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A

abort() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
AbstractArrayLoader<A> - Class in io.scif.img.cell.loaders
Abstract superclass for all SCIFIOArrayLoader implementations.
AbstractArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.AbstractArrayLoader
 
AbstractCacheService<T extends Serializable> - Class in io.scif.img.cell.cache
Abstract superclass for CacheService implementations.
AbstractCacheService() - Constructor for class io.scif.img.cell.cache.AbstractCacheService
 
AbstractChecker - Class in io.scif
Abstract superclass of all SCIFIO Checker implementations.
AbstractChecker() - Constructor for class io.scif.AbstractChecker
 
AbstractCodec - Class in io.scif.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.
AbstractCodec() - Constructor for class io.scif.codec.AbstractCodec
 
AbstractFilter<T> - Class in io.scif.filters
Abstract superclass for Filter implementations.
AbstractFilter(Class<? extends T>) - Constructor for class io.scif.filters.AbstractFilter
 
AbstractFormat - Class in io.scif
Abstract superclass of all SCIFIO Format implementations.
AbstractFormat() - Constructor for class io.scif.AbstractFormat
 
AbstractGroupable - Class in io.scif
Abstract super-class for all Groupable components.
AbstractGroupable() - Constructor for class io.scif.AbstractGroupable
 
AbstractHasFormat - Class in io.scif
Abstract superclass for all classes that implement HasFormat.
AbstractHasFormat() - Constructor for class io.scif.AbstractHasFormat
 
AbstractHasSource - Class in io.scif
Abstract implementation of the HasSource interface.
AbstractHasSource() - Constructor for class io.scif.AbstractHasSource
 
AbstractImageMetadata - Class in io.scif
Abstract superclass of all ImageMetadata implementations.
AbstractImageMetadata() - Constructor for class io.scif.AbstractImageMetadata
 
AbstractImageMetadata(ImageMetadata) - Constructor for class io.scif.AbstractImageMetadata
 
AbstractImgIOComponent - Class in io.scif.img
Abstract superclass for ImgIOComponents (such as ImgOpener or ImgSaver).
AbstractImgIOComponent() - Constructor for class io.scif.img.AbstractImgIOComponent
 
AbstractImgIOComponent(Context) - Constructor for class io.scif.img.AbstractImgIOComponent
 
AbstractMetadata - Class in io.scif
Abstract superclass of all SCIFIO Metadata implementations.
AbstractMetadata() - Constructor for class io.scif.AbstractMetadata
 
AbstractMetadata(Metadata) - Constructor for class io.scif.AbstractMetadata
 
AbstractMetadata(List<ImageMetadata>) - Constructor for class io.scif.AbstractMetadata
 
AbstractMetadataWrapper - Class in io.scif.filters
Abstract superclass for concrete implementations of MetadataWrapper.
AbstractMetadataWrapper() - Constructor for class io.scif.filters.AbstractMetadataWrapper
 
AbstractMetadataWrapper(Metadata) - Constructor for class io.scif.filters.AbstractMetadataWrapper
 
AbstractNIOHandle - Class in io.scif.io
A wrapper for buffered NIO logic that implements the IRandomAccess interface.
AbstractNIOHandle() - Constructor for class io.scif.io.AbstractNIOHandle
 
AbstractParser<M extends TypedMetadata> - Class in io.scif
Abstract superclass of all SCIFIO Parser implementations.
AbstractParser() - Constructor for class io.scif.AbstractParser
 
AbstractPlane<T,P extends DataPlane<T>> - Class in io.scif
Abstract superclass for Plane implementations in SCIFIO.
AbstractPlane(Context) - Constructor for class io.scif.AbstractPlane
 
AbstractPlane(Context, ImageMetadata, long[], long[]) - Constructor for class io.scif.AbstractPlane
 
AbstractPlaneConverter - Class in io.scif.img.converters
Abstract superclass for PlaneConverter implementations.
AbstractPlaneConverter() - Constructor for class io.scif.img.converters.AbstractPlaneConverter
 
AbstractReader<M extends TypedMetadata,P extends DataPlane<?>> - Class in io.scif
Abstract superclass of all SCIFIO Reader implementations.
AbstractReader(Class<P>) - Constructor for class io.scif.AbstractReader
Constructs a reader and stores a reference to its plane type
AbstractReaderCommand - Class in io.scif.cli.commands
Abstract superclass for SCIFIOToolCommand implementations that read images.
AbstractReaderCommand() - Constructor for class io.scif.cli.commands.AbstractReaderCommand
 
AbstractReaderFilter - Class in io.scif.filters
Abstract superclass for all Filter that delegate to Reader instances.
AbstractReaderFilter() - Constructor for class io.scif.filters.AbstractReaderFilter
 
AbstractReaderFilter(Class<? extends MetadataWrapper>) - Constructor for class io.scif.filters.AbstractReaderFilter
 
AbstractSCIFIOPlugin - Class in io.scif
Abstract superclass of all SCIFIOPlugin implementations.
AbstractSCIFIOPlugin() - Constructor for class io.scif.AbstractSCIFIOPlugin
 
