elements.

numer - Variable in class loci.formats.tiff.TiffRational

Components of the rational's fractional representation.

numeric - Variable in class loci.formats.FilePatternBlock

Whether or not this is a numeric block.

NUMERICAL_APERTURE - Static variable in class loci.formats.in.CellSensReader
 
numericalAperture - Variable in class loci.formats.in.CellSensReader.Pyramid
 
NumericComparator() - Constructor for class loci.formats.in.MetamorphTiffReader.NumericComparator
 
numFloatsPerSection - Variable in class loci.formats.in.DeltavisionReader
 
numFrames - Variable in class loci.formats.out.APNGWriter
 
numFramesPointer - Variable in class loci.formats.out.APNGWriter
 
numH - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox
 
numImages - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
numIntsPerSection - Variable in class loci.formats.in.DeltavisionReader

The number of ints in each extended header section.

numLayers - Variable in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

The number of layers.

numLowFields - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

The number of low tag numbered fields in the directory.

numNodes - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
 
NUMOP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

The number of lossless transform operations

NUMPF - Static variable in class org.libjpegturbo.turbojpeg.TJ

The number of pixel formats

numPixelBytes - Variable in class loci.formats.in.GatanReader
 
numPrec - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Maximum number of precincts :

 
  1st dim: component index.
  2nd dim: resolution level index.
 

numPrec - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Maximum number of precincts :

 
 1st dim: tile index.
 2nd dim: component index.
 3nd dim: resolution level index.
 

numRegions - Variable in class loci.formats.in.LiFlimReader
 
NUMSAMP - Static variable in class org.libjpegturbo.turbojpeg.TJ

The number of chrominance subsampling options

numSeries - Variable in class loci.formats.in.LeicaReader

Number of series in the file.

numSeries - Variable in class loci.formats.in.ND2Handler
 
numStrings_ - Variable in class com.sun.media.imageioimpl.common.LZWStringTable
 
numTiles - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
 
numTiles - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
numtp - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
 
numTruncPnts - Variable in class jj2000.j2k.codestream.reader.PktInfo

The number of truncation points that appear in this packet, and all
 previous packets, for this code-block.

numV - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox

The data elements in this box.

numWritten - Variable in class loci.formats.out.LegacyQTWriter

Number of frames written.

numWritten - Variable in class loci.formats.out.QTWriter
 
nVldTrunc - Variable in class jj2000.j2k.entropy.encoder.CBlkRateDistStats

The number of valid truncation points

nXFields - Variable in class loci.formats.in.NativeND2Reader
 
nXFields - Variable in class loci.formats.in.ND2Handler
 
nYFields - Variable in class loci.formats.in.ND2Handler
 




O

OB - Static variable in class loci.formats.in.DicomReader
 
OBFReader - Class in loci.formats.in

OBFReader is the file format reader for Imspector OBF files.

OBFReader() - Constructor for class loci.formats.in.OBFReader
 
OBFReader.Frame - Class in loci.formats.in
 
OBFReader.Stack - Class in loci.formats.in
 
OBJECT - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
OBJECT_DROPPED - Static variable in class loci.formats.cache.CacheEvent

Event type indicating an object has been removed from the cache.

OBJECT_LOADED - Static variable in class loci.formats.cache.CacheEvent

Event type indicating an object has been added to the cache.

objectArrayMaxLength - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
objectArrayMinLength - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
objectClass - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
objectDefaultValue - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
objectEnumerations - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
objective - Variable in class loci.formats.in.BDReader
 
Objective() - Constructor for class loci.formats.in.OIRReader.Objective
 
OBJECTIVE_MAG - Static variable in class loci.formats.in.CellSensReader
 
OBJECTIVE_NAME - Static variable in class loci.formats.in.CellSensReader
 
OBJECTIVE_TYPE - Static variable in class loci.formats.in.CellSensReader
 
objectiveIDs - Variable in class loci.formats.in.FlexReader
 
objectiveManufacturer - Variable in class loci.formats.in.FluoviewReader
 
objectiveModel - Variable in class loci.formats.in.ND2Handler
 
objectiveModels - Variable in class loci.formats.in.LIFReader
 
objectiveName - Variable in class loci.formats.in.CellSensReader.Pyramid
 
objectiveName - Variable in class loci.formats.in.FV1000Reader
 
objectiveNames - Variable in class loci.formats.in.CellSensReader.Pyramid
 
objectiveRefs - Variable in class loci.formats.in.FlexReader
 
objectives - Variable in class loci.formats.in.OIRReader
 
objectiveSettingsID - Variable in class loci.formats.in.ZeissCZIReader
 
objectiveTypes - Variable in class loci.formats.in.CellSensReader.Pyramid
 
objectMaxValue - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
objectMinValue - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
objectValueType - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
objGType - Variable in class loci.formats.services.WlzServiceImpl
 
objMag - Variable in class loci.formats.in.LeicaSCNReader.Image
 
objType - Variable in class loci.formats.services.WlzServiceImpl
 
OBS - Static variable in class loci.formats.gui.AWTImageTools

ImageObserver for working with AWT images.

ocr - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
od - Variable in class loci.plugins.in.IdDialog
 
oddLocations - Variable in class loci.formats.in.DicomReader
 
OECF() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.OECF
 
OECF - Static variable in class loci.formats.tiff.IFD
 
off - Variable in class jj2000.j2k.codestream.reader.CBlkInfo

Offset of each piece of code-block's codewords in the file

offLastROIPkt - Variable in class jj2000.j2k.codestream.writer.FileCodestreamWriter

Offset of end of last packet containing ROI information

offset - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The offset in the source ImageInputStream of the
 start of the data to be decompressed.

offset - Variable in class jj2000.j2k.image.DataBlk

The offset in the array of the top-left coefficient

offset - Variable in class jj2000.j2k.image.input.ImgReaderPGM

The offset of the raw pixel data in the PGM file

offset - Variable in class jj2000.j2k.io.BufferedRandomAccessFile

The current offset of the buffer (which will differ from the offset of
 the file)

offset - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTData

The offset in the array of the top-left coefficient

offset - Variable in class loci.formats.in.APNGReader.PNGBlock
 
offset - Variable in class loci.formats.in.BDReader
 
offset - Variable in class loci.formats.in.BioRadGelReader
 
offset - Variable in class loci.formats.in.BioRadReader
 
offset - Variable in class loci.formats.in.CellSensReader.Pyramid
 
offset - Variable in class loci.formats.in.ICSReader

Offset to pixel data.

offset - Variable in class loci.formats.in.IM3Reader.IM3Record
 
offset - Variable in class loci.formats.in.IvisionReader
 
offset - Variable in class loci.formats.in.KhorosReader

Image offset.

offset - Variable in class loci.formats.in.LeicaHandler.Detector
 
offset - Variable in class loci.formats.in.LeicaReader.Detector
 
offset - Variable in class loci.formats.in.MRWReader

Offset to image data.

offset - Variable in class loci.formats.in.NRRDReader

Offset to pixel data.

offset - Variable in class loci.formats.in.OIRReader.Detector
 
offset - Variable in class loci.formats.in.OIRReader.PixelBlock
 
offset - Variable in class loci.formats.in.PCXReader

Offset to pixel data.

offset - Variable in class loci.formats.in.PGMReader

Offset to pixel data.

offset - Variable in class loci.formats.in.PSDReader

Offset to pixel data.

offset - Variable in class loci.formats.in.SDTInfo
 
offset - Variable in enum loci.formats.in.SPEReader.SpeHeaderEntry
 
offset - Variable in class loci.formats.in.TargaReader
 
offset - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
offsetOfFirstStream - Variable in class loci.formats.in.AmiraReader
 
offsetOfStream - Variable in class loci.formats.in.AmiraReader.HxZip
 
offsetPointCounter - Variable in class loci.formats.in.InCellReader
 
offsets - Variable in class loci.formats.in.AmiraReader.ASCII
 
offsets - Variable in class loci.formats.in.AmiraReader.HxRLE
 
offsets - Variable in class loci.formats.in.AVIReader

Offset to each plane.

offsets - Variable in class loci.formats.in.BaseZeissReader
 
offsets - Variable in class loci.formats.in.DicomReader
 
offsets - Variable in class loci.formats.in.FlexReader.FlexFile
 
offsets - Variable in class loci.formats.in.FluoviewReader
 
offsets - Variable in class loci.formats.in.ImarisReader

Offsets to each image.

offsets - Variable in class loci.formats.in.LIFReader

Offsets to memory blocks, paired with their corresponding description.

offsets - Variable in class loci.formats.in.MNGReader.SeriesInfo
 
offsets - Variable in class loci.formats.in.NAFReader
 
offsets - Variable in class loci.formats.in.NativeND2Reader

Array of image offsets.

offsets - Variable in class loci.formats.in.NativeQTReader

Offsets to each plane's pixel data.

offsets - Variable in class loci.formats.in.OpenlabRawReader

Offset to each image's pixel data.

offsets - Variable in class loci.formats.in.ZeissLMSReader
 
offsets - Variable in class loci.formats.out.QTWriter

Vector of plane offsets.

offX - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The horizontal offsets of the upper-left corner of the current tile
 (not active tile) with respect to the canvas origin, in the component
 hi-res grid, for each component.

offY - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The vertical offsets of the upper-left corner of the current tile (not
 active tile) with respect to the canvas origin, in the component hi-res
 grid, for each component.

OIB_SUFFIX - Static variable in class loci.formats.in.FV1000Reader
 
oibMapping - Variable in class loci.formats.in.FV1000Reader

File mappings for OIB file.

OIF_SUFFIX - Static variable in class loci.formats.in.FV1000Reader
 
OIRReader - Class in loci.formats.in

OIRReader is the file format reader for Olympus .oir files.

OIRReader() - Constructor for class loci.formats.in.OIRReader

Constructs a new OIR reader.

OIRReader.Channel - Class in loci.formats.in
 
OIRReader.Detector - Class in loci.formats.in
 
OIRReader.Laser - Class in loci.formats.in
 
OIRReader.Objective - Class in loci.formats.in
 
OIRReader.PixelBlock - Class in loci.formats.in
 
OLD_PHYSICAL_SIZE_DEFAULT - Static variable in class loci.formats.in.LIFReader
 
OLD_PHYSICAL_SIZE_KEY - Static variable in class loci.formats.in.LIFReader
 
OLD_TOOLS - Static variable in class loci.formats.UpgradeChecker

Name of the previous versions' tools JAR.

OME_TOOLS - Static variable in class loci.formats.UpgradeChecker

Name of the OME tools JAR.

OMEHandler() - Constructor for class loci.formats.out.OMEXMLWriter.OMEHandler
 
omeMeasurementFile - Variable in class loci.formats.in.CellVoyagerReader
 
omeMeta - Variable in class loci.formats.gui.ImageViewer

Attached OME metadata store, if available.

omeMeta - Variable in class loci.formats.out.OMETiffWriter
 
OMETiffPlane() - Constructor for class loci.formats.in.OMETiffReader.OMETiffPlane
 
OMETiffReader - Class in loci.formats.in

OMETiffReader is the file format reader for
 OME-TIFF
 files.

OMETiffReader() - Constructor for class loci.formats.in.OMETiffReader

Constructs a new OME-TIFF reader.

OMETiffReader.OMETiffPlane - Class in loci.formats.in

Structure containing details on where to find a particular image plane.

OMETiffWriter - Class in loci.formats.out

OMETiffWriter is the file format writer for OME-TIFF files.

OMETiffWriter() - Constructor for class loci.formats.out.OMETiffWriter
 
omexml - Variable in class loci.formats.in.OMEXMLReader
 
omeXML - Variable in class loci.plugins.in.ImportProcess
 
OMEXMLHandler() - Constructor for class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
omeXmlMetadata - Variable in class loci.formats.in.FakeReader
 
OMEXMLMetadata - Interface in loci.formats.ome
 
OMEXMLMetadataImpl - Class in loci.formats.ome
 
OMEXMLMetadataImpl() - Constructor for class loci.formats.ome.OMEXMLMetadataImpl
 
OMEXMLReader - Class in loci.formats.in

OMEXMLReader is the file format reader for OME-XML files.

OMEXMLReader() - Constructor for class loci.formats.in.OMEXMLReader

Constructs a new OME-XML reader.

OMEXMLReader.BinData - Class in loci.formats.in
 
OMEXMLReader.OMEXMLHandler - Class in loci.formats.in
 
omexmlService - Variable in class loci.formats.gui.ImageViewer

Service for working with OME-XML metadata.

omeXmlService - Variable in class loci.formats.in.FakeReader
 
OMEXMLService - Interface in loci.formats.services
 
OMEXMLServiceImpl - Class in loci.formats.services
 
OMEXMLServiceImpl() - Constructor for class loci.formats.services.OMEXMLServiceImpl

Default constructor.

OMEXMLWriter - Class in loci.formats.out

OMEXMLWriter is the file format writer for OME-XML files.

OMEXMLWriter() - Constructor for class loci.formats.out.OMEXMLWriter
 
OMEXMLWriter.OMEHandler - Class in loci.formats.out
 
OnDemandLongArray - Class in loci.formats.tiff
 
OnDemandLongArray(RandomAccessInputStream) - Constructor for class loci.formats.tiff.OnDemandLongArray
 
ONE - Static variable in class loci.formats.AxisGuesser
 
oneD - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor

Coding dimensionality: 1 for 2-dimensional, 0 for 1-dimensional.

oneHeaderPerSlice - Variable in class loci.formats.in.SpiderReader
 
oneTimepointPerSeries - Variable in class loci.formats.in.InCellReader
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
op - Variable in class org.libjpegturbo.turbojpeg.TJTransform

Transform operation (one of OP_*)

OP_HFLIP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

Flip (mirror) image horizontally.

OP_NONE - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

Do not transform the position of the image pixels.

OP_ROT180 - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

Rotate image 180 degrees.

OP_ROT270 - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

Rotate image counter-clockwise by 90 degrees.

OP_ROT90 - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

Rotate image clockwise by 90 degrees.

OP_TRANSPOSE - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

Transpose image (flip/mirror along upper left to lower right axis).

OP_TRANSVERSE - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

Transverse transpose image (flip/mirror along upper right to lower left
 axis).

OP_VFLIP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

Flip (mirror) image vertically.

open(String) - Method in class loci.formats.gui.ImageViewer

Opens the given data source using the current format reader.

open(String, IFormatReader) - Method in class loci.formats.gui.ImageViewer

Opens from the given data source using the specified reader
 in a separate thread.

open(String, String) - Method in interface loci.formats.services.WlzService

Initializes the service for the given file path.

open(String, String) - Method in class loci.formats.services.WlzServiceImpl
 
open() - Method in class loci.formats.tools.EditTiffG
 
open(String) - Method in class loci.plugins.shortcut.ShortcutPanel

Opens the given location (e.g., file)
 with the Bio-Formats Importer plugin.

OPEN_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
 
OPEN_BEZIER - Static variable in class loci.formats.in.ZeissLSMReader
 
OPEN_POLYLINE - Static variable in class loci.formats.in.ZeissLSMReader
 
openAllSeries() - Method in class loci.plugins.in.ImporterOptions
 
openAllSeriesBox - Variable in class loci.plugins.in.MainDialog
 
openBitmaskBytes(IFD, int, int) - Method in class loci.formats.in.FlowSightReader

Decode the whole IFD plane using bitmask compression

openBufferedImage(int) - Method in class loci.formats.in.TiffJAIReader

Obtains a BufferedImage from the given data source using JAI.

openBytes(int) - Method in class loci.formats.ChannelFiller
 
openBytes(int, byte[]) - Method in class loci.formats.ChannelFiller
 
openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelFiller
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelFiller
 
openBytes(int) - Method in class loci.formats.ChannelMerger
 
openBytes(int, byte[]) - Method in class loci.formats.ChannelMerger
 
openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelMerger
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelMerger
 
openBytes(int) - Method in class loci.formats.ChannelSeparator
 
openBytes(int, byte[]) - Method in class loci.formats.ChannelSeparator
 
openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelSeparator
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelSeparator
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.DelegateReader
 
openBytes(int) - Method in class loci.formats.DimensionSwapper
 
openBytes(int, int, int, int, int) - Method in class loci.formats.DimensionSwapper
 
openBytes(int, byte[]) - Method in class loci.formats.DimensionSwapper
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.DimensionSwapper
 
openBytes(int) - Method in class loci.formats.FileStitcher
 
openBytes(int, byte[]) - Method in class loci.formats.FileStitcher
 
openBytes(int, int, int, int, int) - Method in class loci.formats.FileStitcher
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.FileStitcher
 
openBytes(int) - Method in class loci.formats.FormatReader
 
openBytes(int, byte[]) - Method in class loci.formats.FormatReader
 
openBytes(int, int, int, int, int) - Method in class loci.formats.FormatReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.FormatReader
 
openBytes(int) - Method in interface loci.formats.IFormatReader

Obtains the specified image plane from the current file as a byte array.

openBytes(int, int, int, int, int) - Method in interface loci.formats.IFormatReader

Obtains a sub-image of the specified image plane,
 whose upper-left corner is given by (x, y).

openBytes(int, byte[]) - Method in interface loci.formats.IFormatReader

Obtains the specified image plane from the current file into a
 pre-allocated byte array of
 (sizeX * sizeY * bytesPerPixel * RGB channel count).

openBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.IFormatReader

Obtains a sub-image of the specified image plane
 into a pre-allocated byte array.

openBytes(int) - Method in class loci.formats.ImageReader
 
openBytes(int, int, int, int, int) - Method in class loci.formats.ImageReader
 
openBytes(int, byte[]) - Method in class loci.formats.ImageReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AFIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AIMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AliconaReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AmiraReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AnalyzeReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.APLReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.APNGReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ARFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AVIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BDReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BIFormatReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadGelReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadSCNReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BMPReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BrukerReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BurleighReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CanonRawReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellH5Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellomicsReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellSensReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellVoyagerReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellWorxReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ColumbusReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DeltavisionReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DicomReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DNGReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.Ecat7Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.EPSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FakeReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FEIReader
 
openBytes(int) - Method in class loci.formats.in.FilePatternReader
 
openBytes(int, int, int, int, int) - Method in class loci.formats.in.FilePatternReader
 
openBytes(int, byte[]) - Method in class loci.formats.in.FilePatternReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FilePatternReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FitsReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FlexReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FlowSightReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FluoviewReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FujiReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FV1000Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GatanDM2Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GatanReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GelReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GIFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HamamatsuVMSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HISReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HitachiReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HRDGDFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.I2IReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ICSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IM3Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImaconReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImagicReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImarisHDFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImarisReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IMODReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImprovisionTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImspectorReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InCell3000Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InCellReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.INRReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InveonReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IPLabReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IPWReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IvisionReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JEOLReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPEG2000Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPKReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPXReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KhorosReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KodakReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.L2DReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaSCNReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LiFlimReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LIFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LIMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MetamorphReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MetamorphTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MIASReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MicromanagerReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MINCReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MinimalTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MolecularImagingReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MRCReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MRWReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NAFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NativeND2Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NativeQTReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NDPIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NDPISReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NiftiReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NikonReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NRRDReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OBFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OIRReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OMETiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OMEXMLReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OpenlabRawReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OpenlabReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OperettaReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OxfordInstrumentsReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCORAWReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCXReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PDSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PerkinElmerReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PGMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PhotoshopTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PictReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PovrayReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PQBinReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PrairieReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PSDReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PyramidTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.QuesantReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.RHKReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SBIGReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ScanrReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ScreenReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SDTReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SeikoReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SIFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SimplePCITiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlidebookReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlidebookTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SMCameraReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SPCReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SPEReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SpiderReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SVSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TargaReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TCSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TextReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TileJPEGReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TillVisionReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TopometrixReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TrestleReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.UBMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.UnisokuReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VarianFDFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VeecoReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VGSAMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VisitechReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VolocityClippingReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VolocityReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.WATOPReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.WlzReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissCZIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissLMSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissLSMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissTIFFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissZVIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZipReader
 
openBytes(int) - Method in class loci.formats.MinMaxCalculator
 
openBytes(int, byte[]) - Method in class loci.formats.MinMaxCalculator
 
openBytes(int, int, int, int, int) - Method in class loci.formats.MinMaxCalculator
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.MinMaxCalculator
 
openBytes(int) - Method in class loci.formats.ReaderWrapper
 
openBytes(int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
 
openBytes(int, byte[]) - Method in class loci.formats.ReaderWrapper
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ReaderWrapper
 
openBytes(int) - Method in class loci.formats.TileStitcher
 
openBytes(int, byte[]) - Method in class loci.formats.TileStitcher
 
openBytes(int, int, int, int, int) - Method in class loci.formats.TileStitcher
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.TileStitcher
 
OPENER_PLUGIN - Static variable in class loci.plugins.shortcut.ShortcutPanel

Name of plugin to use for opening dropped files.

openerIndex - Static variable in class loci.plugins.shortcut.ShortcutPanel

Index of plugin to use to open dropped files.

openFile(String) - Method in class loci.formats.in.LegacyND2Reader
 
openFile(File) - Method in class loci.formats.tools.EditTiffG
 
openFile(String) - Static method in class loci.formats.tools.EditTiffG
 
openFiles - Variable in class loci.formats.in.MetamorphReader
 
openGreyscaleBytes(IFD, int, int) - Method in class loci.formats.in.FlowSightReader

Decode the whole IFD plane using greyscale compression

openImage(byte[], IFormatReader, int, int) - Static method in class loci.formats.gui.AWTImageTools

Creates an image from the given byte array, using the given
 IFormatReader to retrieve additional information.

openImage(int) - Method in class loci.formats.gui.BufferedImageReader

Obtains the specified image from the current file.

openImage(int, int, int, int, int) - Method in class loci.formats.gui.BufferedImageReader

Obtains a sub-image of the specified image, whose upper-left corner is
 given by (x, y).

openImage - Variable in class loci.formats.in.InCellReader.InCellHandler
 
openImage(String, Double) - Method in class loci.plugins.macro.LociFunctions
 
openImagePlus(String) - Static method in class loci.plugins.BF
 
openImagePlus(ImporterOptions) - Static method in class loci.plugins.BF
 
openImagePlus() - Method in class loci.plugins.in.ImagePlusReader

Opens one or more ImagePlus objects
 corresponding to the reader's associated options.

openImagePlus(String) - Method in class loci.plugins.macro.LociFunctions
 
OPENLAB_RAW_MAGIC_STRING - Static variable in class loci.formats.in.OpenlabRawReader
 
OpenlabRawReader - Class in loci.formats.in

OpenlabRawReader is the file format reader for Openlab RAW files.

OpenlabRawReader() - Constructor for class loci.formats.in.OpenlabRawReader

Constructs a new RAW reader.

OpenlabReader - Class in loci.formats.in

OpenlabReader is the file format reader for Openlab LIFF files.

OpenlabReader() - Constructor for class loci.formats.in.OpenlabReader

Constructs a new OpenlabReader.

OpenlabReader.PlaneInfo - Class in loci.formats.in

Helper class for storing plane info.

openPlane(int, int, int, int, int) - Method in class loci.formats.FileStitcher
 
openPlane(int, int, int, int, int) - Method in class loci.formats.FormatReader
 
openPlane(int, int, int, int, int) - Method in interface loci.formats.IFormatReader

Obtains the specified image plane (or sub-image thereof) in the reader's
 native data structure.

openPlane(int, int, int, int, int) - Method in class loci.formats.ImageReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.FilePatternReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.ImageIOReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.LegacyQTReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.MNGReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.TextReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.TiffJAIReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
 
openPlane(int, int, int, int, int) - Method in class loci.plugins.util.ImageProcessorReader
 
openProcessors(int) - Method in class loci.plugins.util.ImageProcessorReader

Creates an ImageJ image processor object
 for the image plane at the given position.

openProcessors(int, int, int, int, int) - Method in class loci.plugins.util.ImageProcessorReader

Returns an array of ImageProcessors that represent the given slice.

openRaw() - Method in class loci.formats.in.IM3Reader

Open the current series in raw-mode, returning the
 interleaved image bytes.

openRead(String) - Method in class loci.formats.services.WlzServiceImpl
 
openROIs(IMetadata, ImagePlus[]) - Static method in class loci.plugins.util.ROIHandler

Look for ROIs in the given OMEXMLMetadata; if any are present, apply
 them to the given images and display them in the ROI manager.

openROIs(IMetadata, ImagePlus[], boolean) - Static method in class loci.plugins.util.ROIHandler

Opens the rois and converts them into ImageJ Rois.

openROIs(IMetadata, ImagePlus[], boolean, String) - Static method in class loci.plugins.util.ROIHandler

Opens the rois and converts them into ImageJ Rois.

openSubImage(String, Double, Double, Double, Double, Double) - Method in class loci.plugins.macro.LociFunctions
 
openThumbBytes(int) - Method in class loci.formats.ChannelSeparator
 
openThumbBytes(int) - Method in class loci.formats.DimensionSwapper
 
openThumbBytes(int) - Method in class loci.formats.FileStitcher
 
openThumbBytes(int) - Method in class loci.formats.FormatReader
 
openThumbBytes(IFormatReader, int) - Static method in class loci.formats.FormatTools

Default implementation for IFormatReader.openThumbBytes(int).

openThumbBytes(int) - Method in interface loci.formats.IFormatReader

Obtains a thumbnail for the specified image plane from the current file,
 as a byte array.

openThumbBytes(int) - Method in class loci.formats.ImageReader
 
openThumbBytes(int) - Method in class loci.formats.in.AFIReader
 
openThumbBytes(int) - Method in class loci.formats.in.CellSensReader
 
openThumbBytes(int) - Method in class loci.formats.in.FilePatternReader
 
openThumbBytes(int) - Method in class loci.formats.in.LeicaSCNReader
 
openThumbBytes(int) - Method in class loci.formats.in.MinimalTiffReader
 
openThumbBytes(int) - Method in class loci.formats.in.NDPIReader
 
openThumbBytes(int) - Method in class loci.formats.in.SVSReader
 
openThumbBytes(int) - Method in class loci.formats.ReaderWrapper
 
openThumbImage(int) - Method in class loci.formats.gui.BufferedImageReader

Obtains a thumbnail for the specified image from the current file.

openThumbImage(String, Double) - Method in class loci.plugins.macro.LociFunctions
 
openThumbImagePlus(String) - Static method in class loci.plugins.BF
 
openThumbImagePlus(ImporterOptions) - Static method in class loci.plugins.BF
 
openThumbImagePlus() - Method in class loci.plugins.in.ImagePlusReader
 
openThumbImagePlus(String) - Method in class loci.plugins.macro.LociFunctions
 
openThumbProcessors(int) - Method in class loci.plugins.util.ImageProcessorReader
 
openWrite(String) - Method in class loci.formats.services.WlzServiceImpl
 
OperettaHandler() - Constructor for class loci.formats.in.OperettaReader.OperettaHandler
 
OperettaReader - Class in loci.formats.in

OperettaReader is the file format reader for PerkinElmer Operetta data.

OperettaReader() - Constructor for class loci.formats.in.OperettaReader

Constructs a new Operetta reader.

OperettaReader.OperettaHandler - Class in loci.formats.in
 
OperettaReader.Plane - Class in loci.formats.in
 
OPT_BYPASS - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The flag bit to indicate that selective arithmetic coding bypass
 should be used.

OPT_CROP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

This option will enable lossless cropping.

OPT_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

This option will discard the color data in the input image and produce
 a grayscale output image.

OPT_NOOUTPUT - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

This option will prevent TJTransformer.transform() from outputting a JPEG image for this
 particular transform.

OPT_PERFECT - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

This option will cause TJTransformer.transform() to throw an exception if the transform is not
 perfect.

OPT_PRED_TERM - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The flag bit to indicate that error resilience info is embedded on MQ
 termination.

OPT_PREFIX - Static variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The prefix for bit stream reader options: 'B'

OPT_PREFIX - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

The prefix for header decoder options: 'H'

OPT_PREFIX - Static variable in class jj2000.j2k.codestream.writer.PktEncoder

The prefix for packet encoding options: 'P'

OPT_PREFIX - Static variable in class jj2000.j2k.entropy.decoder.EntropyDecoder

The prefix for entropy decoder optiojns: 'C'

OPT_PREFIX - Static variable in class jj2000.j2k.entropy.encoder.EntropyCoder

The prefix for entropy coder options: 'C'

OPT_PREFIX - Static variable in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

The prefix for rate allocation options: 'A'

OPT_PREFIX - Static variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

The prefix for component transformation type: 'M'

OPT_PREFIX - Static variable in class jj2000.j2k.image.invcomptransf.InvCompTransf

The prefix for inverse component transformation options: 'M'

OPT_PREFIX - Static variable in class jj2000.j2k.quantization.dequantizer.Dequantizer

The prefix for dequantizer options: 'Q'

OPT_PREFIX - Static variable in class jj2000.j2k.quantization.quantizer.Quantizer

The prefix for quantizer options: 'Q'

OPT_PREFIX - Static variable in class jj2000.j2k.roi.encoder.ROIScaler

The prefix for ROI Scaler options: 'R'

OPT_PREFIX - Static variable in class jj2000.j2k.roi.ROIDeScaler

The prefix for ROI decoder options: 'R'

OPT_PREFIX - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilter

The prefix for wavelet filter options: 'F'

OPT_PREFIX - Static variable in class jj2000.j2k.wavelet.analysis.ForwardWT

The prefix for wavelet transform options: 'W'

OPT_RESET_MQ - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The flag bit to indicate that the MQ states for all contexts should be
 reset at the end of each non-bypass coding pass.

OPT_SEG_SYMBOLS - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The flag bit to indicate that a segmentation marker is to be
 inserted at the end of each normalization coding pass.

OPT_TERM_PASS - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The flag bit to indicate that regular termination should be used.

OPT_TRIM - Static variable in class org.libjpegturbo.turbojpeg.TJTransform

This option will discard any partial MCU blocks that cannot be
 transformed.

OPT_VERT_STR_CAUSAL - Static variable in interface jj2000.j2k.entropy.StdEntropyCoderOptions

The flag bit to indicate the vertically stripe-causal context
 formation should be used.

optbrate - Variable in class jj2000.j2k.entropy.encoder.LayersInfo

The target bitrate to which specified layers should be optimized.

OPTICAL_PATH - Static variable in class loci.formats.in.CellSensReader
 
optimal - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

Whether can write optimally.

optimize - Variable in class jj2000.j2k.entropy.encoder.EBCOTLayer

If true the `maxBytes' value is the hard maximum and the threshold is
 determined iteratively.

optimizeBitstreamLayer(int, float, int, int) - Method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

This function implements the rate-distortion optimization algorithm.

Option - Class in loci.plugins.prefs

Base class for an option for one of the plugins.

Option(String, boolean, String, String) - Constructor for class loci.plugins.prefs.Option

Constructs an option with the given parameters.

options - Variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The options that are turned on, as flag bits.

options - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor

The options bitmask to use in compression

options - Variable in class loci.formats.ClassList

List of options.

options - Variable in class loci.formats.codec.JPEGTileDecoder.TileCache
 
options - Variable in class loci.formats.FormatWriter

The options if required.

options - Variable in class loci.formats.tiff.TiffSaver

The codec options if set.

options - Variable in class loci.plugins.in.DisplayHandler
 
options - Variable in class loci.plugins.in.ImporterDialog
 
options - Variable in class loci.plugins.in.ImportProcess

Associated importer options.

options - Variable in class loci.plugins.prefs.OptionsList

Table of options defining this set of preferences.

options - Variable in class loci.plugins.util.DataBrowser
 
options - Variable in class org.libjpegturbo.turbojpeg.TJTransform

Transform options (bitwise OR of one or more of OPT_*)

OptionsDialog - Class in loci.plugins.prefs

Base class for options dialogs.

OptionsDialog(OptionsList) - Constructor for class loci.plugins.prefs.OptionsDialog

Creates a new options dialog with the given associated options.

optionsList - Variable in class loci.plugins.prefs.OptionsDialog

Options list associated with the dialog.

OptionsList - Class in loci.plugins.prefs

Base class for ImageJ preferences for plugins.

OptionsList(String, Class<?>) - Constructor for class loci.plugins.prefs.OptionsList
 
OptionsList(IniList) - Constructor for class loci.plugins.prefs.OptionsList
 
optionsWindow - Variable in class loci.plugins.util.DataBrowser
 
optName - Static variable in class jj2000.j2k.entropy.CBlkSizeSpec

Name of the option

optName - Static variable in class jj2000.j2k.entropy.PrecinctSizeSpec

Name of the option

opts - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The options that are turned on, as flag bits.

or(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
order - Variable in class loci.formats.cache.CacheStrategy

The order in which planes should be loaded along each axis.

order - Variable in class loci.formats.gui.CacheComponent

Combo boxes for choosing planar ordering.

ORDER - Static variable in class loci.plugins.out.Exporter
 
ORDER_CHANGED - Static variable in class loci.formats.cache.CacheEvent

Event type indicating new planar ordering.

ORDER_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_VALUES - Static variable in class loci.formats.gui.CacheComponent
 
ORDER_XYCTZ - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_XYCZT - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_XYTCZ - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_XYTZC - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_XYZCT - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_XYZTC - Static variable in class loci.plugins.in.ImporterOptions
 
orderCertain - Variable in class loci.formats.CoreMetadata

Indicates whether or not we are confident that the
 dimension order is correct.

orderIndex(int) - Method in class loci.formats.gui.CacheComponent

Converts enumerated order value to order chooser index.

ORDERS - Static variable in class loci.formats.gui.CacheComponent
 
orderValue(int) - Method in class loci.formats.gui.CacheComponent

Converts order chooser index to enumerated order value.

org.libjpegturbo.turbojpeg - package org.libjpegturbo.turbojpeg
 
Orientation() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Orientation
 
orientation - Variable in class jj2000.j2k.wavelet.Subband

The orientation of this subband (WT_ORIENT_LL, WT_ORIENT_HL,
 WT_ORIENT_LH, WT_ORIENT_HH).

orientation - Variable in class loci.formats.in.TargaReader
 
ORIENTATION - Static variable in class loci.formats.tiff.IFD
 
ORIENTATION_ROW_0_BOTTOM_COLUMN_0_LEFT - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "Orientation" tag.

ORIENTATION_ROW_0_BOTTOM_COLUMN_0_RIGHT - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "Orientation" tag.

ORIENTATION_ROW_0_LEFT_COLUMN_0_BOTTOM - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "Orientation" tag.

ORIENTATION_ROW_0_LEFT_COLUMN_0_TOP - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "Orientation" tag.

ORIENTATION_ROW_0_RIGHT_COLUMN_0_BOTTOM - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "Orientation" tag.

ORIENTATION_ROW_0_RIGHT_COLUMN_0_TOP - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "Orientation" tag.

ORIENTATION_ROW_0_TOP_COLUMN_0_LEFT - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "Orientation" tag.

ORIENTATION_ROW_0_TOP_COLUMN_0_RIGHT - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "Orientation" tag.

orientationNames - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
origBitDepth - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
origin - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
original - Variable in class loci.formats.in.DNGReader

The original IFD.

original - Variable in class loci.formats.in.NikonReader

The original IFD.

ORIGINAL_FRAME_RATE - Static variable in class loci.formats.in.CellSensReader
 
ORIGINAL_METADATA_NS - Static variable in class loci.formats.meta.OriginalMetadataAnnotation
 
originalColorModel - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
originalColorModel - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
originalDate - Variable in class loci.formats.in.DicomReader
 
originalDimension - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
originalID - Variable in class loci.plugins.in.FilePatternDialog
 
originalInstance - Variable in class loci.formats.in.DicomReader
 
originalMetadata - Variable in class loci.formats.in.CellSensReader.Pyramid
 
OriginalMetadataAnnotation - Class in loci.formats.meta
 
OriginalMetadataAnnotation() - Constructor for class loci.formats.meta.OriginalMetadataAnnotation
 
originalNumXTiles - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

The orginal number tiles in X direction.

originalOrder - Variable in class loci.formats.FileStitcher.ExternalSeries
 
originalRegion - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
originalSampleModel - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
originalSampleModel - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
originalSampleModel - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

The sample model for the original image.

originalSeries - Variable in class loci.formats.in.DicomReader
 
originalSrcHeight - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullDecompressor

The original value of srcHeight.

originalSrcMinX - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullDecompressor

The original value of srcMinX.

originalSrcMinY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullDecompressor

The original value of srcMinY.

originalSrcWidth - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullDecompressor

The original value of srcWidth.

originalTime - Variable in class loci.formats.in.DicomReader
 
originX - Variable in class loci.formats.in.CellSensReader.Pyramid
 
originX - Variable in class loci.formats.in.PerkinElmerReader
 
originX - Variable in class loci.formats.in.VarianFDFReader
 
originX - Variable in class loci.formats.in.ZeissLSMReader
 
originY - Variable in class loci.formats.in.CellSensReader.Pyramid
 
originY - Variable in class loci.formats.in.PerkinElmerReader
 
originY - Variable in class loci.formats.in.VarianFDFReader
 
originY - Variable in class loci.formats.in.ZeissLSMReader
 
originZ - Variable in class loci.formats.in.PerkinElmerReader
 
originZ - Variable in class loci.formats.in.VarianFDFReader
 
originZ - Variable in class loci.formats.in.ZeissLSMReader
 
origname - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
origSigned - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
origSrc - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

The image data reader.

OTHER_KEYS - Static variable in class loci.formats.in.ICSReader
 
otherChannels - Variable in class loci.plugins.util.RecordedImageProcessor
 
otherCOMMarkSeg - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

Other COM marker segments specified in the command line

otherLength - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter

The length not counted by the orginal JJ2000 packages.

out - Variable in class jj2000.j2k.codestream.writer.FileCodestreamWriter

The file to write

out - Variable in class jj2000.j2k.entropy.encoder.BitToByteOutput

The byte based output

out - Variable in class jj2000.j2k.entropy.encoder.MQCoder

The ByteOutputBuffer used to write the compressed bit stream.

out - Variable in class jj2000.j2k.util.StreamMsgLogger

The 'out' stream

out - Variable in class loci.formats.FormatWriter

Current file.

out - Variable in class loci.formats.tiff.TiffSaver

Output stream to use when saving TIFF data.

outBlk - Variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Output block used instead of the one provided as an argument
        if the later is DataBlkFloat.

outdata - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf

Buffer for each component of output data

outdtype - Variable in class jj2000.j2k.quantization.dequantizer.StdDequantizer

Type of the current output data

output - Variable in class loci.formats.gui.DataConverter
 
output - Variable in class loci.formats.Memoizer.KryoDeser
 
output_ - Variable in class com.sun.media.imageioimpl.common.BitFile
 
outputOrder - Variable in class loci.formats.out.ICSWriter
 
outputOrder - Variable in class loci.formats.out.V3DrawWriter
 
outputOrder - Variable in class loci.formats.out.WlzWriter
 
outputPath - Variable in class loci.formats.out.CellH5Writer
 
OutputStreamAdapter - Class in com.sun.media.imageioimpl.plugins.clib
 
OutputStreamAdapter(ImageOutputStream) - Constructor for class com.sun.media.imageioimpl.plugins.clib.OutputStreamAdapter
 
outT - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The output stream used, for each thread

overfl - Variable in class loci.formats.in.SDTInfo
 
overflowCorrFactor - Variable in class loci.formats.in.SDTInfo
 
overlaps - Variable in class loci.formats.in.TrestleReader
 
overlayFiles - Variable in class loci.formats.in.MIASReader
 
overlayPlanes - Variable in class loci.formats.in.MIASReader
 
overruns - Variable in class loci.formats.in.SDTInfo

No of Fifo overruns
 when > 0  fcs curve & endTime are not valid.

