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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.BioRadSCNReader
 
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.
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.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
 
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.GatanReader
 
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() - 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 - 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.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
 
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.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.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.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.
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.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.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.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.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
 
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_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
 
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.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.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'.
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.
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.
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.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 - 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
 
detType - Variable in class loci.formats.in.SDTInfo
Detector type (SPC-930 in camera mode).
DEVICE_ID - Static variable in class loci.formats.in.CellSensReader
 
DEVICE_MANUFACTURER - Static variable in class loci.formats.in.CellSensReader
 
DEVICE_NAME - Static variable in class loci.formats.in.CellSensReader
 
DEVICE_SUBTYPE - Static variable in class loci.formats.in.CellSensReader
 
deviceIDs - Variable in class loci.formats.in.CellSensReader.Pyramid
 
deviceManufacturers - Variable in class loci.formats.in.CellSensReader.Pyramid
 
deviceNames - Variable in class loci.formats.in.CellSensReader.Pyramid
 
DeviceSettingDescription() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.DeviceSettingDescription
 
deviceTypes - Variable in class loci.formats.in.CellSensReader.Pyramid
 
devModel - Variable in class loci.formats.in.LeicaSCNReader.Image
 
devVersion - Variable in class loci.formats.in.LeicaSCNReader.Image
 
DHP - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
DHT - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
DHT - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
dialog - Variable in class loci.plugins.in.ThumbLoader
 
dichroic - Variable in class loci.formats.in.FlexReader.FilterGroup
 
dichroicMap - Variable in class loci.formats.in.FlexReader
 
dichroicModels - Variable in class loci.formats.in.NikonTiffReader
 
DICOM_MAGIC_STRING - Static variable in class loci.formats.in.DicomReader
 
DICOM_SUFFIXES - Static variable in class loci.formats.in.DicomReader
 
DicomReader - Class in loci.formats.in
DicomReader is the file format reader for DICOM files.
DicomReader() - Constructor for class loci.formats.in.DicomReader
Constructs a new DICOM reader.
diff - Variable in class loci.formats.in.BioRadGelReader
 
difference(byte[], IFD) - Static method in enum loci.formats.tiff.TiffCompression
Performs in-place differencing according to the given predictor value.
DIFFERENTIAL_CORRECTION_APPLIED - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSDifferential" tag.
DIFFERENTIAL_CORRECTION_NONE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSDifferential" tag.
DIGITAL_ZOOM_RATIO - Static variable in class loci.formats.tiff.IFD
 
DigitalZoomRatio() - Constructor for class com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.DigitalZoomRatio
 
digits(int) - Static method in class loci.plugins.in.ImporterMetadata
Computes the given value's number of digits.
dilate() - Method in class loci.plugins.util.RecordedImageProcessor
 
DIM_INDEX_1 - Static variable in class loci.formats.in.CellSensReader
 
DIM_INDEX_2 - Static variable in class loci.formats.in.CellSensReader
 
DIMDESCR - Static variable in class loci.formats.in.LeicaReader
 
Dimension(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Dimension
 
dimension - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
Dimension(Integer) - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
Constructor.
dimension - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
DIMENSION_DESCRIPTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_INCREMENT_ID - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_MEANING - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_NAME - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_NAMES - Static variable in class loci.formats.in.LeicaReader
 
DIMENSION_SIZE - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_START_ID - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_VALUE_ID - Static variable in class loci.formats.in.CellSensReader
 
dimensionCount - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
dimensionEntries - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
DimensionEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DimensionEntry
 
dimensionLength - Variable in class loci.formats.out.ICSWriter
 
dimensionM - Variable in class loci.formats.in.ZeissLSMReader
 
dimensionOffset - Variable in class loci.formats.out.ICSWriter
 
dimensionOrder - Variable in class loci.formats.CoreMetadata
Order in which dimensions are stored.
dimensionOrder - Variable in class loci.formats.in.FluoviewReader
 