AbstractSCIFIOToolCommand - Class in io.scif.cli
Abstract SCIFIOToolCommand superclass.
AbstractSCIFIOToolCommand() - Constructor for class io.scif.cli.AbstractSCIFIOToolCommand
 
AbstractTranslator<M extends Metadata,N extends Metadata> - Class in io.scif
Abstract superclass of all SCIFIO Translator components.
AbstractTranslator() - Constructor for class io.scif.AbstractTranslator
 
AbstractWriter<M extends TypedMetadata> - Class in io.scif
Abstract superclass of all SCIFIO Writer implementations.
AbstractWriter() - Constructor for class io.scif.AbstractWriter
 
accept(File) - Method in class io.scif.gui.ComboFileFilter
Accepts files with the proper filename prefix.
accept(File) - Method in class io.scif.gui.FormatFileFilter
Accepts files in accordance with the associated format's Checker.
accept(String) - Method in class io.scif.NumberFilter
Tests if a specified file should be included in a file list.
accept(File) - Method in class io.scif.NumberFilter
Tests if a specified file should be included in a file list.
accumulate - Variable in class io.scif.lifesci.SDTInfo
 
actionPerformed(ActionEvent) - Method in class io.scif.gui.ImageViewer
Handles menu commands.
activeSrcHeight - Variable in class io.scif.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 io.scif.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 io.scif.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 io.scif.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.
ACTLChunk() - Constructor for class io.scif.formats.APNGFormat.ACTLChunk
 
adcDE - Variable in class io.scif.lifesci.SDTInfo
ADC sample delay (SPC-930).
adcRE - Variable in class io.scif.lifesci.SDTInfo
 
adcZoom - Variable in class io.scif.lifesci.SDTInfo
 
add(ImageMetadata) - Method in class io.scif.AbstractMetadata
 
add(byte) - Method in class io.scif.codec.ByteVector
 
add(byte[]) - Method in class io.scif.codec.ByteVector
 
add(byte[], int, int) - Method in class io.scif.codec.ByteVector
 
add(ImageMetadata, boolean) - Method in class io.scif.filters.AbstractMetadataWrapper
 
add(ImageMetadata) - Method in class io.scif.filters.AbstractMetadataWrapper
 
add(ImageMetadata, boolean) - Method in interface io.scif.filters.MetadataWrapper
 
add(ImageMetadata) - Method in interface io.scif.Metadata
Adds the provided image metadata to this dataset metadata
add1DBits(byte[], int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Get code for run and add to compressed bitstream.
add2DBits(byte[], int, int[][], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Place entry from mode table into compressed bitstream.
addAllowedTagSet(TIFFTagSet) - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageReadParam
Adds a TIFFTagSet object to the list of allowed tag sets.
addAxis(CalibratedAxis) - Method in class io.scif.AbstractImageMetadata
 
addAxis(CalibratedAxis, long) - Method in class io.scif.AbstractImageMetadata
 
addAxis(AxisType, long) - Method in class io.scif.AbstractImageMetadata
 
addAxis(CalibratedAxis) - Method in interface io.scif.ImageMetadata
Appends the provided CalibratedAxis to the metadata's list of axes, with a length of 1.
addAxis(CalibratedAxis, long) - Method in interface io.scif.ImageMetadata
Appends the provided CalibratedAxis to the current CalibratedAxis array and creates a corresponding entry with the specified value in axis lengths.
addAxis(AxisType, long) - Method in interface io.scif.ImageMetadata
addByteArray(byte[], int, int) - Method in class io.scif.jj2000.j2k.entropy.decoder.ByteInputBuffer
Adds the specified data to the end of the byte array stream.
addCache(String) - Method in interface io.scif.img.cell.cache.CacheService
Creates a cache using the specified id
addCache(String) - Method in class io.scif.img.cell.cache.MapDBCache
 
AddCharString(short, byte) - Method in class io.scif.media.imageioimpl.common.LZWStringTable
 
addChunk(APNGFormat.FDATChunk) - Method in class io.scif.formats.APNGFormat.FCTLChunk
 
addComment(String) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
addComponents(Format) - Method in class io.scif.services.DefaultFormatService
 
addComponents(Format) - Method in interface io.scif.services.FormatService
Creates mappings between this Format and its components.
addCubeChannel(Hashtable<Integer, String>) - Method in class io.scif.formats.ICSFormat.Metadata
 
addEOFB(byte[], int) - Method in class io.scif.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 io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Add an End-of-Line (EOL == 0x001) to the compressed bitstream with optional byte alignment.
addFormat(Format) - Method in class io.scif.services.DefaultFormatService
 
addFormat(Format) - Method in interface io.scif.services.FormatService
Makes the provided Format available for image IO operations in this context.
addIdat(APNGFormat.IDATChunk) - Method in class io.scif.formats.APNGFormat.Metadata
 
addImage(Object, int, int, int, String) - Method in class io.scif.formats.imaris.ImarisWriter
 
addLaserWavelength(Hashtable<Integer, Integer>) - Method in class io.scif.formats.ICSFormat.Metadata
 
addLocation(int) - Method in class io.scif.formats.DICOMFormat.DICOMTag
 
addMetadataOnly(OMEXMLMetadata, int) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
addMetadataOnly(OMEXMLMetadata, int) - Method in interface io.scif.ome.services.OMEXMLService
 