OVERVIEW_IMAGE - Static variable in class loci.formats.in.CellSensReader
 
overwriteComment(RandomAccessInputStream, Object) - Method in class loci.formats.tiff.TiffSaver

Convenience method for overwriting a file's first ImageDescription.

overwriteDimensions(MetadataRetrieve) - Method in class loci.formats.out.ICSWriter
 
overwriteIFDValue(RandomAccessInputStream, int, int, Object) - Method in class loci.formats.tiff.TiffSaver

Surgically overwrites an existing IFD value with the given one.

overwriteLastIFDOffset(RandomAccessInputStream) - Method in class loci.formats.tiff.TiffSaver
 
OW - Static variable in class loci.formats.in.DicomReader
 
OXFORD_MAGIC_STRING - Static variable in class loci.formats.in.OxfordInstrumentsReader
 
OxfordInstrumentsReader - Class in loci.formats.in

OxfordInstrumentsReader is the file format reader for
 Oxford Instruments .top files.

OxfordInstrumentsReader() - Constructor for class loci.formats.in.OxfordInstrumentsReader

Constructs a new Oxford Instruments reader.





P

p - Variable in class loci.formats.in.BioRadReader.Note
 
p - Variable in class loci.plugins.in.SeriesDialog
 
p - Variable in class loci.plugins.in.ThumbLoader
 
P_KEY - Static variable in class loci.formats.in.LiFlimReader
 
pack() - Method in class loci.plugins.util.DataBrowser

Overridden pack method to allow us to delay initial window sizing.

PackageUtil - Class in com.sun.media.imageioimpl.common
 
PackageUtil() - Constructor for class com.sun.media.imageioimpl.common.PackageUtil
 
packBits(byte[], int, int, byte[], int) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFPackBitsCompressor

Performs PackBits compression for a single buffer of data.

PACKBITS - Static variable in class loci.formats.in.PhotoshopTiffReader
 
PackbitsCodec - Class in loci.formats.codec

This class implements packbits decompression.

PackbitsCodec() - Constructor for class loci.formats.codec.PackbitsCodec
 
packetData - Variable in class jj2000.j2k.util.CodestreamManipulator

Buffers containing the packet data

packetHeaders - Variable in class jj2000.j2k.util.CodestreamManipulator

Buffers contaning the packet headers

packetIdx - Variable in class jj2000.j2k.codestream.reader.PktInfo

Index of the packet

packetIdx - Variable in class jj2000.j2k.codestream.writer.FileCodestreamWriter

The packet index (when start of packet markers i.e.

packetPerTilePart - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies the maximum number of packets to be put into one tile-part.

packetWritable - Variable in class jj2000.j2k.codestream.writer.PktEncoder

Whether or not the current packet is writable

packPacketHeaderInMain - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Indicates that the packet headers are packed in the main header.

packPacketHeaderInTile - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Indicates that the packet headers are packed in the tiles' headers.

PAD - Static variable in class loci.formats.codec.Base64Codec
 
pad - Variable in class loci.formats.out.QTWriter

Number of padding bytes in each row.

PAD - Static variable in class loci.plugins.config.ConfigWindow
 
PAD_SEQ - Static variable in class jj2000.j2k.entropy.encoder.BitToByteOutput

The alternating sequence of 0's and 1's used for byte padding

paddedMaskLine - Variable in class jj2000.j2k.roi.encoder.ArbROIMaskGenerator

A line or column of the mask with padding

padding - Variable in class loci.formats.in.UBMReader
 
PADDING_BYTES - Static variable in class loci.formats.out.AVIWriter
 
paddingZeros - Variable in class loci.plugins.in.FilePatternDialog
 
padImage(BufferedImage, int, int) - Static method in class loci.formats.gui.AWTImageTools

Pads (or crops) the image to the given width and height.

padImage(byte[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools

Pads (or crops) the byte array to the given width and height.

padImage(short[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools

Pads (or crops) the short array to the given width and height.

padImage(int[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools

Pads (or crops) the int array to the given width and height.

padImage(float[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools

Pads (or crops) the float array to the given width and height.

padImage(double[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools

Pads (or crops) the double array to the given width and height.

PAETH - Static variable in class loci.formats.in.APNGReader
 
page - Variable in class loci.formats.in.SDTInfo
 
PAGE_NAME - Static variable in class loci.formats.tiff.IFD
 
PAGE_NUMBER - Static variable in class loci.formats.tiff.IFD
 
PageName() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.PageName
 
PageNumber() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.PageNumber
 
paintComponent(Graphics) - Method in class loci.formats.gui.CacheIndicator
 
palette - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
 
palette - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
palette - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
palette - Variable in class loci.formats.in.BMPReader

The palette for indexed color images.

PALETTE - Static variable in class loci.formats.in.ZeissLSMReader
 
PALETTE_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
PALETTE_COLOR - Static variable in interface com.sun.media.imageioimpl.plugins.pcx.PCXConstants
 
PALETTE_GRAYSCALE - Static variable in interface com.sun.media.imageioimpl.plugins.pcx.PCXConstants
 
PaletteBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000

This class is designed to represent a palette box for JPEG 2000 JP2 file
  format.

PaletteBox(IndexColorModel) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

Constructs a PlatteBox from an
  IndexColorModel.

PaletteBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

Constructs a PlatteBox from an
  org.w3c.dom.Node.

PaletteBox(int, byte[], byte[][]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

Constructs a PlatteBox from the provided length, bit
  depths of the color components and the LUT.

PaletteBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox

Constructs a PlatteBox from the provided byte array.

PaletteBuilder - Class in com.sun.media.imageioimpl.common

This class implements the octree quantization method 
  as it is described in the "Graphics Gems"
  (ISBN 0-12-286166-3, Chapter 4, pages 297-293)

PaletteBuilder(RenderedImage) - Constructor for class com.sun.media.imageioimpl.common.PaletteBuilder
 
PaletteBuilder(RenderedImage, int) - Constructor for class com.sun.media.imageioimpl.common.PaletteBuilder
 
PaletteBuilder.ColorNode - Class in com.sun.media.imageioimpl.common

The node of color tree.

paletteIndex - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
paletteSize - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
paletteType - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
pane - Variable in class loci.formats.gui.ImageViewer
 
panel - Variable in class loci.plugins.util.SearchableWindow
 
param - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
param - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

The ImageReadParam to create this
  renderedImage.

param - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
param - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
PARAMETER_KEYS - Static variable in class loci.formats.in.ICSReader
 
parameterFile - Variable in class loci.formats.in.JEOLReader
 
paramFile - Variable in class loci.formats.in.PCORAWReader
 
params - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Dequantization parameters of all subbands and all components in the
 current tile.

params - Variable in class jj2000.j2k.quantization.dequantizer.StdDequantizer

The decoding parameters of the dequantizer

PARAMS - Static variable in class loci.plugins.config.ConfigWindow
 
parent - Variable in class jj2000.j2k.wavelet.analysis.SubbandAn

The reference to the parent of this subband.

parent - Variable in class jj2000.j2k.wavelet.synthesis.SubbandSyn

The reference to the parent of this subband.

parentDimension - Variable in class loci.formats.Modulo
 
parentNames - Variable in class loci.formats.in.FEITiffReader.FEIHandler
 
parentQName - Variable in class loci.formats.in.FlexReader.FlexHandler
 
parents - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat

The table to link the child to its parent.

parents - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormat

The table to link the child to its parent.

parentTag - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

The parent TIFFTag of this directory.

parentType - Variable in class loci.formats.Modulo
 
parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Parses the data elements from the byte array.

parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox

Parse the channel definitions from the content data array.

parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox

Parse the component mapping from the provided content data array.

parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox

Parses the content of this box from its content byte array.

parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox
 
parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox

Parse the data elements from the byte array of the content.

parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox
 
parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox

Parse the data elements from the provided content data array.

parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDBox

Parses the data elements from the provided data array.

parse(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.UUIDListBox

Parses the data elements from the provided content data array.

parse(int, long, long) - Method in class loci.formats.in.NativeQTReader

Parse all of the atoms in the file.

parse(Element) - Method in class loci.formats.in.PrairieMetadata.Frame

Parses metadata from the given Frame element.

parse(Element) - Method in class loci.formats.in.PrairieMetadata.PFile

Parses metadata from the given File element.

parse(Element) - Method in class loci.formats.in.PrairieMetadata.Sequence

Parses metadata from the given Sequence element.

parseAlayers(String, float) - Static method in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

Convenience method that parses the 'Alayers' option.

parseAndFind(BufferedRandomAccessFile) - Method in class jj2000.j2k.util.CodestreamManipulator

This method parses the codestream for SOT, SOP and EPH markers and
 removes header header bits signalling SOP and EPH markers if packed
 packet headers are used

parseApplicationTags() - Method in class loci.formats.in.ZeissLSMReader
 
parseArg(String) - Method in class loci.plugins.in.ImporterOptions

Parses the plugin argument for parameter values.

parseArray(String) - Method in class loci.formats.in.VarianFDFReader

Split a String that represents an array into individual elements.

parseAttributes() - Method in class loci.formats.in.ImarisHDFReader
 
parseAttributesAndVariables(List<Group>) - Method in class loci.formats.services.NetCDFServiceImpl

Recursively parses attribute and variable paths, filling
 attributeList and variableList.

parseAxis(Element) - Method in class loci.formats.in.OIRReader
 
parseBoxes() - Method in class loci.formats.in.JPEG2000MetadataParser

Parses the JPEG 2000 JP2 metadata boxes.

parseByteArray(String) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Parses the byte array expressed by a string.

parseCellObjects() - Method in class loci.formats.in.CellH5Reader
 
parseCFG(Document) - Method in class loci.formats.in.PrairieMetadata

Parses metadata from Prairie CFG file.

parseChannel(Element, boolean) - Method in class loci.formats.in.OIRReader
 
parseChannelData(Location) - Method in class loci.formats.in.BDReader
 
parseChannels() - Method in class loci.formats.in.PrairieMetadata

Parses details of the activated channels into the PrairieMetadata.activeChannels
 data structure from the "channel" entry of the configuration.

parseChannelTag() - Method in class loci.formats.in.LeicaReader
 
parseChunks(IRandomAccess) - Method in class loci.formats.in.IM3Reader.ContainerRecord

Parse and return the sub-records for the record container

parseColor(byte, byte, byte) - Static method in class loci.formats.in.BaseZeissReader
 
parseColor(String) - Method in class loci.formats.in.FakeReader
 
parseColor(byte, byte, byte) - Static method in class loci.formats.in.ZeissTIFFHandler
 
parseComment() - Method in class loci.formats.in.FluoviewReader
 
parseCommentGeneric(String) - Method in class loci.formats.in.TiffReader
 
parseCommentImageJ(String) - Method in class loci.formats.in.TiffReader
 
parseCommentMetamorph(String) - Method in class loci.formats.in.TiffReader
 
parseContiguousCodestream(long) - Method in class loci.formats.in.JPEG2000MetadataParser

Parses the JPEG 2000 codestream metadata.

parseCSVFile(String) - Method in class loci.formats.in.PerkinElmerReader
 
parseDatabase() - Method in interface loci.formats.services.MDBService

Read all tables from a pre-initialized .mdb files.

parseDatabase() - Method in class loci.formats.services.MDBServiceImpl
 
parseDeconvolutionLog(MetadataStore) - Method in class loci.formats.in.DeltavisionReader

Parse deconvolution output, if it exists.

parseDimension(String) - Method in class loci.formats.in.APLReader

Parse an integer from the given dimension String.

parseDimensionSizes(String[], String[]) - Method in class loci.formats.in.NikonTiffReader
 
parseDimensionTag(int) - Method in class loci.formats.in.LeicaReader
 
parseDOM(Location) - Method in class loci.formats.in.PrairieReader

Parses a Document from the data in the given file.

parseDouble(String) - Method in class loci.formats.in.LeicaHandler
 
parseDouble(String) - Method in class loci.formats.in.LIFReader
 
parseDouble(String) - Method in class loci.formats.in.TiffReader
 
parseDouble(String) - Static method in class loci.formats.in.ZeissTIFFHandler

Parse a Double from a String.

parseENV(Document) - Method in class loci.formats.in.PrairieMetadata

Parses metadata from Prairie ENV file.

parseETSFile(String, int) - Method in class loci.formats.in.CellSensReader
 
parseExperimentTag() - Method in class loci.formats.in.LeicaReader
 
parseExtraTags() - Method in class loci.formats.in.GatanDM2Reader
 
parseFDF(String) - Method in class loci.formats.in.VarianFDFReader
 
parseFile(String, Class<?>) - Method in class loci.formats.ClassList

Parses a list of classes from a configuration file.

parseFile(String, MetamorphHandler) - Method in class loci.formats.in.MetamorphTiffReader
 
parseFile(DirectoryEntry) - Method in class loci.formats.services.POIServiceImpl
 
parseFileHeader(List<String>) - Method in class loci.formats.in.TextReader

Parses the file looking for the file header.

parseFilename(String[], int, int) - Method in class loci.formats.in.APLReader
 
parseFilenames(int) - Method in class loci.formats.in.LeicaReader
 
parseFilters(String) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterSpec

Parse filters from the given word

parseFlexFile(int, int, int, int, boolean, MetadataStore) - Method in class loci.formats.in.FlexReader

Parses XML metadata from the Flex file corresponding to the given well.

parseFrameProperties(Element) - Method in class loci.formats.in.OIRReader
 
parseHeader() - Method in class loci.formats.in.LiFlimReader
 
parseHeaderRow(String[]) - Method in class loci.formats.in.TextReader

Populates rowLength, xIndex, yIndex, and channels.

parseIdx(String, int) - Static method in class jj2000.j2k.ModuleSpec

This method is responsible of parsing tile indexes set and
 component indexes set for an option.

parseIFD(Node) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
parseImageNames(int) - Method in class loci.formats.in.OpenlabReader
 
parseImageProperties(Element) - Method in class loci.formats.in.OIRReader
 
parseImageTag(int) - Method in class loci.formats.in.LeicaReader
 
parseImageXML(String, int) - Method in class loci.formats.in.ColumbusReader
 
parseInstrumentData(MetadataStore, int) - Method in class loci.formats.in.LeicaReader
 
parseInt(String) - Static method in class loci.formats.in.BaseZeissReader

Parse an Integer from a String.

parseInt(String, int) - Static method in class loci.formats.in.BaseZeissReader

Parse an Integer from a String.

parseInt(String) - Method in class loci.formats.in.TiffReader
 
parseIntArray(String) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Parses the integer array expressed a string.

parseKeyAndValue(String, String, int, int, int) - Method in class loci.formats.in.MicromanagerReader
 
parseKeyAndValue(String, String, String) - Method in class loci.formats.in.ND2Handler
 
parseKeys(Element, PrairieMetadata.ValueTable) - Method in class loci.formats.in.PrairieMetadata

Parses <Key> elements beneath the given element, into the specified
 table.

parseKeyValue(String, String) - Method in class loci.formats.in.PerkinElmerReader
 
parseLength(String, String) - Method in class loci.formats.in.FakeReader
 
parseLine(String) - Method in class loci.formats.ClassList

Parses a class from a string including options and comments.

parseList(String) - Static method in class loci.plugins.prefs.StringOption

Parses a string of comma-separated values into a list of tokens.

parseLogFile(MetadataStore) - Method in class loci.formats.in.DeltavisionReader

Extract metadata from associated log file, if it exists.

parseLUT(int) - Method in class loci.formats.in.LeicaReader
 
parseLUT(Element, String) - Method in class loci.formats.in.OIRReader
 
parseMainTags(int, MetadataStore, ArrayList<BaseZeissReader.Tag>) - Method in class loci.formats.in.BaseZeissReader
 
parseMasks - Variable in class loci.formats.in.MIASReader

Whether or not mask pixel data should be parsed in setId.

parseMasks(MetadataStore) - Method in class loci.formats.in.MIASReader

Parse masks into a separate overlay-specific MetadataStore.

parseMasks(MetadataStore, int, int, String) - Method in class loci.formats.in.MIASReader

Parse Mask ROIs from the given TIFF and place them in the given
 MetadataStore.

parseMDB(String) - Method in class loci.formats.in.ZeissLSMReader

Parse a .mdb file and return a list of referenced .lsm files.

parseMetadata() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
parseNotes(MetadataStore) - Method in class loci.formats.in.BioRadReader
 
parseObjectives(NodeList) - Method in class loci.formats.in.ZeissCZIReader
 
parseOption(String) - Method in class loci.plugins.prefs.BooleanOption
 
parseOption(String) - Method in class loci.plugins.prefs.DoubleOption
 
parseOption(String) - Method in class loci.plugins.prefs.Option

Parses the option's value from the given argument string.

parseOption(String) - Method in class loci.plugins.prefs.StringOption
 
parseOptions(String) - Method in class loci.formats.ClassList

Parses one or more options from a string.

parseOptions(String) - Method in class loci.plugins.in.Importer

Parses core options.

parseOptions(String) - Method in class loci.plugins.prefs.OptionsList

Parses option values from the given argument string.

parseOriginalMetadata(Node) - Method in class loci.formats.in.OIRReader
 
parseOverlays(int, long, String, MetadataStore) - Method in class loci.formats.in.ZeissLSMReader

Parses overlay-related fields.

parsePageName() - Method in class loci.formats.in.FluoviewReader
 
parsePixelsSizeZFromKey(String) - Method in class loci.formats.in.ND2Handler

Parses the physical size from a key.

parsePoints(String) - Static method in class loci.plugins.util.ROIHandler

Parse (x, y) coordinates from a String returned by
 MetadataRetrieve.getPolygonpoints(...) or
 MetadataRetrieve.getPolylinepoints(...)

parsePosition(int) - Method in class loci.formats.in.MicromanagerReader
 
parsePosition(String, int) - Method in class loci.formats.in.MicromanagerReader
 
parsePrairieMetadata() - Method in class loci.formats.in.PrairieReader

This step parses the Prairie metadata files into the Prairie-specific
 metadata structure, PrairieReader.meta.

parsePVStateShard(Element, PrairieMetadata.ValueTable) - Method in class loci.formats.in.PrairieMetadata

Parses the <PVStateShard> element beneath the given element, into
 the specified table.

parser - Variable in class loci.formats.in.APLReader
 
parser - Variable in class loci.formats.in.CellSensReader
 
parser - Variable in class loci.formats.in.FV1000Reader
 
parser - Variable in class loci.formats.in.ZeissCZIReader
 
parseRecord(IRandomAccess) - Static method in class loci.formats.in.IM3Reader

Parse an IM3 record at the current file pointer location

parseResFile(String) - Method in class loci.formats.in.FlexReader
 
parseROIFile(String, MetadataStore, int, int) - Method in class loci.formats.in.FV1000Reader
 
parseROIs(String, int, Vector) - Static method in class jj2000.j2k.roi.encoder.ROIScaler

This function parses the values given for the ROIs with the argument
 -Rroi.

parseROIs(MetadataStore) - Method in class loci.formats.in.BDReader
 
parseROIs(int) - Method in class loci.formats.in.CellH5Reader
 
parseROIs(MetadataStore) - Method in class loci.formats.in.TrestleReader
 
parseROIs(int, String, MetadataStore) - Method in class loci.formats.in.ZeissZVIReader

Parse ROI data from the given RandomAccessInputStream and store it in the
 given MetadataStore.

parseROIString(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
 
parseSeriesTag() - Method in class loci.formats.in.LeicaReader
 
parseSetup(String, String) - Method in class loci.formats.in.SPCReader
 
parseSpectrumRecord(IRandomAccess, IM3Reader.ContainerRecord) - Method in class loci.formats.in.IM3Reader.Spectrum

Parse the spectrum record

parseString(IRandomAccess) - Static method in class loci.formats.in.IM3Reader

Parse a string from the IM3 file at the current file pointer loc

parseStructure() - Method in class loci.formats.in.CellH5Reader
 
parseTableData(List<String>, int) - Method in class loci.formats.in.TextReader

Reads the tabular data into the data array.

parseTags(int, String, String) - Method in class loci.formats.in.GatanReader

Parses Gatan DM3 tags.

parseTags(MetadataStore) - Method in class loci.formats.in.IPLabReader
 
parseTags(int, String, MetadataStore) - Method in class loci.formats.in.ZeissZVIReader

Parse all of the tags in a stream.

parseTemplateFile(MetadataStore) - Method in class loci.formats.in.MIASReader

Parse metadata from the Nugenesistemplate.txt file.

parseText(String, int, boolean) - Method in class loci.formats.in.NativeND2Reader
 
parseTimestamp(String) - Method in class loci.formats.in.BaseZeissReader

Parse timestamp from string.

parseTimeTag(int) - Method in class loci.formats.in.LeicaReader
 
parseTimFile(String) - Method in class loci.formats.in.PerkinElmerReader
 
parseUIC1Tags(long, int) - Method in class loci.formats.in.MetamorphReader

UIC1 entry parser

parseUIC2Tags(long) - Method in class loci.formats.in.MetamorphReader

Populates metadata fields with some contained in MetaMorph UIC2 Tag.

parseUIC4Tags(long) - Method in class loci.formats.in.MetamorphReader

UIC4 metadata parser

 UIC4 Table contains per-plane blocks of metadata
 stage X/Y positions,
 camera chip offsets,
 stage labels...

parseWellLogFile(int, MetadataStore) - Method in class loci.formats.in.CellWorxReader

Parse metadata from a well log file.

parseXML(String, long) - Method in class loci.formats.in.OIRReader
 
parseXML(Document) - Method in class loci.formats.in.PrairieMetadata

Parses metadata from Prairie XML file.

parseXMLFile() - Method in class loci.formats.in.MicromanagerReader

Parse metadata values from the Acqusition.xml file.

parseZpoFile(String) - Method in class loci.formats.in.PerkinElmerReader
 
parsingEnabled - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava

Enable the parsing mode or not when the decoding rate is specified .

pass - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Black and white pass mode table.

PASS_HEIGHTS - Static variable in class loci.formats.in.APNGReader
 
PASS_WIDTHS - Static variable in class loci.formats.in.APNGReader

Interlacing pass dimensions.

passMode - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Pass mode table.

PassthroughCodec - Class in loci.formats.codec

A codec which just returns the exact data it was given, performing no
 compression or decompression.

PassthroughCodec() - Constructor for class loci.formats.codec.PassthroughCodec
 
path - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
 
path - Variable in class loci.plugins.config.ConfigWindow
 
path - Variable in class loci.plugins.config.LibraryEntry
 
pathToImageData - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
pathToPosition - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
pathToSegmentationData - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
pattern - Variable in class loci.formats.FilePattern

The file pattern string.

pattern - Variable in class loci.formats.FileStitcher.ExternalSeries
 
PATTERN_D - Static variable in class loci.formats.in.CellomicsReader
 
PATTERN_O - Static variable in class loci.formats.in.CellomicsReader
 
patternIds - Variable in class loci.formats.FileStitcher

Whether string ids given should be treated
 as file patterns rather than single file paths.

PBM_ASCII - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
PBM_ASCII - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
PBM_RAW - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
PBM_RAW - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
PCI_MAGIC_BYTES - Static variable in class loci.formats.in.PCIReader
 
PCIReader - Class in loci.formats.in

PCIReader is the file format reader for SimplePCI (Compix) .cxd files.

PCIReader() - Constructor for class loci.formats.in.PCIReader

Constructs a new SimplePCI reader.

PCORAWReader - Class in loci.formats.in

PCORAWReader is the file format reader for PCORAW files.

PCORAWReader() - Constructor for class loci.formats.in.PCORAWReader

Constructs a new PCORAW reader.

pcs - Variable in class jj2000.j2k.decoder.DecoderSpecs

The progression changes specifications

PCX_MAGIC_BYTE - Static variable in class loci.formats.in.PCXReader
 
PCXConstants - Interface in com.sun.media.imageioimpl.plugins.pcx
 
PCXImageReader - Class in com.sun.media.imageioimpl.plugins.pcx
 
PCXImageReader(PCXImageReaderSpi) - Constructor for class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
PCXImageReaderSpi - Class in com.sun.media.imageioimpl.plugins.pcx
 
PCXImageReaderSpi() - Constructor for class com.sun.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
PCXImageWriter - Class in com.sun.media.imageioimpl.plugins.pcx
 
PCXImageWriter(PCXImageWriterSpi) - Constructor for class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
PCXImageWriterSpi - Class in com.sun.media.imageioimpl.plugins.pcx
 
PCXImageWriterSpi() - Constructor for class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
PCXMetadata - Class in com.sun.media.imageioimpl.plugins.pcx
 
PCXMetadata() - Constructor for class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
PCXReader - Class in loci.formats.in

PCXReader is the file format reader for PCX files (originally used by
 PC Paintbrush; now used in Zeiss' LSM Image Browser).

PCXReader() - Constructor for class loci.formats.in.PCXReader

Constructs a new PCX reader.

PDS_MAGIC_STRING - Static variable in class loci.formats.in.PDSReader
 
PDSReader - Class in loci.formats.in

PDSReader is the file format reader for Perkin Elmer densitometer files.

PDSReader() - Constructor for class loci.formats.in.PDSReader

Constructs a new PDS reader.

periodX - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
periodY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
PerkinElmerReader - Class in loci.formats.in

PerkinElmerReader is the file format reader for PerkinElmer files.

PerkinElmerReader() - Constructor for class loci.formats.in.PerkinElmerReader

Constructs a new PerkinElmer reader.

PerkinElmerReader.PixelsFile - Class in loci.formats.in
 
pf(Double, String) - Method in class loci.formats.in.PrairieReader

Converts the given double to a PositiveFloat, or
 null if incompatible.

PF_ABGR - Static variable in class org.libjpegturbo.turbojpeg.TJ

ABGR pixel format.

PF_ARGB - Static variable in class org.libjpegturbo.turbojpeg.TJ

ARGB pixel format.

PF_BGR - Static variable in class org.libjpegturbo.turbojpeg.TJ

BGR pixel format.

PF_BGRA - Static variable in class org.libjpegturbo.turbojpeg.TJ

BGRA pixel format.

PF_BGRX - Static variable in class org.libjpegturbo.turbojpeg.TJ

BGRX pixel format.

PF_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJ

Grayscale pixel format.

PF_RGB - Static variable in class org.libjpegturbo.turbojpeg.TJ

RGB pixel format.

PF_RGBA - Static variable in class org.libjpegturbo.turbojpeg.TJ

RGBA pixel format.

PF_RGBX - Static variable in class org.libjpegturbo.turbojpeg.TJ

RGBX pixel format.

PF_XBGR - Static variable in class org.libjpegturbo.turbojpeg.TJ

XBGR pixel format.

PF_XRGB - Static variable in class org.libjpegturbo.turbojpeg.TJ

XRGB pixel format.

PFile(PrairieMetadata.Frame, Element) - Constructor for class loci.formats.in.PrairieMetadata.PFile

Creates a new file by parsing the given <File> element.

pfsOffset - Variable in class loci.formats.in.NativeND2Reader
 
pfsStateOffset - Variable in class loci.formats.in.NativeND2Reader
 
PGM_ASCII - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
PGM_ASCII - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
PGM_MAGIC_CHAR - Static variable in class loci.formats.in.PGMReader
 
PGM_RAW - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
PGM_RAW - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
PGMReader - Class in loci.formats.in

PGMReader is the file format reader for Portable Gray Map (PGM) images.

PGMReader() - Constructor for class loci.formats.in.PGMReader

Constructs a new PGMReader.

PHASE - Static variable in class loci.formats.FormatTools

Identifies the Phase dimensional type,
 representing a dimension consisting of phases.

PHASE - Static variable in class loci.formats.in.CellSensReader
 
phaseLabels - Variable in class loci.formats.in.ZeissCZIReader
 
phases - Variable in class loci.formats.in.LiFlimReader
 
phases - Variable in class loci.formats.in.ZeissCZIReader
 
phases - Variable in class loci.formats.in.ZeissLSMReader
 
PHOTOBLEACHING - Static variable in class loci.formats.in.CellSensReader
 
PhotoInterp - Enum in loci.formats.tiff

Utility class for working with TIFF photometric interpretations.

PhotoInterp(int, String, String) - Constructor for enum loci.formats.tiff.PhotoInterp

Default constructor.

PHOTOMETRIC_INTERPRETATION - Static variable in class loci.formats.in.DicomReader
 
PHOTOMETRIC_INTERPRETATION - Static variable in class loci.formats.tiff.IFD
 
PHOTOMETRIC_INTERPRETATION_BLACK_IS_ZERO - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PhotometricInterpretation" tag.

PHOTOMETRIC_INTERPRETATION_CIELAB - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PhotometricInterpretation" tag.

PHOTOMETRIC_INTERPRETATION_CMYK - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PhotometricInterpretation" tag.

PHOTOMETRIC_INTERPRETATION_ICCLAB - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PhotometricInterpretation" tag.

PHOTOMETRIC_INTERPRETATION_PALETTE_COLOR - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PhotometricInterpretation" tag.

PHOTOMETRIC_INTERPRETATION_RGB - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PhotometricInterpretation" tag.

PHOTOMETRIC_INTERPRETATION_TRANSPARENCY_MASK - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PhotometricInterpretation" tag.

PHOTOMETRIC_INTERPRETATION_WHITE_IS_ZERO - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PhotometricInterpretation" tag.

PHOTOMETRIC_INTERPRETATION_Y_CB_CR - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PhotometricInterpretation" tag.

PhotometricInterpretation() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.PhotometricInterpretation
 
photometricInterpretation - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The value of the PhotometricInterpretation tag.

photometricInterpretation - Variable in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam
 
photometricInterpretation - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
photometricInterpretation - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
photon(int) - Method in class loci.formats.in.SPCReader
 
PHOTON_IMAGING_MODE - Static variable in class loci.formats.in.CellSensReader
 
photosensorReading - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Photosensor reading.

PhotoshopTiffReader - Class in loci.formats.in

PhotoshopTiffReader is the file format reader for
 Adobe Photoshop TIFF files.

PhotoshopTiffReader() - Constructor for class loci.formats.in.PhotoshopTiffReader

Constructs a new Photoshop TIFF reader.

PHYSICAL_SIZE_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
 
physicalSizes - Variable in class loci.formats.in.LeicaReader
 
physicalSizeX - Variable in class loci.formats.in.BaseZeissReader
 
physicalSizeX - Variable in class loci.formats.in.BioRadSCNReader
 
physicalSizeX - Variable in class loci.formats.in.CellSensReader.Pyramid
 
physicalSizeX - Variable in class loci.formats.in.FakeReader
 
physicalSizeX - Variable in class loci.formats.in.LeicaHandler
 
physicalSizeX - Variable in class loci.formats.in.NikonTiffReader
 
physicalSizeX - Variable in class loci.formats.in.OIRReader
 
physicalSizeX - Variable in class loci.formats.in.SISReader
 
physicalSizeXs - Variable in class loci.formats.in.LIFReader
 
physicalSizeY - Variable in class loci.formats.in.BaseZeissReader
 
physicalSizeY - Variable in class loci.formats.in.BioRadSCNReader
 
physicalSizeY - Variable in class loci.formats.in.CellSensReader.Pyramid
 
physicalSizeY - Variable in class loci.formats.in.FakeReader
 
physicalSizeY - Variable in class loci.formats.in.LeicaHandler
 
physicalSizeY - Variable in class loci.formats.in.NikonTiffReader
 
physicalSizeY - Variable in class loci.formats.in.OIRReader
 
physicalSizeY - Variable in class loci.formats.in.SISReader
 
physicalSizeYs - Variable in class loci.formats.in.LIFReader
 
physicalSizeZ - Variable in class loci.formats.in.BaseZeissReader
 
physicalSizeZ - Variable in class loci.formats.in.FakeReader
 
physicalSizeZ - Variable in class loci.formats.in.NikonTiffReader
 
physicalSizeZ - Variable in class loci.formats.in.OIRReader
 
physicalSizeZ - Variable in class loci.formats.in.TiffReader
 
physicalX - Variable in class loci.formats.in.VolocityReader.Stack
 
physicalY - Variable in class loci.formats.in.VolocityReader.Stack
 
physicalZ - Variable in class loci.formats.in.VolocityReader.Stack
 
PIC_FILE_ID - Static variable in class loci.formats.in.BioRadReader

Numerical ID of a valid Bio-Rad PIC file.

PIC_SUFFIX - Static variable in class loci.formats.in.BioRadReader
 
picFiles - Variable in class loci.formats.in.BioRadReader
 
pict - Variable in class loci.formats.in.OpenlabReader

Helper reader to read PICT data.

pict - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
PICT_9A - Static variable in class loci.formats.in.PictReader
 
PICT_BITSRECT - Static variable in class loci.formats.in.PictReader
 
PICT_BITSRGN - Static variable in class loci.formats.in.PictReader
 
PICT_CLIP_RGN - Static variable in class loci.formats.in.PictReader
 
PICT_END - Static variable in class loci.formats.in.PictReader
 
PICT_JPEG - Static variable in class loci.formats.in.PictReader
 
PICT_LONGCOMMENT - Static variable in class loci.formats.in.PictReader
 
PICT_PACKBITSRECT - Static variable in class loci.formats.in.PictReader
 
PICT_PACKBITSRGN - Static variable in class loci.formats.in.PictReader
 
PICT_TYPE_1 - Static variable in class loci.formats.in.PictReader
 
PICT_TYPE_2 - Static variable in class loci.formats.in.PictReader
 
PictReader - Class in loci.formats.in

PictReader is the file format reader for Apple PICT files.

PictReader() - Constructor for class loci.formats.in.PictReader

Constructs a new PICT reader.

pictToImage(byte[]) - Method in class loci.formats.gui.LegacyQTTools

Converts the given byte array in PICT format to a Java image.

PictWidgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats PICT support.

PictWidgets() - Constructor for class loci.plugins.config.PictWidgets
 
pinfo - Static variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The list of parameters that is accepted by the bit stream
 readers.

pinfo - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

The list of parameters that is accepted for quantization.

pinfo - Static variable in class jj2000.j2k.codestream.writer.PktEncoder

The list of parameters that is accepted for packet encoding.

pinfo - Static variable in class jj2000.j2k.entropy.decoder.EntropyDecoder

The list of parameters that is accepted by the entropy
 decoders.

pinfo - Static variable in class jj2000.j2k.entropy.encoder.EntropyCoder

The list of parameters that is accepted for entropy coding.

pinfo - Static variable in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

The list of parameters that is accepted for entropy coding.

pinfo - Static variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

The list of parameters that is accepted by the forward
 component transformation module.

pinfo - Static variable in class jj2000.j2k.image.invcomptransf.InvCompTransf

The list of parameters that is accepted by the inverse
 component transformation module.

pinfo - Static variable in class jj2000.j2k.quantization.dequantizer.Dequantizer

The list of parameters that is accepted by the bit stream
 readers.

pinfo - Static variable in class jj2000.j2k.quantization.quantizer.Quantizer

The list of parameters that is accepted for quantization.

pinfo - Static variable in class jj2000.j2k.roi.encoder.ROIScaler

The list of parameters that are accepted for ROI coding.

pinfo - Static variable in class jj2000.j2k.roi.ROIDeScaler

The list of parameters that is accepted by the entropy decoders.

pinfo - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilter

The list of parameters that is accepted for wavelet filters.

pinfo - Static variable in class jj2000.j2k.wavelet.analysis.ForwardWT

The list of parameters that is accepted for wavelet transform.

pinhole - Variable in class loci.formats.in.ImarisHDFReader
 
pinhole - Variable in class loci.formats.in.LeicaHandler
 
pinhole - Variable in class loci.formats.in.LeicaReader
 
pinhole - Variable in class loci.formats.in.OIRReader.Channel
 
pinhole - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
pinhole - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
pinholes - Variable in class loci.formats.in.LIFReader
 
pinholeSize - Variable in class loci.formats.in.FV1000Reader
 
pinholeSize - Variable in class loci.formats.in.ND2Handler
 
pinholeSize - Variable in class loci.formats.in.NikonTiffReader
 
pix - Variable in class loci.formats.in.CanonRawReader
 
pixbuf - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
pixClk - Variable in class loci.formats.in.SDTInfo
 
PIXEL_CLOCK - Static variable in class loci.formats.in.CellSensReader
 
PIXEL_DATA - Static variable in class loci.formats.in.DicomReader
 
PIXEL_INFO_TYPE - Static variable in class loci.formats.in.CellSensReader
 
PIXEL_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
 
PIXEL_OFFSET - Static variable in class loci.formats.in.VGSAMReader
 
PIXEL_REPRESENTATION - Static variable in class loci.formats.in.DicomReader
 
PIXEL_SIGN - Static variable in class loci.formats.in.DicomReader
 
PIXEL_SPACING - Static variable in class loci.formats.in.DicomReader
 
PIXEL_X_DIMENSION - Static variable in class loci.formats.tiff.IFD
 
PIXEL_Y_DIMENSION - Static variable in class loci.formats.tiff.IFD
 
pixelAspectRatio - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
pixelBits - Variable in class loci.formats.gui.SignedColorModel
 
PixelBlock() - Constructor for class loci.formats.in.OIRReader.PixelBlock
 
pixelBlocks - Variable in class loci.formats.in.OIRReader
 
pixelBytes - Variable in class loci.formats.in.NativeQTReader

Total number of bytes of pixel data.

pixelData - Variable in class loci.formats.in.MINCReader
 
pixelFile - Variable in class loci.formats.in.AnalyzeReader

File containing the pixel data.

pixelFile - Variable in class loci.formats.in.NiftiReader

File containing the pixel data.

pixelLengths - Variable in class loci.formats.in.SlidebookReader
 
pixelOffset - Variable in class loci.formats.in.AIMReader
 
pixelOffset - Variable in class loci.formats.in.AnalyzeReader

Offset to the pixel data in the .img file.

pixelOffset - Variable in class loci.formats.in.FitsReader
 
pixelOffset - Variable in class loci.formats.in.GatanReader

Offset to pixel data.

pixelOffset - Variable in class loci.formats.in.HISReader

Offsets to pixel data for each series.

pixelOffset - Variable in class loci.formats.in.JEOLReader
 
pixelOffset - Variable in class loci.formats.in.KodakReader
 
pixelOffset - Variable in class loci.formats.in.MolecularImagingReader
 
pixelOffset - Variable in class loci.formats.in.NativeQTReader

Offset to start of pixel data.

pixelOffset - Variable in class loci.formats.in.NiftiReader

Offset to the pixel data in the .img file.

pixelOffset - Variable in class loci.formats.in.RHKReader
 
pixelOffset - Variable in class loci.formats.in.SIFReader
 
pixelOffset - Variable in class loci.formats.in.TopometrixReader
 
pixelOffset - Variable in class loci.formats.in.VolocityClippingReader
 
pixelOffset - Variable in class loci.formats.out.ICSWriter
 
pixelOffset - Variable in class loci.formats.out.V3DrawWriter
 
pixelOffsets - Variable in class loci.formats.in.JPXReader
 
pixelOffsets - Variable in class loci.formats.in.SlidebookReader
 
pixelOffsets - Variable in class loci.formats.in.VarianFDFReader
 
pixelOffsets - Variable in class loci.formats.in.VisitechReader
 
pixelPtr - Variable in class loci.formats.codec.RPZACodec
 
pixels - Variable in class loci.formats.in.AFIReader
 
pixels - Variable in class loci.formats.in.GIFReader
 
pixels - Variable in class loci.formats.in.ImagicReader
 
pixels - Variable in class loci.formats.in.LeicaSCNReader.Image
 
Pixels(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Pixels
 
pixels - Variable in class loci.formats.in.ZeissCZIReader
 
pixels - Variable in class loci.formats.out.ICSWriter
 
pixels - Variable in class loci.formats.out.V3DrawWriter
 
pixels2 - Variable in class loci.formats.out.LegacyQTWriter
 
PIXELS_MARKER - Static variable in class loci.formats.in.VisitechReader
 
PIXELS_OFFSET - Static variable in class loci.formats.in.ARFReader
 
PIXELS_OFFSET - Static variable in class loci.formats.in.LIMReader
 
PIXELS_STRING - Static variable in class loci.formats.in.KodakReader
 
PIXELS_SUFFIXES - Static variable in class loci.formats.in.InCellReader
 
PIXELS_TAG - Static variable in class loci.formats.in.ImaconReader
 
pixelsDone - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
pixelsFile - Variable in class loci.formats.in.FujiReader
 
pixelsFile - Variable in class loci.formats.in.ImagicReader
 
pixelsFile - Variable in class loci.formats.in.PDSReader
 
PixelsFile() - Constructor for class loci.formats.in.PerkinElmerReader.PixelsFile
 
pixelsFilename - Variable in class loci.formats.in.AnalyzeReader
 
pixelsFilename - Variable in class loci.formats.in.NiftiReader
 
pixelsFiles - Variable in class loci.formats.in.BrukerReader
 
pixelsFiles - Variable in class loci.formats.in.TillVisionReader
 
pixelsFiles - Variable in class loci.formats.in.VolocityReader.Stack
 
pixelSize - Variable in class loci.formats.in.FV1000Reader
 
pixelSize - Variable in class loci.formats.in.IPLabReader
 
pixelSize - Variable in class loci.formats.in.MicromanagerReader.Position
 
pixelSize - Variable in class loci.formats.in.ScanrReader
 
pixelSize - Variable in class loci.formats.in.SVSReader
 
pixelSize - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
pixelSizes - Variable in class loci.formats.in.GatanReader

List of pixel sizes.

pixelSizes - Variable in class loci.formats.in.NRRDReader
 
pixelSizeT - Variable in class loci.formats.in.FV1000Reader
 
pixelSizeT - Variable in class loci.formats.in.ImprovisionTiffReader
 
pixelSizeUnits - Variable in class loci.formats.in.GatanDM2Reader
 
pixelSizeX - Variable in class loci.formats.in.DicomReader
 
pixelSizeX - Variable in class loci.formats.in.FV1000Reader
 
pixelSizeX - Variable in class loci.formats.in.GatanDM2Reader
 
pixelSizeX - Variable in class loci.formats.in.ImarisHDFReader
 
pixelSizeX - Variable in class loci.formats.in.ImprovisionTiffReader
 
pixelSizeX - Variable in class loci.formats.in.MetamorphHandler
 
pixelSizeX - Variable in class loci.formats.in.ND2Handler
 
pixelSizeX - Variable in class loci.formats.in.PerkinElmerReader
 
pixelSizeX - Variable in class loci.formats.in.VarianFDFReader
 
pixelSizeX - Variable in class loci.formats.in.ZeissLSMReader
 
pixelSizeY - Variable in class loci.formats.in.DicomReader
 
pixelSizeY - Variable in class loci.formats.in.FV1000Reader
 
pixelSizeY - Variable in class loci.formats.in.GatanDM2Reader
 
pixelSizeY - Variable in class loci.formats.in.ImarisHDFReader
 
pixelSizeY - Variable in class loci.formats.in.ImprovisionTiffReader
 
pixelSizeY - Variable in class loci.formats.in.MetamorphHandler
 
pixelSizeY - Variable in class loci.formats.in.ND2Handler
 
pixelSizeY - Variable in class loci.formats.in.PerkinElmerReader
 
pixelSizeY - Variable in class loci.formats.in.VarianFDFReader
 
pixelSizeY - Variable in class loci.formats.in.ZeissLSMReader
 
pixelSizeZ - Variable in class loci.formats.in.DicomReader
 
pixelSizeZ - Variable in class loci.formats.in.FV1000Reader
 
pixelSizeZ - Variable in class loci.formats.in.ImarisHDFReader
 
pixelSizeZ - Variable in class loci.formats.in.ImprovisionTiffReader
 
pixelSizeZ - Variable in class loci.formats.in.ND2Handler
 
pixelSizeZ - Variable in class loci.formats.in.VarianFDFReader
 
pixelSizeZ - Variable in class loci.formats.in.ZeissLSMReader
 
pixelsOffset - Variable in class loci.formats.in.BioRadSCNReader
 
pixelsOffset - Variable in class loci.formats.in.BurleighReader
 
pixelsOffset - Variable in class loci.formats.in.InCell3000Reader
 
pixelsOffset - Variable in class loci.formats.in.JPEG2000Reader
 
pixelsOffset - Variable in class loci.formats.in.QuesantReader
 
pixelsOffsets - Variable in class loci.formats.in.ImspectorReader

List of offsets to each block of pixel data.

pixelsPerPlane - Variable in class loci.formats.in.AmiraReader.ASCII
 
pixelsRead - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
pixelsStream - Variable in class loci.formats.in.TillVisionReader
 
pixelStack - Variable in class loci.formats.in.GIFReader
 
pixelsToRead - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
pixelType - Variable in class loci.formats.CoreMetadata

Describes the number of bytes per pixel.

pixelType - Variable in class loci.formats.in.AmiraReader.ASCII
 
pixelType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
pixelType - Variable in class loci.formats.services.WlzServiceImpl
 
pixelTypeFromBytes(int, boolean, boolean) - Static method in class loci.formats.FormatTools

Returns an appropriate pixel type given the number of bytes per pixel.

pixelTypeFromString(String) - Static method in class loci.formats.FormatTools

Takes a string value and maps it to one of the pixel type enumerations.

pixelTypeIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
pixelTypes - Static variable in class loci.formats.FormatTools

Human readable pixel type.

pixelUIDs - Variable in class loci.formats.in.OIRReader
 
PixelXDimension() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.PixelXDimension
 
PixelYDimension() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.PixelYDimension
 
pixTime - Variable in class loci.formats.in.SDTInfo
 
pkdPktHeaders - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

The packed packet headers if the PPM or PPT markers are used

pktDec - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Reference to the PktDecoder instance

PktDecoder - Class in jj2000.j2k.codestream.reader

This class is used to read packet's head and body.