dimensionOrdering - Variable in class loci.formats.in.CellSensReader.Pyramid
 
dimensionP - Variable in class loci.formats.in.ZeissLSMReader
 
DIMENSIONS_STRING - Static variable in class loci.formats.in.KodakReader
 
DimensionSwapper - Class in loci.formats
Handles swapping the dimension order of an image series.
DimensionSwapper() - Constructor for class loci.formats.DimensionSwapper
Constructs a DimensionSwapper around a new image reader.
DimensionSwapper(IFormatReader) - Constructor for class loci.formats.DimensionSwapper
Constructs a DimensionSwapper with the given reader.
dimensionSwapper - Variable in class loci.plugins.in.ImportProcess
 
dimensionTag - Variable in class loci.formats.in.CellSensReader
 
dimOrder - Variable in class loci.formats.AxisGuesser
Original ordering of internal dimensional axes.
dims - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
dims - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
 
dir - Variable in class loci.formats.in.VolocityReader
 
DIRECTION_REF_MAGNETIC - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSTrackRef", "GPSImgDirectionRef", and "GPSDestBearingRef" tags.
DIRECTION_REF_TRUE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSTrackRef", "GPSImgDirectionRef", and "GPSDestBearingRef" tags.
Directory() - Constructor for class loci.formats.in.ZeissCZIReader.Directory
 
directory - Variable in class loci.formats.Memoizer
Directory where all memo files should be created.
directory - Variable in class loci.formats.services.EXIFServiceImpl
 
DirectoryEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
directoryEntry - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
directoryList - Variable in class loci.formats.in.CellWorxReader
 
directoryPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
directoryRoot - Variable in class loci.formats.tools.FakeImage
 
dirty - Variable in class loci.formats.cache.CacheStrategy
Whether load order array needs to be recomputed before building the next load list.
DISPLAY_COLOR - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_LIMITS - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_LUT - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_MAPPING_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_PROCESSOR_TYPE - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_STACK_ID - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_STACK_INDEX - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_VISIBLE - Static variable in class loci.formats.in.CellSensReader
 
displayDataBrowser(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
 
displayDialog(GenericDialog) - Method in class loci.plugins.in.IdDialog
Asks user whether Bio-Formats should automatically check for upgrades, and if so, checks for an upgrade and prompts user to install it.
displayDialog(GenericDialog) - Method in class loci.plugins.in.ImporterDialog
Displays the dialog, or grabs values from macro options.
displayDialog(GenericDialog) - Method in class loci.plugins.in.SeriesDialog
 
displayDialog(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog
Asks user whether Bio-Formats should automatically check for upgrades, and if so, checks for an upgrade and prompts user to install it.
DISPLAYED_LUT_ID - Static variable in class loci.formats.in.CellSensReader
 
DisplayHandler - Class in loci.plugins.in
Logic for displaying images and metadata onscreen using ImageJ.
DisplayHandler(ImportProcess) - Constructor for class loci.plugins.in.DisplayHandler
 
displayImage(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
Displays the given image according to the configured options.
displayImage5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
 
displayImages(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler
Displays the given images according to the configured options.
displayName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
displayNormal(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
Displays in a normal ImageJ window.
displayOMEXML() - Method in class loci.plugins.in.DisplayHandler
Displays OME-XML metadata in a tree in its own window.
displayOriginalMetadata() - Method in class loci.plugins.in.DisplayHandler
Displays standard metadata in a table in its own window.
displayROIs(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler
 
displayTag - Variable in class loci.formats.in.BaseZeissReader.Shape
 
displayUsage() - Method in class loci.formats.tools.MakeTestOmeTiff
 
displayView5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
 
disposalMethod - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
disposalMethodNames - Static variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
dispose() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
dispose() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
dispose() - Method in class loci.formats.gui.CacheComponent
 
dispose - Variable in class loci.formats.in.GIFReader
 
distance(int, int) - Method in class loci.formats.cache.CacheStrategy
Computes the distance from the given axis value to the axis center, taking into account the axis ordering scheme.
distbufT - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder
The buffer for distortion values (avoids reallocation for each code-block), for each thread.
dither - Variable in class loci.formats.in.SDTInfo
 
dl - Variable in class jj2000.j2k.entropy.decoder.DecLyrdCBlk
The coded (compressed) data length.
DLL_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
For .sdt files created using DLL function SPC_save_data_to_sdtfile (no setup, only data).
dls - Variable in class jj2000.j2k.decoder.DecoderSpecs
Number of decomposition levels specifications
dls - Variable in class jj2000.j2k.entropy.PrecinctSizeSpec
Reference to wavelet number of decomposition levels for each tile-component.
dls - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull
The number of decomposition levels specification
DM2_MAGIC_BYTES - Static variable in class loci.formats.in.GatanDM2Reader
 