addNode(Box) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
addNTP(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
Adds the number of new truncation for specified layer.
addOptPoint(float, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.LayersInfo
Adds a new optimization point, with target bitrate 'brate' and with 'elyrs' (unoptimized) extra layers after it.
addRange(AxisType, String) - Method in class io.scif.img.ImageRegion
 
addReader(Class<IFormatReader>) - Method in class io.scif.bf.BioFormatsFormat
Adds the given reader class to this format's supported reader list.
addShortOrLongField(int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
addStepChannel(Hashtable<Integer, String>) - Method in class io.scif.formats.ICSFormat.Metadata
 
addStringToTable(byte[], byte) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
Add a new string to the string table.
addStringToTable(byte[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
Add a new string to the string table.
addStringToTable(byte[], byte) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWUtil
Add a new string to the string table.
addStringToTable(byte[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWUtil
Add a new string to the string table.
addTagSet(TIFFTagSet) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Adds an element to the group of TIFFTagSets of which this directory is aware.
addTIFFField(TIFFField) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Adds a TIFF field to the directory.
addValueName(int, String) - Method in class io.scif.media.imageio.plugins.tiff.TIFFTag
Adds a mnemonic name for a particular value that this tag's data may take on.
ALL_DOMAINS - Static variable in class io.scif.util.FormatTools
List of all supported domains.
allocate(long...) - Static method in class io.scif.common.DataTools
Deprecated.
Allocates a 1-dimensional byte array matching the product of the given sizes.
allocate(FileChannel, FileChannel.MapMode, long, int) - Method in class io.scif.io.DefaultNIOService
 
allocate(FileChannel, FileChannel.MapMode, long, int) - Method in interface io.scif.io.NIOService
Allocates or maps the desired file data into memory.
ALPHA - Static variable in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
The value of the first lifting step coefficient
ALPHA - Static variable in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
The value of the first lifting step coefficient
alphaMask - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
ALT_ZVI - Static variable in class io.scif.common.DateTools
 
ALT_ZVI_EPOCH - Static variable in class io.scif.common.DateTools
 
ALTITUDE_REF_SEA_LEVEL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSAltitudeRef" tag.
ALTITUDE_REF_SEA_LEVEL_REFERENCE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSAltitudeRef" tag.
analyze_hpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.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.
anbytes - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Actual number of read bytes
anGainExp - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The base 2 exponent of the analysis gain of the subband.
AnWTFilter - Class in io.scif.jj2000.j2k.wavelet.analysis
This abstract class defines the methods of all analysis wavelet filters.
AnWTFilter() - Constructor for class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilter
 
AnWTFilterFloat - Class in io.scif.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 io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloat
 
AnWTFilterFloatLift9x7 - Class in io.scif.jj2000.j2k.wavelet.analysis
This class inherits from the analysis wavelet filter definition for int data.
AnWTFilterFloatLift9x7() - Constructor for class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
 
AnWTFilterInt - Class in io.scif.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 io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterInt
 
AnWTFilterIntLift5x3 - Class in io.scif.jj2000.j2k.wavelet.analysis
This class inherits from the analysis wavelet filter definition for int data.
AnWTFilterIntLift5x3() - Constructor for class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
 
AnWTFilterSpec - Class in io.scif.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 io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterSpec
Constructs a new 'AnWTFilterSpec' for the specified number of components and tiles.
APERTURE_VALUE - Static variable in class io.scif.formats.tiff.IFD
 
APNGChunk(byte[]) - Constructor for class io.scif.formats.APNGFormat.APNGChunk
 
APNGFormat - Class in io.scif.formats
SCIFIO Format supporting the PNG and APNG image formats.
APNGFormat() - Constructor for class io.scif.formats.APNGFormat
 
APNGFormat.ACTLChunk - Class in io.scif.formats
Represents the acTL chunk of the APNG image format.
APNGFormat.APNGChunk - Class in io.scif.formats
A parent class for all APNG Chunk classes.
APNGFormat.APNGTranslator - Class in io.scif.formats
This class can be used for translating any io.scif.Metadata to Metadata for writing Animated Portable Network Graphics (APNG) files.
APNGFormat.Checker - Class in io.scif.formats
File format SCIFIO Checker for Animated Portable Network Graphics (APNG) images.
APNGFormat.FCTLChunk - Class in io.scif.formats
Represents the fcTL chunk of the APNG image format.
APNGFormat.FDATChunk - Class in io.scif.formats
Represents the fdAT chunk of the APNG image format.
APNGFormat.IDATChunk - Class in io.scif.formats
Represents the IDAT chunk of the APNG image format.
APNGFormat.IENDChunk - Class in io.scif.formats
This class represents the critical IEND chunk that signifies the end of a PNG stream.
APNGFormat.IHDRChunk - Class in io.scif.formats
Represents the IHDR chunk of the APNG image format.
APNGFormat.Metadata - Class in io.scif.formats
File format SCIFIO Metadata for Animated Portable Network Graphics (APNG) images.
APNGFormat.Parser - Class in io.scif.formats
File format SCIFIO Parser for Animated Portable Network Graphics (APNG) images.
APNGFormat.PLTEChunk - Class in io.scif.formats
Represents the PLTE chunk of the APNG image format.
APNGFormat.Reader - Class in io.scif.formats
File format SCIFIO Reader for Animated Portable Network Graphics (APNG) images.
APNGFormat.Writer - Class in io.scif.formats
The SCIFIO file format writer for PNG and APNG files.
APNGOMETranslator() - Constructor for class io.scif.ome.translators.APNGTranslator.APNGOMETranslator
 