PktDecoder(DecoderSpecs, HeaderDecoder, RandomAccessIO, BitstreamReaderAgent, boolean, int) - Constructor for class jj2000.j2k.codestream.reader.PktDecoder

Creates an empty PktDecoder object associated with given decoder
 specifications and HeaderDecoder.

pktEnc - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Packet encoder.

PktEncoder - Class in jj2000.j2k.codestream.writer

This class builds packets and keeps the state information of packet
 interdependencies.

PktEncoder(CodedCBlkDataSrcEnc, J2KImageWriteParamJava, Point[][][]) - Constructor for class jj2000.j2k.codestream.writer.PktEncoder

Creates a new packet header encoder, using the information from the
 'infoSrc' object.

PktHeaderBitReader - Class in jj2000.j2k.codestream.reader

This class provides a bit based reading facility from a byte based one,
 applying the bit unstuffing procedure as required by the packet headers.

PktHeaderBitReader(RandomAccessIO) - Constructor for class jj2000.j2k.codestream.reader.PktHeaderBitReader

Instantiates a 'PktHeaderBitReader' that gets the byte data from the
 given source.

PktHeaderBitReader(ByteArrayInputStream) - Constructor for class jj2000.j2k.codestream.reader.PktHeaderBitReader

Instantiates a 'PktHeaderBitReader' that gets the byte data from the
 given source.

pktHL - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Length of each packet head found in the tile

pktIdx - Variable in class jj2000.j2k.codestream.reader.CBlkInfo

Index of the packet where each layer has been found

pktIdx - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Index of the current packet in the tile.

PktInfo - Class in jj2000.j2k.codestream.reader

This class defines an object used to countain informations about a packet
 to which the current code-block belongs.

PktInfo(int, int) - Constructor for class jj2000.j2k.codestream.reader.PktInfo

Classe's constructor.

placeWindow(Window) - Static method in class loci.plugins.util.WindowTools

Places the given window at a nice location on screen, either centered
 below the ImageJ window if there is one, or else centered on screen.

planar - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

true if the image is encoded using separate planes.

PLANAR_CONFIGURATION - Static variable in class loci.formats.in.DicomReader
 
PLANAR_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
 
PLANAR_CONFIGURATION_CHUNKY - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PlanarConfiguration" tag.

PLANAR_CONFIGURATION_PLANAR - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "PlanarConfiguration" tag.

planarCache - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
PlanarConfiguration() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.PlanarConfiguration
 
planarConfiguration - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
plane - Variable in class loci.formats.in.CanonRawReader
 
Plane() - Constructor for class loci.formats.in.ColumbusReader.Plane
 
Plane() - Constructor for class loci.formats.in.OperettaReader.Plane
 
plane - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
 
Plane(String, ZeissTIFFHandler.TagSet) - Constructor for class loci.formats.in.ZeissTIFFHandler.Plane

Constructor

Plane() - Constructor for class loci.formats.in.ZeissTIFFReader.Plane
 
PLANE_ORIGIN_RWC - Static variable in class loci.formats.in.CellSensReader
 
PLANE_SCALE_RWC - Static variable in class loci.formats.in.CellSensReader
 
PLANE_UNIT - Static variable in class loci.formats.in.CellSensReader
 
planeCount() - Method in class loci.formats.out.OMETiffWriter
 
PlaneData() - Constructor for class loci.formats.in.FV1000Reader.PlaneData
 
planeDeltaT - Variable in class loci.formats.in.FlexReader
 
planeExposureTime - Variable in class loci.formats.in.FlexReader
 
planeIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
planeIndexes - Variable in class loci.plugins.util.BFVirtualStack
 
PlaneInfo() - Constructor for class loci.formats.in.OpenlabReader.PlaneInfo
 
planeMax - Variable in class loci.formats.MinMaxCalculator

Max values for each plane.

planeMin - Variable in class loci.formats.MinMaxCalculator

Min values for each plane.

planeName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
planeNames - Variable in class loci.formats.in.ZeissTIFFHandler
 
planeOffset - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
planeOffset - Variable in class loci.formats.in.SlidebookReader
 
planeOffset - Variable in class loci.formats.out.EPSWriter
 
planeOffsets - Variable in class loci.formats.in.OpenlabReader
 
planePadding - Variable in class loci.formats.in.VolocityReader.Stack
 
planePositionX - Variable in class loci.formats.in.FlexReader
 
planePositionY - Variable in class loci.formats.in.FlexReader
 
planePositionZ - Variable in class loci.formats.in.FlexReader
 
planeReader - Variable in class loci.formats.in.AmiraReader
 
planes - Variable in class loci.formats.in.ColumbusReader
 
planes - Variable in class loci.formats.in.FV1000Reader
 
planes - Variable in class loci.formats.in.OpenlabReader
 
planes - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
planes - Variable in class loci.formats.in.OperettaReader
 
planes - Variable in class loci.formats.in.ZeissCZIReader
 
planes - Variable in class loci.formats.in.ZeissTIFFHandler
 
planes - Variable in class loci.formats.in.ZeissTIFFReader

Image planes

planeSize - Variable in class loci.formats.in.AmiraReader.HxRLE
 
planeSize - Variable in class loci.formats.in.AmiraReader.HxZip
 
planesPerBlock - Variable in class loci.formats.in.ImspectorReader

Number of planes in each block of pixel data.

planesWritten - Variable in class loci.formats.out.AVIWriter
 
PLATE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
plate - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
plate - Variable in class loci.formats.in.MIASReader.AnalysisFile
 
PLATE - Static variable in class loci.formats.ResourceNamer
 
plateAcqStartTime - Variable in class loci.formats.in.FlexReader
 
plateBarcode - Variable in class loci.formats.in.FlexReader
 
plateCols - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
plateColumns - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
plateCount - Variable in class loci.formats.in.FlexReader
 
plateDescription - Variable in class loci.formats.in.BDReader
 
plateDescription - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
plateID - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
plateLogFile - Variable in class loci.formats.in.CellWorxReader
 
plateMap - Variable in class loci.formats.in.InCellReader
 
plateMaps - Variable in class loci.formats.in.ScreenReader
 
plateMetadataFiles - Variable in class loci.formats.in.ScreenReader
 
plateName - Variable in class loci.formats.in.BDReader
 
plateName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
plateName - Variable in class loci.formats.in.FlexReader
 
plateName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
plateName - Variable in class loci.formats.in.ScanrReader
 
plateRows - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
plateRows - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
plateType - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
PLM - Static variable in interface jj2000.j2k.codestream.Markers

Packet length, main header (PLM): 0xFF57

PLM_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for PLM marker segment found

PLT - Static variable in interface jj2000.j2k.codestream.Markers

Packet length, tile-part header (PLT): 0xFF58

PLT_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for PLT marker segment found

plugin - Variable in class loci.plugins.in.Importer

A handle to the plugin wrapper, for toggling
 the canceled and success flags.

plugin - Variable in class loci.plugins.out.Exporter
 
plugins - Static variable in class loci.plugins.shortcut.ShortcutPanel

Details for installed plugins.

PN - Static variable in class loci.formats.in.DicomReader
 
PNG - Static variable in class loci.formats.in.CellSensReader
 
PNG_SIG - Static variable in class loci.formats.out.APNGWriter
 
PNGBlock() - Constructor for class loci.formats.in.APNGReader.PNGBlock
 
PNGInputStream(String) - Constructor for class loci.formats.in.APNGReader.PNGInputStream
 
PNGInputStream(String, int) - Constructor for class loci.formats.in.APNGReader.PNGInputStream
 
PNMImageReader - Class in com.sun.media.imageioimpl.plugins.pnm

This class is the Java Image IO plugin reader for PNM images.

PNMImageReader(ImageReaderSpi) - Constructor for class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

Constructs PNMImageReader from the provided
  ImageReaderSpi.

PNMImageReaderSpi - Class in com.sun.media.imageioimpl.plugins.pnm
 
PNMImageReaderSpi() - Constructor for class com.sun.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
PNMImageWriteParam - Class in com.sun.media.imageio.plugins.pnm

A subclass of ImageWriteParam for writing images in
 the PNM format.

PNMImageWriteParam() - Constructor for class com.sun.media.imageio.plugins.pnm.PNMImageWriteParam

Constructs a PNMImageWriteParam object with default values
 for parameters.

PNMImageWriter - Class in com.sun.media.imageioimpl.plugins.pnm

The Java Image IO plugin writer for encoding a binary RenderedImage into
 a PNM format.

PNMImageWriter(ImageWriterSpi) - Constructor for class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter

Constructs PNMImageWriter based on the provided
  ImageWriterSpi.

PNMImageWriterSpi - Class in com.sun.media.imageioimpl.plugins.pnm
 
PNMImageWriterSpi() - Constructor for class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
PNMMetadata - Class in com.sun.media.imageioimpl.plugins.pnm

Metadata for the PNM plug-in.

PNMMetadata() - Constructor for class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata

Constructor containing code shared by other constructors.

PNMMetadata(IIOMetadata) - Constructor for class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
PNMMetadata(ImageTypeSpecifier, ImageWriteParam) - Constructor for class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata

Constructs a default image PNMMetadata object appropriate
 for the given image type and write parameters.

PNMMetadataFormat - Class in com.sun.media.imageioimpl.plugins.pnm
 
PNMMetadataFormat() - Constructor for class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormat

Constructs PNMMetadataFormat.

PNMMetadataFormatResources - Class in com.sun.media.imageioimpl.plugins.pnm
 
PNMMetadataFormatResources() - Constructor for class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormatResources
 
poc - Variable in class jj2000.j2k.codestream.HeaderInfo

Reference to the POC marker segments found in main and first tile-part
 header.

POC() - Constructor for class jj2000.j2k.codestream.HeaderInfo.POC
 
POC - Static variable in interface jj2000.j2k.codestream.Markers
 
POC_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for POC marker segment found

poi - Variable in class loci.formats.in.FV1000Reader
 
poi - Variable in class loci.formats.in.IPWReader

Helper reader - parses embedded files from the OLE document.

poi - Variable in class loci.formats.in.PCIReader
 
poi - Variable in class loci.formats.in.ZeissZVIReader
 
POINT - Static variable in class loci.formats.in.FV1000Reader

ROI types.

pointCount - Variable in class loci.formats.in.BaseZeissReader.Shape
 
points - Variable in enum loci.formats.in.BaseZeissReader.FeatureType
 
points - Variable in class loci.formats.in.BaseZeissReader.Shape
 
points - Variable in class loci.formats.in.FakeReader
 
points - Variable in class loci.formats.in.IMODReader
 
points - Variable in class loci.formats.in.LiFlimReader.ROI
 
pointsToString() - Method in class loci.formats.in.LiFlimReader.ROI
 
PointStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.PointStyle
 
pointStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
 
POIService - Interface in loci.formats.services

Interface defining methods for reading Microsoft OLE2 documents using
 OME's fork of Apache POI.

POIServiceImpl - Class in loci.formats.services
 
POIServiceImpl() - Constructor for class loci.formats.services.POIServiceImpl

Default constructor.

polarityF - Variable in class loci.formats.in.SDTInfo
 
polarityL - Variable in class loci.formats.in.SDTInfo

2 = disabled line markers.

polarityP - Variable in class loci.formats.in.SDTInfo
 
POLARIZATION - Static variable in class loci.formats.FormatTools

Identifies the Polarization dimensional type,
 representing a dimension consisting of polarization states.

POLYGON - Static variable in class loci.formats.in.FV1000Reader
 
POLYGON - Static variable in class loci.formats.in.LeicaHandler.ROI
 
POLYGON - Static variable in class loci.formats.in.LIFReader.ROI
 
polygons - Variable in class loci.formats.in.FakeReader
 
POLYLINE - Static variable in class loci.formats.in.FV1000Reader
 
POLYLINE_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
 
polylines - Variable in class loci.formats.in.FakeReader
 
poolName - Variable in class jj2000.j2k.util.ThreadPool

The name of the pool

poolPriority - Variable in class jj2000.j2k.util.ThreadPool

The priority for the pool

populateCircles(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
 
populateCore - Variable in class loci.formats.in.FlexReader.FlexHandler
 
populateCoreMetadata(int, int, int, List<String>) - Method in class loci.formats.in.FlexReader

Populate core metadata using the given list of image names.

populateCoreMetadata() - Method in class loci.formats.in.PrairieReader

This step populates the CoreMetadata by extracting relevant values
 from the parsed PrairieReader.meta structure.

populateCoreMetadata(int, int, int, int, int) - Method in class loci.formats.in.TextReader

Populates the CoreMetadata values.

populateExtendedMetadata() - Method in class loci.formats.in.NiftiReader
 
populateGlobalMetaData() - Method in class loci.formats.in.SPEReader

This function is used to populate values not contained in Core Meta Data to the Global Meta Data

populateImage(OMEXMLMetadata, int) - Method in class loci.formats.out.OMETiffWriter
 
populateLines(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
 
populateMaskPixels(int, int, int, MetadataStore) - Method in class loci.formats.in.MIASReader

Populate the MaskPixels.BinData attribute for the Mask identified by the
 given Image index, ROI index, and Shape index.

populateMetadata() - Method in class loci.formats.in.MicromanagerReader
 
populateMetadata(MetadataStore, int, String, CoreMetadata) - Static method in class loci.formats.MetadataTools

Populates the given MetadataStore, for the specified series, using
 the values from the provided CoreMetadata.

populateMetadata(MetadataStore, int, String, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools

Populates the given MetadataStore, for the specified series, using
 the provided values.

populateMetadata(MetadataStore, String, int, String, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools

Populates the given MetadataStore, for the specified series, using
 the provided values.

populateMetadataStore(MetadataStore) - Method in class loci.formats.in.FlexReader
 
populateMetadataStore(MetadataStore, String) - Method in class loci.formats.in.FV1000Reader
 
populateMetadataStore(String[]) - Method in class loci.formats.in.MicromanagerReader
 
populateMetadataStore(ND2Handler) - Method in class loci.formats.in.NativeND2Reader
 
populateMetadataStore() - Method in class loci.formats.in.TillVisionReader
 
populateMetadataStore(ZeissLSMReader.SubBlock, MetadataStore, int) - Method in class loci.formats.in.ZeissLSMReader
 
populateMetadataStoreImageJ(MetadataStore) - Method in class loci.formats.in.TiffReader

Checks the original metadata table for ImageJ-specific information
 to propagate into the metadata store.

populateObjective(MetadataStore, int) - Method in class loci.formats.in.DeltavisionReader

Populate an Objective based upon the lens ID.

populateOMEMetadata(IniTable, MetadataStore) - Method in class loci.formats.in.HitachiReader
 
populateOMEMetadata() - Method in class loci.formats.in.PrairieReader

This step populates the OME MetadataStore by extracting relevant
 values from the parsed PrairieReader.meta structure.

populateOriginalMetadata(Element, Deque<String>) - Method in class loci.formats.in.LIFReader
 
populateOriginalMetadata() - Method in class loci.formats.in.PrairieReader

This steps populates the original metadata table (the tables returned by
 FormatReader.getGlobalMetadata() and FormatReader.getSeriesMetadata()).

populateOriginalMetadata(Element, Deque<String>) - Method in class loci.formats.in.ZeissCZIReader
 
populateOriginalMetadata(OMEXMLMetadata, Hashtable<String, Object>) - Method in interface loci.formats.services.OMEXMLService

Adds the key/value pairs in the specified Hashtable as new
 OriginalMetadata annotations in the given OME-XML metadata object.

populateOriginalMetadata(OMEXMLMetadata, String, String) - Method in interface loci.formats.services.OMEXMLService

Adds the specified key/value pair as a new OriginalMetadata node
 to the given OME-XML metadata object.

populateOriginalMetadata(OMEXMLMetadata, Hashtable<String, Object>) - Method in class loci.formats.services.OMEXMLServiceImpl
 
populateOriginalMetadata(OMEXMLMetadata, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
 
populatePixels(MetadataStore, IFormatReader) - Static method in class loci.formats.MetadataTools

Populates the Pixels element of the given metadata store, using core
 metadata from the given reader.

populatePixels(MetadataStore, IFormatReader, boolean) - Static method in class loci.formats.MetadataTools

Populates the Pixels element of the given metadata store, using core
 metadata from the given reader.

populatePixels(MetadataStore, IFormatReader, boolean, boolean) - Static method in class loci.formats.MetadataTools

Populates the Pixels element of the given metadata store, using core
 metadata from the given reader.

populatePixelsOnly(MetadataStore, IFormatReader) - Static method in class loci.formats.MetadataTools
 
populatePixelsOnly(MetadataStore, int, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
 
populatePixelType(int) - Method in class loci.formats.in.NiftiReader
 
populatePolylines(NodeList, int, int, boolean) - Method in class loci.formats.in.ZeissCZIReader
 
populateRectangles(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
 
populateROI(List<String>, String[], int, int, int, int, MetadataStore) - Method in class loci.formats.in.MIASReader
 
populateRoiMetaData(MetadataStore) - Method in class loci.formats.in.SPEReader

Reads and populates ROI Meta Data values.

populateROIs(MetadataStore) - Method in class loci.formats.in.ND2Handler
 
populateSPW(MetadataStore, int, int, int, int, int, int, boolean) - Method in class loci.formats.in.FakeReader
 
populateTiffData(OMEXMLMetadata, int[], int, int, int) - Method in class loci.formats.out.OMETiffWriter
 
populateXY - Variable in class loci.formats.in.ND2Handler
 
pos - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
 
pos - Variable in class jj2000.j2k.decoder.DecoderSpecs

Progression order specifications

pos - Variable in class jj2000.j2k.entropy.decoder.ByteInputBuffer

The index of the next character to read from the input stream buffer

pos - Variable in class jj2000.j2k.io.BufferedRandomAccessFile

The current position in the byte-buffer

pos - Variable in class jj2000.j2k.util.ISRandomAccessIO
 
pos(int) - Method in class loci.formats.cache.CacheStrategy

Shortcut for converting rasterized position to N-D position.

pos(int, int[]) - Method in class loci.formats.cache.CacheStrategy

Shortcut for converting rasterized position to N-D position,
 using the given array instead of allocating a new one.

pos - Variable in class loci.formats.in.AVIReader
 
POS_COMP_RES_LY_PROG - Static variable in interface jj2000.j2k.codestream.ProgressionType

The bit stream is Position/Component/Resolution/Layer progressive : 3

position - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

The position of the first sample of this image in the stream.

position - Variable in class loci.formats.in.MicromanagerReader.Index
 
Position() - Constructor for class loci.formats.in.MicromanagerReader.Position
 
position - Variable in class loci.formats.in.NativeND2Reader.ChunkMapEntry
 
position - Variable in class loci.formats.in.OBFReader.Stack
 
POSITION_CHANGED - Static variable in class loci.formats.cache.CacheEvent

Event type indicating an updated current dimensional position.

positionCount - Variable in class loci.formats.in.NativeND2Reader
 
positions - Variable in class jj2000.j2k.util.CodestreamManipulator

The positions of the SOT, SOP and EPH markers

positions - Variable in class loci.formats.cache.CacheStrategy

The list of dimensional positions to consider caching, in order of
 preference based on strategy, axis priority and planar ordering.

positions - Variable in class loci.formats.in.MicromanagerReader.Position
 
positions - Variable in class loci.formats.in.MicromanagerReader
 
positions - Variable in class loci.formats.in.ZeissCZIReader
 
positionsMatch(int, int) - Method in class loci.formats.in.PrairieReader

Verifies that stage coordinates match for all (P, Z) across time.

positionsX - Variable in class loci.formats.in.ZeissCZIReader
 
positionsY - Variable in class loci.formats.in.ZeissCZIReader
 
positionsZ - Variable in class loci.formats.in.ZeissCZIReader
 
positionToRaster(int[], int[]) - Static method in class loci.formats.FormatTools

Computes a unique 1-D index corresponding
 to the given multidimensional position.

positionX - Variable in class loci.formats.in.ColumbusReader.Plane
 
positionX - Variable in class loci.formats.in.DicomReader
 
positionX - Variable in class loci.formats.in.FV1000Reader.PlaneData
 
positionX - Variable in class loci.formats.in.MetamorphHandler
 
positionX - Variable in class loci.formats.in.OperettaReader.Plane
 
positionY - Variable in class loci.formats.in.ColumbusReader.Plane
 
positionY - Variable in class loci.formats.in.DicomReader
 
positionY - Variable in class loci.formats.in.FV1000Reader.PlaneData
 
positionY - Variable in class loci.formats.in.MetamorphHandler
 
positionY - Variable in class loci.formats.in.OperettaReader.Plane
 
positionZ - Variable in class loci.formats.in.ColumbusReader.Plane
 
positionZ - Variable in class loci.formats.in.DicomReader
 
positionZ - Variable in class loci.formats.in.FV1000Reader.PlaneData
 
positionZ - Variable in class loci.formats.in.OperettaReader.Plane
 
posNames - Variable in class loci.formats.in.ND2Handler
 
possibleValues - Variable in class loci.plugins.prefs.StringOption

List of possible values.

post - Variable in class loci.formats.NumberFilter

String appearing after the numerical block.

PostCompRateAllocator - Class in jj2000.j2k.entropy.encoder

This is the abstract class from which post-compression rate allocators
 which generate layers should inherit.

PostCompRateAllocator(CodedCBlkDataSrcEnc, int, CodestreamWriter, J2KImageWriteParamJava) - Constructor for class jj2000.j2k.entropy.encoder.PostCompRateAllocator

Initializes the source of entropy coded data.

posX - Variable in class loci.formats.in.GatanReader
 
posX - Variable in class loci.formats.in.InCellReader
 
posX - Variable in class loci.formats.in.LIFReader
 
posX - Variable in class loci.formats.in.NativeND2Reader
 
posX - Variable in class loci.formats.in.ND2Handler
 
posY - Variable in class loci.formats.in.GatanReader
 
posY - Variable in class loci.formats.in.InCellReader
 
posY - Variable in class loci.formats.in.LIFReader
 
posY - Variable in class loci.formats.in.NativeND2Reader
 
posY - Variable in class loci.formats.in.ND2Handler
 
posZ - Variable in class loci.formats.in.GatanReader
 
posZ - Variable in class loci.formats.in.LIFReader
 
posZ - Variable in class loci.formats.in.NativeND2Reader
 
posZ - Variable in class loci.formats.in.ND2Handler
 
PovrayReader - Class in loci.formats.in

PovrayReader is the file format reader for POV-Ray .df3 files.

PovrayReader() - Constructor for class loci.formats.in.PovrayReader

Constructs a new POV-Ray reader.

power - Variable in class loci.formats.in.ND2Handler
 
power - Variable in class loci.formats.in.OIRReader.Laser
 
power - Variable in class loci.formats.in.ZeissLSMReader.Laser
 
power1 - Static variable in class com.sun.media.imageioimpl.common.InvertedCMYKColorSpace

The exponent for gamma correction.

power1 - Static variable in class com.sun.media.imageioimpl.common.SimpleCMYKColorSpace

The exponent for gamma correction.

pph - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Flag indicating whether packed packet header was used for this tile

pphbais - Variable in class jj2000.j2k.codestream.reader.PktDecoder

The packed packet header if it was used

pphs - Variable in class jj2000.j2k.decoder.DecoderSpecs

Packed packet header specifications

ppinfo - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Array containing the coordinates, width, height, indexes, ...

ppinfo - Variable in class jj2000.j2k.codestream.writer.PktEncoder

Array containing the coordinates, width, height, indexes, ...

PPM - Static variable in interface jj2000.j2k.codestream.Markers

Packed packet headers, main header (PPM): 0xFF60

PPM_ASCII - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
PPM_ASCII - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
PPM_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for SOD marker segment found

PPM_RAW - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
PPM_RAW - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
pPMMarkerData - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Array containing the Nppm and Ippm fields of the PPM marker segments

ppmUsed - Variable in class jj2000.j2k.util.CodestreamManipulator

Flag indicating whether packed packet headers in main header is used

ppoc - Variable in class jj2000.j2k.codestream.HeaderInfo.POC
 
PPT - Static variable in interface jj2000.j2k.codestream.Markers

Packed packet headers, tile-part header (PPT): 0xFF61

ppt - Variable in class jj2000.j2k.util.CodestreamManipulator

The number of packets per tile

PPT_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for SOD marker segment found

pptp - Variable in class jj2000.j2k.util.CodestreamManipulator

The number of packets per tile-part

pptUsed - Variable in class jj2000.j2k.util.CodestreamManipulator

Flag indicating whether packed packet headers in tile headers is used

PQBinReader - Class in loci.formats.in

PQBinReader is the file format reader for PicoQuant .bin files.

PQBinReader() - Constructor for class loci.formats.in.PQBinReader

Constructs a new PQBin reader.

PRAIRIE_SUFFIXES - Static variable in class loci.formats.in.PrairieReader
 
PRAIRIE_TAG_1 - Static variable in class loci.formats.in.PrairieReader
 
PRAIRIE_TAG_2 - Static variable in class loci.formats.in.PrairieReader
 
PRAIRIE_TAG_3 - Static variable in class loci.formats.in.PrairieReader
 
PrairieMetadata - Class in loci.formats.in

Metadata structure for Prairie Technologies' TIFF-based format.

PrairieMetadata(Document, Document, Document) - Constructor for class loci.formats.in.PrairieMetadata

Creates a new Prairie metadata by parsing the given XML, CFG and/or ENV
 documents.

PrairieMetadata.Frame - Class in loci.formats.in

A Prairie <Frame>, beneath a <Sequence>.

PrairieMetadata.PFile - Class in loci.formats.in

A Prairie <File> beneath a <Frame>.

PrairieMetadata.Sequence - Class in loci.formats.in

A Prairie <Sequence>.

PrairieMetadata.Value - Interface in loci.formats.in

A value in a Prairie metadata dictionary.

PrairieMetadata.ValueItem - Class in loci.formats.in

A leaf value with an actual PrairieMetadata.ValueItem.value() as well as an optional
 PrairieMetadata.ValueItem.description().

PrairieMetadata.ValueTable - Class in loci.formats.in

A table of values.

PrairieReader - Class in loci.formats.in

PrairieReader is the file format reader for
 Prairie Technologies' TIFF variant.

PrairieReader() - Constructor for class loci.formats.in.PrairieReader

Constructs a new Prairie TIFF reader.

pre - Variable in class loci.formats.NumberFilter

String appearing before the numerical block.

PRE_AMP_SETTING - Static variable in class loci.formats.in.FluoviewReader
 
PREAMP_GAIN_VALUE - Static variable in class loci.formats.in.CellSensReader
 
PrecCoordInfo - Class in jj2000.j2k.codestream

This class is used to store the coordinates of precincts.

PrecCoordInfo(int, int, int, int, int, int) - Constructor for class jj2000.j2k.codestream.PrecCoordInfo

Constructor.

PrecCoordInfo() - Constructor for class jj2000.j2k.codestream.PrecCoordInfo

Empty Constructor.

precedence - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
PRECINCT_PARTITION_DEF_SIZE - Static variable in interface jj2000.j2k.codestream.Markers

The default size exponent of the precincts

precinctPartition - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies precinct partition dimensions for tiles/components.

precinctPartition - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

boolean used to signal if the precinct partition is used for
  each component and each tile.

precinctPartitionIsUsed - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Is the precinct partition used

precinctPartitionUsed() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Returns the boolean used to know if the precinct partition is used

precinctPartitionUsed(int, int) - Method in interface jj2000.j2k.entropy.encoder.CodedCBlkDataSrcEnc

Returns true if the precinct partition is used for the
 specified component and tile, returns false otherwise

precinctPartitionUsed(int, int) - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Returns true if precinct partition is used for the specified
 component and tile, returns false otherwise.

PrecinctSizeSpec - Class in jj2000.j2k.entropy

This class extends ModuleSpec class for precinct partition sizes holding
 purposes.

PrecinctSizeSpec(int, int, byte, IntegerSpec) - Constructor for class jj2000.j2k.entropy.PrecinctSizeSpec

Creates a new PrecinctSizeSpec object for the specified number of tiles
 and components.

PrecinctSizeSpec(int, int, byte, BlkImgDataSrc, IntegerSpec, J2KImageWriteParamJava, String) - Constructor for class jj2000.j2k.entropy.PrecinctSizeSpec

Creates a new PrecinctSizeSpec object for the specified number of tiles
 and components and the J2KImageWriteParamJava instance.

PrecInfo - Class in jj2000.j2k.codestream

Class that holds precinct coordinates and references to contained
 code-blocks in each subband.

PrecInfo(int, int, int, int, int, int, int, int, int) - Constructor for class jj2000.j2k.codestream.PrecInfo

Class constructor.

preDefinedColorSpaces - Static variable in class com.sun.media.imageio.stream.RawImageInputStream
 
preDefinedTypes - Static variable in class com.sun.media.imageio.stream.RawImageInputStream
 
PREDICTED_CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
Predictor() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Predictor
 
predictor - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFDeflateDecompressor
 
predictor - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFDeflater
 
predictor - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
predictor - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWCompressor
 
predictor - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
predictor - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
PREDICTOR - Static variable in class loci.formats.tiff.IFD
 
PREDICTOR_HORIZONTAL_DIFFERENCING - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "Predictor" tag.

PREDICTOR_NONE - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "Predictor" tag.

PREF_CZI_ATTACHMENT - Static variable in class loci.plugins.util.LociPrefs
 
PREF_CZI_AUTOSTITCH - Static variable in class loci.plugins.util.LociPrefs
 
PREF_LEICA_LIF_PHYSICAL_SIZE - Static variable in class loci.plugins.util.LociPrefs
 
PREF_ND2_CHUNKMAP - Static variable in class loci.plugins.util.LociPrefs
 
PREF_ND2_NIKON - Static variable in class loci.plugins.util.LociPrefs
 
PREF_PICT_QTJAVA - Static variable in class loci.plugins.util.LociPrefs
 
PREF_QT_QTJAVA - Static variable in class loci.plugins.util.LociPrefs
 
PREF_READER_ENABLED - Static variable in class loci.plugins.util.LociPrefs
 
PREF_READER_WINDOWLESS - Static variable in class loci.plugins.util.LociPrefs
 
PREF_SDT_INTENSITY - Static variable in class loci.plugins.util.LociPrefs
 
PREF_TIFF_IMAGEIO - Static variable in class loci.plugins.util.LociPrefs
 
prefix - Variable in class loci.formats.in.GIFReader
 
prefix - Variable in class loci.formats.in.ND2Handler
 
PREFIX - Static variable in class loci.formats.in.TCSReader
 
prefix - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
prefix_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor

the prefix code which represents the predecessor string to current input point

PREFIX_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
preLoad - Variable in class loci.formats.in.SDTReader

Whether to pre-load all lifetime bins for faster loading.

prepareGZipStream(int) - Method in class loci.formats.in.LiFlimReader
 
prepareInsertEmpty(int, ImageTypeSpecifier, int, int, IIOMetadata, List, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
prepareRead(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
prepareReplacePixels(int, Rectangle) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
prepareToWriteImage(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.TiffWriter

Performs the preparation for work prior to the usage of the TIFF saver.

prepareWriteEmpty(IIOMetadata, ImageTypeSpecifier, int, int, IIOMetadata, List, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
prepareWriteSequence(IIOMetadata) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
prepareWriteSequence(IIOMetadata) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
prepend(ClassList<T>) - Method in class loci.formats.ClassList

Prepends a class list which must be assignable to the base class

prepend(List<Class<? extends T>>) - Method in class loci.formats.ClassList

Prepends a list of classes which must be assignable to the base class

preprocess(RandomAccessInputStream) - Method in class loci.formats.codec.JPEGTileDecoder

Pre-process the stream to make sure that the
 image width and height are non-zero.

PRESCANS - Static variable in class loci.formats.in.FluoviewReader
 
PRESENT - Static variable in class loci.plugins.config.LibraryEntry

HTML markup for installed library.

prestitched - Variable in class loci.formats.in.ZeissCZIReader
 
prevBuf - Variable in class loci.formats.in.ZeissLSMReader
 
prevChangingElems - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
prevChannel - Variable in class loci.formats.in.ZeissLSMReader
 
prevElement - Variable in class loci.formats.in.ND2Handler
 
PREVIEWNAME_PREFIXES - Static variable in class loci.formats.in.FV1000Reader
 
previewNames - Variable in class loci.formats.in.FV1000Reader
 
PreviewPane - Class in loci.formats.gui

PreviewPane is a panel for use as a JFileChooser accessory, displaying
 a thumbnail for the selected image, loaded in a separate thread.

PreviewPane(JFileChooser) - Constructor for class loci.formats.gui.PreviewPane

Constructs a preview pane for the given file chooser.

prevImage - Variable in class loci.formats.in.ICSReader
 
previousChannel - Variable in class loci.formats.in.ZeissCZIReader
 
previousImage - Variable in class loci.formats.codec.CodecOptions

Pixels for preceding image (READ/WRITE).

previousTag - Variable in class loci.formats.in.CellSensReader
 
prevPixels - Variable in class loci.formats.in.NativeQTReader

Pixel data for the previous image plane.

prevPlane - Variable in class loci.formats.in.NativeQTReader

Previous plane number.

prevPlane - Variable in class loci.formats.in.ZeissLSMReader
 
prevRegion - Variable in class loci.formats.in.ZeissLSMReader
 
prevRuntype - Variable in class loci.formats.in.ND2Handler
 
prevtIdxs - Variable in class jj2000.j2k.codestream.writer.PktEncoder

The last encoded truncation point for each code-block.

PRIMARY_CHROMATICITIES - Static variable in class loci.formats.tiff.IFD
 
PrimaryChromaticities() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.PrimaryChromaticities
 
primaryFileGUID - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
print(PrintWriter, int, int, String) - Method in class jj2000.j2k.util.MsgPrinter

Formats the message to print in the current line width, by
 breaking the message into lines between words.

print(int, long, String) - Method in class loci.formats.in.NativeQTReader

Debugging method; prints information on an atom.

printArray(String, int[]) - Static method in class loci.formats.tools.CacheConsole

Helper utility for outputing contents of an int array, used by main.

printIFD() - Method in class loci.formats.tiff.IFD

Prints the contents of this IFD.

printInfo - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Whether or not to print information found in codestream

println(String, int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
println(String, int, int) - Method in interface jj2000.j2k.util.MsgLogger

Prints the string 'str' to the output device, appending a line
 return.

println(String, int, int) - Method in class jj2000.j2k.util.StreamMsgLogger

Prints the string 'str' to the 'out' stream, appending a newline.

printmsg(int, String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
printmsg(int, String) - Method in interface jj2000.j2k.util.MsgLogger

Prints the message 'msg' to the output device, appending a newline,
 with severity 'sev'.

printmsg(int, String) - Method in class jj2000.j2k.util.StreamMsgLogger

Prints the message 'msg' to the output device, appending a newline,
 with severity 'sev'.

printOrder(String, Cache) - Static method in class loci.formats.tools.CacheConsole

Helper utility for outputing cache strategy's order, used by main.

printSizes(Component) - Static method in class loci.plugins.config.SpringUtilities

A debugging utility that prints to stdout the component's
 minimum, preferred, and maximum sizes.

printSource(String, Cache) - Static method in class loci.formats.tools.CacheConsole

Helper utility for outputing cache's associated source, used by main.

printStrategy(String, Cache) - Static method in class loci.formats.tools.CacheConsole

Helper utility for outputing cache's associated strategy, used by main.

priorities - Variable in class loci.formats.cache.CacheStrategy

Priority for caching each axis.

