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.