APNGTranslator() - Constructor for class io.scif.formats.APNGFormat.APNGTranslator
 
APNGTranslator - Class in io.scif.ome.translators
Container class for translators between OME and APNG formats.
APNGTranslator() - Constructor for class io.scif.ome.translators.APNGTranslator
 
APNGTranslator.APNGOMETranslator - Class in io.scif.ome.translators
Translator class from APNGFormat.Metadata to OMEMetadata
APNGTranslator.OMEAPNGTranslator - Class in io.scif.ome.translators
Translator class from APNGFormat.Metadata to OMEMetadata.
appendChild(Node) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
appendToken(String, String, Object...) - Static method in class io.scif.formats.FakeFormat.FakeUtils
Appends the provided key:value pair to the provided base and returns the result.
applicationData - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
applicationIDs - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
arate - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Actual decoding rate in bpp
ArbROIMaskGenerator - Class in io.scif.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 io.scif.jj2000.j2k.roi.encoder.ArbROIMaskGenerator
The constructor of the arbitrary mask generator
arbShape - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
Where or not the ROI shape is arbitrary
ArrayDataAccessConverter - Class in io.scif.img.converters
PlaneConverter implementation specialized for populating ArrayImg instances.
ArrayDataAccessConverter() - Constructor for class io.scif.img.converters.ArrayDataAccessConverter
 
ArrayUtil - Class in io.scif.jj2000.j2k.util
This class contains a colleaction of utility static methods for arrays.
ArrayUtil() - Constructor for class io.scif.jj2000.j2k.util.ArrayUtil
 
ARTIST - Static variable in class io.scif.formats.tiff.IFD
 
AsciiImage - Class in io.scif.util
A utility class for outputting a BufferedImage as ASCII text.
AsciiImage(BufferedImage) - Constructor for class io.scif.util.AsciiImage
 
asRetrieve(MetadataStore) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
asRetrieve(MetadataStore) - Method in interface io.scif.ome.services.OMEXMLService
 
assertId(Object, boolean, int) - Static method in class io.scif.util.FormatTools
Asserts that the current file is either null, or not, according to the given flag.
assertStream(RandomAccessInputStream, boolean, int) - Static method in class io.scif.util.FormatTools
Asserts that the current file is either null, or not, according to the given flag.
asStore(MetadataRetrieve) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
asStore(MetadataRetrieve) - Method in interface io.scif.ome.services.OMEXMLService
 
ASTRONOMY_DOMAIN - Static variable in class io.scif.util.FormatTools
Identifies the astronomy domain.
attrInfoMap - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
authenticationCodes - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
autoscale(BufferedImage) - Static method in class io.scif.gui.AWTImageTools
Perform autoscaling on the given BufferedImage.
autoscale(BufferedImage, int, int) - Static method in class io.scif.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 io.scif.util.ImageTools
Perform autoscaling on the given byte array; map min to 0 and max to 255.
available() - Method in class io.scif.bf.wrapper.RandomAccessInputStreamWrapper
 
available() - Method in class io.scif.common.RandomAccessInputStreamWrapper
Deprecated.
 
available() - Method in class io.scif.io.NIOInputStream
 
available() - Method in class io.scif.io.RandomAccessInputStream
 
AVI_MAGIC_STRING - Static variable in class io.scif.formats.AVIFormat.Checker
 
AVIFormat - Class in io.scif.formats
AVIReader is the file format reader for AVI files.
AVIFormat() - Constructor for class io.scif.formats.AVIFormat
 
AVIFormat.Checker - Class in io.scif.formats
 
AVIFormat.Metadata - Class in io.scif.formats
 
AVIFormat.Parser - Class in io.scif.formats
 
AVIFormat.Reader - Class in io.scif.formats
 
AVIFormat.Translator - Class in io.scif.formats
 
AVIFormat.Writer - Class in io.scif.formats
 
avoidUndeclaredNamespaces(String) - Method in class io.scif.xml.DefaultXMLService
 
avoidUndeclaredNamespaces(String) - Method in interface io.scif.xml.XMLService
Replaces NS:tag with NS_tag for undeclared namespaces
AWTImageTools - Class in io.scif.gui
A utility class with convenience methods for manipulating images in BufferedImage form.
ax - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The horizontal coordinate of the image origin in the canvas system, on the reference grid.
AxisGuesser - Class in io.scif
AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T or C), potentially recommending an adjustment in dimension order within the files, depending on the confidence of each guess.
AxisGuesser(FilePattern, AxisType[], long, long, long, boolean) - Constructor for class io.scif.AxisGuesser
Guesses dimensional axis assignments corresponding to the given file pattern, using the specified dimensional information from within each file as a guide.
AxisValue(AxisType, long) - Constructor for class io.scif.util.SCIFIOMetadataTools.AxisValue
 
ay - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The vertical coordinate of the image origin in the canvas system, on the reference grid.