PRIORITIES - Static variable in class loci.formats.gui.CacheComponent
 
PRIORITIES_CHANGED - Static variable in class loci.formats.cache.CacheEvent

Event type indicating new axis priorities.

priority - Variable in class loci.formats.gui.CacheComponent

Combo boxes for choosing axis priority.

PRIORITY_VALUES - Static variable in class loci.formats.gui.CacheComponent
 
priorityIndex(int) - Method in class loci.formats.gui.CacheComponent

Converts enumerated priority value to priority chooser index.

priorityValue(int) - Method in class loci.formats.gui.CacheComponent

Converts priority chooser index to enumerated priority value.

probeLabel - Variable in class loci.formats.gui.ImageViewer
 
proc - Variable in class loci.plugins.util.RecordedImageProcessor
 
process - Variable in class loci.plugins.in.Calibrator
 
process - Variable in class loci.plugins.in.Colorizer
 
process - Variable in class loci.plugins.in.DisplayHandler
 
process - Variable in class loci.plugins.in.ImagePlusReader

Import preparation process managing Bio-Formats readers and other state.

process - Variable in class loci.plugins.in.ImporterDialog
 
process - Variable in class loci.plugins.in.ImporterPrompter
 
processBuffer(int) - Method in class loci.formats.in.SPCReader
 
processElement(String) - Method in class loci.formats.in.FEITiffReader.FEIHandler
 
processImageProgressWrapper(float) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

Wrapper for the protected method processImageProgress
  So it can be access from the classes which are not in
  ImageReader hierarchy.

processImageProgressWrapper(float) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter

Wrapper for the protected method processImageProgress
  So it can be access from the classes which are not in
  ImageWriter hierachy.

processImageProgressWrapper(float) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader

Wrapper for the protected method processImageProgress
  So it can be access from the classes which are not in
  ImageReader hierachy.

processImageUpdateWrapper(BufferedImage, int, int, int, int, int, int, int[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

Wrapper for the protected method processImageUpdate
  So it can be access from the classes which are not in
  ImageReader hierarchy.

processImageUpdateWrapper(BufferedImage, int, int, int, int, int, int, int[]) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader

Wrapper for the protected method processImageUpdate
  So it can be access from the classes which are not in
  ImageReader hierachy.

processOnRegistration(ServiceRegistry, Class, String, ImageReaderWriterSpi, int, int) - Static method in class com.sun.media.imageioimpl.common.ImageUtil
 
producer - Variable in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
profile - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
profile - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader

ICC profile

PROFILE_EMBEDDED - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
PROFILE_LINKED - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
prog - Variable in class jj2000.j2k.entropy.decoder.DecLyrdCBlk

The progressive flag, false by default (see above).

progress - Variable in class loci.formats.gui.DataConverter
 
progress(boolean, int, int) - Static method in class loci.plugins.BF
 
Progression - Class in jj2000.j2k.entropy

This class holds one of the different progression orders defined in
 the bit stream.

Progression(int, int, int, int, int, int) - Constructor for class jj2000.j2k.entropy.Progression

Constructor.

progressionName - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

The specified (tile-component) progression.

ProgressionSpec - Class in jj2000.j2k.entropy

This class extends ModuleSpec class for progression type(s) and progression
 order changes holding purposes.

ProgressionSpec(int, int, byte) - Constructor for class jj2000.j2k.entropy.ProgressionSpec

Creates a new ProgressionSpec object for the specified number of tiles
 and components.

ProgressionSpec(int, int, int, IntegerSpec, byte, J2KImageWriteParamJava, String) - Constructor for class jj2000.j2k.entropy.ProgressionSpec

Creates a new ProgressionSpec object for the specified number of
 tiles, components and the J2KImageWriteParamJava instance.

progressionType - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

See above.

progressionType - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies which type of progression should be used when generating
  the codestream.

ProgressionType - Interface in jj2000.j2k.codestream

This interface defines the identifiers for the different bit stream
 profiles and progression types.

progressive - Variable in class jj2000.j2k.image.DataBlk

The progressive attribute (false by default)

ProgressWatch - Interface in jj2000.j2k.util
 
promptColors() - Method in class loci.plugins.in.ImporterPrompter

Prompts for color details, if necessary.

promptCrop() - Method in class loci.plugins.in.ImporterPrompter

Prompts for cropping details, if necessary.

promptFilePattern() - Method in class loci.plugins.in.ImporterPrompter

Prompts for the file pattern, if necessary.

promptId() - Method in class loci.plugins.in.ImporterPrompter
 
promptLicenseCode(String, boolean) - Static method in class loci.plugins.util.LuraWave

Prompts the user to enter their LuraWave
 license code in an ImageJ dialog window.

promptLocation() - Method in class loci.plugins.in.ImporterPrompter
 
promptMain() - Method in class loci.plugins.in.ImporterPrompter
 
promptMemory() - Method in class loci.plugins.in.ImporterPrompter

Prompts for confirmation of memory usage, if necessary.

promptRange() - Method in class loci.plugins.in.ImporterPrompter

Prompts for the range of planes to import, if necessary.

promptSeries() - Method in class loci.plugins.in.ImporterPrompter

Prompts for which series to import, if necessary.

promptSwap() - Method in class loci.plugins.in.ImporterPrompter

Prompts for dimension swapping parameters, if necessary.

promptUpgrade() - Method in class loci.plugins.in.ImporterPrompter
 
PROP_LUT - Static variable in class loci.plugins.in.ImagePlusReader

Special property prefix for storing planar LUTs.

PROP_SERIES - Static variable in class loci.plugins.in.ImagePlusReader

Special property for storing series number associated with the image.

properties - Variable in class com.sun.media.imageioimpl.common.SimpleRenderedImage

A Hashtable containing the image properties.

PROPERTY_FILE - Static variable in class loci.formats.FormatTools

Deprecated.
The property file is no longer used.


PROPERTY_SET_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
propertyChange(PropertyChangeEvent) - Method in class loci.formats.gui.PreviewPane

Property change event, to listen for when a new
 file is selected, or the file chooser closes.

props - Variable in class loci.formats.in.DynamicMetadataOptions
 
pruneNodes(Node, boolean) - Static method in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor

Removes nonessential nodes from a JPEG native image metadata tree.

PSD_MAGIC_STRING - Static variable in class loci.formats.in.PSDReader
 
PSDReader - Class in loci.formats.in

PSDReader is the file format reader for Photoshop PSD files.

PSDReader() - Constructor for class loci.formats.in.PSDReader

Constructs a new PSD reader.

psot - Variable in class jj2000.j2k.codestream.HeaderInfo.SOT
 
pss - Variable in class jj2000.j2k.decoder.DecoderSpecs

Precinct partition specifications

pss - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The precinct partition specifications

pss - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull

The precinct partition specifications

ptyEnd - Variable in class loci.formats.in.FV1000Reader
 
ptyPattern - Variable in class loci.formats.in.FV1000Reader
 
ptyStart - Variable in class loci.formats.in.FV1000Reader
 
put(String, Object) - Method in class loci.formats.in.BaseTiffReader
 
put(String, int) - Method in class loci.formats.in.BaseTiffReader
 
put(String, boolean) - Method in class loci.formats.in.BaseTiffReader
 
put(String, byte) - Method in class loci.formats.in.BaseTiffReader
 
put(String, char) - Method in class loci.formats.in.BaseTiffReader
 
put(String, double) - Method in class loci.formats.in.BaseTiffReader
 
put(String, float) - Method in class loci.formats.in.BaseTiffReader
 
put(String, long) - Method in class loci.formats.in.BaseTiffReader
 
put(String, short) - Method in class loci.formats.in.BaseTiffReader
 
put(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
 
putColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
 
putIFDValue(int, Object) - Method in class loci.formats.tiff.IFD

Adds a directory entry to this IFD.

putIFDValue(int, short) - Method in class loci.formats.tiff.IFD

Adds a directory entry of type BYTE to this IFD.

putIFDValue(int, int) - Method in class loci.formats.tiff.IFD

Adds a directory entry of type SHORT to this IFD.

putIFDValue(int, long) - Method in class loci.formats.tiff.IFD

Adds a directory entry of type LONG to this IFD.

putInIdleList(ThreadPool.ThreadPoolThread) - Method in class jj2000.j2k.util.ThreadPool

Puts the thread 't' in the idle list.

putInt(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
 
putPixel(int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
putPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
putPixelValue(int, int, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
putRow(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
 
putString(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
 
pw - Variable in class jj2000.j2k.wavelet.synthesis.InvWTFull

Reference to the ProgressWatch instance if any

px - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The horizontal coordinate of the tiling origin in the canvas system, on
 the reference grid.

pxlStride - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

The strides for pixel, band, and scanline.

py - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

The vertical coordinate of the tiling origin in the canvas system, on
 the reference grid.

Pyramid() - Constructor for class loci.formats.in.CellSensReader.Pyramid
 
pyramidHeight - Variable in class loci.formats.in.NDPIReader
 
pyramids - Variable in class loci.formats.in.CellSensReader
 
PyramidTiffReader - Class in loci.formats.in

PyramidTiffReader is the file format reader for pyramid TIFFs.

PyramidTiffReader() - Constructor for class loci.formats.in.PyramidTiffReader

Constructs a new pyramid TIFF reader.

pyramidType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 




Q

Q_TYPE_SCALAR_DZ - Static variable in interface jj2000.j2k.quantization.QuantizationType

The ID of the scalar deadzone dequantizer

qcc - Variable in class jj2000.j2k.codestream.HeaderInfo

Reference to the QCC marker segments found in main and first tile-part
 header.

QCC() - Constructor for class jj2000.j2k.codestream.HeaderInfo.QCC
 
QCC - Static variable in interface jj2000.j2k.codestream.Markers

Quantization component (QCC): 0xFF5D

QCC_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for QCC marker segment found

qcd - Variable in class jj2000.j2k.codestream.HeaderInfo

Reference to the QCD marker segments found in main and first tile-part
 header.

QCD() - Constructor for class jj2000.j2k.codestream.HeaderInfo.QCD
 
QCD - Static variable in interface jj2000.j2k.codestream.Markers

Quantization default (QCD): 0xFF5C

QCD_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for QCD marker segment found

qe - Static variable in class jj2000.j2k.entropy.decoder.MQDecoder

The data structures containing the probabilities for the LPS

qe - Static variable in class jj2000.j2k.entropy.encoder.MQCoder

The data structures containing the probabilities for the LPS

qName - Variable in class loci.formats.in.ImaconReader.ImaconHandler
 
qName - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
QQ - Static variable in class loci.formats.in.DicomReader
 
qsss - Variable in class jj2000.j2k.decoder.DecoderSpecs

Quantization normalized base step size specifications

qsss - Variable in class jj2000.j2k.quantization.dequantizer.StdDequantizer

The quantizer step sizes  spec

qsss - Variable in class jj2000.j2k.quantization.quantizer.StdQuantizer

The quantization step size specifications

QSTEP_EXPONENT_BITS - Static variable in class jj2000.j2k.quantization.quantizer.StdQuantizer

The number of exponent bits for the quantization steps

QSTEP_MANTISSA_BITS - Static variable in class jj2000.j2k.quantization.quantizer.StdQuantizer

The number of mantissa bits for the quantization steps

QSTEP_MAX_EXPONENT - Static variable in class jj2000.j2k.quantization.quantizer.StdQuantizer

The maximum value of the exponent for the quantization steps

QSTEP_MAX_MANTISSA - Static variable in class jj2000.j2k.quantization.quantizer.StdQuantizer

The maximum value of the mantissa for the quantization steps

qtJava - Variable in class loci.formats.gui.DataConverter
 
QTReader - Class in loci.formats.in

QTReader is the file format reader for QuickTime movie files.

QTReader() - Constructor for class loci.formats.in.QTReader

Constructs a new QuickTime reader.

QTRLECodec - Class in loci.formats.codec

Methods for compressing and decompressing data using QuickTime RLE.

QTRLECodec() - Constructor for class loci.formats.codec.QTRLECodec
 
qts - Variable in class jj2000.j2k.decoder.DecoderSpecs

Quantization type specifications

qts - Variable in class jj2000.j2k.quantization.dequantizer.StdDequantizer

The quantizer type spec

qts - Variable in class jj2000.j2k.quantization.quantizer.StdQuantizer

The quantization type specifications

qtTools - Variable in class loci.formats.in.PictReader

Helper reader in case this one fails.

QTWidgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats QuickTime support.

QTWidgets() - Constructor for class loci.plugins.config.QTWidgets
 
QTWriter - Class in loci.formats.out

QTWriter is the file format writer for uncompressed QuickTime movie files.

QTWriter() - Constructor for class loci.formats.out.QTWriter
 
qType - Variable in class jj2000.j2k.codestream.HeaderInfo.QCC
 
qType - Variable in class jj2000.j2k.codestream.HeaderInfo.QCD
 
quality - Variable in class loci.formats.codec.CodecOptions

Compression quality level as it would be provided to:
 ImageWriteParam.compressionQuality (WRITE).

QUALITY - Static variable in class loci.formats.in.NikonReader
 
quality - Variable in class loci.formats.out.LegacyQTWriter

The quality to use.

quality - Variable in class loci.formats.out.QTWriter

The quality to use.

QUALITY_HIGH - Static variable in class loci.formats.out.QTWriter

Value indicating High quality.

QUALITY_LOW - Static variable in class loci.formats.out.QTWriter

Value indicating Low quality.

QUALITY_MAXIMUM - Static variable in class loci.formats.out.QTWriter

Value indicating Maximum quality.

QUALITY_NORMAL - Static variable in class loci.formats.out.QTWriter

Value indicating Normal quality.

quantizationStep - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

This parameter specifies the base normalized quantization step
  size for the tiles/components.

quantizationType - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies which quantization type to use for specified
  tiles/components.

QuantizationType - Interface in jj2000.j2k.quantization

This interface defines the IDs of the possible quantization types.

Quantizer - Class in jj2000.j2k.quantization.quantizer

This abstract class provides the general interface for quantizers.

Quantizer(CBlkWTDataSrc) - Constructor for class jj2000.j2k.quantization.quantizer.Quantizer

Initializes the source of wavelet transform coefficients.

QuantStepSizeSpec - Class in jj2000.j2k.quantization

This class extends ModuleSpec class in order to hold specifications about
 the quantization base normalized step size to use in each tile-component.

QuantStepSizeSpec(int, int, byte) - Constructor for class jj2000.j2k.quantization.QuantStepSizeSpec

Constructs an empty 'QuantStepSizeSpec' with specified number of
 tile and components.

QuantStepSizeSpec(int, int, byte, J2KImageWriteParamJava, String) - Constructor for class jj2000.j2k.quantization.QuantStepSizeSpec

Constructs a new 'QuantStepSizeSpec' for the specified number of
 components and tiles and the arguments of "-Qstep" option.

QuantTypeSpec - Class in jj2000.j2k.quantization

This class extends ModuleSpec class in order to hold specifications about
 the quantization type to use in each tile-component.

QuantTypeSpec(int, int, byte) - Constructor for class jj2000.j2k.quantization.QuantTypeSpec

Constructs an empty 'QuantTypeSpec' with specified number of tile and
 components.

QuantTypeSpec(int, int, byte, J2KImageWriteParamJava, String) - Constructor for class jj2000.j2k.quantization.QuantTypeSpec

Constructs a new 'QuantTypeSpec' for the specified number of components
 and tiles and the arguments of "-Qtype" option.

QuesantReader - Class in loci.formats.in

QuesantReader is the file format reader for Quesant .afm files.

QuesantReader() - Constructor for class loci.formats.in.QuesantReader

Constructs a new Quesant reader.

quit - Variable in class loci.formats.cache.CacheUpdater
 
quit() - Method in class loci.formats.cache.CacheUpdater
 




R

r - Variable in class jj2000.j2k.codestream.PrecInfo

Resolution level index

r - Variable in class jj2000.j2k.roi.encoder.ROI

radius of circular ROI

r - Variable in class loci.formats.gui.LegacyQTTools

Reflection tool for QuickTime for Java calls.

r - Variable in class loci.formats.in.LegacyQTReader

Reflection tool for QuickTime for Java calls.

r - Variable in class loci.formats.in.LeicaSCNReader.Dimension
 
r - Variable in class loci.formats.in.TiffJAIReader

Reflection tool for JAI calls.

r - Variable in class loci.formats.out.LegacyQTWriter

Reflection tool for QuickTime for Java calls.

r - Variable in class loci.plugins.macro.LociFunctions
 
r - Variable in class loci.plugins.util.VirtualImagePlus
 
ralloc - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

Reference to the rate allocator

RandomAccessDeser() - Constructor for class loci.formats.Memoizer.RandomAccessDeser
 
RandomAccessIO - Interface in jj2000.j2k.io

This abstract class defines the interface to perform random access I/O.

range - Variable in class loci.formats.cache.CacheStrategy

Number of planes to cache along each axis.

range - Variable in class loci.formats.gui.CacheComponent

Spinners for choosing range of slices to cache.

RANGE_CHANGED - Static variable in class loci.formats.cache.CacheEvent

Event type indicating new planar ordering.

RangeDialog - Class in loci.plugins.in

Bio-Formats Importer range chooser dialog box.

RangeDialog(ImportProcess) - Constructor for class loci.plugins.in.RangeDialog

Creates a range chooser dialog for the Bio-Formats Importer.

ras - Variable in class com.sun.media.imageioimpl.common.SingleTileRenderedImage
 
rasForATile - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

The raster for medialib tiles to share.

raster - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
 
raster - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

The input source raster.

raster(int[]) - Method in class loci.formats.cache.CacheStrategy

Shortcut for converting N-D position to rasterized position.

rasterToPosition(int[], int) - Static method in class loci.formats.FormatTools

Computes a unique N-D position corresponding
 to the given rasterized index value.

rasterToPosition(int[], int, int[]) - Static method in class loci.formats.FormatTools

Computes a unique N-D position corresponding
 to the given rasterized index value.

ratebufT - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The buffer for rate values (avoids reallocation for each
        code-block), for each thread.

rateReached - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
 
raw - Variable in class com.sun.media.imageio.plugins.pnm.PNMImageWriteParam
 
RAW - Static variable in class loci.formats.in.BMPReader

Compression types.

RAW - Static variable in class loci.formats.in.CellSensReader
 
rawBits - Variable in class loci.formats.in.PGMReader
 
rawBuf - Variable in class loci.formats.in.SPCReader
 
rawCount - Variable in class loci.formats.in.BaseZeissReader
 
rawImage - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

A BufferedImage for the decodeRaw
 method to write into.

RawImageInputStream - Class in com.sun.media.imageio.stream

This class defines the content of the ImageInputStream
 containing several raw images with the same image type: the number of
 the images, the image type, the offset for the first sample of each image,
 and the image size information.

RawImageInputStream(ImageInputStream, ImageTypeSpecifier, long[], Dimension[]) - Constructor for class com.sun.media.imageio.stream.RawImageInputStream

Constructor.

RawImageInputStream(ImageInputStream, SampleModel, long[], Dimension[]) - Constructor for class com.sun.media.imageio.stream.RawImageInputStream

Constructor.

RawImageInputStream(ImageInputStream, InputSource) - Constructor for class com.sun.media.imageio.stream.RawImageInputStream

Constructor.

RawImageReader - Class in com.sun.media.imageioimpl.plugins.raw

This class is the Java Image IO plugin reader for Raw images.

RawImageReader(ImageReaderSpi) - Constructor for class com.sun.media.imageioimpl.plugins.raw.RawImageReader

Constructs RawImageReader from the provided
  ImageReaderSpi.

RawImageReaderSpi - Class in com.sun.media.imageioimpl.plugins.raw
 
RawImageReaderSpi() - Constructor for class com.sun.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
RawImageWriteParam - Class in com.sun.media.imageioimpl.plugins.raw

A subclass of ImageWriteParam for writing images in
 the RAW format.

RawImageWriteParam(Locale) - Constructor for class com.sun.media.imageioimpl.plugins.raw.RawImageWriteParam

Constructor to set locales.

RawImageWriter - Class in com.sun.media.imageioimpl.plugins.raw

The Java Image IO plugin writer for encoding a binary RenderedImage into
 a Raw format.

RawImageWriter(ImageWriterSpi) - Constructor for class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

Constructs RawImageWriter based on the provided
  ImageWriterSpi.

RawImageWriterSpi - Class in com.sun.media.imageioimpl.plugins.raw
 
RawImageWriterSpi() - Constructor for class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
rawMagRefPass(DataBlk, ByteToBitInput, int, int[], boolean) - Method in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Performs the magnitude refinement pass on the specified data and
 bit-plane.

rawMagRefPass(CBlkWTData, BitToByteOutput, boolean, int, int[], int[], int[], int, int, int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Performs the magnitude refinement pass on the specified data and
 bit-plane, without using the arithmetic coder.

RawRenderedImage - Class in com.sun.media.imageioimpl.plugins.raw
 
RawRenderedImage(RawImageInputStream, RawImageReader, ImageReadParam, int) - Constructor for class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
rawSigProgPass(DataBlk, ByteToBitInput, int, int[], boolean) - Method in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Performs the significance propagation pass on the specified data and
 bit-plane.

rawSigProgPass(CBlkWTData, BitToByteOutput, boolean, int, int[], int[], int[], int, int, int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Performs the significance propagation pass on the specified data and
 bit-plane, without using the arithmetic coder.

rawSize - Variable in class loci.formats.in.NativeQTReader

Raw plane size, in bytes.

rb - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

The number of bits that determine the nominal dynamic range

rb - Variable in class jj2000.j2k.image.input.ImgReaderPGM

The number of bits that determine the nominal dynamic range

rb - Variable in class jj2000.j2k.quantization.dequantizer.Dequantizer

The "range bits" for each transformed component

rc - Variable in class loci.formats.gui.DataConverter
 
rcom - Variable in class jj2000.j2k.codestream.HeaderInfo.COM
 
RCOM_GEN_USE - Static variable in interface jj2000.j2k.codestream.Markers

General use registration value (COM): 0x0001

RD_SUMMARY_OFF - Static variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

The normalization offset for the R-D summary table

RD_SUMMARY_SIZE - Static variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

The size of the summary table

RDSlopesRates - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

The R-D summary information collected from the coding of all
 code-blocks.

rdThreshold - Variable in class jj2000.j2k.entropy.encoder.EBCOTLayer

The rate-distortion threshold associated with the bit-stream
 layer.

re - Variable in class jj2000.j2k.entropy.Progression

Resolution index for the end of a progression.

read() - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream
 
read(byte[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream
 
read() - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream
 
read(byte[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream
 
read() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
read(byte[]) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
read(byte[], int, int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
read() - Method in class com.sun.media.imageio.stream.SegmentedImageInputStream

Reads the next byte of data from the input stream.

read(byte[], int, int) - Method in class com.sun.media.imageio.stream.SegmentedImageInputStream

Reads up to len bytes of data from the input stream into
 an array of bytes.

read(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
read() - Method in class com.sun.media.imageioimpl.plugins.clib.InputStreamAdapter
 
read(byte[], int, int) - Method in class com.sun.media.imageioimpl.plugins.clib.InputStreamAdapter
 
read(ImageInputStream, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Reads a box from the ImageInputStream

read() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
read() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
read(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
read(byte[], int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
read(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
read(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
read(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
read(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
read(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
read(Rectangle) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
read(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
read() - Method in class jj2000.j2k.entropy.decoder.ByteInputBuffer

Reads the next byte of data from this input stream.

read() - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Reads an unsigned byte of data from the stream.

read() - Method in interface jj2000.j2k.io.RandomAccessIO

Reads a byte of data from the stream.

read() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads a byte of data from the stream.

read(int, byte[]) - Method in class loci.formats.in.AmiraReader.ASCII
 
read(byte[], int) - Method in class loci.formats.in.AmiraReader.HxRLE
 
read(int, byte[]) - Method in class loci.formats.in.AmiraReader.HxRLE
 
read(int, byte[]) - Method in class loci.formats.in.AmiraReader.HxZip
 
read(int, byte[]) - Method in interface loci.formats.in.AmiraReader.PlaneReader
 
read() - Method in class loci.formats.in.APNGReader.PNGInputStream
 
read(byte[], int, int) - Method in class loci.formats.in.APNGReader.PNGInputStream
 
read() - Method in class loci.formats.in.ZeissLSMReader.BeamSplitter
 
read() - Method in class loci.formats.in.ZeissLSMReader.DataChannel
 
read() - Method in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
read() - Method in class loci.formats.in.ZeissLSMReader.IlluminationChannel
 
read() - Method in class loci.formats.in.ZeissLSMReader.Laser
 
read() - Method in class loci.formats.in.ZeissLSMReader.Recording
 
read() - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
read() - Method in class loci.formats.in.ZeissLSMReader.Track
 
read(Kryo, Input) - Method in class loci.formats.services.NetCDFServiceImpl
 
read16Bit(short[]) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
read1Bit(byte[]) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
read1Bit(byte[]) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
read24Bit(byte[]) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
read32Bit(int[]) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
read4Bit(byte[]) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
read4Bit(byte[]) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
read8Bit(byte[]) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
read8Bit(byte[]) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
readAborted(ImageReader) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader.EmbeddedProgressAdapter
 
readAbsoluteZValid() - Method in class loci.formats.in.MetamorphReader
 
readAndBuffer(BufferedRandomAccessFile) - Method in class jj2000.j2k.util.CodestreamManipulator

This method reads and buffers the tile headers, packet headers and
 packet data.

readArea(Element, int, double, double, int, int) - Method in class loci.formats.in.CellVoyagerReader
 
readAsRaster() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
readAsRaster(WritableRaster) - Method in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
readAsRenderedImage(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
readAsRenderedImage(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
readAsRenderedImage(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
readAttachments() - Method in class loci.formats.in.ZeissCZIReader
 
readBit() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readBit() - Method in class jj2000.j2k.codestream.reader.PktHeaderBitReader

Reads a single bit from the input.

readBit() - Method in class jj2000.j2k.entropy.decoder.ByteToBitInput

Reads from the bit stream one bit.

readBits(int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readBits(int) - Method in class jj2000.j2k.codestream.reader.PktHeaderBitReader

Reads a specified number of bits and returns them in a single
 integer.

readBitsPerComponentBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

Read the bits per component.

readBlock() - Method in class loci.formats.in.GIFReader

Reads the next variable length block.

readBoolean() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readBufferedImage() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
readByte() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readByte() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readByte() - Method in interface jj2000.j2k.io.BinaryDataInput

Should read a signed byte (i.e., 8 bit) from the input.

readByte() - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Reads a signed byte (i.e., 8 bit) from the input.

readByte() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads a signed byte (8 bit) from the input.

readByte() - Method in class loci.formats.in.APNGReader.PNGInputStream
 
readByte() - Method in class loci.formats.tools.AmiraParameters
 
readByteArray(String) - Method in interface loci.formats.services.JHDFService

Reads a multi-dimensional byte array from path.

readByteArray(String) - Method in class loci.formats.services.JHDFServiceImpl
 
readByteBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService

Reads a multi-dimensional sub-block byte array from path.

readByteBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
 
readBytes(IIOByteBuffer, int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.services.WlzService

Reads a rectangle of bytes in an x-y plane from the opened Woolz
 object.

readBytes(int, byte[], int, int, int, int) - Method in class loci.formats.services.WlzServiceImpl
 
readBytes2DDomObj(byte[], int, int, int, int) - Method in class loci.formats.services.WlzServiceImpl
 
readBytes3DDomObj(byte[], int, int, int, int, int) - Method in class loci.formats.services.WlzServiceImpl
 
readChannel(Element) - Method in class loci.formats.in.CellVoyagerReader
 
readChannelDefinitionBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method reads the Channel Definition box

readChar() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readChecked() - Method in class jj2000.j2k.entropy.decoder.ByteInputBuffer

Reads the next byte of data from this input stream.

readChunk() - Method in class loci.formats.in.AVIReader
 
readChunkHeader() - Method in class loci.formats.in.AVIReader
 
readCOC(DataInputStream, boolean, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads the COC marker segment and realigns the codestream where the next
 marker should be found.

readCOD(DataInputStream, boolean, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads a COD marker segment and realigns the codestream where the next
 marker should be found.

readColourSpecificationBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

Read the color specifications.

readCOM(DataInputStream, boolean, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads a COM marker segments and realigns the bit stream at the point
 where the next marker segment should be found.

readComments(ImageInputStream, PNMMetadata) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

Reads the comments.

readComponentMappingBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

Read the component mapping channel.

readCompoundArrayDataMap(String) - Method in interface loci.formats.services.JHDFService

Reads Compound array of any type

readCompoundArrayDataMap(String) - Method in class loci.formats.services.JHDFServiceImpl
 
readCompPosResLy(int[][], int, int, int, int, int) - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Reads packets of the current tile according to the
 component-position-resolution-layer progressiveness.

readContiguousCodeStreamBox(int, long) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method skips the Contiguous codestream box and adds position
 of contiguous codestream to a vector

readCRG(DataInputStream) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads a CRG marker segment and checks its length.

readCString() - Method in class loci.formats.in.OpenlabReader
 
readCString() - Method in class loci.formats.in.SlidebookReader
 
readDate() - Method in class loci.formats.in.OxfordInstrumentsReader
 
readDouble() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readDouble() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readDouble() - Method in class jj2000.j2k.io.BEBufferedRandomAccessFile

Reads an IEEE double precision (i.e., 64 bit) floating-point number
 from the input.

readDouble() - Method in interface jj2000.j2k.io.BinaryDataInput

Should read an IEEE double precision (i.e., 64 bit)
 floating-point number from the input.

readDouble() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads an IEEE double precision (i.e., 64 bit) floating-point number
 from the input.

readDoubleArray(int) - Method in class loci.formats.tools.AmiraParameters
 
readEmbedded(int, BufferedImage, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

Decodes the jpeg/png image embedded in the bitmap using any jpeg
  ImageIO-style plugin.

readEntry() - Method in class loci.formats.in.ZeissLSMReader
 
readEPHMarker(PktHeaderBitReader) - Method in class jj2000.j2k.codestream.reader.PktDecoder

Try to read an EPH marker.

reader - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The ImageReader calling this
 TIFFDecompressor.

reader - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState

Cache the J2KImageReader which creates this object.

reader - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

Caches the RawImageReader which creates this object.

reader - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
reader - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
reader - Variable in class loci.formats.cache.CacheSource

Reader from which to draw image planes.

reader - Variable in class loci.formats.FileInfo

IFormatReader implementation that would be used to read this file.

reader - Variable in class loci.formats.gui.BufferedImageSource

Image reader from which to draw BufferedImages.

reader - Variable in class loci.formats.gui.DataConverter
 
reader - Variable in class loci.formats.gui.FormatFileFilter

Associated file format reader.

reader - Variable in class loci.formats.gui.PreviewPane

Reader for use when loading thumbnails.

reader - Variable in class loci.formats.in.AFIReader
 
reader - Variable in class loci.formats.in.BDReader
 
reader - Variable in class loci.formats.in.ColumbusReader
 
reader - Variable in class loci.formats.in.L2DReader
 
reader - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane

Reader to use for accessing this plane.

reader - Variable in class loci.formats.in.OperettaReader
 
reader - Variable in class loci.formats.in.PCORAWReader
 
reader - Variable in class loci.formats.in.ScanrReader
 
reader - Variable in class loci.formats.in.ZeissTIFFHandler
 
reader - Variable in class loci.formats.in.ZipReader
 
reader - Variable in class loci.formats.ReaderWrapper

FormatReader used to read the file.

reader - Variable in class loci.formats.services.MetakitServiceImpl
 
reader - Variable in class loci.plugins.config.FormatEntry
 
reader - Variable in class loci.plugins.in.ImportProcess
 
reader - Variable in class loci.plugins.util.BFVirtualStack
 
reader - Variable in class loci.plugins.util.ImageProcessorSource

Image reader from which to draw ImageProcessors.

READER_VALIDATE_DEFAULT - Static variable in class loci.formats.in.DynamicMetadataOptions
 
READER_VALIDATE_KEY - Static variable in class loci.formats.in.DynamicMetadataOptions
 
readerClassName - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
readerFromBytes(Class<IFormatReader>, byte[]) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
readerName - Variable in class loci.plugins.config.FormatEntry
 
readers - Variable in class loci.formats.FileStitcher.ExternalSeries
 
readers - Variable in class loci.formats.ImageReader

List of supported file format readers.

readers - Variable in class loci.formats.in.ImprovisionTiffReader
 
readers - Variable in class loci.formats.in.MIASReader

Delegate readers.

readers - Variable in class loci.formats.in.NDPISReader
 
readers - Variable in class loci.formats.in.ScreenReader
 
readers - Variable in class loci.formats.in.SlidebookTiffReader
 
readerSpiNames - Static variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
readerSpiNames - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
readerSpiNames - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
readerSpiNames - Static variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
readerSpiNames - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
readerSpiNames - Static variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
readerSpiNames - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
readerSpiNames - Static variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
ReaderWrapper - Class in loci.formats

Abstract superclass of reader logic that wraps other readers.

ReaderWrapper() - Constructor for class loci.formats.ReaderWrapper

Constructs a reader wrapper around a new image reader.

ReaderWrapper(IFormatReader) - Constructor for class loci.formats.ReaderWrapper

Constructs a reader wrapper around the given reader.

readExtraMetadata(MetadataStore) - Method in class loci.formats.in.KodakReader
 
readField(Element) - Method in class loci.formats.in.CellVoyagerReader
 
readFile(String) - Method in class loci.formats.in.TextReader
 
readFile(String) - Method in class loci.formats.tools.AmiraParameters
 
readFile(RandomAccessInputStream) - Method in class loci.formats.tools.AmiraParameters
 
readFileFormat() - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method checks whether the given RandomAccessIO is a valid JP2 file
 and if so finds the first codestream in the file.

readFileInfoMetadata(MetadataStore) - Method in class loci.formats.in.KodakReader
 
readFileTypeBox(int, long) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method reads the File Type box

readFilter(DataInputStream, int[]) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads a wavelet filter from the codestream and returns the filter
 object that implements it.

readFloat() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readFloat() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readFloat() - Method in class jj2000.j2k.io.BEBufferedRandomAccessFile

Reads an IEEE single precision (i.e., 32 bit) floating-point number
 from the input.

readFloat() - Method in interface jj2000.j2k.io.BinaryDataInput

Should read an IEEE single precision (i.e., 32 bit)
 floating-point number from the input.

readFloat() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads an IEEE single precision (i.e., 32 bit) floating-point number
 from the input.

readFoundMainMarkSeg() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Retrieves and reads all marker segments found in the main header during
 the first pass.

readFoundTilePartMarkSeg(int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Return the DecoderSpecs instance filled when reading the headers

 Retrieves and reads all marker segments previously found in the
 tile-part header.

readFrameInterval(Document) - Method in class loci.formats.in.CellVoyagerReader
 
readFromOverlays() - Static method in class loci.plugins.util.ROIHandler

Returns rois if any from the overlay.

readFromRoiManager() - Static method in class loci.plugins.util.ROIHandler

Returns the rois if any stored in the ROI manager.

readFully(char[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream
 
readFully(short[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream
 
readFully(int[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream
 
readFully(long[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream
 
readFully(float[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream
 
readFully(double[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream
 
readFully(char[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream
 
readFully(short[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream
 
readFully(int[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream
 
readFully(long[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream
 
readFully(float[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream
 
readFully(double[], int, int) - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream
 
readFully(byte[], int, int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readFully(byte[]) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readFully(short[], int, int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readFully(char[], int, int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readFully(int[], int, int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readFully(long[], int, int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readFully(float[], int, int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readFully(double[], int, int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readFully(byte[], int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readFully(byte[], int, int) - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Reads up to len bytes of data from this file into an array of
 bytes.

readFully(byte[], int, int) - Method in interface jj2000.j2k.io.RandomAccessIO

Reads up to len bytes of data from this file into an array of
 bytes.

readFully(byte[], int, int) - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads 'len' bytes of data from this file into an array of bytes.

readHeader() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
readHeader() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
readHeader() - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
readHeader() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
readHeader() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
readHeader() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
readHeaderInt() - Method in class jj2000.j2k.image.input.ImgReaderPGM

Returns an int read from the header of the PGM file.

readIFD(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
readImage(byte[]) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
readImage(long) - Method in class loci.formats.in.MNGReader
 
readImage(InputStream, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService

Reads an image using JAI Image I/O using the JPEG 2000 codec.

readImage(InputStream) - Method in interface loci.formats.services.JAIIIOService

Reads an image using JAI Image I/O using the JPEG 2000 codec.

readImage(InputStream, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
 
readImage(InputStream) - Method in class loci.formats.services.JAIIIOServiceImpl
 
readImage(int, boolean) - Method in class loci.plugins.in.ImagePlusReader
 
readImageBlock() - Method in class loci.formats.in.GIFReader
 
readImageHeader(int) - Method in class loci.formats.in.PictReader
 
readImageHeaderBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method reads the Image Header box

readImages() - Method in class loci.plugins.in.ImagePlusReader
 
readImages(boolean) - Method in class loci.plugins.in.ImagePlusReader
 
readInfo(Document, Document) - Method in class loci.formats.in.CellVoyagerReader
 
readInput() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads data from the wrapped InputStream and places it in the cache
 buffer.

readInt() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readInt() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readInt() - Method in class jj2000.j2k.io.BEBufferedRandomAccessFile

Reads a signed int (i.e., 32 bit) from the input.

readInt() - Method in interface jj2000.j2k.io.BinaryDataInput

Should read a signed int (i.e., 32 bit) from the input.

readInt() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads a signed int (32 bit) from the input.

readIntArray(String) - Method in interface loci.formats.services.JHDFService

Reads a multi-dimensional int array from path.

readIntArray(String) - Method in class loci.formats.services.JHDFServiceImpl
 
readIntArray() - Method in class loci.formats.tools.AmiraParameters
 
readIntArray(int) - Method in class loci.formats.tools.AmiraParameters
 
readIntBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService

Reads a multi-dimensional sub-block int array from path.

readIntBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
 
readInteger(ImageInputStream) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

Reads the next integer.

readIntPropertyBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method reads the contents of the Intellectual property box

readJP2HeaderBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method reads the JP2Header box

readKey() - Method in class loci.formats.tools.AmiraParameters
 
readLine() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readLine() - Method in class loci.formats.in.EPSReader
 
readLong() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readLong() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readLong() - Method in class jj2000.j2k.io.BEBufferedRandomAccessFile

Reads a signed long (i.e., 64 bit) from the input.

readLong() - Method in interface jj2000.j2k.io.BinaryDataInput

Should read a signed long (i.e., 64 bit) from the input.

readLong() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads a signed long (64 bit) from the input.

readLookupTables(RandomAccessInputStream) - Method in class loci.formats.in.BioRadReader

Read all lookup tables from the given file into the 'lut' variable.

readLut(int) - Method in class loci.formats.in.GIFReader

Read a color lookup table of the specified size.

readLyResCompPos(int[][], int, int, int, int, int) - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Reads packets of the current tile according to the
 layer-resolution-component-position progressiveness.

readMap() - Method in class loci.formats.tools.AmiraParameters
 
readMetadata() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
readMetaData(String) - Method in class loci.formats.in.BDReader
 
readMetadataFile() - Method in class loci.formats.in.OMETiffReader

Extracts the OME-XML from the current OMETiffReader.metadataFile.