DM3_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader
 
DM4_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader
 
DNGReader - Class in loci.formats.in
DNGReader is the file format reader for Canon DNG (TIFF) files.
DNGReader() - Constructor for class loci.formats.in.DNGReader
Constructs a new DNG reader.
DNL - Static variable in class loci.formats.codec.LosslessJPEGCodec
 
DO_TIMING - Static variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder
Whether to collect timing information or not: false.
DO_TIMING - Static variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator
Whether to collect timing information or not: false.
DO_TIMING - Static variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder
Whether to collect timing information or not: false.
doc - Variable in class loci.formats.gui.XMLWindow
 
doCaching - Variable in class loci.formats.tiff.TiffParser
 
doChannels - Variable in class loci.formats.in.CellWorxReader
 
doCodestreamManipulation() - Method in class jj2000.j2k.util.CodestreamManipulator
This method performs the actual manipulation of the codestream which is the reparsing for tile parts and packed packet headers
doCrop() - Method in class loci.plugins.in.ImporterOptions
 
DOCUMENT_AUTHOR - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_COMPANY - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_BUILD_NUMBER - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_MAJOR_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_MINOR_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_NAME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_PACKAGE - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_SUB_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_KEYS - Static variable in class loci.formats.in.ICSReader
 
DOCUMENT_NAME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_NAME - Static variable in class loci.formats.tiff.IFD
 
DOCUMENT_NOTE - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PRODUCT - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PRODUCT_NAME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PRODUCT_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_THUMB - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_TIME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_TYPE_HINT - Static variable in class loci.formats.in.CellSensReader
 
DocumentName() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.DocumentName
 
documentUpdate() - Method in class loci.plugins.config.FlexWidgets
 
doer - Variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder
Flag to indicate if we should try to detect errors or just ignore any error resilient information
doFormatLayout(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
 
doInPlaceCaching - Variable in class loci.formats.Memoizer
If true, then all memo files will be created in the same directory as the original file.
domains - Variable in class loci.formats.FormatReader
List of domains in which this format is used.
doMustGroup() - Method in class loci.plugins.in.ImporterOptions
 
doNotChangePattern - Variable in class loci.formats.FileStitcher
 
doNotifyAll - Variable in class jj2000.j2k.util.ThreadPool.ThreadPoolThread
 
doRecording - Variable in class loci.plugins.util.RecordedImageProcessor
 
doStitchTiles() - Method in class loci.plugins.in.ImporterOptions
 
doT - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
DOT - Static variable in class loci.formats.ResourceNamer
 
DOT_RANGE - Static variable in class loci.formats.tiff.IFD
 
DotRange() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.DotRange
 
DOUBLE - Static variable in class loci.formats.FormatTools
Identifies the DOUBLE data type used to store pixel values.
DOUBLE - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE - Static variable in class loci.formats.in.GatanReader
 
DOUBLE_2 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_2_2 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_3 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_3_3 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_4 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_4_4 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_ARRAY_2 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_ARRAY_3 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_INTERVAL - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_RECT - Static variable in class loci.formats.in.CellSensReader
 
doubleCapacity() - Method in class loci.formats.codec.ByteVector
 
DoubleOption - Class in loci.plugins.prefs
A double option for one of the plugins.
DoubleOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.DoubleOption
Constructs a double option with the parameters from the given map.
DoubleOption(String, boolean, String, String, double) - Constructor for class loci.plugins.prefs.DoubleOption
Constructs a double option with the given parameters.
doubleValue() - Method in class loci.formats.tiff.TiffRational
Returns the value of the specified number as a double.