B

backgroundColorIndex - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
baos - Variable in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
The ByteArrayOutputStream to store header data.
Base64Codec - Class in io.scif.codec
Implements encoding (compress) and decoding (decompress) methods for Base64.
Base64Codec() - Constructor for class io.scif.codec.Base64Codec
 
BaseHandler - Class in io.scif.xml
Top-level SAX handler.
BaseHandler(LogService) - Constructor for class io.scif.xml.BaseHandler
 
BaselineTIFFTagSet - Class in io.scif.media.imageio.plugins.tiff
A class representing the set of tags found in the baseline TIFF specification as well as some common additional tags.
baseTiff - Variable in class io.scif.formats.MicromanagerFormat.Position
 
BaseTIFFParser() - Constructor for class io.scif.formats.TIFFFormat.BaseTIFFParser
 
BEBufferedRandomAccessFile - Class in io.scif.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 io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Constructor.
BEBufferedRandomAccessFile(File, String) - Constructor for class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Constructor.
BEBufferedRandomAccessFile(String, String, int) - Constructor for class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Constructor.
BEBufferedRandomAccessFile(String, String) - Constructor for class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Constructor.
beginDecoding() - Method in class io.scif.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 io.scif.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 io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
beginDecoding() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFNullDecompressor
 
beginDecoding() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
BETA - Static variable in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
The value of the second lifting step coefficient
BETA - Static variable in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
The value of the second lifting step coefficient
bgrToRgb(byte[], boolean, int, int) - Static method in class io.scif.util.ImageTools
Reorganizes the provided BGR buffer to be in RGB order.
BH_HEADER_CHKSUM - Static variable in class io.scif.lifesci.SDTInfo
 
BH_HEADER_NOT_VALID - Static variable in class io.scif.lifesci.SDTInfo
 
BH_HEADER_VALID - Static variable in class io.scif.lifesci.SDTInfo
 
BI_BITFIELDS - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
BI_JPEG - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
BI_PNG - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
BI_RGB - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
BI_RLE4 - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
BI_RLE8 - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
BIG - Static variable in class io.scif.formats.tiff.TiffConstants
 
BIG_ENDIAN - Static variable in interface io.scif.jj2000.j2k.io.EndianType
Identifier for big-endian byte ordering (i.e.
BIG_TIFF - Static variable in class io.scif.formats.tiff.IFD
 
BIG_TIFF_BYTES_PER_ENTRY - Static variable in class io.scif.formats.tiff.TiffConstants
The number of bytes in each IFD entry of a BigTIFF file.
BIG_TIFF_KEY - Static variable in class io.scif.formats.TIFFFormat.Writer
 
BIG_TIFF_MAGIC_NUMBER - Static variable in class io.scif.formats.tiff.TiffConstants
 
BinaryDataInput - Interface in io.scif.jj2000.j2k.io
This interface defines the input of binary data from streams and/or files.
BinaryDataOutput - Interface in io.scif.jj2000.j2k.io
This interface defines the output of binary data to streams and/or files.
binning - Variable in class io.scif.formats.MicromanagerFormat.Position
 
BioFormatsFormat - Class in io.scif.bf
Wraps an ImageReader in a SCIFIO Format, allowing proprietary Bio-Formats readers to be used in SCIFIO-based applications.
BioFormatsFormat() - Constructor for class io.scif.bf.BioFormatsFormat
Constructs a new Format with the default list of reader classes from readers.txt.
BioFormatsFormat.Checker - Class in io.scif.bf
 
BioFormatsFormat.Metadata - Class in io.scif.bf
 
BioFormatsFormat.Parser - Class in io.scif.bf
 
BioFormatsFormat.Reader - Class in io.scif.bf
 
BioFormatsOMETranslator() - Constructor for class io.scif.bf.ome.BioFormatsTranslator.BioFormatsOMETranslator
 
BioFormatsTranslator - Class in io.scif.bf.ome
Container class for translators between BioFormats and OME formats.
BioFormatsTranslator() - Constructor for class io.scif.bf.ome.BioFormatsTranslator
 
BioFormatsTranslator.BioFormatsOMETranslator - Class in io.scif.bf.ome
Translator class from BioFormatsFormat.Metadata to OMEMetadata
BitBuffer - Class in io.scif.codec
A class for reading arbitrary numbers of bits from a byte array.
BitBuffer(byte[]) - Constructor for class io.scif.codec.BitBuffer
Default constructor.
BitFile - Class in io.scif.media.imageioimpl.common
Came from GIFEncoder initially.
BitFile(ImageOutputStream, boolean) - Constructor for class io.scif.media.imageioimpl.common.BitFile
 
BitOutputBuffer - Class in io.scif.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 io.scif.jj2000.j2k.codestream.writer.BitOutputBuffer
Creates a new BitOutputBuffer width a buffer of length 'SZ_INIT'.
bits - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Output bit buffer.
BITS_PER_COMPONENT_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
BITS_PER_SAMPLE - Static variable in class io.scif.formats.tiff.IFD
 