readMultiByteInteger(ImageInputStream) - Static method in class com.sun.media.imageioimpl.common.ImageUtil
 
readNewBuffer(int) - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Reads a new buffer from the file.

readNotes(RandomAccessInputStream, boolean) - Method in class loci.formats.in.BioRadReader

Read all of the note strings from the given file.

readNumber() - Method in class loci.formats.tools.AmiraParameters
 
readNumberArray() - Method in class loci.formats.tools.AmiraParameters
 
readNumberString() - Method in class loci.formats.in.AmiraReader.ASCII
 
READOUT_TIME - Static variable in class loci.formats.in.FluoviewReader
 
readOutRate - Variable in class loci.formats.in.MetamorphHandler
 
readoutTime - Variable in class loci.formats.in.FluoviewReader
 
readPaletteBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method reads the content of the palette box

readPixelBlock(long) - Method in class loci.formats.in.OIRReader
 
readPixelData() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
readPixelData(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
readPixelData(RandomAccessInputStream, Region, byte[]) - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
readPixels(byte[], RandomAccessInputStream, ZipInputStream, int) - Method in class loci.formats.in.SDTReader
 
readPixels(ImagePlusReader, ImporterOptions, DisplayHandler) - Method in class loci.plugins.in.Importer
 
readPktBody(int, int, int, int, CBlkInfo[][][], int[]) - Method in class jj2000.j2k.codestream.reader.PktDecoder

Reads specificied packet body in order to find offset of each
 code-block's piece of codeword.

readPktHead(int, int, int, int, CBlkInfo[][][], int[]) - Method in class jj2000.j2k.codestream.reader.PktDecoder

Read specified packet head and found length of each code-block's piece
 of codewords as well as number of skipped most significant bit-planes.

readPlane(RandomAccessInputStream, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader

Reads a raw plane from disk.

readPlane(RandomAccessInputStream, int, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader

Reads a raw plane from disk.

readPlaneData() - Method in class loci.formats.in.MetamorphReader
 
readPlanes(ImportProcess, int, List<LUT>, boolean) - Method in class loci.plugins.in.ImagePlusReader
 
readPLM(DataInputStream) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads PLM marker segment and realigns the codestream where the next
 marker should be found.

readPLTFields(DataInputStream) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads the PLT fields and realigns the codestream where the next marker
 should be found.

readPOC(DataInputStream, boolean, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads the POC marker segment and realigns the codestream where the next
 marker should be found.

readPosCompResLy(int[][], int, int, int, int, int) - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Reads packets of the current tile according to the
 position-component-resolution-layer progressiveness.

readPPM(DataInputStream) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads the PPM marker segment of the main header.

readPPT(DataInputStream, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Teads the PPT marker segment of the main header.

readProcessors(ImportProcess, int, Region, boolean) - Method in class loci.plugins.in.ImagePlusReader

HACK: This method mainly exists to prompt the user for a missing
 LuraWave license code, in the case of LWF-compressed Flex.

readQCC(DataInputStream, boolean, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads a QCC marker segment and realigns the codestream at the point
 where the next marker should be found.

readQCD(DataInputStream, boolean, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads a QCD marker segment and realigns the codestream at the point
 where the next marker should be found.

readQuotedString() - Method in class loci.formats.tools.AmiraParameters
 
readRaster(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
readRaster(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
readRaster(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
readRaster(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
readRaster(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
readRaster(int, ImageReadParam) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
readRaster(InputStream, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService

Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.

readRaster(InputStream) - Method in interface loci.formats.services.JAIIIOService

Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.

readRaster(InputStream, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
 
readRaster(InputStream) - Method in class loci.formats.services.JAIIIOServiceImpl
 
readRational(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphReader
 
readRational(RandomAccessInputStream, long) - Method in class loci.formats.in.MetamorphReader
 
readRationals(String[]) - Method in class loci.formats.in.MetamorphReader
 
readResLyCompPos(int[][], int, int, int, int, int) - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Reads packets of the current tile according to the
 resolution-layer-component-position progressiveness.

readResolutionBox(int, int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

Read the resolution.

readResPosCompLy(int[][], int, int, int, int, int) - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Reads packets of the current tile according to the
 resolution-position-component-layer progressiveness.

readRGN(DataInputStream, boolean, int, int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads the RGN marker segment of the codestream header.

readRLE4(byte[]) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
readRLE8(byte[]) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
readScanLine(byte[]) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
readSegment(String) - Method in class loci.formats.in.ZeissCZIReader
 
readSegments(String) - Method in class loci.formats.in.ZeissCZIReader
 
readShort() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readShort() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readShort() - Method in class jj2000.j2k.io.BEBufferedRandomAccessFile

Reads a signed short (i.e., 16 bit) from the input.

readShort() - Method in interface jj2000.j2k.io.BinaryDataInput

Should read a signed short (i.e., 16 bit) from the input.

readShort() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads a signed short (16 bit) from the input.

readShortBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService

Reads a multi-dimensional sub-block short array from path.

readShortBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
 
readSIZ(DataInputStream) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads the SIZ marker segment and realigns the codestream at the point
 where the next marker segment should be found.

readSOPMarker(int[], int, int, int) - Method in class jj2000.j2k.codestream.reader.PktDecoder

Try to read a SOP marker and check that its sequence number if not out
 of sequence.

readSpecialPixels(byte[]) - Static method in class loci.formats.in.FakeReader

Read byte-encoded metadata from the given plane.

readSpecialPixels(byte[], int, boolean) - Static method in class loci.formats.in.FakeReader

Read byte-encoded metadata from the given plane.

readSpecialPixels(byte[], int, boolean, int, boolean) - Static method in class loci.formats.in.FakeReader

Read byte-encoded metadata from the given plane.

readStackHeader() - Method in class loci.formats.in.ImspectorReader

Read the header for an image stack.

readStageLabels() - Method in class loci.formats.in.MetamorphReader
 
readStagePositions() - Method in class loci.formats.in.MetamorphReader
 
readStamps() - Method in class loci.formats.in.FluoviewReader
 
readState - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

The J2KReadState for this reading session based on the current input
  and J2KImageReadParam.

readState - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
 
readStream - Variable in class com.sun.media.imageio.stream.FileChannelImageOutputStream

An ImageInputStream used for reading.

readString() - Method in class loci.formats.in.OBFReader
 
readStringArray(String) - Method in interface loci.formats.services.JHDFService

Reads String array array from path.

readStringArray(String) - Method in class loci.formats.services.JHDFServiceImpl
 
readSubsampledRaster(WritableRaster) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
readSubsampledRaster(WritableRaster) - Method in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
readSupportsThumbnails() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
readTagHeader() - Method in class loci.formats.in.OpenlabReader

Read the next tag.

readTags(RandomAccessInputStream, boolean, String) - Method in class loci.formats.in.CellSensReader
 
readThumbImages() - Method in class loci.plugins.in.ImagePlusReader
 
readTiffIFDEntry() - Method in class loci.formats.tiff.TiffParser
 
readTile(int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
readTilePartHeader() - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Reads SOT marker segment of the tile-part header and calls related
 methods of the HeaderDecoder to read other markers segments.

readTilePkts(int) - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Finish initialization of members for specified tile, reads packets head
 of each tile and keeps location of each code-block's codewords.

readTimePoints(Document) - Method in class loci.formats.in.CellVoyagerReader
 
readTLM(DataInputStream) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Reads TLM marker segment and realigns the codestream where the next
 marker should be found.

readTopLevel() - Method in class loci.formats.tools.AmiraParameters
 
readTypeAndSize() - Method in class loci.formats.in.AVIReader
 
readUnsignedByte() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readUnsignedByte() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readUnsignedByte() - Method in interface jj2000.j2k.io.BinaryDataInput

Should read an unsigned byte (i.e., 8 bit) from the input.

readUnsignedByte() - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Reads an unsigned byte (i.e., 8 bit) from the input.

readUnsignedByte() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads an unsigned byte (8 bit) from the input.

readUnsignedInt() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readUnsignedInt() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readUnsignedInt() - Method in class jj2000.j2k.io.BEBufferedRandomAccessFile

Reads an unsigned int (i.e., 32 bit) from the input.

readUnsignedInt() - Method in interface jj2000.j2k.io.BinaryDataInput

Should read an unsigned int (i.e., 32 bit) from the input.

readUnsignedInt() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads a unsigned int (32 bit) from the input.

readUnsignedLong(RandomAccessInputStream) - Method in class loci.formats.in.SDTInfo
 
readUnsignedShort() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readUnsignedShort() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readUnsignedShort() - Method in class jj2000.j2k.io.BEBufferedRandomAccessFile

Reads an unsigned short (i.e., 16 bit) from the input.

readUnsignedShort() - Method in interface jj2000.j2k.io.BinaryDataInput

Should read an unsigned short (i.e., 16 bit) from the input.

readUnsignedShort() - Method in class jj2000.j2k.util.ISRandomAccessIO

Reads an unsigned short (16 bit) from the input.

readURLBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method reads the contents of the XML box

readUTF() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
readUUIDBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method reads the contents of the Intellectual property box

readUUIDListBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method reads the contents of the UUID List box

readValue(int) - Method in class loci.formats.in.GatanReader
 
readValue() - Method in class loci.formats.in.ZeissLSMReader
 
readVariable() - Method in class loci.formats.in.OpenlabReader
 
readVariable() - Method in class loci.formats.in.QuesantReader
 
readWavelength(int, MetadataStore) - Method in class loci.formats.in.DeltavisionReader
 
readWellInfo(Element, double, double, int, int) - Method in class loci.formats.in.CellVoyagerReader
 
readXMLBlock() - Method in class loci.formats.in.OIRReader
 
readXMLBox(int) - Method in class jj2000.j2k.fileformat.reader.FileFormatReader

This method reads the contents of the XML box

realChannel - Variable in class loci.formats.in.LIFReader
 
realColors - Variable in class loci.formats.in.ND2Handler
 
realFile - Variable in class loci.formats.Memoizer
 
realHeight - Variable in class loci.formats.in.BaseZeissReader
 
realWidth - Variable in class loci.formats.in.BaseZeissReader
 
rebuild(GenericDialog) - Method in class loci.plugins.in.FilePatternDialog
 
rebuildDialog(GenericDialog) - Method in class loci.plugins.in.MainDialog

Fancies up the importer dialog to look much nicer.

rebuildDialog(GenericDialog, int) - Method in class loci.plugins.in.SeriesDialog
 
REC_BOOLEAN - Static variable in class loci.formats.in.IM3Reader
 
REC_CONTAINER - Static variable in class loci.formats.in.IM3Reader

A record that is a container of
 other records.

REC_FLOAT - Static variable in class loci.formats.in.IM3Reader
 
REC_IMAGE - Static variable in class loci.formats.in.IM3Reader

Image format
 int: pixel type? 3 = RGBA
 int: width
 int: height
 int: depth
 data bytes follow

REC_INT - Static variable in class loci.formats.in.IM3Reader

32-bit integer values

REC_NESTED - Static variable in class loci.formats.in.IM3Reader

A nested record of records

REC_STRING - Static variable in class loci.formats.in.IM3Reader

A string
 int: ?
 int: length
 8-byte characters follow

REC_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
 
recache(int) - Method in class loci.formats.cache.Cache

Updates the given plane.

recache() - Method in class loci.formats.cache.Cache

Updates all planes on the load list.

recalcTreeV() - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Recalculates the values of the elements in the tag tree, in
 levels 1 and up, based on the values of the leafs (level 0).

reconstructedComps - Variable in class jj2000.j2k.wavelet.synthesis.InvWTFull

block storing the reconstructed image for each component

record - Variable in class loci.plugins.util.BFVirtualStack
 
record(String) - Method in class loci.plugins.util.RecordedImageProcessor
 
record(String, Object, Class<?>) - Method in class loci.plugins.util.RecordedImageProcessor
 
record(String, Object[], Class<?>[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
RecordedImageProcessor - Class in loci.plugins.util

Image processor extension that records commands executed upon it.

RecordedImageProcessor(ImageProcessor) - Constructor for class loci.plugins.util.RecordedImageProcessor
 
RecordedImageProcessor(ImageProcessor, int, ImageProcessor[]) - Constructor for class loci.plugins.util.RecordedImageProcessor
 
RecordedImageProcessor.MethodEntry - Class in loci.plugins.util
 
Recording() - Constructor for class loci.formats.in.ZeissLSMReader.Recording
 
RECORDING_CAMERA_BINNING - Static variable in class loci.formats.in.ZeissLSMReader
 
RECORDING_DESCRIPTION - Static variable in class loci.formats.in.ZeissLSMReader
 
RECORDING_NAME - Static variable in class loci.formats.in.ZeissLSMReader

Data types.

RECORDING_OBJECTIVE - Static variable in class loci.formats.in.ZeissLSMReader
 
RECORDING_SAMPLE_0TIME - Static variable in class loci.formats.in.ZeissLSMReader
 
RECORDING_ZOOM - Static variable in class loci.formats.in.ZeissLSMReader
 
records - Variable in class loci.formats.in.IM3Reader
 
recordWidth - Variable in class loci.formats.in.PDSReader
 
rect - Variable in class jj2000.j2k.roi.encoder.ROI

Flag indicating whether the ROI is rectangular or not

RECTANGLE - Static variable in class loci.formats.in.FV1000Reader
 
RECTANGLE - Static variable in class loci.formats.in.LeicaHandler.ROI
 
RECTANGLE - Static variable in class loci.formats.in.LIFReader.ROI
 
RECTANGLE - Static variable in class loci.formats.in.ZeissLSMReader
 
rectangles - Variable in class loci.formats.in.FakeReader
 
RectangleStrategy - Class in loci.formats.cache

A rectangle strategy caches planes extending from the the current
 dimensional position along each axis and combination of axes.

RectangleStrategy(int[]) - Constructor for class loci.formats.cache.RectangleStrategy

Constructs a rectangle strategy.

RectROIMaskGenerator - Class in jj2000.j2k.roi.encoder

This class generates the ROI masks when there are only rectangular ROIs in
 the image.

RectROIMaskGenerator(ROI[], int) - Constructor for class jj2000.j2k.roi.encoder.RectROIMaskGenerator

The constructor of the mask generator.

red - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
red - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
RED_GAIN - Static variable in class loci.formats.in.CellSensReader
 
RED_MAX - Static variable in class loci.plugins.in.Colorizer
 
RED_OFFSET - Static variable in class loci.formats.in.CellSensReader
 
redGain - Variable in class loci.formats.in.CellSensReader.Pyramid
 
redMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
redMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
redOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
 
redOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
redShort - Variable in class loci.formats.gui.Index16ColorModel

Lookup tables.

reduce() - Method in class loci.formats.tiff.TiffRational

Reduces this rational's fraction to lowest terms.

reduceList - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
 
reduceTree() - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
 
redX - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
redY - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
redZ - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
refCount - Variable in class loci.plugins.util.VirtualReader
 
REFERENCE_BLACK_WHITE - Static variable in class loci.formats.tiff.IFD
 
referenceBlackCb - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
referenceBlackCb - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
referenceBlackCr - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
referenceBlackCr - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
ReferenceBlackWhite() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ReferenceBlackWhite
 
referenceBlackY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
referenceBlackY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
referenceWhiteCb - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
referenceWhiteCb - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
referenceWhiteCr - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
referenceWhiteCr - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
referenceWhiteY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
referenceWhiteY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
reformatData(byte[], int, int, short[], int[], int, int) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Reformats data read as bytes into a short or int buffer.

reformatDiscontiguousData(byte[], int, int, int, WritableRaster) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Reformats bit-discontiguous data into the DataBuffer
 of the supplied WritableRaster.

refractive - Variable in class loci.formats.in.InCellReader
 
REFRACTIVE_INDEX - Static variable in class loci.formats.in.CellSensReader
 
refractiveIndex - Variable in class loci.formats.in.CellSensReader.Pyramid
 
refractiveIndex - Variable in class loci.formats.in.IvisionReader
 
refractiveIndex - Variable in class loci.formats.in.LIFReader
 
refractiveIndex - Variable in class loci.formats.in.NativeND2Reader
 
refractiveIndex - Variable in class loci.formats.in.ND2Handler
 
refractiveIndex - Variable in class loci.formats.in.ZeissCZIReader
 
refresher - Variable in class loci.formats.gui.PreviewPane

Method for syncing the view to the model.

registered - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
registered - Variable in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
registerMsgLogger(Thread, MsgLogger) - Static method in class jj2000.j2k.util.FacilityManager

Registers the MsgLogger 'ml' as the logging facility of the
 thread 't'.

registerProgressWatch(Thread, ProgressWatch) - Static method in class jj2000.j2k.util.FacilityManager
 
registerServiceProviders() - Static method in class loci.formats.services.JAIIIOServiceImpl

Register the JPEG-2000 readers with the reader service.

REGISTRY - Static variable in class loci.formats.UpgradeChecker

Location of the OME registry.

REGISTRY_IMAGEJ - Static variable in class loci.formats.UpgradeChecker

Registry ID identifying usage of Bio-Formats in ImageJ.

REGISTRY_LIBRARY - Static variable in class loci.formats.UpgradeChecker

Registry ID identifying usage of Bio-Formats as a library in general.

REGISTRY_PROPERTIES - Static variable in class loci.formats.UpgradeChecker

Properties that are sent to the OME registry.

RELATED_SOUND_FILE - Static variable in class loci.formats.tiff.IFD
 
RelatedSoundFile() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.RelatedSoundFile
 
relativeTime - Variable in class loci.formats.in.PrairieMetadata.Frame

relativeTime attribute of this <Frame>.

remainingTileParts - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

The number of tile-parts that remain to read

removeAllowedTagSet(TIFFTagSet) - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam

Removes a TIFFTagSet object from the list of
 allowed tag sets.

removeBinData(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService

Remove all of the BinData elements from the given OME-XML metadata object.

removeBinData(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
 
removeCacheListener(CacheListener) - Method in class loci.formats.cache.Cache
 
removeCacheListener(CacheListener) - Method in interface loci.formats.cache.CacheReporter

Removes a listener for status update events.

removeCacheListener(CacheListener) - Method in class loci.formats.cache.CacheStrategy
 
removeChannels(OMEXMLMetadata, int, int) - Method in interface loci.formats.services.OMEXMLService

Remove all but the first sizeC valid Channel elements from the given
 OME-XML metadata object.

removeChannels(OMEXMLMetadata, int, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
removeChild(Node) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
removeClass(Class<? extends T>) - Method in class loci.formats.ClassList

Removes the given class from the list.

removeExtension(String) - Method in class loci.plugins.out.Exporter

Removes the extension of the specified name.

removeGST(String) - Method in class loci.formats.in.FV1000Reader
 
removePossible(String) - Method in class loci.plugins.prefs.StringOption

Removes a possible value from the list.

removeStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
 
removeStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
 
removeTagSet(TIFFTagSet) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Removes an element from the group of TIFFTagSets of which this
 directory is aware.

removeTiffData(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService

Remove all of the TiffData elements from the given OME-XML metadata object.

removeTiffData(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
 
removeTIFFField(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Removes a TIFF field from the directory.

removeTIFFField(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
removeTIFFFields() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory

Removes all TIFF fields from the directory.

removeUpdate(DocumentEvent) - Method in class loci.plugins.config.FlexWidgets
 
RENDER_OPERATION_ID - Static variable in class loci.formats.in.CellSensReader
 
RenderedImageSrc - Class in com.sun.media.imageioimpl.plugins.jpeg2000
 
RenderedImageSrc(Raster, J2KImageWriteParamJava, J2KImageWriter) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Creates RenderedImageSrc for encoding a Raster.

RenderedImageSrc(RenderedImage, J2KImageWriteParamJava, J2KImageWriter) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Creates RenderedImageSrc for encoding a
 RenderedImage.

reopenFile() - Method in class loci.formats.DelegateReader
 
reopenFile() - Method in class loci.formats.FileStitcher
 
reopenFile() - Method in class loci.formats.FormatReader
 
reopenFile() - Method in interface loci.formats.IFormatReader

Reopen any files that were closed, and which are expected to be open
 while the reader is open.

reopenFile() - Method in class loci.formats.ImageReader
 
reopenFile() - Method in class loci.formats.in.AnalyzeReader
 
reopenFile() - Method in class loci.formats.in.CellH5Reader
 
reopenFile() - Method in class loci.formats.in.CellSensReader
 
reopenFile() - Method in class loci.formats.in.FakeReader
 
reopenFile() - Method in class loci.formats.in.FlowSightReader
 
reopenFile() - Method in class loci.formats.in.HitachiReader
 
reopenFile() - Method in class loci.formats.in.ICSReader
 
reopenFile() - Method in class loci.formats.in.ImagicReader
 
reopenFile() - Method in class loci.formats.in.MinimalTiffReader
 
reopenFile() - Method in class loci.formats.in.NiftiReader
 
reopenFile() - Method in class loci.formats.in.OMETiffReader
 
reopenFile() - Method in class loci.formats.in.ScreenReader
 
reopenFile() - Method in class loci.formats.in.SPCReader
 
reopenFile() - Method in class loci.formats.ReaderWrapper
 
reorder(int) - Method in class loci.formats.DimensionSwapper
 
reorder(ImagePlus, String, String) - Static method in class loci.plugins.Slicer

Reorder the given ImagePlus's stack.

reorderResolutions() - Method in class loci.formats.in.SVSReader

Validate the order of resolutions for the current series, in
 decending order of size.

reorderXSLT - Static variable in class loci.formats.services.OMEXMLServiceImpl

Reordering stylesheet.

repeat(String, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
replace(String, Box) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
replaceChild(Node, Node) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
replaceExtension(String, String, String) - Method in class loci.formats.in.FV1000Reader
 
replacementMetadataStore - Variable in class loci.formats.Memoizer

MetadataStore created internally.

replacePixels(RenderedImage, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
replacePixels(Raster, ImageWriteParam) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
replacePixelsByteCounts - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
replacePixelsByteCountsPosition - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
replacePixelsIndex - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
replacePixelsLock - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
replacePixelsMetadata - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
replacePixelsOffsetsPosition - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
replacePixelsRegion - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
replacePixelsTileOffsets - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
repoc - Variable in class jj2000.j2k.codestream.HeaderInfo.POC
 
reportException(Throwable) - Static method in class loci.plugins.util.WindowTools

Reports the given exception with stack trace in an ImageJ error dialog.

reportException(Throwable, boolean) - Static method in class loci.plugins.util.WindowTools

Reports the given exception with stack trace in an ImageJ error dialog.

reportException(Throwable, boolean, String) - Static method in class loci.plugins.util.WindowTools

Reports the given exception with stack trace in an ImageJ error dialog.

reportProgress() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
REPRESENTATION_KEYS - Static variable in class loci.formats.in.ICSReader
 
repT - Variable in class loci.formats.in.SDTInfo
 
requiredSize - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
 
RES_CODES - Static variable in class com.sun.media.imageioimpl.common.LZWStringTable

codesize + Reserved Codes

RES_LY_COMP_POS_PROG - Static variable in interface jj2000.j2k.codestream.ProgressionType

The bit stream is Resolution/Layer/Component/Position progressive : 1

RES_POS_COMP_LY_PROG - Static variable in interface jj2000.j2k.codestream.ProgressionType

The bit stream is Resolution/Position/Component/Layer progressive : 2

RES_SUFFIX - Static variable in class loci.formats.in.FlexReader
 
rescale(int, int) - Method in class loci.formats.gui.SignedColorModel
 
rescale(int) - Method in class loci.formats.gui.SignedColorModel
 
RESCALE_INTERCEPT - Static variable in class loci.formats.in.DicomReader
 
RESCALE_SLOPE - Static variable in class loci.formats.in.DicomReader
 
rescaleIntercept - Variable in class loci.formats.in.DicomReader
 
rescaleSlope - Variable in class loci.formats.in.DicomReader
 
reserved1 - Variable in class loci.formats.in.SDTInfo
 
reserved2 - Variable in class loci.formats.in.SDTInfo
 
reset() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
reset() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
reset() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
reset() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
reset() - Method in class com.sun.media.imageioimpl.plugins.clib.InputStreamAdapter
 
reset() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
reset() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
reset() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
reset() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableImageMetadata
 
reset() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableStreamMetadata
 
reset() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
reset() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
reset() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
reset() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
reset() - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
reset() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
reset() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
reset() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
reset() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
reset() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
reset() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
reset() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
reset() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
reset() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
reset() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
reset() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
reset() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
reset() - Method in class jj2000.j2k.codestream.writer.BitOutputBuffer

Resets the buffer.

reset() - Method in class jj2000.j2k.codestream.writer.HeaderEncoder

Resets the contents of this HeaderEncoder to its initial state.

reset() - Method in class jj2000.j2k.codestream.writer.PktEncoder

Resets the state of the object to the initial state, as if the object
 was just created.

reset() - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Resets the tree values and state.

reset(int[]) - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Resets the tree values and state.

reset() - Method in class jj2000.j2k.entropy.encoder.BitToByteOutput

Resets the bit buffer to empty, without writing anything to the
 underlying byte output, and resets the byte count.

reset() - Method in class jj2000.j2k.entropy.encoder.ByteOutputBuffer

Discards all the buffered data, by resetting the counter of written
 bytes to 0.

reset() - Method in class jj2000.j2k.entropy.encoder.MQCoder

Reinitializes the MQ coder and the underlying 'ByteOutputBuffer' buffer
 as if a new object was instantaited.

reset() - Method in class loci.formats.cache.Cache

Reallocates the cache.

reset() - Method in class loci.plugins.util.RecordedImageProcessor
 
reset(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
 
resetBinaryThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
resetCtxt(int) - Method in class jj2000.j2k.entropy.decoder.MQDecoder

Resets a context to the original probability distribution.

resetCtxt(int) - Method in class jj2000.j2k.entropy.encoder.MQCoder

Resets a context to the original probability distribution, and sets its
 more probable symbol to 0.

resetCtxts() - Method in class jj2000.j2k.entropy.decoder.MQDecoder

Resets a context to the original probability distribution.

resetCtxts() - Method in class jj2000.j2k.entropy.encoder.MQCoder

Resets all contexts to their original probability distribution and sets
 all more probable symbols to 0.

resetHeaderInfo() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
resetHeaderMarkers() - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Method that resets members indicating which markers have already been
 found

resetLocal() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter

Resets locally defined instance variables.

resetLocal() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
resetMinAndMax() - Method in class loci.plugins.util.RecordedImageProcessor
 
resetMQ - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

If this is enabled the probability estimates of the MQ coder are
  reset after each arithmetically coded (i.e.

resetRoi() - Method in class loci.plugins.util.RecordedImageProcessor
 
resetThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
ResHandler() - Constructor for class loci.formats.in.FlexReader.ResHandler
 
resize(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
resize(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
resLabel - Variable in class loci.formats.gui.PreviewPane

Labels containing thumbnail and dimensional information.

reslice(ImagePlus, boolean, boolean, boolean, String) - Method in class loci.plugins.Slicer
 
resLvl - Variable in class jj2000.j2k.wavelet.Subband

The resolution level to which this subband contributes.

reslvl - Variable in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

The resquested image resolution level for reconstruction.

resolution - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageReadParam

Specifies the resolution level wanted for the decoded image
  (0 means the lowest available resolution, the resolution
  level gives an image with the original dimension).

resolution - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState

The resolution level requested.

resolution - Variable in class loci.formats.codec.JPEG2000CodecOptions

The resolution level as would be provided to:
 J2KImageReadParam.setResolution(int)
 (READ).

resolution - Variable in class loci.formats.FormatReader

The number of the current resolution.

RESOLUTION_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
RESOLUTION_UNIT - Static variable in class loci.formats.tiff.IFD
 
RESOLUTION_UNIT_CENTIMETER - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "ResolutionUnit" tag.

RESOLUTION_UNIT_INCH - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "ResolutionUnit" tag.

RESOLUTION_UNIT_NONE - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "ResolutionUnit" tag.

ResolutionBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000

This class is defined to represent a Resolution Box of JPEG JP2
  file format.

ResolutionBox(int, byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox

Constructs a ResolutionBox from the provided type and
  content data array.

ResolutionBox(int, float, float) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox

Constructs a ResolutionBox from the provided type and
  horizontal/vertical resolutions.

ResolutionBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ResolutionBox

Constructs a ResolutionBox based on the provided
  org.w3c.dom.Node.

resolutionCount - Variable in class loci.formats.CoreMetadata
 
resolutionCount - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
resolutionIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
resolutionLevels - Variable in class loci.formats.in.JPEG2000MetadataParser

Number of JPEG 2000 resolution levels the file has.

resolutionLevels - Variable in class loci.formats.in.JPEG2000Reader

The number of JPEG 2000 resolution levels the file has.

resolutionLevels - Variable in class loci.formats.in.JPXReader

The number of JPEG 2000 resolution levels the file has.

resolutionLevels - Variable in class loci.formats.in.MinimalTiffReader

Number of JPEG 2000 resolution levels.

ResolutionUnit() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ResolutionUnit
 
resolutionX - Variable in class loci.formats.in.OperettaReader.Plane
 
resolutionY - Variable in class loci.formats.in.OperettaReader.Plane
 
resourceBaseName - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
resourceBaseName - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormat
 
resourceBaseName - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
resourceCount - Variable in class loci.formats.ResourceNamer
 
ResourceNamer - Class in loci.formats

Utility class helping with generating human-readable resource names
 based on alphanumeric indexing.

ResourceNamer(int) - Constructor for class loci.formats.ResourceNamer
 
resourceNamer - Variable in class loci.formats.tools.FakeImage
 
restart(int, int[], int, CBlkInfo[][][][][], boolean, ByteArrayInputStream) - Method in class jj2000.j2k.codestream.reader.PktDecoder

Re-initialize the PktDecoder instance at the beginning of a new tile.

restartAlphabet() - Method in class loci.formats.ResourceNamer

Resets the internal state of the class so that it starts alphabet
 generation from the first letter (ASCII A).

restartInterval - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
restartMarkers - Variable in class loci.formats.in.HamamatsuVMSReader
 
restartMarkers - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
resText - Variable in class loci.formats.gui.PreviewPane
 
resTip - Variable in class loci.formats.gui.PreviewPane
 
restore() - Method in class jj2000.j2k.codestream.writer.PktEncoder

Restores the last saved state of this object.

restore() - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Restores the saved values and state of the tree.

resultFile - Variable in class loci.formats.in.MIASReader

Path to file containing analysis results for all plates.

REUSE - Static variable in class loci.formats.tiff.IFD
 
rev - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor

The reversible flag to use in compression

REV_FILTER_STR - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterSpec

The reversible default filter

reverseFileMapping - Variable in class loci.formats.in.FlexReader
 
reverseX - Variable in class loci.formats.in.PDSReader
 
reverseY - Variable in class loci.formats.in.PDSReader
 
reversible - Variable in class jj2000.j2k.wavelet.synthesis.InvWTFull

The reversible flag for each component in each tile.

revision - Variable in class loci.formats.in.SDTInfo

Software revision number (lower 4 bits >= 10(decimal)).

rgb - Variable in class loci.formats.CoreMetadata

Indicates whether or not the images are stored as RGB
 (multiple channels per plane).

RGB - Static variable in class loci.formats.in.CellSensReader
 
RGB_MASK - Static variable in class loci.formats.in.BMPReader
 
rgh - Variable in class jj2000.j2k.codestream.PrecInfo

Precinct height reported in the reference grid

rgn - Variable in class jj2000.j2k.codestream.HeaderInfo

Reference to the RGN marker segments found in main and first tile-part
 header.

RGN() - Constructor for class jj2000.j2k.codestream.HeaderInfo.RGN
 
RGN - Static variable in interface jj2000.j2k.codestream.Markers

Region-of-interest (RGN): 0xFF5E

RGN_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for RGN marker segment found

rgulx - Variable in class jj2000.j2k.codestream.PrecInfo

Precinct horizontal upper-left coordinate in the reference grid

rguly - Variable in class jj2000.j2k.codestream.PrecInfo

Precinct vertical upper-left coordinate in the reference grid

rgw - Variable in class jj2000.j2k.codestream.PrecInfo

Precinct width reported in the reference grid

RHKReader - Class in loci.formats.in

RHKReader is the file format reader for RHK Technologies files.

RHKReader() - Constructor for class loci.formats.in.RHKReader

Constructs a new RHK reader.

ri - Variable in class loci.formats.in.OIRReader.Objective
 
RLC_CTXT - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The RLC context

RLC_CTXT - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The RLC context

RLC_MASK_R1R2 - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The mask to isolate the bits necessary to identify RLC coding state
 (significant, visited and non-zero context, for row 1 and 2).

RLC_MASK_R1R2 - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The mask to isolate the bits necessary to identify RLC coding state
 (significant, visited and non-zero context, for row 1 and 2).

RLE_4 - Static variable in class loci.formats.in.BMPReader
 
RLE_8 - Static variable in class loci.formats.in.BMPReader
 
ROI - Class in jj2000.j2k.roi.encoder

This class contains the shape of a single ROI.

ROI(int, ImgReaderPGM) - Constructor for class jj2000.j2k.roi.encoder.ROI

Constructor for ROI with arbitrary shape

ROI(int, int, int, int, int) - Constructor for class jj2000.j2k.roi.encoder.ROI

Constructor for rectangular ROIs

ROI(int, int, int, int) - Constructor for class jj2000.j2k.roi.encoder.ROI

Constructor for circular ROIs

roi - Variable in class jj2000.j2k.roi.encoder.ROIScaler

Flag indicating the presence of ROIs

roi - Variable in class loci.formats.in.LeicaHandler
 
ROI() - Constructor for class loci.formats.in.LeicaHandler.ROI
 
ROI() - Constructor for class loci.formats.in.LiFlimReader.ROI
 
ROI() - Constructor for class loci.formats.in.LIFReader.ROI
 
ROI_PREFIX - Static variable in class loci.formats.in.FakeReader
 
ROI_SIGNATURE - Static variable in class loci.formats.in.ZeissZVIReader
 
ROI_SPACING - Static variable in class loci.formats.in.FakeReader
 
roiCount - Variable in class loci.formats.in.FakeReader
 
ROIDeScaler - Class in jj2000.j2k.roi

This class takes care of the de-scaling of ROI coefficients.

ROIDeScaler(CBlkQuantDataSrcDec, MaxShiftSpec) - Constructor for class jj2000.j2k.roi.ROIDeScaler

Constructor of the ROI descaler, takes EntropyDEcoder as source of data
 to de-scale.

roiDrawFile - Variable in class loci.formats.in.TrestleReader
 
roids - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
roiFile - Variable in class loci.formats.in.BDReader
 
roiFile - Variable in class loci.formats.in.TrestleReader
 
roiFilenames - Variable in class loci.formats.in.FV1000Reader
 
roiFiles - Variable in class loci.formats.in.MIASReader
 
ROIHandler - Class in loci.plugins.util

Utility class for managing regions of interest within ImageJ.

ROIHandler() - Constructor for class loci.plugins.util.ROIHandler
 
roiIDs - Variable in class loci.formats.in.BaseZeissReader
 
roiInPkt - Variable in class jj2000.j2k.codestream.writer.PktEncoder

Whether or not there is ROI information in the last encoded Packet

roiInTile - Variable in class jj2000.j2k.roi.encoder.ArbROIMaskGenerator

Flag indicating if any ROI was found to be in this tile

roiInTile - Variable in class jj2000.j2k.roi.encoder.ROIMaskGenerator
 
roiLen - Variable in class jj2000.j2k.codestream.writer.PktEncoder

Length to read in current packet body to get all the ROI information

roiMask - Variable in class jj2000.j2k.roi.encoder.ArbROIMaskGenerator

The ROI mask for the current tile for all components

roiMask - Variable in class jj2000.j2k.roi.encoder.ROIScaler

The ROI mask

ROIMaskGenerator - Class in jj2000.j2k.roi.encoder

This class generates the ROI masks for the ROIScaler.It gives the scaler
 the ROI mask for the current code-block.

ROIMaskGenerator(ROI[], int) - Constructor for class jj2000.j2k.roi.encoder.ROIMaskGenerator

The constructor of the mask generator

ROIs - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies ROIs shape and location.

rois - Variable in class jj2000.j2k.decoder.DecoderSpecs

ROI maxshift value specifications

rois - Variable in class jj2000.j2k.roi.encoder.ROIMaskGenerator

Array containing the ROIs

rois - Variable in class loci.formats.in.LiFlimReader
 
rois - Variable in class loci.formats.in.ND2Handler
 
ROIS_MODE_MANAGER - Static variable in class loci.plugins.in.ImporterOptions
 
ROIS_MODE_OVERLAY - Static variable in class loci.plugins.in.ImporterOptions
 
roiSc - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder

Reference to the ROI module

ROIScaler - Class in jj2000.j2k.roi.encoder

This class deals with the ROI functionality.

ROIScaler(Quantizer, ROIMaskGenerator, boolean, int, boolean, J2KImageWriteParamJava) - Constructor for class jj2000.j2k.roi.encoder.ROIScaler

Constructor of the ROI scaler, takes a Quantizer as source of data to
 scale.

roisModeChoice - Variable in class loci.plugins.in.MainDialog
 
root - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
 
root - Variable in class loci.formats.services.NetCDFServiceImpl

Root of the NetCDF file.

root - Variable in class loci.formats.services.POIServiceImpl
 
rootIFD - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
rootList - Variable in class loci.formats.in.BDReader
 
rootName - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
rotate(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
rotate90(Point) - Method in class jj2000.j2k.ModuleSpec

Rotate the ModuleSpec instance by 90 degrees (this modifies only tile
 and tile-component specifications).

rotateLeft() - Method in class loci.plugins.util.RecordedImageProcessor
 
rotateRight() - Method in class loci.plugins.util.RecordedImageProcessor
 
ROTATION - Static variable in class loci.formats.FormatTools

Identifies the Rotation dimensional type,
 representing a dimension consisting of rotations.

ROTATION - Static variable in class loci.formats.in.FV1000Reader
 
rotation - Variable in class loci.formats.in.LeicaHandler.ROI
 
rotation - Variable in class loci.formats.in.LIFReader.ROI
 
rotationLabels - Variable in class loci.formats.in.ZeissCZIReader
 
rotations - Variable in class loci.formats.in.ZeissCZIReader
 
rotations - Variable in class loci.formats.in.ZeissLSMReader
 
roundBpp(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
row - Variable in class loci.formats.codec.JPEGTileDecoder.TileCache
 
row - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
row - Variable in class loci.formats.in.ColumbusReader.Plane
 
row - Variable in class loci.formats.in.FlexReader.FlexFile
 
row - Variable in class loci.formats.in.OMEXMLReader.BinData
 
row - Variable in class loci.formats.in.OperettaReader.Plane
 
row - Variable in class loci.formats.in.TextReader

Current row number.

row - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
row - Variable in class loci.formats.tools.AmiraParameters
 
ROW_COUNT - Static variable in class loci.formats.codec.JPEGTileDecoder.TileCache
 
rowBytes - Variable in class loci.formats.in.PictReader

Number of bytes in a row of pixel data (variable).

rowCount - Variable in class loci.formats.in.BaseZeissReader
 
rowLength - Variable in class loci.formats.in.TextReader

Number of tokens per row.

rowName - Variable in class loci.formats.in.InCellReader
 
RowPanel() - Constructor for class loci.formats.gui.DataConverter.RowPanel
 
rowPtr - Variable in class loci.formats.codec.RPZACodec
 
rows - Variable in class loci.formats.in.CellSensReader
 
ROWS - Static variable in class loci.formats.in.DicomReader
 
ROWS_PER_STRIP - Static variable in class loci.formats.tiff.IFD
 
rowsDone - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
RowsPerStrip() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.RowsPerStrip
 
rPad - Variable in class loci.formats.gui.CacheIndicator
 
RPZACodec - Class in loci.formats.codec

Implements encoding and decoding methods for Apple RPZA.