BitsPerComponentBox - Class in io.scif.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 io.scif.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 io.scif.media.imageioimpl.plugins.jpeg2000.BitsPerComponentBox
Constructs a BitsPerComponentBox based on the provide org.w3c.dom.Node.
bitsPerPixel - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
bitsPerSample - Variable in class io.scif.codec.CodecOptions
Number of bits per channel.
bitsPerSample - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The value of the BitsPerSample tag.
BitstreamReaderAgent - Class in io.scif.jj2000.j2k.codestream.reader
This is the generic interface for bit stream reader agents.
BitstreamReaderAgent(HeaderDecoder, DecoderSpecs) - Constructor for class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Initializes members of this class.
BitWriter - Class in io.scif.codec
A class for writing arbitrary numbers of bits to a byte array.
BitWriter() - Constructor for class io.scif.codec.BitWriter
Constructs a new bit writer.
BitWriter(int) - Constructor for class io.scif.codec.BitWriter
Constructs a new bit writer with the given initial buffer size.
BLACK - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
The CCITT numerical definition of black.
blankImage(ImageMetadata, long[], int) - Static method in class io.scif.gui.AWTImageTools
Creates a blank image with the given dimensions and transfer type.
blankPlane(long[], long[]) - Method in class io.scif.AbstractPlane
 
blankPlane(long[], long[]) - Method in class io.scif.BufferedImagePlane
 
blankPlane(long[], long[]) - Method in class io.scif.ByteArrayPlane
 
BlkImgDataSrc - Interface in io.scif.jj2000.j2k.image
This interface defines the methods to transfer image data in blocks, without following any particular order (random access).
BLOCK_END - Static variable in class io.scif.FilePatternBlock
 
BLOCK_START - Static variable in class io.scif.FilePatternBlock
 
blockLength - Variable in class io.scif.lifesci.SDTInfo
reserved2 now contains block (set) length.
blockNo - Variable in class io.scif.lifesci.SDTInfo
Number of the block in the file.
blockType - Variable in class io.scif.lifesci.SDTInfo
See blockType defines below.
blue - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
blue - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
blueMask - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
blueX - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
blueY - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
blueZ - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
BMP_MAGIC_STRING - Static variable in class io.scif.formats.BMPFormat
 
BMPConstants - Interface in io.scif.media.imageioimpl.plugins.bmp
 
BMPFormat - Class in io.scif.formats
BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
BMPFormat() - Constructor for class io.scif.formats.BMPFormat
 
BMPFormat.Checker - Class in io.scif.formats
 
BMPFormat.Metadata - Class in io.scif.formats
 
BMPFormat.Parser - Class in io.scif.formats
 
BMPFormat.Reader - Class in io.scif.formats
 
BMPImageReader - Class in io.scif.media.imageioimpl.plugins.bmp
This class is the Java Image IO plugin reader for BMP images.
BMPImageReader(ImageReaderSpi) - Constructor for class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
Constructs BMPImageReader from the provided ImageReaderSpi.
BMPImageReaderSpi - Class in io.scif.media.imageioimpl.plugins.bmp
 
BMPImageReaderSpi() - Constructor for class io.scif.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
BMPImageWriteParam - Class in io.scif.media.imageio.plugins.bmp
A subclass of ImageWriteParam for encoding images in the BMP format.
BMPImageWriteParam(Locale) - Constructor for class io.scif.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 io.scif.media.imageio.plugins.bmp.BMPImageWriteParam
Constructs an BMPImageWriteParam object with default values for all parameters and a null Locale.
BMPImageWriter - Class in io.scif.media.imageioimpl.plugins.bmp
The Java Image IO plugin writer for encoding a binary RenderedImage into a BMP format.
BMPImageWriter(ImageWriterSpi) - Constructor for class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
Constructs BMPImageWriter based on the provided ImageWriterSpi.
BMPImageWriterSpi - Class in io.scif.media.imageioimpl.plugins.bmp
 
BMPImageWriterSpi() - Constructor for class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
BMPMetadata - Class in io.scif.media.imageioimpl.plugins.bmp
 
BMPMetadata() - Constructor for class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
BMPMetadata(IIOMetadata) - Constructor for class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
BMPMetadataFormat - Class in io.scif.media.imageioimpl.plugins.bmp
 
BMPMetadataFormatResources - Class in io.scif.media.imageioimpl.plugins.bmp
 
BMPMetadataFormatResources() - Constructor for class io.scif.media.imageioimpl.plugins.bmp.BMPMetadataFormatResources
 
BMPOMETranslator() - Constructor for class io.scif.ome.translators.BMPTranslator.BMPOMETranslator
 
BMPTranslator - Class in io.scif.ome.translators
Container class for translators between OME and BMP formats.
BMPTranslator() - Constructor for class io.scif.ome.translators.BMPTranslator
 
BMPTranslator.BMPOMETranslator - Class in io.scif.ome.translators
Translator class from BMPFormat.Metadata to OMEMetadata
bmpVersion - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
bms - Variable in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
By-pass mode specifications
BogusColorSpace - Class in io.scif.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 io.scif.media.imageioimpl.common.BogusColorSpace
Constructs a bogus ColorSpace.
bordL - Variable in class io.scif.lifesci.SDTInfo
 
bordU - Variable in class io.scif.lifesci.SDTInfo
 
Box - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is defined to create the box of JP2 file format.
Box(int, int, byte[]) - Constructor for class io.scif.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 io.scif.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 io.scif.media.imageioimpl.plugins.jpeg2000.Box
Constructs a Box instance from the provided ImageInputStream at the specified position.
Box(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Constructs a Box from an "unknown" Node.
BRIGHTNESS_VALUE - Static variable in class io.scif.formats.tiff.IFD
 
BUF_DEF_LEN - Static variable in class io.scif.jj2000.j2k.entropy.encoder.ByteOutputBuffer
The default initial buffer size
BUF_INC - Static variable in class io.scif.jj2000.j2k.entropy.encoder.ByteOutputBuffer
The buffer increase size
BufferedImagePlane - Class in io.scif
A Plane implementation using a BufferedImage for the underlying data representation.
BufferedImagePlane(Context) - Constructor for class io.scif.BufferedImagePlane
 
BufferedImagePlane(Context, ImageMetadata, long[], long[]) - Constructor for class io.scif.BufferedImagePlane
 
BufferedImageReader<M extends TypedMetadata> - Class in io.scif.gui
BufferedImageReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.
BufferedImageReader() - Constructor for class io.scif.gui.BufferedImageReader
Constructs a new BIFormatReader.
BufferedImageTools - Class in io.scif.gui
Collection of static utility methods for working with BufferedImage.
BufferedImageTools() - Constructor for class io.scif.gui.BufferedImageTools
 
BufferedRandomAccessFile - Class in io.scif.jj2000.j2k.io
This class defines a Buffered Random Access File.
BufferedRandomAccessFile(File, String, int) - Constructor for class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Constructor.
BufferedRandomAccessFile(File, String) - Constructor for class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Constructor.
BufferedRandomAccessFile(String, String, int) - Constructor for class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Constructor.
BufferedRandomAccessFile(String, String) - Constructor for class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Constructor.
bugaddr - Static variable in class io.scif.jj2000.j2k.JJ2KInfo
The bug reporting e-mail address
buildFileChooser(Collection<Format>) - Method in class io.scif.gui.DefaultGUIService
 
buildFileChooser(Collection<Format>, boolean) - Method in class io.scif.gui.DefaultGUIService
 
buildFileChooser(FileFilter[]) - Method in class io.scif.gui.DefaultGUIService
 
buildFileChooser(FileFilter[], boolean) - Method in class io.scif.gui.DefaultGUIService
 
buildFileChooser(Collection<Format>) - Method in interface io.scif.gui.GUIService
Constructs a file chooser for the given file format handler.
buildFileChooser(Collection<Format>, boolean) - Method in interface io.scif.gui.GUIService
Constructs a file chooser for the given file format handler.
buildFileChooser(FileFilter[]) - Method in interface io.scif.gui.GUIService
Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter.
buildFileChooser(FileFilter[], boolean) - Method in interface io.scif.gui.GUIService
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(Collection<Format>) - Method in class io.scif.gui.DefaultGUIService
 
buildFileFilters(Collection<Format>) - Method in interface io.scif.gui.GUIService
Constructs a list of file filters for the given file format handler.
buildPalette() - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
ByteArrayHandle - Class in io.scif.io
A wrapper for a byte array that implements the IRandomAccess interface.
ByteArrayHandle(byte[]) - Constructor for class io.scif.io.ByteArrayHandle
Creates a random access byte stream to read from, and write to, the bytes specified by the byte[] argument.
ByteArrayHandle(ByteBuffer) - Constructor for class io.scif.io.ByteArrayHandle
 
ByteArrayHandle(int) - Constructor for class io.scif.io.ByteArrayHandle
Creates a random access byte stream to read from, and write to.
ByteArrayHandle() - Constructor for class io.scif.io.ByteArrayHandle
Creates a random access byte stream to write to a byte array.
ByteArrayLoader - Class in io.scif.img.cell.loaders
SCIFIOArrayLoader implementation for ByteArray types.
ByteArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.ByteArrayLoader
 
ByteArrayPlane - Class in io.scif
A naive Plane implementation that uses byte[] for its underlying data type.
ByteArrayPlane(Context) - Constructor for class io.scif.ByteArrayPlane
 
ByteArrayPlane(Context, ImageMetadata, long[], long[]) - Constructor for class io.scif.ByteArrayPlane
 
ByteArrayReader<M extends TypedMetadata> - Class in io.scif
Abstract superclass for all Reader implementations that return a ByteArrayPlane when reading datasets.
ByteArrayReader() - Constructor for class io.scif.ByteArrayReader
 
byteArraySet(byte[], byte) - Static method in class io.scif.jj2000.j2k.util.ArrayUtil
Reinitializes a byte array to the given value in an optimized way.
byteBuffer - Variable in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Buffer of bytes containing the part of the file that is currently being accessed
byteBufferChanged - Variable in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Boolean keeping track of whether the byte buffer has been changed since it was read.
byteCount - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The number of bytes of data from the source ImageInputStream to be decompressed.
ByteInputBuffer - Class in io.scif.jj2000.j2k.entropy.decoder
This class provides a byte input facility from byte buffers.
ByteInputBuffer(byte[]) - Constructor for class io.scif.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 io.scif.jj2000.j2k.entropy.decoder.ByteInputBuffer
Creates a new byte array input stream that reads data from the specified byte array.
byteOrder - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
byteOrdering - Variable in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
 