RPZACodec() - Constructor for class loci.formats.codec.RPZACodec
 
rQuit - Variable in class jj2000.j2k.codestream.reader.PktDecoder

The resolution in which the ncb quit condition was reached

rs - Variable in class jj2000.j2k.entropy.Progression

Resolution index for the start of a progression

rsiz - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
RSIZ_BASELINE - Static variable in interface jj2000.j2k.codestream.Markers

No special capabilities (baseline) in codestream, in Rsiz field of SIZ
 marker: 0x00.

RSIZ_ER_FLAG - Static variable in interface jj2000.j2k.codestream.Markers

Error resilience marker flag bit in Rsiz field in SIZ marker: 0x01

RSIZ_ROI - Static variable in interface jj2000.j2k.codestream.Markers

ROI present marker flag bit in Rsiz field in SIZ marker: 0x02

rspoc - Variable in class jj2000.j2k.codestream.HeaderInfo.POC
 
RST0 - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
RST7 - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
RST_0 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
RST_1 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
RST_2 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
RST_3 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
RST_4 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
RST_5 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
RST_6 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
RST_7 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
rts - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Regular termination specifications

run() - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor

Calls the 'compressCodeBlock()' method with thread local
 arguments.

run() - Method in class jj2000.j2k.util.ThreadPool.ThreadPoolThread

The method that is run by the thread.

run() - Method in class loci.formats.cache.CacheUpdater
 
run() - Method in class loci.formats.gui.DataConverter
 
run() - Method in class loci.formats.gui.ImageViewer

Handles animation.

run() - Method in class loci.formats.gui.PreviewPane

Thumbnail loading routine.

RUN - Static variable in class loci.formats.ResourceNamer
 
run(String) - Method in class loci.plugins.About
 
run() - Method in class loci.plugins.config.ConfigWindow

Populate configuration information in a separate thread.

run(String) - Method in class loci.plugins.config.LociConfig

Executes the plugin.

run(String) - Method in class loci.plugins.config.LociInstaller

Executes the plugin.

run(String) - Method in class loci.plugins.in.Importer

Executes the plugin.

run() - Method in class loci.plugins.in.ThumbLoader

Does the work of loading the thumbnails.

run(ImageProcessor) - Method in class loci.plugins.LociExporter

Executes the plugin.

run(String) - Method in class loci.plugins.LociImporter

Executes the plugin.

run(String) - Method in class loci.plugins.macro.LociFunctions
 
run(String) - Method in class loci.plugins.macro.MacroFunctions
 
run() - Method in class loci.plugins.out.Exporter

Executes the plugin.

run(String) - Method in class loci.plugins.shortcut.ShortcutPanel

Executes the plugin.

run(ImageProcessor) - Method in class loci.plugins.Slicer
 
run(String) - Method in class loci.plugins.Updater
 
runAndWrite() - Method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator

Runs the rate allocation algorithm and writes the data to the bit
 stream writer object provided to the constructor.

runAndWrite() - Method in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

Runs the rate allocation algorithm and writes the data to the
 bit stream.

runPlugIn(String, String) - Static method in class loci.plugins.shortcut.ShortcutPanel

Executes the given plugin, in a separate thread.

runTarget(Runnable, Object) - Method in class jj2000.j2k.util.ThreadPool

Runs the run method of the specified target in an idle thread of this
 pool.

runTarget(Runnable, Object, boolean) - Method in class jj2000.j2k.util.ThreadPool

Runs the run method of the specified target in an idle thread of this
 pool.

runTarget(Runnable, Object, boolean, boolean) - Method in class jj2000.j2k.util.ThreadPool

Runs the run method of the specified target in an idle thread of this
 pool.

RWC_FRAME_ORIGIN - Static variable in class loci.formats.in.CellSensReader
 
RWC_FRAME_SCALE - Static variable in class loci.formats.in.CellSensReader
 
RWC_FRAME_UNIT - Static variable in class loci.formats.in.CellSensReader
 




S

S_AXIS - Static variable in class loci.formats.AxisGuesser

Axis type for series.

S_MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
 
S_MIN_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
 
S_PREFIXES - Static variable in class loci.formats.AxisGuesser

Prefixes indicating series dimension.

SAMP_420 - Static variable in class org.libjpegturbo.turbojpeg.TJ

4:2:0 chrominance subsampling.

SAMP_422 - Static variable in class org.libjpegturbo.turbojpeg.TJ

4:2:2 chrominance subsampling.

SAMP_440 - Static variable in class org.libjpegturbo.turbojpeg.TJ

4:4:0 chrominance subsampling.

SAMP_444 - Static variable in class org.libjpegturbo.turbojpeg.TJ

4:4:4 chrominance subsampling (no chrominance subsampling).

SAMP_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJ

Grayscale.

SAMPLE_FLAGS_LIST - Static variable in class loci.formats.in.CellSensReader
 
SAMPLE_FORMAT - Static variable in class loci.formats.tiff.IFD
 
SAMPLE_FORMAT_FLOATING_POINT - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "SampleFormat" tag.

SAMPLE_FORMAT_SIGNED_INTEGER - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "SampleFormat" tag.

SAMPLE_FORMAT_UNDEFINED - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "SampleFormat" tag.

SAMPLE_FORMAT_UNSIGNED_INTEGER - Static variable in class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet

A value to be used with the "SampleFormat" tag.

SAMPLE_ID_LIST - Static variable in class loci.formats.in.CellSensReader
 
SAMPLE_MASK - Static variable in class loci.formats.in.CellSensReader
 
SampleFormat() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.SampleFormat
 
sampleFormat - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The value of the SampleFormat tag.

sampleFormat - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
sampleFormat - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
sampleModel - Variable in class com.sun.media.imageioimpl.common.SimpleRenderedImage

The image's SampleModel.

sampleModel - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
sampleModel - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
sampleModel - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
sampleModel - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
sampleModel - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter

The sample model of the image to be compressed.

SAMPLES_PER_PIXEL - Static variable in class loci.formats.in.DicomReader
 
SAMPLES_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
 
sampleSize - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
SamplesPerPixel() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.SamplesPerPixel
 
samplesPerPixel - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The value of the SamplesPerPixel tag.

samplesPerPixel - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
samplesPerPixel - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
sampleTable - Variable in class loci.formats.in.VolocityReader
 
sampleTime - Variable in class loci.formats.in.GatanReader
 
sanitize(String, boolean) - Method in class loci.formats.gui.XMLCellRenderer.XMLItem

Sanitizes strings to appear correctly in HTML.

sanitizeControl(String) - Static method in class loci.formats.in.NativeND2Reader

Remove control and invalid characters from the given string.

sanitizeFile(String, String) - Method in class loci.formats.in.FV1000Reader
 
sanitizeValue(String) - Method in class loci.formats.in.FV1000Reader
 
Saturation() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.Saturation
 
SATURATION - Static variable in class loci.formats.in.CellSensReader
 
SATURATION - Static variable in class loci.formats.tiff.IFD
 
SATURATION_HIGH - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "Saturation" tag.

SATURATION_LOW - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "Saturation" tag.

SATURATION_NORMAL - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "Saturation" tag.

save() - Method in class jj2000.j2k.codestream.writer.PktEncoder

Saves the current state of this object.

save() - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Saves the current values and state of the tree.

save(String) - Method in class loci.formats.gui.ImageViewer

Saves the current images to the given destination
 using the current format writer.

save(String, IFormatWriter) - Method in class loci.formats.gui.ImageViewer

Saves to the given data destination using the specified writer
 in a separate thread.

save() - Method in class loci.formats.tools.EditTiffG
 
save - Variable in class loci.plugins.prefs.Option

Whether option state should be saved to ImageJ preferences file.

SAVE_FILE_SIZE - Static variable in class loci.formats.out.AVIWriter
 
SAVE_JUNK_SIG - Static variable in class loci.formats.out.AVIWriter
 
SAVE_LIST1_SIZE - Static variable in class loci.formats.out.AVIWriter
 
SAVE_LIST1_SUBSIZE - Static variable in class loci.formats.out.AVIWriter
 
SAVE_LIST2_SIZE - Static variable in class loci.formats.out.AVIWriter
 
SAVE_MOVI - Static variable in class loci.formats.out.AVIWriter
 
SAVE_STRF_SIZE - Static variable in class loci.formats.out.AVIWriter
 
SAVE_STRN_POS - Static variable in class loci.formats.out.AVIWriter
 
saveBytes(int, byte[]) - Method in class loci.formats.FormatWriter
 
saveBytes(int, byte[], Region) - Method in class loci.formats.FormatWriter
 
saveBytes(int, byte[]) - Method in interface loci.formats.IFormatWriter

Saves the given image to the current series in the current file.

saveBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.IFormatWriter

Saves the given image tile to the current series in the current file.

saveBytes(int, byte[], Region) - Method in interface loci.formats.IFormatWriter

Saves the given image tile to the current series in the current file.

saveBytes(int, byte[]) - Method in class loci.formats.ImageWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageWriter
 
saveBytes(int, byte[], Region) - Method in class loci.formats.ImageWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.APNGWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.AVIWriter
 
saveBytes(int, byte[]) - Method in class loci.formats.out.CellH5Writer

Saves the given image to the specified (possibly already open) file.

saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.CellH5Writer
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.EPSWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ICSWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JavaWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.LegacyQTWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
 
saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMEXMLWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.QTWriter
 
saveBytes(int, byte[], IFD) - Method in class loci.formats.out.TiffWriter

Saves the given image to the specified (possibly already open) file.

saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.TiffWriter

Saves the given image to the specified series in the current file.

saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.TiffWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.V3DrawWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.WlzWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.services.WlzService

Adds a rectangle of bytes in an x-y plane to the opened Woolz object.

saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.services.WlzServiceImpl
 
saveBytes(int, byte[]) - Method in class loci.formats.WriterWrapper
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WriterWrapper
 
saveBytes(int, byte[], Region) - Method in class loci.formats.WriterWrapper
 
saveComment(String, String) - Method in class loci.formats.out.OMETiffWriter
 
saved - Variable in class jj2000.j2k.codestream.writer.PktEncoder

The saved state

saved - Variable in class jj2000.j2k.codestream.writer.TagTreeEncoder

The saved state.

SAVED_INC - Static variable in class jj2000.j2k.entropy.encoder.MQCoder

The increase in length for the arrays to save states

SAVED_LEN - Static variable in class jj2000.j2k.entropy.encoder.MQCoder

The initial length of the arrays to save sates

savedA - Variable in class jj2000.j2k.entropy.encoder.MQCoder

Saved values of the A register.

savedB - Variable in class jj2000.j2k.entropy.encoder.MQCoder

Saved values of the B byte buffer.

savedbLength - Variable in class loci.formats.out.AVIWriter
 
savedC - Variable in class jj2000.j2k.entropy.encoder.MQCoder

Saved values of the C register.

savedCT - Variable in class jj2000.j2k.entropy.encoder.MQCoder

Saved values of CT counter.

savedDelFF - Variable in class jj2000.j2k.entropy.encoder.MQCoder

Saved values of the delFF (i.e.

saveDefaults() - Method in class loci.plugins.in.ImportProcess

Performed following ImportStep.FILE notification.

savedToMemo - Variable in class loci.formats.Memoizer

Whether the ReaderWrapper.reader instance was saved to a memo file on
 Memoizer.setId(String).

saveFile(File) - Method in class loci.formats.tools.EditTiffG
 
saveidx1Length - Variable in class loci.formats.out.AVIWriter
 
saveImage(int, BufferedImage) - Method in class loci.formats.gui.BufferedImageWriter

Saves the given BufferedImage to the current file.

saveImage(int, BufferedImage, int, int, int, int) - Method in class loci.formats.gui.BufferedImageWriter

Saves the given BufferedImage to the current file.

saveLUTs(ImagePlus, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
 
saveMemo() - Method in class loci.formats.Memoizer

Save a reader including all reader wrappers inside a memo file.

saveOption() - Method in class loci.plugins.prefs.BooleanOption
 
saveOption() - Method in class loci.plugins.prefs.DoubleOption
 
saveOption() - Method in class loci.plugins.prefs.Option

Saves the option's value to the ImageJ preferences file.

saveOption() - Method in class loci.plugins.prefs.StringOption
 
saveOptions() - Method in class loci.plugins.prefs.OptionsList

Saves option values to the ImageJ preferences file.

saveOriginalMetadata - Variable in class loci.formats.FormatReader

Whether or not to save proprietary metadata in the MetadataStore.

savePlane(int, Object) - Method in class loci.formats.FormatWriter
 
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.FormatWriter
 
savePlane(int, Object, Region) - Method in class loci.formats.FormatWriter
 
savePlane(int, Object) - Method in interface loci.formats.IFormatWriter

Saves the given image plane to the current series in the current file.

savePlane(int, Object, int, int, int, int) - Method in interface loci.formats.IFormatWriter

Saves the given image plane to the current series in the current file.

savePlane(int, Object, Region) - Method in interface loci.formats.IFormatWriter

Saves the given image plane to the current series in the current file.

savePlane(int, Object) - Method in class loci.formats.ImageWriter
 
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.ImageWriter
 
savePlane(int, Object, Region) - Method in class loci.formats.ImageWriter
 
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
 
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.out.LegacyQTWriter
 
savePlane(int, Object) - Method in class loci.formats.WriterWrapper
 
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.WriterWrapper
 
savePlane(int, Object, Region) - Method in class loci.formats.WriterWrapper
 
saveReader(IFormatReader) - Method in interface loci.formats.Memoizer.Deser
 
saveReader(IFormatReader) - Method in class loci.formats.Memoizer.KryoDeser
 
saveReader(IFormatReader) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
saveReleaseVersion(String) - Method in interface loci.formats.Memoizer.Deser
 
saveReleaseVersion(String) - Method in class loci.formats.Memoizer.KryoDeser
 
saveReleaseVersion(String) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
saveRevision(String) - Method in interface loci.formats.Memoizer.Deser
 
saveRevision(String) - Method in class loci.formats.Memoizer.KryoDeser
 
saveRevision(String) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
saveROIs(MetadataStore) - Static method in class loci.plugins.util.ROIHandler

Save ROIs in the ROI manager to the given MetadataStore.

saveStart(File) - Method in interface loci.formats.Memoizer.Deser
 
saveStart(File) - Method in class loci.formats.Memoizer.KryoDeser
 
saveStart(File) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
saveState() - Method in class jj2000.j2k.entropy.encoder.MQCoder

Saves the current state of the MQ coder (just the registers, not the
 contexts) so that a near optimal length calculation can be performed
 later.

saveStop() - Method in interface loci.formats.Memoizer.Deser
 
saveStop() - Method in class loci.formats.Memoizer.KryoDeser
 
saveStop() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
saveStream - Variable in class loci.formats.Memoizer.RandomAccessDeser
 
saveVersion(Integer) - Method in interface loci.formats.Memoizer.Deser
 
saveVersion(Integer) - Method in class loci.formats.Memoizer.KryoDeser
 
saveVersion(Integer) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
sb - Variable in class jj2000.j2k.entropy.encoder.CBlkRateDistStats

The subband to which the code-block belongs

sb - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTData

The subband in which this code-block is found

sb - Variable in class loci.formats.gui.ImageViewer
 
sb - Variable in class loci.formats.in.FEITiffReader.FEIHandler
 
sbandIdx - Variable in class jj2000.j2k.wavelet.Subband

The subband index within its resolution level.

SBIGReader - Class in loci.formats.in

SBIGReader is the file format reader for SBIG files.

SBIGReader() - Constructor for class loci.formats.in.SBIGReader

Constructs a new SBIG reader.

SC_LUT - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Sign Coding context lookup table.

SC_LUT - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Sign Coding context lookup table.

SC_LUT_BITS - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Number of bits used for the Sign Coding lookup table

SC_LUT_BITS - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Number of bits used for the Sign Coding lookup table

SC_LUT_MASK - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The mask to obtain the context index from the 'SC_LUT'

SC_LUT_MASK - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The mask to obtain the context index from the 'SC_LUT'

SC_MASK - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The bit mask to isolate the state bits relative to the sign coding
 lookup table ('SC_LUT').

SC_MASK - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The bit mask to isolate the state bits relative to the sign coding
 lookup table ('SC_LUT').

SC_SHIFT_R1 - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The shift to obtain the SC index to 'SC_LUT' from the 'state'
 information, for row 1.

SC_SHIFT_R1 - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The shift to obtain the SC index to 'SC_LUT' from the state
 information, for row 1.

SC_SHIFT_R2 - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The shift to obtain the SC index to 'SC_LUT' from the state
 information, for row 2.

SC_SHIFT_R2 - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The shift to obtain the SC index to 'SC_LUT' from the state
 information, for row 2.

SC_SPRED_SHIFT - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The shift to obtain the sign predictor from the 'SC_LUT'.

SC_SPRED_SHIFT - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The shift to obtain the sign predictor from the 'SC_LUT'.

scale - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
scale(BufferedImage, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools

Scales the image using the most appropriate API, with the resultant image
 having the same color model as the original image.

SCALE - Static variable in class loci.formats.in.FV1000Reader
 
scale - Variable in class loci.formats.in.NativeQTReader

Amount to subtract from each offset.

scale(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
scale0 - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
scale2D(BufferedImage, int, int, Object, GraphicsConfiguration) - Static method in class loci.formats.gui.AWTImageTools

Scales the image using the Java2D API, with the resultant
 image optimized for the given graphics configuration.

scale2D(BufferedImage, int, int, Object, ColorModel) - Static method in class loci.formats.gui.AWTImageTools

Scales the image using the Java2D API, with the
 resultant image having the given color model.

SCALE_BAR - Static variable in class loci.formats.in.LeicaHandler.ROI
 
SCALE_BAR - Static variable in class loci.formats.in.LIFReader.ROI
 
SCALE_BAR - Static variable in class loci.formats.in.ZeissLSMReader
 
scaleAWT(BufferedImage, int, int, int) - Static method in class loci.formats.gui.AWTImageTools

Scales the image using the AWT Image API.

scaleFactor - Variable in class loci.formats.in.FakeReader

Scale factor for gradient, if any.

scaleFactor - Variable in class loci.formats.in.ZeissCZIReader
 
scaleh - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
scalel - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
scaleX - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

The scaling factors.

scaleX - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState

Source to destination transform

scaleX - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

The source -> destination transformation

scaleX - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader

The scaling factors.

scaleX - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
scaleX - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

The source -> destination transformation

scaleX - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

The subsampling parameters.

scaleX - Variable in class loci.formats.in.LeicaHandler.ROI
 
scaleX - Variable in class loci.formats.in.LIFReader.ROI
 
scaleY - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

The scaling factors.

scaleY - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState

Source to destination transform

scaleY - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

The source -> destination transformation

scaleY - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader

The scaling factors.

scaleY - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
scaleY - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

The source -> destination transformation

scaleY - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage

The subsampling parameters.

scaleY - Variable in class loci.formats.in.LeicaHandler.ROI
 
scaleY - Variable in class loci.formats.in.LIFReader.ROI
 
scaling - Variable in class loci.formats.in.SimplePCITiffReader
 
Scaling() - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling
 
scalingBitDepth - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
scalings - Variable in class loci.formats.in.ZeissTIFFHandler
 
scanData(byte[], int, boolean) - Static method in class loci.formats.ImageTools

Scan a plane for the channel min and max values.

scanDim - Variable in class loci.formats.in.ZeissCZIReader
 
scanDirectory(Location, boolean) - Method in class loci.formats.in.DicomReader

Scan the given directory for files that belong to this dataset.

scanFormat(String, String) - Static method in class loci.formats.in.FV1000Reader
 
SCANNERSET - Static variable in class loci.formats.in.LeicaReader
 
ScanrHandler() - Constructor for class loci.formats.in.ScanrReader.ScanrHandler
 
ScanrReader - Class in loci.formats.in

ScanrReader is the file format reader for Olympus ScanR datasets.

ScanrReader() - Constructor for class loci.formats.in.ScanrReader

Constructs a new ScanR reader.

ScanrReader.ScanrHandler - Class in loci.formats.in
 
scanRX - Variable in class loci.formats.in.SDTInfo
 
scanRY - Variable in class loci.formats.in.SDTInfo
 
scanValues - Variable in class loci.formats.in.PrairieMetadata

Table of key/value pairs at the top level.

scanw - Variable in class jj2000.j2k.image.DataBlk

The width of the scanlines used to store the data in the array

scanw - Variable in class jj2000.j2k.wavelet.analysis.CBlkWTData

The width of the scanlines used to store the data in the array

scanX - Variable in class loci.formats.in.SDTInfo
 
scanY - Variable in class loci.formats.in.SDTInfo
 
SCENE_CAPTURE_TYPE - Static variable in class loci.formats.tiff.IFD
 
SCENE_CAPTURE_TYPE_LANDSCAPE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SceneCaptureType" tag.

SCENE_CAPTURE_TYPE_NIGHT_SCENE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SceneCaptureType" tag.

SCENE_CAPTURE_TYPE_PORTRAIT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SceneCaptureType" tag.

SCENE_CAPTURE_TYPE_STANDARD - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SceneCaptureType" tag.

SCENE_TYPE - Static variable in class loci.formats.tiff.IFD
 
SCENE_TYPE_DSC - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SceneType" tag.

SceneCaptureType() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.SceneCaptureType
 
SceneType() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.SceneType
 
SCHEMA_2010_03 - Static variable in class loci.formats.in.LeicaSCNReader
 
SCHEMA_2010_10 - Static variable in class loci.formats.in.LeicaSCNReader
 
SCHEMA_CLASSPATH_READER - Static variable in class loci.formats.services.OMEXMLServiceImpl

Finds OME-XML schema definitions in specifications.jar.

SCHEMA_PATH - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
SCHEMA_URL_PATTERN - Static variable in class loci.formats.services.OMEXMLServiceImpl

The pattern of system ID URLs for OME-XML schema definitions.

schemaType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
schemaType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
SCNHandler() - Constructor for class loci.formats.in.BioRadSCNReader.SCNHandler
 
scoc - Variable in class jj2000.j2k.codestream.HeaderInfo.COC
 
scod - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
SCOX_HOR_CB_PART - Static variable in interface jj2000.j2k.codestream.Markers

Horizontal code-block partition origin is at x=1

SCOX_PRECINCT_PARTITION - Static variable in interface jj2000.j2k.codestream.Markers

Precinct used flag

SCOX_USE_EPH - Static variable in interface jj2000.j2k.codestream.Markers

Use end of packet header marker

SCOX_USE_SOP - Static variable in interface jj2000.j2k.codestream.Markers

Use start of packet marker

SCOX_VER_CB_PART - Static variable in interface jj2000.j2k.codestream.Markers

Vertical code-block partition origin is at y=1

SCREENING - Static variable in class loci.formats.in.FlexReader
 
screenName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
ScreenReader - Class in loci.formats.in

ScreenReader is a generic reader for files in non-HCS formats that have been
 organized into a screen.

ScreenReader() - Constructor for class loci.formats.in.ScreenReader

Constructs a new screen reader.

SDTInfo - Class in loci.formats.in

SDTInfo encapsulates the header information for
 Becker & Hickl SPC-Image SDT files.

SDTInfo(RandomAccessInputStream, Hashtable) - Constructor for class loci.formats.in.SDTInfo

Constructs a new SDT header by reading values from the given input source,
 populating the given metadata table.

SDTReader - Class in loci.formats.in

SDTReader is the file format reader for
 Becker & Hickl SPC-Image SDT files.

SDTReader() - Constructor for class loci.formats.in.SDTReader

Constructs a new SDT reader.

SDTWidgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats SDT support.

SDTWidgets() - Constructor for class loci.plugins.config.SDTWidgets
 
SearchableWindow - Class in loci.plugins.util

Text panel with search capabilities.

SearchableWindow(String, String, String, int, int) - Constructor for class loci.plugins.util.SearchableWindow
 
SearchableWindow.SearchBox - Class in loci.plugins.util
 
SearchBox(SearchableWindow) - Constructor for class loci.plugins.util.SearchableWindow.SearchBox
 
searchBox - Variable in class loci.plugins.util.SearchableWindow.SearchBox
 
searchPane - Variable in class loci.plugins.util.SearchableWindow.SearchBox
 
SectorStreamSegmentMapper - Class in com.sun.media.imageio.stream

An implementation of the StreamSegmentMapper interface
 for segments of equal length.

SectorStreamSegmentMapper(long[], int, int) - Constructor for class com.sun.media.imageio.stream.SectorStreamSegmentMapper
 
SEED - Static variable in class loci.formats.in.FakeReader
 
seek(long) - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream

Invokes the superclass method and sets the position within the
 memory mapped buffer.

seek(long) - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream

Invokes the superclass method, writes any unwritten data,
 and sets the channel position to the supplied parameter.

seek(long) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
seek(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
seek(int) - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Moves the current position to the given offset at which the
 next read or write occurs.

seek(int) - Method in interface jj2000.j2k.io.RandomAccessIO

Moves the current position for the next read or write operation to
 offset.

seek(int) - Method in class jj2000.j2k.util.ISRandomAccessIO

Moves the current position for the next read operation to
 offset.

seekStartOfPlane(int, long, long) - Method in class loci.formats.in.LIFReader
 
seekToImage(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
seekToNextMarker() - Method in class loci.formats.in.ZeissLMSReader
 
seekToPlaneOffset(long, int, int) - Method in class loci.formats.FormatWriter

Seek to the given (x, y) coordinate of the image that starts at
 the given offset.

SEG_SYMB_CTXTS - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The 4 contexts for the segmentation marker (always the UNIFORM context,
 UNIF_CTXT)

SEG_SYMBOL - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The 4 symbol segmentation marker (decimal 10, which is binary sequence
        1010)

SEG_SYMBOLS - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The 4 symbol segmentation marker (1010)

segLen - Variable in class jj2000.j2k.codestream.reader.CBlkInfo

The length of each segment (used with regular termination or
 in selective arithmetic bypass coding mode)

segLengths - Variable in class jj2000.j2k.codestream.reader.PktInfo

The length of each terminated segment in the packet.

Segment() - Constructor for class loci.formats.in.ZeissCZIReader.Segment
 
Segment(String) - Constructor for class loci.formats.in.ZeissCZIReader.Segment
 
Segment(ZeissCZIReader.Segment) - Constructor for class loci.formats.in.ZeissCZIReader.Segment
 
SEGMENTATION_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
SegmentedImageInputStream - Class in com.sun.media.imageio.stream

A SegmentedImageInputStream provides a view of a
 subset of another ImageInputStream consiting of a series
 of segments with given starting positions in the source stream and
 lengths.

SegmentedImageInputStream(ImageInputStream, StreamSegmentMapper) - Constructor for class com.sun.media.imageio.stream.SegmentedImageInputStream

Constructs a SegmentedImageInputStream
 given a ImageInputStream as input
 and an instance of StreamSegmentMapper.

SegmentedImageInputStream(ImageInputStream, long[], int[]) - Constructor for class com.sun.media.imageio.stream.SegmentedImageInputStream

Constructs a SegmentedImageInputStream given a
 ImageInputStream as input and a list of the starting
 positions and lengths of the segments of the source stream.

SegmentedImageInputStream(ImageInputStream, long[], int, int) - Constructor for class com.sun.media.imageio.stream.SegmentedImageInputStream

Constructs a SegmentedImageInputStream given a
 ImageInputStream as input, a list of the starting
 positions of the segments of the source stream, the common
 length of each segment, and the total length of the segments.

segmentLength - Variable in class com.sun.media.imageio.stream.SectorStreamSegmentMapper
 
segmentLength - Variable in class com.sun.media.imageio.stream.StreamSegment
 
segmentLengths - Variable in class com.sun.media.imageio.stream.StreamSegmentMapperImpl
 
segmentPositions - Variable in class com.sun.media.imageio.stream.SectorStreamSegmentMapper
 
segmentPositions - Variable in class com.sun.media.imageio.stream.StreamSegmentMapperImpl
 
segments - Variable in class loci.formats.in.ZeissCZIReader
 
SeikoReader - Class in loci.formats.in

SeikoReader is the file format reader for Seiko .xqd/.xqf files.

SeikoReader() - Constructor for class loci.formats.in.SeikoReader

Constructs a new Seiko reader.

seleBand - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

Indicates whether subband is selected.

seleBand - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader

Indicates whether subband is selected.

selectConvexHull(int[], double[], boolean[], int, boolean) - Method in class jj2000.j2k.entropy.encoder.CBlkRateDistStats

Compute the rate-distorsion slopes and selects those that lie in a
 convex hull.

SELECTED_CHANNELS - Static variable in class loci.formats.in.CellSensReader
 
SELECTED_FRAMES - Static variable in class loci.formats.in.CellSensReader
 
selectLine(int) - Method in class loci.plugins.util.SearchableWindow
 
SEM_DOMAIN - Static variable in class loci.formats.FormatTools

Identifies the scanning electron microscopy domain.

SENSING_METHOD - Static variable in class loci.formats.tiff.IFD
 
SENSING_METHOD_COLOR_SEQUENTIAL_AREA_SENSOR - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SensingMethod" tag.

SENSING_METHOD_COLOR_SEQUENTIAL_LINEAR_SENSOR - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SensingMethod" tag.

SENSING_METHOD_NOT_DEFINED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SensingMethod" tag.

SENSING_METHOD_ONE_CHIP_COLOR_AREA_SENSOR - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SensingMethod" tag.

SENSING_METHOD_THREE_CHIP_COLOR_AREA_SENSOR - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SensingMethod" tag.

SENSING_METHOD_TRILINEAR_SENSOR - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SensingMethod" tag.

SENSING_METHOD_TWO_CHIP_COLOR_AREA_SENSOR - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "SensingMethod" tag.

SensingMethod() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.SensingMethod
 
SENSOR_KEYS - Static variable in class loci.formats.in.ICSReader
 
sensorHeight - Variable in class loci.formats.in.MRWReader
 
sensorWidth - Variable in class loci.formats.in.MRWReader
 
separatedFork - Variable in class loci.formats.in.NativeQTReader

Flag indicating whether the resource and data fork are separated.

SEQ_FILTERSET - Static variable in class loci.formats.in.LeicaReader
 
SEQ_FILTERSET_END - Static variable in class loci.formats.in.LeicaReader
 
SEQ_SCANNERSET - Static variable in class loci.formats.in.LeicaReader
 
SEQ_SCANNERSET_END - Static variable in class loci.formats.in.LeicaReader
 
SEQReader - Class in loci.formats.in

SEQReader is the file format reader for Image-Pro Sequence files.

SEQReader() - Constructor for class loci.formats.in.SEQReader

Constructs a new Image-Pro SEQ reader.

sequence - Variable in class loci.formats.in.PrairieMetadata.Frame

The <Sequence> containing this <Frame>.

Sequence(Element) - Constructor for class loci.formats.in.PrairieMetadata.Sequence

Creates a new sequence by parsing the given <Sequence> element.

sequence(int) - Method in class loci.formats.in.PrairieReader

Gets the first sequence associated with the given series.

sequence(int, int) - Method in class loci.formats.in.PrairieReader

Gets the sequence associated with the given series and time point.

sequence(int, int, int) - Method in class loci.formats.in.PrairieReader

Gets the sequence associated with the given time point and stage position.

SEQUENCE_DELIMINATION - Static variable in class loci.formats.in.DicomReader
 
sequenceComplete(ImageReader) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader.EmbeddedProgressAdapter
 
sequences - Variable in class loci.formats.in.PrairieMetadata

<Sequence> elements, keyed on each sequence's cycle.

sequences - Variable in class loci.formats.in.PrairieReader

List of Prairie metadata Sequences, ordered by cycle.

sequenceStarted(ImageReader, int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader.EmbeddedProgressAdapter
 
sequenceValues - Variable in class loci.formats.in.PrairieMetadata.Sequence

Table of key/value pairs for this <Sequence>.

sequential - Variable in class loci.formats.FormatWriter

Whether or not we are writing planes sequentially.

sequential - Variable in class loci.formats.in.LeicaReader
 
SEQUENTIALSET - Static variable in class loci.formats.in.LeicaReader
 
sequentialTileFilePointer - Variable in class loci.formats.tiff.TiffSaver
 
sequentialTileOffsets - Variable in class loci.formats.tiff.TiffSaver

Store tile offsets and original file pointer when writing sequentially.

sequentialWrite - Variable in class loci.formats.tiff.TiffSaver
 
ser - Variable in class loci.formats.Memoizer
 
SERIALIZED_MASK - Static variable in class loci.formats.in.CellSensReader
 
serialNumber - Variable in class loci.formats.in.BioRadSCNReader
 
serialNumber - Variable in class loci.formats.in.LIFReader
 
serialNumber - Variable in class loci.formats.in.NDPIReader
 
serialVersionUID - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
 
series - Variable in class loci.formats.FileStitcher

The number of the current series (non flat).

series - Variable in class loci.formats.FormatReader

The number of the current series (non flat).

series - Variable in class loci.formats.FormatWriter

Current series.

series - Variable in class loci.formats.gui.DataConverter
 
series - Variable in class loci.formats.in.ColumbusReader.Plane
 
SERIES - Static variable in class loci.formats.in.LeicaReader

IFD tags.

series - Variable in class loci.formats.in.OBFReader.Frame
 
series - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
series - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
 
series - Variable in class loci.plugins.macro.LociFunctions
 
series - Variable in class loci.plugins.util.BFVirtualStack
 
SERIES_NAME - Static variable in class loci.formats.FormatTools
 
SERIES_NUM - Static variable in class loci.formats.FormatTools

Patterns to be used when constructing a pattern for output filenames.

seriesCount - Variable in class loci.formats.in.CellH5Reader
 
seriesCount - Variable in class loci.formats.in.ImarisHDFReader
 
seriesCounts - Variable in class loci.formats.in.ZeissLSMReader
 
seriesDescriptions - Variable in class loci.formats.in.LeicaReader
 
SeriesDialog - Class in loci.plugins.in

Bio-Formats Importer series chooser dialog box.

SeriesDialog(ImportProcess) - Constructor for class loci.plugins.in.SeriesDialog

Creates a series chooser dialog for the Bio-Formats Importer.

seriesFiles - Variable in class loci.formats.in.ScanrReader
 
seriesIndex - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
seriesInfo - Variable in class loci.formats.in.MNGReader
 
SeriesInfo() - Constructor for class loci.formats.in.MNGReader.SeriesInfo
 
SeriesInfo(int, int) - Constructor for class loci.plugins.in.ThumbLoader.SeriesInfo
 
seriesLabels - Variable in class loci.plugins.in.ImportProcess

A descriptive label for each series.

seriesMetadata - Variable in class loci.formats.CoreMetadata

Non-core metadata associated with this series.

seriesNames - Variable in class loci.formats.in.LeicaReader
 
seriesOn - Variable in class loci.plugins.in.ImporterOptions
 
seriesRow - Variable in class loci.formats.gui.DataConverter
 
seriesStream - Variable in class loci.formats.in.BrukerReader
 
seriesToCoreIndex(int) - Method in class loci.formats.FileStitcher
 
seriesToCoreIndex(int) - Method in class loci.formats.FormatReader
 
seriesToCoreIndex(int) - Method in interface loci.formats.IFormatReader

Returns the first core index corresponding to the specified series.

seriesToCoreIndex(int) - Method in class loci.formats.ImageReader
 
seriesToCoreIndex(int) - Method in class loci.formats.in.FilePatternReader
 
seriesToCoreIndex(int) - Method in class loci.formats.ReaderWrapper
 
seriesToWellArea(int) - Method in class loci.formats.in.CellVoyagerReader

Returns the well index (in the field CellVoyagerReader.wells) and the area index
 (in the field CellVoyagerReader.WellInfo.areas corresponding to the specified
 series.

serverMap - Static variable in class loci.formats.in.FlexReader

Mapping from server names stored in the .mea file to actual server names.

service - Variable in class loci.formats.codec.JPEG2000Codec
 
service - Variable in class loci.formats.codec.JPEGXRCodec
 
service - Variable in class loci.formats.codec.LuraWaveCodec
 
service - Variable in class loci.formats.FormatReader
 
service - Variable in class loci.formats.in.CellWorxReader
 
service - Variable in class loci.formats.in.HamamatsuVMSReader
 
service - Variable in class loci.formats.in.NDPIReader
 
service - Variable in class loci.formats.in.OMETiffReader
 
service - Variable in class loci.formats.in.TileJPEGReader
 
service - Variable in class loci.formats.Memoizer
 
service - Variable in class loci.formats.out.OMETiffWriter
 
service - Variable in class loci.formats.out.OMEXMLWriter
 
serviceRegistry - Variable in class loci.formats.services.JAIIIOServiceImpl
 
set(String, String) - Method in class loci.formats.in.DynamicMetadataOptions

Set property name to value.

set(List<T>, int, T, T) - Method in class loci.plugins.in.ImporterOptions
 
set(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
set(int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setActiveSrcHeight(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the activeSrcHeight field.

setActiveSrcHeight(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setActiveSrcMinX(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the activeSrcMinX field.

setActiveSrcMinX(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setActiveSrcMinY(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the activeSrcMinY field.

setActiveSrcMinY(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setActiveSrcWidth(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the activeSrcWidth field.

setActiveSrcWidth(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setAlignROI(boolean) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets alignROI

setAllowOpenFiles(boolean) - Method in class loci.formats.ImageReader

Toggles whether or not file system access is allowed when doing type
 detection.

setAntialiasedText(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
setAssumeEqualStrips(boolean) - Method in class loci.formats.tiff.TiffParser

Sets whether or not to assume that strips are of equal size.

setAutomaticallyParseMasks(boolean) - Method in class loci.formats.in.MIASReader

Toggle whether or not Mask pixel data should be parsed in setId.

setAutoscale(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setAutoThreshold(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setAxisTypes(int[]) - Method in class loci.formats.AxisGuesser

Sets the axis type for each dimensional block.

setAxisTypes(int[]) - Method in class loci.formats.FileStitcher

Sets the axis type for each dimensional block.

setBackgroundValue(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
setBigTiff(boolean) - Method in class loci.formats.out.TiffWriter

Sets whether or not BigTIFF files should be written.

setBigTiff(boolean) - Method in class loci.formats.tiff.TiffSaver

Sets whether or not BigTIFF data should be written.

setBitOffset(int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
setBitsPerSample(int[]) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the bitsPerSample field.

setBitsPerSample(int[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions

Set property name to Boolean value.

setBypass(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets bypass

setByte(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader

Private method used to set a Byte value in the SPE header

setByteArray(byte[], int, int) - Method in class jj2000.j2k.entropy.decoder.ByteInputBuffer

Sets the underlying buffer byte array to the given one, with the given
 offset and length.

setByteArray(byte[], int, int) - Method in class jj2000.j2k.entropy.decoder.ByteToBitInput

Resets the underlying byte input to start a new segment.

setByteCount(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the byteCount field.

setByteCount(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setByteOrder(ByteOrder) - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream
 
setByteOrder(ByteOrder) - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream
 
setByteOrder(ByteOrder) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
setCalibrationTable(float[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
setCanChangePattern(boolean) - Method in class loci.formats.FileStitcher
 
setCanDoUpgradeCheck(boolean) - Method in class loci.formats.UpgradeChecker

Set whether or not we are ever allowed to perform an upgrade check.

setCanLookForND(boolean) - Method in class loci.formats.in.MetamorphReader
 
setCategory(int) - Method in class loci.formats.in.BaseZeissReader.Tag
 
setCausalCXInfo(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets causalCXInfo

setCBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setCEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setChannelGlobalMinMax(int, double, double, int) - Method in interface loci.formats.meta.IMinMaxStore

Populates the channel global minimum and maximum.

setClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions

Set property name to Class value.

setClipRect(Rectangle) - Method in class loci.plugins.util.RecordedImageProcessor
 
setCodeBlockSize(int[]) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Sets codeBlockSize.

setCodeBlockSize(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets codeBlockSize

setCodec(int) - Method in class loci.formats.out.LegacyQTWriter

Sets the encoded movie's codec.

setCodec(int) - Method in class loci.formats.out.QTWriter

Sets the encoded movie's codec.

setCodec() - Method in class loci.formats.out.QTWriter
 
setCodecOptions(CodecOptions) - Method in class loci.formats.FormatWriter
 
setCodecOptions(CodecOptions) - Method in interface loci.formats.IFormatWriter

Sets the codec options.

setCodecOptions(CodecOptions) - Method in class loci.formats.ImageWriter
 
setCodecOptions(CodecOptions) - Method in class loci.formats.tiff.TiffParser

Sets the codec options to be used when decompressing pixel data.

setCodecOptions(CodecOptions) - Method in class loci.formats.tiff.TiffSaver

Sets the codec options.

setCodecOptions(CodecOptions) - Method in class loci.formats.WriterWrapper
 
setCodeSegSymbol(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets codeSegSymbol

setColor(Color) - Method in class loci.plugins.util.RecordedImageProcessor
 
setColor(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setColorConverter(TIFFColorConverter) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the TIFFColorConverter object describing the color
 space of the encoded data in the input stream.

setColorConverter(TIFFColorConverter) - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam

Sets the TIFFColorConverter object for the pixel data
 being read.

setColorConverter(TIFFColorConverter, int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam

Sets the TIFFColorConverter object describing the
 color space to which the input data should be converted for
 storage in the input stream.

setColorMap(char[]) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the colorMap field.

setColorMap(char[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setColorMode(String) - Method in class loci.plugins.in.ImporterOptions
 
setColorModel(ColorModel) - Method in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
setColorModel(ColorModel) - Method in class loci.formats.FormatWriter
 
setColorModel(ColorModel) - Method in interface loci.formats.IFormatWriter

Sets the color model.

setColorModel(ColorModel) - Method in class loci.formats.ImageWriter
 
setColorModel(ColorModel) - Method in class loci.formats.WriterWrapper
 
setColorModel(ColorModel) - Method in class loci.plugins.util.RecordedImageProcessor
 
setCompDef(int, Object) - Method in class jj2000.j2k.entropy.CBlkSizeSpec

Sets default value for specified component and specValType tag if
 allowed by its priority.

setCompDef(int, Object) - Method in class jj2000.j2k.ModuleSpec

Sets default value for specified component and specValType tag if
 allowed by its priority.

setComponentTransformation(boolean) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Sets componentTransformation.

setComponentTransformation(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets componentTransformation

setCompression(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the compression field.

setCompression(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setCompression(String) - Method in class loci.formats.FormatWriter
 
setCompression(String) - Method in interface loci.formats.IFormatWriter

Sets the current compression type.

setCompression(String) - Method in class loci.formats.ImageWriter
 
setCompression(String) - Method in class loci.formats.WriterWrapper
 
setCompressionMode(int) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriteParam
 
setCompressionType(String) - Method in class com.sun.media.imageio.plugins.bmp.BMPImageWriteParam

Sets the compression type to one of the values indicated by
 getCompressionTypes.

setConcatenate(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setContent(byte[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Sets the box content.

setCoreIndex(int) - Method in class loci.formats.DelegateReader
 
setCoreIndex(int) - Method in class loci.formats.FileStitcher
 
setCoreIndex(int) - Method in class loci.formats.FormatReader
 
setCoreIndex(int) - Method in interface loci.formats.IFormatReader

Set the current resolution/series (ignores subresolutions).

setCoreIndex(int) - Method in class loci.formats.ImageReader
 
setCoreIndex(int) - Method in class loci.formats.in.FilePatternReader
 
setCoreIndex(int) - Method in class loci.formats.ReaderWrapper
 
setCrop(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setCropRegion(int, Region) - Method in class loci.plugins.in.ImporterOptions
 
setCStep(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setCurrentPos(int[]) - Method in class loci.formats.cache.Cache

Sets the current dimensional position.

setCustomColor(int, int, Color) - Method in class loci.plugins.in.ImporterOptions
 
setData(Object) - Method in class jj2000.j2k.image.DataBlk

Sets the data array to the specified one.

setData(Object) - Method in class jj2000.j2k.image.DataBlkFloat

Sets the data array to the specified one.

setData(Object) - Method in class jj2000.j2k.image.DataBlkInt

Sets the data array to the specified one.

setData(Object) - Method in class jj2000.j2k.wavelet.analysis.CBlkWTData

Sets the data array to the specified one.

setData(Object) - Method in class jj2000.j2k.wavelet.analysis.CBlkWTDataFloat

Sets the data array to the specified one.

setData(Object) - Method in class jj2000.j2k.wavelet.analysis.CBlkWTDataInt

Sets the data array to the specified one.

setDataFloat(float[]) - Method in class jj2000.j2k.image.DataBlkFloat

Sets the data array to the specified one.

setDataFloat(float[]) - Method in class jj2000.j2k.wavelet.analysis.CBlkWTDataFloat

Sets the data array to the specified one.

setDataInt(int[]) - Method in class jj2000.j2k.image.DataBlkInt

Sets the data array to the specified one.

setDataInt(int[]) - Method in class jj2000.j2k.wavelet.analysis.CBlkWTDataInt

Sets the data array to the specified one.

setDataType(String) - Method in class loci.formats.in.InveonReader
 
setDecodingRate(double) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageReadParam

Sets decodingRate.

setDecompositionLevel(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets decompositionLevel

setDefault(Object) - Method in class jj2000.j2k.entropy.CBlkSizeSpec

Sets default value for this module

setDefault(Object) - Method in class jj2000.j2k.ModuleSpec

Sets default value for this module

setDefaultAttributes(IIOMetadataNode) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Sets the default attributes, "Length", "Type", and "ExtraLength", to
  the provided IIOMetadataNode.

setDefaultCreationDate(MetadataStore, String, int) - Static method in class loci.formats.MetadataTools

Sets a default creation date.

setDefaultDateEnabled(boolean) - Static method in class loci.formats.MetadataTools

Disables the setting of a default creation date.

setDefaults() - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Set source

setDefaults(Raster) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Set source

setDefaults(RenderedImage) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Set source

setDefaults() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
 
setDestImage(BufferedImage) - Method in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
setDestinationBands(int[]) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the destinationBands field.

setDestinationBands(int[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDimensions(int, int) - Method in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
setDoCaching(boolean) - Method in class loci.formats.tiff.TiffParser

Sets whether or not IFD entries should be cached.

setDocument(Document) - Method in class loci.formats.gui.XMLWindow

Displays XML from the given document.

setDocumentLocator(Locator) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
setDoRecording(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
setDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions

Set property name to Double value.

setDstHeight(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the dstHeight field.

setDstHeight(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstMinX(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the dstMinX field.

setDstMinX(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstMinY(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the dstMinY field.

setDstMinY(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstWidth(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the dstWidth field.

setDstWidth(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstXOffset(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the dstXOffset field.

setDstXOffset(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstYOffset(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the dstYOffset field.

setDstYOffset(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
 
setElem(int, int, int) - Method in class loci.formats.gui.SignedByteBuffer
 
setElem(int, int, int) - Method in class loci.formats.gui.SignedShortBuffer
 
setElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setElem(int, int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setElemDouble(int, double) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setElemDouble(int, int, double) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setElemFloat(int, float) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setElemFloat(int, int, float) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setEncodingRate(double) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Sets encodingRate.

setEncodingRate(double) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets encodingRate

setEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions

Set property name to enumerated type value.

setEPH(boolean) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Sets EPH.

setEPH(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets EPH

setExtraLength(long) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Sets the box extra length length to the provided value.

setExtraSamples(int[]) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the extraSamples field.

setExtraSamples(int[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setf(int, float) - Method in class loci.plugins.util.RecordedImageProcessor
 
setf(int, int, float) - Method in class loci.plugins.util.RecordedImageProcessor
 
setFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions

Set property name to file object value.

setFile(String) - Method in interface loci.formats.services.JHDFService

Initializes the service on a given file path.

setFile(String) - Method in class loci.formats.services.JHDFServiceImpl
 
setFile(String) - Method in interface loci.formats.services.NetCDFService

Initializes the service on a given file path.

setFile(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
setFileForWrite(String) - Method in interface loci.formats.services.JHDFService

Initializes the service on a given file path.

setFileForWrite(String) - Method in class loci.formats.services.JHDFServiceImpl
 
setFilled(boolean) - Method in class loci.formats.ChannelFiller

Toggles whether the indices should be factored out.

setFilter(String) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Sets filter.

setFilters(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets filters

setFirstTime(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setFixed() - Method in class loci.formats.FilePatternBlock
 
setFlattenedResolutions(boolean) - Method in class loci.formats.DelegateReader
 
setFlattenedResolutions(boolean) - Method in class loci.formats.FormatReader
 
setFlattenedResolutions(boolean) - Method in interface loci.formats.IFormatReader

Set whether or not to flatten resolutions into individual series.

setFlattenedResolutions(boolean) - Method in class loci.formats.ImageReader
 
setFlattenedResolutions(boolean) - Method in class loci.formats.in.FilePatternReader
 
setFlattenedResolutions(boolean) - Method in class loci.formats.ReaderWrapper
 
setFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions

Set property name to Float value.

setFloatArray(float[][]) - Method in class loci.plugins.util.RecordedImageProcessor
 
setFont(Font) - Method in class loci.plugins.util.RecordedImageProcessor
 
setForceThumbnails(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setFramesPerSecond(int) - Method in class loci.formats.FormatWriter
 
setFramesPerSecond(int) - Method in interface loci.formats.IFormatWriter

Sets the frames per second to use when writing.

setFramesPerSecond(int) - Method in class loci.formats.ImageWriter
 
setFramesPerSecond(int) - Method in class loci.formats.WriterWrapper
 
setFromTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
setFromTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
setFromTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableImageMetadata
 
setFromTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFWritableStreamMetadata
 
setFromTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
setFromTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
setFromTree(String, Node) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
setGroupFiles(boolean) - Method in class loci.formats.DelegateReader
 
setGroupFiles(boolean) - Method in class loci.formats.FileStitcher
 
setGroupFiles(boolean) - Method in class loci.formats.FormatReader
 
setGroupFiles(boolean) - Method in interface loci.formats.IFormatReader

Specifies whether or not to force grouping in multi-file formats.

setGroupFiles(boolean) - Method in class loci.formats.ImageReader
 
setGroupFiles(boolean) - Method in class loci.formats.in.FilePatternReader
 
setGroupFiles(boolean) - Method in class loci.formats.in.ZipReader
 
setGroupFiles(boolean) - Method in class loci.formats.ReaderWrapper
 
setGroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setGroupFiles(String) - Method in class loci.plugins.macro.LociFunctions
 
setGuardBits(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets guardBits

setHeader(byte[]) - Method in class loci.formats.in.SPEReader.SpeHeader
 
setHeaderEncoder(HeaderEncoder) - Method in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

Keep a reference to the header encoder.

setHeight(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
setHints(int) - Method in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
setHistogramRange(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
setHistogramSize(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setId(String) - Method in class loci.formats.ChannelFiller
 
setId(String) - Method in class loci.formats.ChannelSeparator
 
setId(String) - Method in class loci.formats.DelegateReader
 
setId(String) - Method in class loci.formats.DimensionSwapper
 
setId(String) - Method in class loci.formats.FileStitcher
 
setId(String) - Method in class loci.formats.FormatReader

Initializes a reader from the input file name.

setId(String) - Method in class loci.formats.FormatWriter

Initializes a writer from the input file name.

setId(String) - Method in interface loci.formats.IFormatHandler

Sets the current file name.

setId(String) - Method in class loci.formats.ImageReader
 
setId(String) - Method in class loci.formats.ImageWriter
 
setId(String) - Method in class loci.formats.in.JPEGReader
 
setId(String) - Method in class loci.formats.Memoizer
 
setId(String) - Method in class loci.formats.out.APNGWriter
 
setId(String) - Method in class loci.formats.out.AVIWriter
 
setId(String) - Method in class loci.formats.out.CellH5Writer
 
setId(String) - Method in class loci.formats.out.ICSWriter
 
setId(String) - Method in class loci.formats.out.JavaWriter
 
setId(String) - Method in class loci.formats.out.OMETiffWriter
 
setId(String) - Method in class loci.formats.out.OMEXMLWriter
 
setId(String) - Method in class loci.formats.out.QTWriter
 
setId(String) - Method in class loci.formats.out.TiffWriter
 
setId(String) - Method in class loci.formats.out.V3DrawWriter
 
setId(String) - Method in class loci.formats.out.WlzWriter
 
setId(String) - Method in class loci.formats.ReaderWrapper
 
setId(String) - Method in class loci.formats.TileStitcher
 
setId(String) - Method in class loci.formats.WriterWrapper
 
setId(String) - Method in class loci.plugins.in.ImporterOptions
 
setId() - Method in class loci.plugins.in.ImportProcess

HACK: This method mainly exists to prompt the user for a missing
 LuraWave license code, in the case of LWF-compressed Flex.

setId(String) - Method in class loci.plugins.macro.LociFunctions
 
setImage(BufferedImage) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the image field.

setImage(BufferedImage) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setImages(BufferedImage[]) - Method in class loci.formats.gui.ImageViewer

Sets the viewer to display the given images.

setImages(IFormatReader, BufferedImage[]) - Method in class loci.formats.gui.ImageViewer

Sets the viewer to display the given images, obtaining
 corresponding core metadata from the specified format reader.

setImgResLevel(int) - Method in interface jj2000.j2k.wavelet.synthesis.InvWT

Sets the image reconstruction resolution level.

setImgResLevel(int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Sets the image reconstruction resolution level.

setIndex(int) - Method in class loci.formats.in.BaseZeissReader.Tag
 
setInput(Object, boolean, boolean) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

Overrides the method defined in the superclass.

setInput(Object, boolean, boolean) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader

Overrides the method defined in the superclass.

setInput(Object, boolean, boolean) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
setInput(Object, boolean, boolean) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader

Overrides the method defined in the superclass.

setInput(Object, boolean, boolean) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader

Overrides the method defined in the superclass.

setInput(Object, boolean, boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
setInput(Object, boolean, boolean) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader

Overrides the method defined in the superclass.

setInput(RandomAccessIO) - Method in class jj2000.j2k.codestream.reader.PktHeaderBitReader

Sets the underlying byte based input to the given object.

setInput(ByteArrayInputStream) - Method in class jj2000.j2k.codestream.reader.PktHeaderBitReader

Sets the underlying byte based input to the given object.

setInputOrder(int, String) - Method in class loci.plugins.in.ImporterOptions
 
setInt(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader

Private method used to set an Integer value in the SPE header

setIntArray(int[][]) - Method in class loci.plugins.util.RecordedImageProcessor
 
setInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions

Set property name to Integer value.

setIntensity(boolean) - Method in class loci.formats.in.SDTReader

Toggles whether the reader should return intensity
 data only (the sum of each lifetime histogram).

setInterleaved(boolean) - Method in class loci.formats.FormatWriter
 
setInterleaved(boolean) - Method in interface loci.formats.IFormatWriter

Sets whether or not the channels in an image are interleaved.

setInterleaved(boolean) - Method in class loci.formats.ImageWriter
 
setInterleaved(boolean) - Method in class loci.formats.WriterWrapper
 
setInterpolate(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
setJPEGImage(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor

Associate the JPEG image of length imageSize bytes stored in
 jpegImage with this decompressor instance.

setJPEGQuality(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor

Set the JPEG image quality level for subsequent compress operations.

setJustification(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setKey(int) - Method in class loci.formats.in.BaseZeissReader.Tag
 
setKeyValue(String, String) - Method in class loci.formats.meta.OriginalMetadataAnnotation

Set the key/value metadata pair for this annotation.

setLayers(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets the layers

setLegacy(boolean) - Method in class loci.formats.DelegateReader

Sets whether to use the legacy reader by default.

setLegacy(boolean) - Method in class loci.formats.in.PictReader

Control whether or not legacy reader (QT Java) is used.

setLenCalcType(int) - Method in class jj2000.j2k.entropy.encoder.MQCoder

Set the length calculation type to the specified type

setLength(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.Box

Sets the box length to the provided value.

setLicenseCode(String) - Method in interface loci.formats.services.LuraWaveService

Overrides the license code to use when initializing the LuraWave decoder.

setLicenseCode(String) - Method in class loci.formats.services.LuraWaveServiceImpl
 
setLineWidth(int) - Method in class jj2000.j2k.util.MsgPrinter

Sets the line width to the specified value.

setLineWidth(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setLittleEndian(boolean) - Method in class loci.formats.tiff.TiffSaver

Sets whether or not little-endian data should be written.

setLocation(String) - Method in class loci.plugins.in.ImporterOptions
 
setLong(String, Long) - Method in class loci.formats.in.DynamicMetadataOptions

Set property name to Long value.

setLong(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader

Private method used to set a Long value in the SPE header

setLossless(boolean) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Sets lossless.

setLossless(boolean) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets lossless

setLutAnimation(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
setLUTs(LUT[]) - Method in class loci.plugins.util.VirtualImagePlus
 
setMainCompDefDecompType(int, int, int) - Method in class jj2000.j2k.wavelet.WTDecompSpec

Sets the "component main default" decomposition type and number of
 levels for the specified component.

setMask(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
 
setMaxBitDepth(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata

Set the maximum sample size and maximum sample value.

setMetadata(IIOMetadata) - Method in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Sets the value of the metadata field.

setMetadata(IIOMetadata) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the metadata field.

setMetadata(IIOMetadata) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFEXIFJPEGCompressor
 
setMetadata(IIOMetadata) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor

Sets the value of the metadata field.

setMetadata(IIOMetadata) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGCompressor

Sets the value of the metadata field.

setMetadata(IIOMetadata) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFT4Compressor

Sets the value of the metadata field.

setMetadata(IIOMetadata) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setMetadataFiltered(boolean) - Method in class loci.formats.DelegateReader
 
setMetadataFiltered(boolean) - Method in class loci.formats.FormatReader
 
setMetadataFiltered(boolean) - Method in interface loci.formats.IFormatReader

Specifies whether ugly metadata (entries with unprintable characters,
 and extremely large entries) should be discarded from the metadata table.

setMetadataFiltered(boolean) - Method in class loci.formats.ImageReader
 
setMetadataFiltered(boolean) - Method in class loci.formats.in.FilePatternReader
 
setMetadataFiltered(boolean) - Method in class loci.formats.ReaderWrapper
 
setMetadataFiltered(String) - Method in class loci.plugins.macro.LociFunctions
 
setMetadataLevel(MetadataLevel) - Method in class loci.formats.in.DefaultMetadataOptions
 
setMetadataLevel(MetadataLevel) - Method in class loci.formats.in.DynamicMetadataOptions
 
setMetadataLevel(MetadataLevel) - Method in interface loci.formats.in.MetadataOptions

Set the metadata level.

setMetadataOptions(MetadataOptions) - Method in class loci.formats.DelegateReader
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.FileStitcher
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.FormatHandler
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageReader
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageWriter
 
setMetadataOptions(MetadataOptions) - Method in interface loci.formats.IMetadataConfigurable
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ReaderWrapper
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.WriterWrapper
 
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.FormatWriter
 
setMetadataRetrieve(MetadataRetrieve) - Method in interface loci.formats.IFormatWriter

Sets the metadata retrieval object from
 which to retrieve standardized metadata.

setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.ImageWriter
 
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.WriterWrapper
 
setMetadataStore(MetadataStore) - Method in class loci.formats.DelegateReader
 
setMetadataStore(MetadataStore) - Method in class loci.formats.FileStitcher
 
setMetadataStore(MetadataStore) - Method in class loci.formats.FormatReader
 
setMetadataStore(MetadataStore) - Method in interface loci.formats.IFormatReader

Sets the default metadata store for this reader.

setMetadataStore(MetadataStore) - Method in class loci.formats.ImageReader
 
setMetadataStore(MetadataStore) - Method in class loci.formats.in.FilePatternReader
 
setMetadataStore(MetadataStore) - Method in class loci.formats.Memoizer
 
setMetadataStore(MetadataStore) - Method in class loci.formats.ReaderWrapper
 
setMethodForMQLengthCalc(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets methodForMQLengthCalc

setMethodForMQTermination(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets methodForMQTermination

setMinAndMax(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
setMinMaxStore(IMinMaxStore) - Method in class loci.formats.MinMaxCalculator

Sets the active min-max store for the calculator.

setMinX(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets minX

setMinY(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets minY

setModulo(OMEXMLMetadata, Modulo) - Method in class loci.formats.meta.ModuloAnnotation

Set the value of this annotation using the given Modulo object

setMustGroup(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setNormalized(boolean) - Method in class loci.formats.DelegateReader
 
setNormalized(boolean) - Method in class loci.formats.FileStitcher
 
setNormalized(boolean) - Method in class loci.formats.FormatReader
 
setNormalized(boolean) - Method in interface loci.formats.IFormatReader

Specifies whether or not to normalize float data.

setNormalized(boolean) - Method in class loci.formats.ImageReader
 
setNormalized(boolean) - Method in class loci.formats.in.FilePatternReader
 
setNormalized(boolean) - Method in class loci.formats.ReaderWrapper
 
setNormalized(Boolean) - Method in class loci.plugins.macro.LociFunctions
 
setNoROIDescaling(boolean) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava

Sets noROIDescaling

setNumDecompositionLevels(int) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Sets numDecompositionLevels.

setNumeric() - Method in class loci.formats.FilePatternBlock
 
setOffset(long) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the offset field.

setOffset(long) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setOffsetInfo(int, int, int, int) - Method in class loci.formats.in.DeltavisionReader

This method calculates the size of a w, t, z section depending on which
 sequence is being used (either ZTW, WZT, or ZWT)

setOpenAllSeries(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setOrder(int, int) - Method in class loci.formats.cache.CacheStrategy
 
setOrder(int, int) - Method in interface loci.formats.cache.ICacheStrategy

Sets the order in which objects should be loaded along each axis.

setOriginalMetadataPopulated(boolean) - Method in class loci.formats.DelegateReader
 
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FileStitcher
 
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FormatReader
 
setOriginalMetadataPopulated(boolean) - Method in interface loci.formats.IFormatReader

Specifies whether or not to save proprietary metadata
 in the MetadataStore.

setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ImageReader
 
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.in.FilePatternReader
 
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ReaderWrapper
 
setOriginalMetadataPopulated(Boolean) - Method in class loci.plugins.macro.LociFunctions
 
setOutput(Object) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
setOutput(Object) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
setOutput(Object) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
setOutput(Object) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
setOutput(Object) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
setOutput(Object) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
setOutput(Object) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
setOutput(Object) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
setOutputOrder(String) - Method in class loci.formats.DimensionSwapper

Sets the output dimension order according to the given string (e.g.,
 "XYZCT").

setOutputOrder(String) - Method in class loci.formats.out.ICSWriter

Set the order in which dimensions should be written to the file.

setOutputOrder(String) - Method in class loci.formats.out.V3DrawWriter

Set the order in which dimensions should be written to the file.

setOutputOrder(String) - Method in class loci.formats.out.WlzWriter

Set the order in which dimensions should be written to the file.

setPackedBinaryData(byte[], WritableRaster, Rectangle) - Static method in class com.sun.media.imageioimpl.common.ImageUtil

Sets the supplied Raster's data from an array
 of packed binary data of the form returned by
 getPackedBinaryData().

setPacketPerTilePart(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets packetPerTilePart

setPackPacketHeaderInMain(boolean) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets packPacketHeaderInMain

setPackPacketHeaderInTile(boolean) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets packPacketHeaderInTile

setParsingEnabled(boolean) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava

Sets parsingEnabled

setPhotometricInterpretation(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the photometricInterpretation
 field.

setPhotometricInterpretation(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setPixels(int, int, int, int, ColorModel, byte[], int, int) - Method in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
setPixels(int, int, int, int, ColorModel, int[], int, int) - Method in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
setPixels() - Method in class loci.formats.in.GIFReader
 
setPixels(int, FloatProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
 
setPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor
 
setPlanar(boolean) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the planar field.

setPlanar(boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setPlaneIndexes(int[]) - Method in class loci.plugins.util.BFVirtualStack
 
setPositions(long, long, long) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFIFD
 
setPrecinctPartition(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets precinctPartition

setPredTerm(boolean) - Method in class jj2000.j2k.entropy.encoder.BitToByteOutput

Set the flag according to whether or not the predictable termination is
 requested.

setPreLoad(boolean) - Method in class loci.formats.in.SDTReader

Toggles whether the reader should pre-load data for increased performance.

setPriority(int, int) - Method in class loci.formats.cache.CacheStrategy
 
setPriority(int, int) - Method in interface loci.formats.cache.ICacheStrategy

Sets the priority for caching the given axis.

setProgressBar(ProgressBar) - Method in class loci.plugins.util.RecordedImageProcessor
 
setProgressionName(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets progressionName

setProgressionType(String) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Sets progressionType.

setProgressionType(LayersInfo, String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets progressionType

setProperties(Hashtable) - Method in class loci.formats.codec.JPEGTileDecoder.TileConsumer
 
setQuality(int) - Method in class loci.formats.out.LegacyQTWriter

Sets the quality of the encoded movie.

setQuality(int) - Method in class loci.formats.out.QTWriter

Sets the quality of the encoded movie.

setQuantizationStep(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets quantizationStep

setQuantizationType(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets quantizationType

setQuiet(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setRange(int, int) - Method in class loci.formats.cache.CacheStrategy
 
setRange(int, int) - Method in interface loci.formats.cache.ICacheStrategy

Sets the number of objects to cache along the given axis.

setRaw(boolean) - Method in class com.sun.media.imageio.plugins.pnm.PNMImageWriteParam

Sets the representation to be used.

setReader(ImageReader) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the reader field.

setReader(ImageReader) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setReader(IFormatReader) - Method in class loci.plugins.util.VirtualImagePlus
 
setReaderClassList(ClassList<IFormatReader>) - Method in class loci.formats.FileStitcher

Set the ClassList object to use when constructing any helper readers.

setReaderEnabled(FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
 
setReaderPref(String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
 
setReaderWindowless(FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
 
setRefCount(int) - Method in class loci.plugins.util.VirtualReader
 
setResetMQ(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets resetMQ

setResolution(int) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageReadParam

Sets resolution.

setResolution(int) - Method in class loci.formats.DelegateReader
 
setResolution(int) - Method in class loci.formats.FormatReader
 
setResolution(int) - Method in interface loci.formats.IFormatReader

Set the resolution level.

setResolution(int) - Method in class loci.formats.ImageReader
 
setResolution(int) - Method in class loci.formats.in.FilePatternReader
 
setResolution(int) - Method in class loci.formats.ReaderWrapper
 
setResolutionLevel(IFD) - Method in class loci.formats.in.MinimalTiffReader

Sets the resolution level when we have JPEG 2000 compressed data.

setRestartMarkers(long[]) - Method in interface loci.formats.services.JPEGTurboService
 
setRestartMarkers(long[]) - Method in class loci.formats.services.JPEGTurboServiceImpl
 
setRoi(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setRoi(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
 
setRoi(Rectangle) - Method in class loci.plugins.util.RecordedImageProcessor
 
setRoi(Roi) - Method in class loci.plugins.util.RecordedImageProcessor
 
setROIs(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets ROIs

setROIsMode(String) - Method in class loci.plugins.in.ImporterOptions
 
setSampleFormat(int[]) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the sampleFormat field.

setSampleFormat(int[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSampleModelAndMore() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
setSamplesPerPixel(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the samplesPerPixel field.

setSamplesPerPixel(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSegmentLength(int) - Method in class com.sun.media.imageio.stream.StreamSegment

Sets the length of the segment.

setSeries(int) - Method in class loci.formats.DelegateReader
 
setSeries(int) - Method in class loci.formats.FileStitcher
 
setSeries(int) - Method in class loci.formats.FormatReader
 
setSeries(int) - Method in class loci.formats.FormatWriter
 
setSeries(int) - Method in interface loci.formats.IFormatReader

Activates the specified series.

setSeries(int) - Method in interface loci.formats.IFormatWriter

Sets the current series.

setSeries(int) - Method in class loci.formats.ImageReader
 
setSeries(int) - Method in class loci.formats.ImageWriter
 
setSeries(int) - Method in class loci.formats.in.FilePatternReader
 
setSeries(int) - Method in class loci.formats.in.IM3Reader
 
setSeries(int) - Method in class loci.formats.in.ZeissLSMReader
 
setSeries(int) - Method in class loci.formats.ReaderWrapper
 
setSeries(int) - Method in class loci.formats.WriterWrapper
 
setSeries(Double) - Method in class loci.plugins.macro.LociFunctions
 
setSeriesList(String) - Method in class loci.plugins.in.ImportProcess
 
setSeriesOn(int, boolean) - Method in class loci.plugins.in.ImporterOptions
 
setShort(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader

Private method used to set a Short value in the SPE header

setShowMetadata(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setShowOMEXML(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setShowROIs(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setSize(int) - Method in class loci.formats.tiff.OnDemandLongArray
 
setSlice(int) - Method in class loci.plugins.util.VirtualImagePlus
 
setSnapshotCopyMode(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
setSnapshotPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor
 
setSOP(boolean) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Sets SOP.

setSOP(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets SOP

setSource(ICacheSource) - Method in class loci.formats.cache.Cache

Sets the cache's caching source.

setSourceBands(int[]) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the sourceBands field.

setSourceBands(int[]) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Override the method setSourceBands in the super class.

setSourceBands(int[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSourceImage(byte[], int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor

Associate an uncompressed source image with this compressor instance.

setSourceSubsampling(int, int, int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Override the method setSourceSubsampling in the super class.

setSourceXOffset(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the sourceXOffset field.

setSourceXOffset(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSourceYOffset(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the sourceYOffset.

setSourceYOffset(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSpecifyRanges(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setSplitChannels(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setSplitFocalPlanes(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setSplitTimepoints(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setSrcHeight(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the srcHeight field.

setSrcHeight(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSrcMinX(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the srcMinX field.

setSrcMinX(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSrcMinY(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the srcMinY field.

setSrcMinY(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSrcWidth(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the srcWidth field.

setSrcWidth(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setStackFormat(String) - Method in class loci.plugins.in.ImporterOptions
 
setStackOrder(String) - Method in class loci.plugins.in.ImporterOptions
 
setStartLevelROI(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets the startLevelROI

setStartPos(long) - Method in class com.sun.media.imageio.stream.StreamSegment

Sets the starting position of the segment.

setStitchTiles(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setStrategy(ICacheStrategy) - Method in class loci.formats.cache.Cache

Sets the cache's caching strategy.

setStream(ImageOutputStream) - Method in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Sets the ImageOutputStream to be written.

setStream(ImageInputStream) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the stream field.

setStream(ImageOutputStream) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWCompressor
 
setStream(ImageInputStream) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setStream(RandomAccessInputStream) - Method in class loci.formats.tiff.OnDemandLongArray
 
setString(int, String) - Method in class loci.formats.in.SPEReader.SpeHeader

Private method used to set a String value in the SPE header

setSubsamp(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor

Set the level of chrominance subsampling for subsequent compress/encode
 operations.

setSubsampleX(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the subsampleX field.

setSubsampleY(int) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

Sets the value of the subsampleY field.

setSuperProperties() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
 
setSwapDimensions(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setTarget(Runnable, Object, boolean) - Method in class jj2000.j2k.util.ThreadPool.ThreadPoolThread

Assigns a target to this thread, with an optional notify lock and a
 notify mode.

setTBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setTEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setTerminateOnByte(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Sets terminateOnByte

setTermType(int) - Method in class jj2000.j2k.entropy.encoder.MQCoder

Set termination type to the specified type

setThreadConcurrency(int) - Static method in class jj2000.j2k.util.NativeServices

Sets the concurrency level of the threading system of the Java Virtual
 Machine (JVM) to the specified level.

setThreadConcurrencyN(int) - Static method in class jj2000.j2k.util.NativeServices

Calls the POSIX threads 'pthread_setconcurrency', or equivalent,
 function with 'level' as the argument.

setThreshold(double, double, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setTIFFCompressor(TIFFCompressor) - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam

Sets the TIFFCompressor object to be used by the
 ImageWriter to encode each image strip or tile.

setTIFFDecompressor(TIFFDecompressor) - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam

Sets the TIFFDecompressor object to be used by the
 ImageReader to decode each image strip or tile.

setTile(int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

Changes the current tile, given the new coordinates.

setTile(int, int) - Method in class jj2000.j2k.codestream.reader.BitstreamReaderAgent

Changes the current tile, given the new indexes.

setTile(int, int) - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent

Changes the current tile, given the new indexes.

setTile(int, int) - Method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Changes the current tile, given the new indexes.

setTile(int, int) - Method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

Changes the current tile, given the new indexes.

setTile(int, int) - Method in interface jj2000.j2k.image.ImgData

Changes the current tile, given the new indices.

setTile(int, int) - Method in class jj2000.j2k.image.ImgDataAdapter

Changes the current tile, given the new indexes.

setTile(int, int) - Method in class jj2000.j2k.image.ImgDataJoiner

Changes the current tile, given the new coordinates.

setTile(int, int) - Method in class jj2000.j2k.image.input.ImgReader

Changes the current tile, given the new coordinates.

setTile(int, int) - Method in class jj2000.j2k.image.invcomptransf.InvCompTransf

Changes the current tile, given the new indexes.

setTile(int, int) - Method in class jj2000.j2k.image.Tiler

Changes the current tile, given the new tile indexes.

setTile(int, int) - Method in class jj2000.j2k.quantization.dequantizer.Dequantizer

Changes the current tile, given the new indexes.

setTile(int, int) - Method in class jj2000.j2k.roi.encoder.ROIScaler

Changes the current tile, given the new indexes.

setTile(int, int) - Method in class jj2000.j2k.wavelet.analysis.ForwWTFull

Changes the current tile, given the new coordinates.

setTile(int, int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTAdapter

Changes the current tile, given the new indices.

setTile(int, int) - Method in class jj2000.j2k.wavelet.synthesis.InvWTFull

Changes the current tile, given the new indexes.

setTile(int, int) - Method in interface jj2000.j2k.wavelet.synthesis.MultiResImgData

Changes the current tile, given the new indexes.

setTile(int, int) - Method in class jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter

Changes the current tile, given the new indexes.

setTileCompVal(int, int, Object) - Method in class jj2000.j2k.entropy.CBlkSizeSpec

Sets value for specified tile-component.

setTileCompVal(int, int, Object) - Method in class jj2000.j2k.ModuleSpec

Sets value for specified tile-component.

setTileDef(int, Object) - Method in class jj2000.j2k.entropy.CBlkSizeSpec

Sets default value for specified tile and specValType tag if allowed by
 its priority.

setTileDef(int, Object) - Method in class jj2000.j2k.ModuleSpec

Sets default value for specified tile and specValType tag if
 allowed by its priority.

setTileOfTileParts(int) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder

Sets the tile of each tile part in order.

setTileSizeX(int) - Method in class loci.formats.FormatWriter
 
setTileSizeX(int) - Method in interface loci.formats.IFormatWriter

Will attempt to set the tile width to the desired value and return the actual value which will be used

setTileSizeX(int) - Method in class loci.formats.ImageWriter
 
setTileSizeX(int) - Method in class loci.formats.out.TiffWriter
 
setTileSizeX(int) - Method in class loci.formats.WriterWrapper
 
setTileSizeY(int) - Method in class loci.formats.FormatWriter
 
setTileSizeY(int) - Method in interface loci.formats.IFormatWriter

Will attempt to set the tile height to the desired value and return the actual value which will be used

setTileSizeY(int) - Method in class loci.formats.ImageWriter
 
setTileSizeY(int) - Method in class loci.formats.out.TiffWriter
 
setTileSizeY(int) - Method in class loci.formats.WriterWrapper
 
setTiling(int, int, int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Override the method setTiling in the super class.

setToBlack(int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
setTopDown(boolean) - Method in class com.sun.media.imageio.plugins.bmp.BMPImageWriteParam

If set, the data will be written out in a top-down manner, the first
 scanline being written first.

setTruncatedFileFlag(boolean) - Method in class loci.formats.in.DeltavisionReader

This flag indicates if the file is known to be truncated.

setTStep(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setUngroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setUnpackedBinaryData(byte[], WritableRaster, Rectangle) - Static method in class com.sun.media.imageioimpl.common.ImageUtil

Copies data into the packed array of the Raster
 from an array of unpacked data of the form returned by
 getUnpackedBinaryData().

setup - Variable in class loci.formats.in.SDTInfo
 
setup(String, ImagePlus) - Method in class loci.plugins.LociExporter

Sets up the writer.

setup(String, ImagePlus) - Method in class loci.plugins.Slicer
 
SETUP_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo

For .set files (setup only).

setUpgradeCheck(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setupLength - Variable in class loci.formats.in.SDTInfo

Length of the setup data.

setupMetadata(ColorModel, SampleModel, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter

Sets up the output metadata adding, removing, and overriding fields
 as needed.

setupOffs - Variable in class loci.formats.in.SDTInfo

Offset of the setup text data
 (system parameters, display parameters, trace parameters etc.).

setupReader() - Method in class loci.formats.in.MicromanagerReader

Initialize the TIFF reader with the first file in the current series.

setupService() - Method in class loci.formats.FormatReader

Initialize the OMEXMLService needed by FormatReader.setId(String)

setupService() - Method in class loci.formats.in.OMETiffReader
 
setupServiceAndMetadata() - Method in class loci.formats.out.OMETiffWriter
 
setupTiffSaver() - Method in class loci.formats.out.TiffWriter
 
setupWrite(int, int, int, int, int, int, int, int, double, double, double, int) - Method in interface loci.formats.services.WlzService

Sets up the service, which must have already been opened for writing.

setupWrite(int, int, int, int, int, int, int, int, double, double, double, int) - Method in class loci.formats.services.WlzServiceImpl
 
setUse64BitOffsets(boolean) - Method in class loci.formats.tiff.TiffParser

Sets whether or not 64-bit offsets are used for non-BigTIFF files.

setUsingPatternIds(boolean) - Method in class loci.formats.FileStitcher

Sets whether the reader is using file patterns for IDs.

setValidate(boolean) - Method in class loci.formats.in.DefaultMetadataOptions
 
setValidate(boolean) - Method in class loci.formats.in.DynamicMetadataOptions
 
setValidate(boolean) - Method in interface loci.formats.in.MetadataOptions

Specifies whether or not to validate files when reading.

setValidBitsPerPixel(int) - Method in class loci.formats.FormatWriter
 
setValidBitsPerPixel(int) - Method in interface loci.formats.IFormatWriter

Sets the number of valid bits per pixel.

setValidBitsPerPixel(int) - Method in class loci.formats.ImageWriter
 
setValidBitsPerPixel(int) - Method in class loci.formats.WriterWrapper
 
setValue(int, int, int) - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Changes the value of a leaf in the tag tree.

setValue(String) - Method in class loci.formats.in.BaseZeissReader.Tag
 
setValue(boolean) - Method in class loci.plugins.prefs.BooleanOption

Sets the current value of the option.

setValue(double) - Method in class loci.plugins.prefs.DoubleOption

Sets the current value of the option.

setValue(String, boolean) - Method in class loci.plugins.prefs.OptionsList

Sets the value of the boolean option with the given key.

setValue(String, String) - Method in class loci.plugins.prefs.OptionsList

Sets the value of the string option with the given key.

setValue(String) - Method in class loci.plugins.prefs.StringOption

Sets the current value of the option.

setValue(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
setValues(int[]) - Method in class jj2000.j2k.codestream.writer.TagTreeEncoder

Sets the values of the leafs to the new set of values and
 updates the tag tree accordingly.

setVariant(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata

Sets the variant: '1' - '6'.

setVersionChecking(boolean) - Method in class loci.formats.Memoizer

Set whether version checking is done based upon major/minor version
 numbers.

setView(Attributes) - Method in class loci.formats.in.LeicaSCNReader.Image
 
setVirtual(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setVisible(boolean) - Method in class loci.formats.gui.ImageViewer
 
setVisible(boolean) - Method in class loci.plugins.util.DataBrowser

Overridden show method to allow us to delay initial window display.

setWidth(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
setWindowless(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setWriteCodeStreamOnly(boolean) - Method in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Sets writeCodeStreamOnly.

setWriter(ImageWriter) - Method in class com.sun.media.imageio.plugins.tiff.TIFFCompressor

Sets the value of the writer field.

setWriteSequentially(boolean) - Method in class loci.formats.FormatWriter
 
setWriteSequentially(boolean) - Method in interface loci.formats.IFormatWriter

Sets whether or not we know that planes will be written sequentially.

setWriteSequentially(boolean) - Method in class loci.formats.ImageWriter
 
setWriteSequentially(boolean) - Method in class loci.formats.WriterWrapper
 
setWritingSequentially(boolean) - Method in class loci.formats.tiff.TiffSaver

Sets whether or not we know that the planes will be written sequentially.

setXML(String) - Method in class loci.formats.gui.XMLWindow

Displays XML from the given string.

setXML(File) - Method in class loci.formats.gui.XMLWindow

Displays XML from the given file.

setXML(String) - Method in class loci.formats.tools.EditTiffG
 
setXML(String) - Method in class loci.plugins.util.DataBrowser

Sets XML block associated with this window.

setYCbCrCorrection(boolean) - Method in class loci.formats.tiff.TiffParser

Sets whether or not YCbCr color correction is allowed.

setZBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setZEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setZStep(int, int) - Method in class loci.plugins.in.ImporterOptions
 
SFEG_TAG - Static variable in class loci.formats.in.FEITiffReader
 
sgcod_mct - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
sgcod_nl - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
sgcod_po - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
SH - Static variable in class loci.formats.in.DicomReader
 
SHADING_MUL - Static variable in class loci.formats.in.CellSensReader
 
SHADING_SUB - Static variable in class loci.formats.in.CellSensReader
 
Shape() - Constructor for class loci.formats.in.BaseZeissReader.Shape
 
shape_count - Variable in class loci.formats.in.ZeissTIFFHandler
 
SHAPE_PREFIX - Static variable in class loci.formats.in.FakeReader
 
shapes - Variable in class loci.formats.in.BaseZeissReader.Layer
 
sharpen() - Method in class loci.plugins.util.RecordedImageProcessor
 
SHARPENING - Static variable in class loci.formats.in.NikonReader
 
Sharpness() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.Sharpness
 
SHARPNESS - Static variable in class loci.formats.in.CellSensReader
 
SHARPNESS - Static variable in class loci.formats.tiff.IFD
 
SHARPNESS_HARD - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "Sharpness" tag.

SHARPNESS_NORMAL - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "Sharpness" tag.

SHARPNESS_SOFT - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet

A value to be used with the "Sharpness" tag.

SHLIB_NAME - Static variable in class jj2000.j2k.util.NativeServices

The name of the shared library containing the implementation of the
 native methods: 'jj2000'.

SHORT - Static variable in class loci.formats.in.CellSensReader
 
SHORT - Static variable in class loci.formats.in.GatanReader
 
SHORT_DATE_FORMAT - Static variable in class loci.formats.in.MetamorphReader
 
shortArrayToBytes(short[]) - Method in class loci.formats.in.FluoviewReader
 
SHORTCUT_PLUGIN - Static variable in class loci.plugins.shortcut.ShortcutPanel

Name of this plugin, ignored when parsing the plugins list.

ShortcutPanel - Class in loci.plugins.shortcut

A plugin that displays a small window containing shortcuts to the
 plugins, including the Bio-Formats Importer, Bio-Formats Exporter,
 Stack Colorizer and Stack Slicer.

ShortcutPanel() - Constructor for class loci.plugins.shortcut.ShortcutPanel

Constructs a shortcut panel.

shortcutPanel - Variable in class loci.plugins.shortcut.ShortcutTransferHandler

Associated shortcut panel.

ShortcutTransferHandler - Class in loci.plugins.shortcut

Drag and drop transfer handler for Bio-Formats Plugins Shortcut Window.

ShortcutTransferHandler(ShortcutPanel) - Constructor for class loci.plugins.shortcut.ShortcutTransferHandler

Constructs a new shortcut panel drag and drop transfer handler.

shortLut - Variable in class loci.formats.in.DicomReader
 
shortValue() - Method in class loci.formats.tiff.TiffRational

Returns the value of the specified number as a short.

showDialog() - Method in class loci.plugins.in.ImporterDialog
 
showDialog() - Method in class loci.plugins.prefs.OptionsDialog

Displays the options dialog, returning the status of the operation.

showDialogs(ImportProcess) - Method in class loci.plugins.in.Importer
 
showError(Throwable) - Method in class loci.formats.tools.EditTiffG
 
showMetadataBox - Variable in class loci.plugins.in.MainDialog
 
showMetadataWindow() - Method in class loci.plugins.util.DataBrowser

Displays the OME-XML metadata window onscreen.

showOMEXMLBox - Variable in class loci.plugins.in.MainDialog
 
showOptionsWindow() - Method in class loci.plugins.util.DataBrowser

Displays the caching options window onscreen.

showROIs() - Method in class loci.plugins.in.ImporterOptions
 
showROIsBox - Variable in class loci.plugins.in.MainDialog
 
shuffle(int, int[]) - Static method in class loci.formats.in.FakeReader

Fisher-Yates shuffle with constant seeds to ensure reproducibility.

shuffleAllTypesToFront(FileFilter[]) - Static method in class loci.formats.gui.GUITools

Looks for an "All supported file types" combo filter
 and shuffles it to the front of the list.

shutdown - Variable in class loci.formats.gui.DataConverter
 
SHUTTER_SPEED_VALUE - Static variable in class loci.formats.tiff.IFD
 
ShutterSpeedValue() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.ShutterSpeedValue
 
SIFReader - Class in loci.formats.in

SIFReader is the file format reader for Andor SIF files.

SIFReader() - Constructor for class loci.formats.in.SIFReader

Constructs a new SIF reader.

SIG_MASK_R1R2 - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The mask to isolate the significance bits for row 1 and 2 of the state
 array.

SIG_MASK_R1R2 - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The mask to isolate the significance bits for row 1 and 2 of the state
 array.

SIGNAL_OUTPUT - Static variable in class loci.formats.in.CellSensReader
 
SIGNATURE_SIZE - Static variable in class loci.formats.in.VolocityReader
 
SignatureBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000

This class is defined to represent a Signature Box of JPEG JP2
  file format.

SignatureBox() - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.SignatureBox

Constructs a SignatureBox.

SignatureBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.SignatureBox

Constructs a SignatureBox based on the provided
  org.w3c.dom.Node.

SignatureBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.SignatureBox

Constructs a SignatureBox based on the provided
  byte array.

signed - Variable in class loci.formats.codec.CodecOptions

Indicates whether or not the pixel data is signed.

signed - Variable in class loci.formats.in.GatanReader
 
SignedByteBuffer - Class in loci.formats.gui

DataBuffer that stores signed bytes.

SignedByteBuffer(byte[], int) - Constructor for class loci.formats.gui.SignedByteBuffer

Construct a new buffer of signed bytes using the given byte array.

SignedByteBuffer(byte[][], int) - Constructor for class loci.formats.gui.SignedByteBuffer

Construct a new buffer of signed bytes using the given 2D byte array.

SignedColorModel - Class in loci.formats.gui

ColorModel that handles 8, 16 and 32 bits per channel signed data.

SignedColorModel(int, int, int) - Constructor for class loci.formats.gui.SignedColorModel
 
SignedShortBuffer - Class in loci.formats.gui

DataBuffer that stores signed shorts.

SignedShortBuffer(int) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SignedShortBuffer(int, int) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SignedShortBuffer(short[], int) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SignedShortBuffer(short[], int, int) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SignedShortBuffer(short[][], int) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SignedShortBuffer(short[][], int, int[]) - Constructor for class loci.formats.gui.SignedShortBuffer
 
sigProgPass(DataBlk, MQDecoder, int, int[], int[], boolean) - Method in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

Performs the significance propagation pass on the specified data and
 bit-plane.

sigProgPass(CBlkWTData, MQCoder, boolean, int, int[], int[], int[], int[], int[], int[], int, int, int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Performs the significance propagation pass on the specified data and
 bit-plane.

SimpleCMYKColorSpace - Class in com.sun.media.imageioimpl.common

Singleton class representing a simple, mathematically defined CMYK
 color space.

SimpleCMYKColorSpace() - Constructor for class com.sun.media.imageioimpl.common.SimpleCMYKColorSpace
 
SimplePCITiffReader - Class in loci.formats.in

SimplePCITiffReader is the file format reader for TIFF files produced by
 SimplePCI software.

SimplePCITiffReader() - Constructor for class loci.formats.in.SimplePCITiffReader
 
SimpleRenderedImage - Class in com.sun.media.imageioimpl.common
 
SimpleRenderedImage() - Constructor for class com.sun.media.imageioimpl.common.SimpleRenderedImage
 
SINGLE_TIFF_PATH_BUILDER - Static variable in class loci.formats.in.CellVoyagerReader
 
singleInstance(String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
singleTiffMode - Variable in class loci.formats.in.PrairieReader

Flag indicating that the reader is operating in a mode where grouping of
 files is disallowed.

SingleTileRenderedImage - Class in com.sun.media.imageioimpl.common

A simple class that provides RenderedImage functionality
 given a Raster and a ColorModel.

SingleTileRenderedImage(Raster, ColorModel) - Constructor for class com.sun.media.imageioimpl.common.SingleTileRenderedImage

Constructs a SingleTileRenderedImage based on a Raster
 and a ColorModel.

SIS_INI_TAG - Static variable in class loci.formats.in.SISReader
 
SIS_TAG - Static variable in class loci.formats.in.SISReader
 
SIS_TAG_2 - Static variable in class loci.formats.in.SISReader
 
SISReader - Class in loci.formats.in

SISReader is the file format reader for Olympus Soft Imaging Solutions
 TIFF files.

SISReader() - Constructor for class loci.formats.in.SISReader
 
SITE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
site - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
site - Variable in class loci.formats.in.ZeissTIFFReader.Plane
 
siz - Variable in class jj2000.j2k.codestream.HeaderInfo

Reference to the SIZ marker segment found in main header

SIZ() - Constructor for class jj2000.j2k.codestream.HeaderInfo.SIZ
 
SIZ - Static variable in interface jj2000.j2k.codestream.Markers

SIZ marker (Image and tile size): 0xFF51

SIZ_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for SIZ marker segment found

size() - Method in class jj2000.j2k.entropy.encoder.ByteOutputBuffer

Returns the number of valid bytes in the output buffer (count class
 variable).

size - Variable in class loci.formats.codec.ByteVector
 
size() - Method in class loci.formats.codec.ByteVector
 
size - Variable in class loci.formats.in.AVIReader
 
size - Variable in class loci.formats.in.FV1000Reader
 
size - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
size - Variable in class loci.formats.tiff.OnDemandLongArray
 
size() - Method in class loci.formats.tiff.OnDemandLongArray
 
size - Variable in class loci.plugins.in.ThumbLoader.SeriesInfo
 
sizeC - Variable in class loci.formats.CoreMetadata

Number of channels.

sizeC - Variable in class loci.formats.FileStitcher

Dimensional axis lengths per file.

sizeC - Variable in class loci.formats.gui.ImageViewer
 
sizeC - Variable in class loci.formats.in.FakeReader
 
sizeC - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
sizeCsub - Variable in class loci.formats.tools.MakeTestOmeTiff
 
sizeOfType - Static variable in class com.sun.media.imageio.plugins.tiff.TIFFTag
 
sizeR - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
sizeT - Variable in class loci.formats.CoreMetadata

Number of timepoints.

sizeT - Variable in class loci.formats.FileStitcher

Dimensional axis lengths per file.

sizeT - Variable in class loci.formats.gui.ImageViewer
 
sizeT - Variable in class loci.formats.in.FakeReader
 
sizeTsub - Variable in class loci.formats.tools.MakeTestOmeTiff
 
sizeX - Variable in class loci.formats.CoreMetadata

Width (in pixels) of images in this series.

sizeX - Variable in class loci.formats.in.ColumbusReader.Plane
 
sizeX - Variable in class loci.formats.in.FakeReader
 
sizeX - Variable in class loci.formats.in.FEITiffReader
 
sizeX - Variable in class loci.formats.in.LeicaSCNReader.Dimension
 
sizeX - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
sizeX - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
sizeX - Variable in class loci.formats.in.MetamorphReader
 
sizeX - Variable in class loci.formats.in.TextReader

Image width.

sizeY - Variable in class loci.formats.CoreMetadata

Height (in pixels) of images in this series.

sizeY - Variable in class loci.formats.in.ColumbusReader.Plane
 
sizeY - Variable in class loci.formats.in.FakeReader
 
sizeY - Variable in class loci.formats.in.FEITiffReader
 
sizeY - Variable in class loci.formats.in.LeicaSCNReader.Dimension
 
sizeY - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
sizeY - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
sizeY - Variable in class loci.formats.in.MetamorphReader
 
sizeY - Variable in class loci.formats.in.TextReader

Image height.

sizeZ - Variable in class loci.formats.CoreMetadata

Number of Z sections.

sizeZ - Variable in class loci.formats.FileStitcher

Dimensional axis lengths per file.

sizeZ - Variable in class loci.formats.gui.ImageViewer
 
sizeZ - Variable in class loci.formats.in.FakeReader
 
sizeZ - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
sizeZ - Variable in class loci.formats.in.NDPIReader
 
sizeZsub - Variable in class loci.formats.tools.MakeTestOmeTiff
 
skip(long) - Method in class com.sun.media.imageioimpl.plugins.clib.InputStreamAdapter
 
skip(long) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
skip(InputStream, long) - Method in class loci.formats.in.LiFlimReader
 
skipBits(long) - Method in class loci.formats.codec.BitBuffer

Deprecated.
Skips a number of bits in the BitBuffer.

skipBlocks() - Method in class loci.formats.in.GIFReader
 
skipBytes(int) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
skipBytes(long) - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
skipBytes(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
skipBytes(int) - Method in interface jj2000.j2k.io.BinaryDataInput

Skips n bytes from the input.

skipBytes(int) - Method in class jj2000.j2k.io.BufferedRandomAccessFile

Skips n bytes from the input.

skipBytes(int) - Method in class jj2000.j2k.util.ISRandomAccessIO

Skips 'n' bytes from the input.

skipComment() - Method in class loci.formats.tools.AmiraParameters
 
skipCommentAndWhiteSpace() - Method in class jj2000.j2k.image.input.ImgReaderPGM

Skips any line in the header starting with '#' and any space, tab, line
 feed or carriage return.

skipData() - Method in class loci.formats.in.ZeissCZIReader.Metadata
 
skipInteger(ImageInputStream, int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
skipLoad - Variable in class loci.formats.Memoizer
 
skipMSBP - Variable in class jj2000.j2k.entropy.CodedCBlk

The number of skipped most significant bit-planes.

skipPadding() - Method in class loci.formats.in.GatanReader
 
skipPixelBlock(boolean) - Method in class loci.formats.in.OIRReader
 
skipSave - Variable in class loci.formats.Memoizer
 
skipTagBlock() - Method in class loci.formats.in.ImspectorReader

Skip an unknown tag.

skipTags(int) - Method in class loci.formats.in.ImspectorReader

Skip a block of unknown string values.

skipWhiteSpace() - Method in class loci.formats.in.AmiraReader.ASCII
 
skipWhiteSpace() - Method in class loci.formats.tools.AmiraParameters
 
SL - Static variable in class loci.formats.in.DicomReader
 
SLD_MAGIC_BYTES_1_0 - Static variable in class loci.formats.in.SlidebookReader
 
SLD_MAGIC_BYTES_1_1 - Static variable in class loci.formats.in.SlidebookReader
 
SLD_MAGIC_BYTES_1_2 - Static variable in class loci.formats.in.SlidebookReader
 
SLD_MAGIC_BYTES_2_0 - Static variable in class loci.formats.in.SlidebookReader
 
SLD_MAGIC_BYTES_2_1 - Static variable in class loci.formats.in.SlidebookReader
 
SLD_MAGIC_BYTES_3 - Static variable in class loci.formats.in.SlidebookReader
 
sleep(long) - Method in class loci.plugins.prefs.OptionsDialog

Blocks the current thread for the specified number of milliseconds.

Slice(int) - Constructor for class loci.formats.in.ZeissTIFFReader.Slice
 
SLICE_SPACING - Static variable in class loci.formats.in.DicomReader
 
Slicer - Class in loci.plugins

A plugin for splitting an image stack into separate
 channels, focal planes and/or time points.

Slicer() - Constructor for class loci.plugins.Slicer
 
slices - Variable in class loci.formats.in.ZeissTIFFReader
 
sliceSpace - Variable in class loci.formats.in.PerkinElmerReader
 
sliceThickness - Variable in class loci.formats.in.MicromanagerReader.Position
 
sliceThickness - Variable in class loci.formats.in.NiftiReader
 
SLIDE_INFO - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_NAME - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_PREPARATION - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_SPECIMEN - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_STAINING - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_TISSUE - Static variable in class loci.formats.in.CellSensReader
 
SLIDEBOOK_MAGIC_STRING - Static variable in class loci.formats.in.SlidebookTiffReader
 
SlidebookReader - Class in loci.formats.in

SlidebookReader is the file format reader for 3I Slidebook files.

SlidebookReader() - Constructor for class loci.formats.in.SlidebookReader

Constructs a new Slidebook reader.

SlidebookTiffReader - Class in loci.formats.in
 
SlidebookTiffReader() - Constructor for class loci.formats.in.SlidebookTiffReader
 
sliderName - Variable in class loci.formats.in.FlexReader.FlexHandler
 
sliderPanel - Variable in class loci.formats.gui.ImageViewer
 
sm - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
smallPalette - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
sMasks - Variable in class jj2000.j2k.roi.encoder.RectROIMaskGenerator

The tree of subbandmask.

SMaxSampleValue() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.SMaxSampleValue
 
SMC_MAGIC - Static variable in class loci.formats.in.SMCameraReader
 
SMCameraReader - Class in loci.formats.in

SMCameraReader is the file format reader for SM camera files.

SMCameraReader() - Constructor for class loci.formats.in.SMCameraReader

Constructs a new SM camera reader.

SMinSampleValue() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.SMinSampleValue
 
smooth() - Method in class loci.plugins.util.RecordedImageProcessor
 
snapshot() - Method in class loci.plugins.util.RecordedImageProcessor
 
SOC - Static variable in interface jj2000.j2k.codestream.Markers

Start of codestream (SOC): 0xFF4F

SOD - Static variable in interface jj2000.j2k.codestream.Markers

Start of data (SOD): 0xFF93

SOD_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for SOD marker segment found

SOF0 - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
SOF0 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF0 - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
SOF1 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF10 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF11 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF13 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF14 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF15 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF2 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF3 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF5 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF6 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF7 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOF9 - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOFPosition - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
Software() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Software
 
SOFTWARE - Static variable in class loci.formats.tiff.IFD
 
SOI - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
SOI - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOP - Variable in class com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

Specifies whether start of packet (SOP) markers should be used.

SOP - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

Specifies whether start of packet (SOP) markers should be used.

SOP - Static variable in interface jj2000.j2k.codestream.Markers

Start pf packet (SOP): 0xFF91

SOP_LENGTH - Static variable in interface jj2000.j2k.codestream.Markers

Length of SOP marker (in bytes)

SOP_MARKER_LIMIT - Static variable in class jj2000.j2k.codestream.writer.FileCodestreamWriter

The upper limit for the value of the Nsop field of the SOP marker

sopMarker - Variable in class jj2000.j2k.codestream.writer.FileCodestreamWriter

Array used to store the SOP markers values

sopMarkSeg - Variable in class jj2000.j2k.util.CodestreamManipulator

Buffers containing the SOP marker segments

sops - Variable in class jj2000.j2k.decoder.DecoderSpecs

The Start Of Packet (SOP) markers specifications

sopUsed - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Whether or not SOP marker segment are used

sortFilters(FileFilter[]) - Static method in class loci.formats.gui.ComboFileFilter

Sorts the given list of file filters, and combines filters with identical
 descriptions into a combination filter that accepts anything any of its
 constituant filters do.

sortFilters(Vector) - Static method in class loci.formats.gui.ComboFileFilter

Sorts the given list of file filters, and combines filters with identical
 descriptions into a combination filter that accepts anything any of its
 constituant filters do.

sortFilters(FileFilter[]) - Static method in class loci.formats.gui.GUITools

Sorts the given list of file filters, keeping the "All supported
 file types" combo filter (if any) at the front of the list.

sortFilters(Vector) - Static method in class loci.formats.gui.GUITools

Sorts the given list of file filters, keeping the "All supported
 file types" combo filter (if any) at the front of the list.

sortFlag - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
sortFlag - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
SOS - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
SOS - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
SOS - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
sos - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
SOSMarker - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
sot - Variable in class jj2000.j2k.codestream.HeaderInfo

Reference to the SOT marker segments found in tile-part headers.

SOT() - Constructor for class jj2000.j2k.codestream.HeaderInfo.SOT
 
SOT - Static variable in interface jj2000.j2k.codestream.Markers

Start of tile-part (SOT): 0xFF90

SOT_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder

Flag bit for SOT marker segment found

source - Variable in class com.sun.media.imageio.stream.RawImageInputStream

The wrapperred ImageInputStream.

source - Variable in class loci.formats.cache.Cache

Current cache source.

source - Variable in class loci.formats.cache.CacheEvent

Source of the cache update.

SOURCE_CHANGED - Static variable in class loci.formats.cache.CacheEvent

Event type indicating a new cache source.

SOURCE_LENS - Static variable in class loci.formats.in.NDPIReader
 
SOURCE_PARAMS - Static variable in class loci.formats.gui.CacheComponent
 
SOURCE_VALUES - Static variable in class loci.formats.gui.CacheComponent
 
sourceBands - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The sequence of source bands that are to be copied into the
 destination.

sourceBands - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

source and destination bands.

sourceBands - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
sourceBands - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc

The source bands to be encoded.

sourceBands - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader

source and destination bands.

sourceBands - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter

The source bands to be encoded.

sourceBands - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
sourceBands - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
sourceBands - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
sourceBandsCache - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
sourceChooser - Variable in class loci.formats.gui.CacheComponent

Combo box for choosing cache source.

sourceHeight - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
sourceIndex(ICacheSource) - Method in class loci.formats.gui.CacheComponent

Converts cache source to source chooser index.

sourceOrigin - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
sourceOrigin - Variable in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
sourceRegion - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader

The source region.

sourceRegion - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
sourceRegion - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader

The source region.

sourceRegion - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
sources - Variable in class com.sun.media.imageioimpl.common.SimpleRenderedImage

The image's sources, stored in a Vector.

SOURCES - Static variable in class loci.formats.gui.CacheComponent
 
sourceValue(int) - Method in class loci.formats.gui.CacheComponent

Generates a new cache source matching the source chooser index.

sourceWidth - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
sourceXOffset - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The source X offset used, along with dstXOffset
 and subsampleX, to map between horizontal source
 and destination pixel coordinates.

sourceXOffset - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
sourceXOffset - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
sourceYOffset - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The source Y offset used, along with dstYOffset
 and subsampleY, to map between vertical source and
 destination pixel coordinates.

sourceYOffset - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
sourceYOffset - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
SPACE - Static variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
SPATIAL_FREQUENCY_RESPONSE - Static variable in class loci.formats.tiff.IFD
 
SpatialFrequencyResponse() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.SpatialFrequencyResponse
 
spatialUnit - Variable in class loci.formats.in.NiftiReader
 
spcId - Variable in class loci.formats.in.SPCReader
 
spcoc_ch - Variable in class jj2000.j2k.codestream.HeaderInfo.COC
 
spcoc_cs - Variable in class jj2000.j2k.codestream.HeaderInfo.COC
 
spcoc_cw - Variable in class jj2000.j2k.codestream.HeaderInfo.COC
 
spcoc_ndl - Variable in class jj2000.j2k.codestream.HeaderInfo.COC
 
spcoc_ps - Variable in class jj2000.j2k.codestream.HeaderInfo.COC
 
spcoc_t - Variable in class jj2000.j2k.codestream.HeaderInfo.COC
 
spcod_ch - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
spcod_cs - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
spcod_cw - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
spcod_ndl - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
spcod_ps - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
spcod_t - Variable in class jj2000.j2k.codestream.HeaderInfo.COD
 
SPCReader - Class in loci.formats.in

SPCReader is the file format reader for
 Becker & Hickl SPC-Image SPC FIFO files.

SPCReader() - Constructor for class loci.formats.in.SPCReader

Constructs a new SPC reader.

SPEC_COMP_DEF - Static variable in class jj2000.j2k.ModuleSpec

The identifier for "component default" specification

SPEC_DEF - Static variable in class jj2000.j2k.ModuleSpec

The identifier for default specification

SPEC_TILE_COMP - Static variable in class jj2000.j2k.ModuleSpec

The identifier for a "tile-component" specification

SPEC_TILE_DEF - Static variable in class jj2000.j2k.ModuleSpec

The identifier for "tile default" specification

SPEC_TYPE_COMP - Static variable in class jj2000.j2k.ModuleSpec

The identifier for a specification module that applies only to
 components

SPEC_TYPE_TILE - Static variable in class jj2000.j2k.ModuleSpec

The identifier for a specification module that applies only to
        tiles

SPEC_TYPE_TILE_COMP - Static variable in class jj2000.j2k.ModuleSpec

The identifier for a specification module that applies both to
 tiles and components

specialPlateNames - Variable in class loci.formats.in.OpenlabReader
 
specified - Variable in class jj2000.j2k.ModuleSpec

The specified value in string format

specified - Variable in class jj2000.j2k.StringSpec
 
specifyRangesBox - Variable in class loci.plugins.in.MainDialog
 
specTitle - Static variable in class com.sun.media.imageioimpl.common.PackageUtil

Specification Title derived from Manifest.

SPECTRA - Static variable in class loci.formats.FormatTools

Identifies the Spectra dimensional type,
 representing a dimension consisting of spectral channels.

spectra - Variable in class loci.formats.in.IM3Reader
 
SPECTRAL_SENSITIVITY - Static variable in class loci.formats.tiff.IFD
 
spectralMode - Variable in class loci.formats.in.PrairieMetadata.Sequence

SpectralMode of this <Sequence>.

SpectralSensitivity() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.SpectralSensitivity
 
Spectrum(IRandomAccess, IM3Reader.ContainerRecord) - Constructor for class loci.formats.in.IM3Reader.Spectrum

Construct a spectrum by parsing a Spectrum record

specType - Variable in class jj2000.j2k.ModuleSpec

The type of the specification module

specValType - Variable in class jj2000.j2k.ModuleSpec

The spec type for each tile-component.

specValType - Variable in class jj2000.j2k.wavelet.WTDecompSpec

The spec type for each tile and component.

specValType - Variable in class jj2000.j2k.wavelet.WTFilterSpec

The spec type for each tile and component.

speed - Variable in class loci.formats.in.ND2Handler
 
SPEED_REF_KILOMETERS_PER_HOUR - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSSpeedRef" tag.

SPEED_REF_KNOTS - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSSpeedRef" tag.

SPEED_REF_MILES_PER_HOUR - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet

A value to be used with the "GPSSpeedRef" tag.

SpeHeader(byte[]) - Constructor for class loci.formats.in.SPEReader.SpeHeader

Constructor for SpeHeader

SpeHeaderEntry(int, SPEReader.SpeHeaderType) - Constructor for enum loci.formats.in.SPEReader.SpeHeaderEntry

Constructor for SpeHeaderEntry

SpeHeaderType() - Constructor for enum loci.formats.in.SPEReader.SpeHeaderType
 
SPEReader - Class in loci.formats.in

SPEReader is the file format reader for Princeton Instruments SPE .spe files.

SPEReader() - Constructor for class loci.formats.in.SPEReader

Constructs a new SPE reader.

SPEReader.SpeHeader - Class in loci.formats.in

SpeHeader holds a byte array containing the SPE binary data header along
  with associated methods for reading SPE Header Entry values in various formats

SPEReader.SpeHeaderEntry - Enum in loci.formats.in

SpeHeaderEntry is an Enum which provides a list of all available SPE header entries along 
 with the offset value from the top of the header in bytes and their associated data type

SPEReader.SpeHeaderType - Enum in loci.formats.in

SpeHeaderType is an Enum representing the available data types stored in the SPE header

SPEReader.SpeROI - Class in loci.formats.in

Private class to represent the data for a single ROI in the SPE format

SpeROI(int, int, int, int, int, int) - Constructor for class loci.formats.in.SPEReader.SpeROI

Constructor for SpeROI objects

SpiderReader - Class in loci.formats.in

SpiderReader is the file format reader for SPIDER files.

SpiderReader() - Constructor for class loci.formats.in.SpiderReader

Constructs a new SPIDER reader.

SPIN_DISK_CONFOCAL - Static variable in class loci.formats.in.LegacyND2Reader
 
spixels - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
split(WaveletFilter, WaveletFilter) - Method in class jj2000.j2k.wavelet.analysis.SubbandAn

Splits the current subband in its four subbands.

split(WaveletFilter, WaveletFilter) - Method in class jj2000.j2k.wavelet.Subband

Splits the current subband in its four subbands.

split(WaveletFilter, WaveletFilter) - Method in class jj2000.j2k.wavelet.synthesis.SubbandSyn

Splits the current subband in its four subbands.

split - Variable in class loci.formats.codec.NikonCodecOptions
 
split - Variable in class loci.formats.in.NativeND2Reader
 
split - Variable in class loci.formats.in.NikonReader
 
SPLIT_LOSSY_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
 
SPLIT_LOSSY_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
 
splitCBox - Variable in class loci.plugins.in.MainDialog
 
splitChannels(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools

Splits the given multi-channel image into single-channel images.

splitChannels(byte[], int, int, int, boolean, boolean) - Static method in class loci.formats.ImageTools

Splits the given multi-channel array into a 2D array.

splitChannels(byte[], byte[], int, int, int, boolean, boolean, int) - Static method in class loci.formats.ImageTools

Splits the given multi-channel array into a 2D array.

splitDims(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
 
splitDoubles(String) - Method in class loci.formats.in.ICSReader

Splits the given string into a list of Doubles.

splitPlanes - Variable in class loci.formats.in.ZeissLSMReader
 
splitTBox - Variable in class loci.plugins.in.MainDialog
 
splitZBox - Variable in class loci.plugins.in.MainDialog
 
SPM_DOMAIN - Static variable in class loci.formats.FormatTools

Identifies the scanning probe microscopy domain.

spqcc - Variable in class jj2000.j2k.codestream.HeaderInfo.QCC
 
spqcd - Variable in class jj2000.j2k.codestream.HeaderInfo.QCD
 
sprgn - Variable in class jj2000.j2k.codestream.HeaderInfo.RGN
 
SpringUtilities - Class in loci.plugins.config

A 1.4 file that provides utility methods for
 creating form- or grid-style layouts with SpringLayout.

SpringUtilities() - Constructor for class loci.plugins.config.SpringUtilities
 
SPURIOUS_NOISE_REMOVAL - Static variable in class loci.formats.in.CellSensReader
 
SQ - Static variable in class loci.formats.in.DicomReader
 
sqcc - Variable in class jj2000.j2k.codestream.HeaderInfo.QCC
 
sqcd - Variable in class jj2000.j2k.codestream.HeaderInfo.QCD
 
SQCX_EXP_MASK - Static variable in interface jj2000.j2k.codestream.Markers

Exponent bitmask in SPQCX when no quantization: 3

SQCX_EXP_SHIFT - Static variable in interface jj2000.j2k.codestream.Markers

Exponent shift in SPQCX when no quantization: 3

SQCX_GB_MSK - Static variable in interface jj2000.j2k.codestream.Markers

Guard bits mask in SQCX field: 7

SQCX_GB_SHIFT - Static variable in interface jj2000.j2k.codestream.Markers

Guard bits shift in SQCX field: 5

SQCX_NO_QUANTIZATION - Static variable in interface jj2000.j2k.codestream.Markers

No quantization (i.e.

SQCX_SCALAR_DERIVED - Static variable in interface jj2000.j2k.codestream.Markers

Scalar derived (i.e.

SQCX_SCALAR_EXPOUNDED - Static variable in interface jj2000.j2k.codestream.Markers

Scalar expounded (i.e.

sqr() - Method in class loci.plugins.util.RecordedImageProcessor
 
sqrt() - Method in class loci.plugins.util.RecordedImageProcessor
 
SQUARE_ROOT - Static variable in class loci.formats.in.GelReader
 
squareRoot - Variable in class loci.formats.in.IvisionReader
 
sQuit - Variable in class jj2000.j2k.codestream.reader.PktDecoder

The subband in which the ncb quit condition was reached

src - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
 
src - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper

The ImageInputStream to be wrapped.

src - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
src - Variable in class jj2000.j2k.codestream.reader.PktDecoder

Reference to the codestream reader agent

src - Variable in class jj2000.j2k.entropy.decoder.EntropyDecoder

The bit stream transport from where to get the compressed data
 (the source)

src - Variable in class jj2000.j2k.entropy.encoder.EntropyCoder

The source of quantized wavelet coefficients

src - Variable in class jj2000.j2k.entropy.encoder.PostCompRateAllocator

The source of entropy coded data

src - Variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf

The source of image data

src - Variable in class jj2000.j2k.image.ImgDataConverter

The source of image data

src - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf

The source of image data

src - Variable in class jj2000.j2k.image.Tiler

The source of image data

src - Variable in class jj2000.j2k.quantization.dequantizer.Dequantizer

The entropy decoder from where to get the quantized data (the
 source).

src - Variable in class jj2000.j2k.quantization.quantizer.Quantizer

The source of wavelet transform coefficients

src - Variable in class jj2000.j2k.roi.encoder.ArbROIMaskGenerator

The source of quantized wavelet transform coefficients

src - Variable in class jj2000.j2k.roi.encoder.ROIScaler

The source of quantized wavelet transform coefficients

src - Variable in class jj2000.j2k.roi.ROIDeScaler

The entropy decoder from where to get the compressed data (the source)

src - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull

The source of image data

src - Variable in class jj2000.j2k.wavelet.synthesis.InvWTFull

the code-block buffer's source i.e.

srcblk - Variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The source code-block to entropy code (avoids reallocation for each
        code-block).

srcBlk - Variable in class jj2000.j2k.image.ImgDataConverter

The block used to request data from the source in the case that a
 conversion seems necessary.

srcblkT - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The source code-block to entropy code (avoids reallocation for each
        code-block), for each thread.

srcBuf - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
srcColorModel - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
 
srcData - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
srcData - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
srcHeight - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The height of the source region being decoded from the source
 stream.

srcHeight - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
srcIndex - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
srcIndex - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
srcMinX - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The X coordinate of the upper-left pixel of the source region
 being decoded from the source stream.

srcMinY - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The Y coordinate of the upper-left pixel of the source region
 being decoded from the source stream.

srcPitch - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
srcPixelFormat - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
srcRaster - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder
 
srcWidth - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor

The width of the source region being decoded from the source
 stream.

srcWidth - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
srcXSubsampling - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
srcYSubsampling - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
srgn - Variable in class jj2000.j2k.codestream.HeaderInfo.RGN
 
SRGN_IMPLICIT - Static variable in interface jj2000.j2k.codestream.Markers

Implicit (i.e.

SS - Static variable in class loci.formats.in.DicomReader
 
ssiz - Variable in class jj2000.j2k.codestream.HeaderInfo.SIZ
 
SSIZ_DEPTH_BITS - Static variable in interface jj2000.j2k.codestream.Markers

Component bitdepth bits in Ssiz field in SIZ marker: 7

sss - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

Error resilience segment symbol use specifications

ST - Static variable in class loci.formats.in.DicomReader
 
STABLE - Static variable in class loci.plugins.Updater
 
STABLE_BUILD - Static variable in class loci.formats.UpgradeChecker

Location of the JAR artifacts for the stable releases.

STABLE_VERSION - Static variable in class loci.formats.UpgradeChecker

Version number of the latest stable release.

Stack() - Constructor for class loci.formats.in.OBFReader.Stack
 
Stack() - Constructor for class loci.formats.in.VolocityReader.Stack
 
STACK_DISPLAY_LUT - Static variable in class loci.formats.in.CellSensReader
 
STACK_MAGIC_STRING - Static variable in class loci.formats.in.OBFReader
 
STACK_NAME - Static variable in class loci.formats.in.CellSensReader
 
STACK_TYPE - Static variable in class loci.formats.in.CellSensReader
 
stackFormatChoice - Variable in class loci.plugins.in.MainDialog
 
stackOrderChoice - Variable in class loci.plugins.in.MainDialog
 
stacks - Variable in class loci.formats.in.OBFReader
 
stacks - Variable in class loci.formats.in.VolocityReader
 
stageLabel - Variable in class loci.formats.in.MetamorphHandler
 
stageNames - Variable in class loci.formats.in.MetamorphReader
 
stageX - Variable in class loci.formats.in.BaseZeissReader
 
stageX - Variable in class loci.formats.in.FEITiffReader
 
stageX - Variable in class loci.formats.in.MetamorphReader
 
stageX - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
stageXCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

X stage coordinates.

stageY - Variable in class loci.formats.in.BaseZeissReader
 
stageY - Variable in class loci.formats.in.FEITiffReader
 
stageY - Variable in class loci.formats.in.MetamorphReader
 
stageY - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
stageYCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Y stage coordinates.

stageZ - Variable in class loci.formats.in.FEITiffReader
 
stageZ - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
stageZCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields

Z stage coordinates.

stamps - Variable in class loci.formats.in.FluoviewReader

Timestamps for each plane, in seconds.

stampValues - Variable in class loci.formats.in.LiFlimReader
 
STANDARD_METADATA_NAME - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
start - Variable in class loci.formats.in.EPSReader

Starting line of pixel data.

start - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
start - Variable in class loci.formats.Modulo
 
start - Variable in class loci.formats.tiff.OnDemandLongArray
 
START_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
 
START_TIME - Static variable in class loci.formats.in.ZeissLSMReader
 
startCoordinate - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.AFIReader.AFIHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.BioRadReader.BioRadHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FEITiffReader.FEIHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.FlexHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.MeaHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.ResHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ImaconReader.ImaconHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.InCellReader.InCellHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.InCellReader.MinimalInCellHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.IvisionReader.IvisionHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.MetamorphHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.MicromanagerReader.MicromanagerHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ND2Handler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ScanrReader.ScanrHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ZeissTIFFHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
 
startIndex - Variable in class loci.formats.FilePattern

Indices into the pattern indicating the start of a numerical block.

startingPosition - Variable in class loci.formats.in.ZeissCZIReader.Segment
 
startLevelROI - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava

This parameter defines the lowest resolution levels to belong to
  the ROI.

startPos - Variable in class com.sun.media.imageio.stream.StreamSegment
 
startTime - Variable in class loci.formats.in.PerkinElmerReader
 
startTime - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
startTime - Variable in class loci.plugins.in.ImagePlusReader
 
startTiming() - Method in class loci.plugins.in.ImagePlusReader
 
startX - Variable in class loci.formats.in.SPEReader.SpeROI
 
startY - Variable in class loci.formats.in.SPEReader.SpeROI
 
state - Variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The state array for entropy coding.

state - Variable in class loci.formats.services.WlzServiceImpl
 
STATE_D_DL_R1 - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The flag bit for the diagonal down-left significance in the state
        array, for row 1.

STATE_D_DL_R1 - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The flag bit for the diagonal down-left significance in the state
        array, for row 1.

STATE_D_DL_R2 - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The flag bit for the diagonal down-left significance in the state
        array, for row 2.

STATE_D_DL_R2 - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The flag bit for the diagonal down-left significance in the state
        array, for row 2.

STATE_D_DR_R1 - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The flag bit for the diagonal down-right significance in the state
        array , for row 1.

STATE_D_DR_R1 - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The flag bit for the diagonal down-right significance in the state
        array , for row 1.

STATE_D_DR_R2 - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The flag bit for the diagonal down-right significance in the state
        array , for row 2.

STATE_D_DR_R2 - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The flag bit for the diagonal down-right significance in the state
        array , for row 2.

STATE_D_UL_R1 - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The flag bit for the diagonal up-left significance in the state array,
        for row 1.

STATE_D_UL_R1 - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder

The flag bit for the diagonal up-left significance in the state array,
        for row 1.

STATE_D_UL_R2 - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder

The flag bit for the dia