ByteOutputBuffer - Class in io.scif.jj2000.j2k.entropy.encoder
This class provides a buffering output stream similar to ByteArrayOutputStream, with some additional methods.
ByteOutputBuffer() - Constructor for class io.scif.jj2000.j2k.entropy.encoder.ByteOutputBuffer
Creates a new byte array output stream.
ByteOutputBuffer(int) - Constructor for class io.scif.jj2000.j2k.entropy.encoder.ByteOutputBuffer
Creates a new byte array output stream, with a buffer capacity of the specified size, in bytes.
BYTES_PER_ENTRY - Static variable in class io.scif.formats.tiff.TiffConstants
The number of bytes in each IFD entry.
bytesToDouble(byte[], int, int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first len bytes of a byte array beyond the given offset to a double.
bytesToDouble(byte[], int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 8 bytes of a byte array beyond the given offset to a double.
bytesToDouble(byte[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 8 bytes of a byte array to a double.
bytesToDouble(short[], int, int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first len bytes of a byte array beyond the given offset to a double.
bytesToDouble(short[], int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 8 bytes of a byte array beyond the given offset to a double.
bytesToDouble(short[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 8 bytes of a byte array to a double.
bytesToFloat(byte[], int, int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first len bytes of a byte array beyond the given offset to a float.
bytesToFloat(byte[], int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 4 bytes of a byte array beyond a given offset to a float.
bytesToFloat(byte[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 4 bytes of a byte array to a float.
bytesToFloat(short[], int, int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first len bytes of a byte array beyond a given offset to a float.
bytesToFloat(short[], int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 4 bytes of a byte array beyond a given offset to a float.
bytesToFloat(short[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 4 bytes of a byte array to a float.
bytesToHex(byte[]) - Static method in class io.scif.common.DataTools
Deprecated.
Translates the given byte array into a String of hexadecimal digits.
bytesToInt(byte[], int, int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first len bytes of a byte array beyond the given offset to an int.
bytesToInt(byte[], int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 4 bytes of a byte array beyond the given offset to an int.
bytesToInt(byte[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 4 bytes of a byte array to an int.
bytesToInt(short[], int, int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first len bytes of a byte array beyond the given offset to an int.
bytesToInt(short[], int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 4 bytes of a byte array beyond the given offset to an int.
bytesToInt(short[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 4 bytes of a byte array to an int.
bytesToLong(byte[], int, int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first len bytes of a byte array beyond the given offset to a long.
bytesToLong(byte[], int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 8 bytes of a byte array beyond the given offset to a long.
bytesToLong(byte[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 8 bytes of a byte array to a long.
bytesToLong(short[], int, int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first len bytes of a byte array beyond the given offset to a long.
bytesToLong(short[], int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 8 bytes of a byte array beyond the given offset to a long.
bytesToLong(short[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 8 bytes of a byte array to a long.
bytesToShort(byte[], int, int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first len bytes of a byte array beyond the given offset to a short.
bytesToShort(byte[], int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 2 bytes of a byte array beyond the given offset to a short.
bytesToShort(byte[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 2 bytes of a byte array to a short.
bytesToShort(short[], int, int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first len bytes of a byte array byond the given offset to a short.
bytesToShort(short[], int, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 2 bytes of a byte array byond the given offset to a short.
bytesToShort(short[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates up to the first 2 bytes of a byte array to a short.
byteTable - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
 
byteValue() - Method in class io.scif.formats.tiff.TiffRational
Returns the value of the specified number as a byte.
ByteVector - Class in io.scif.codec
A growable array of bytes.
ByteVector() - Constructor for class io.scif.codec.ByteVector
 
ByteVector(int) - Constructor for class io.scif.codec.ByteVector
 
ByteVector(byte[]) - Constructor for class io.scif.codec.ByteVector
 
BZip2Handle - Class in io.scif.io
StreamHandle implementation for reading from BZip2-compressed files or byte arrays.
BZip2Handle() - Constructor for class io.scif.io.BZip2Handle
Zero-parameter constructor.
BZip2Handle(Context) - Constructor for class io.scif.io.BZip2Handle
 
BZip2Handle(Context, String) - Constructor for class io.scif.io.BZip2Handle
Construct a new BZip2Handle corresponding to the given file.

C

c() - Method in class io.scif.gui.XYCTuple
 
C_AXIS - Static variable in class io.scif.AxisGuesser
Axis type for channels.
C_STRING1 - Static variable in class io.scif.lifesci.SDTInfo
 
C_STRING2 - Static variable in class io.scif.lifesci.SDTInfo
 
cache(String, int, T) - Method in interface io.scif.img.cell.cache.CacheService
Caches the provided object.
cache(String, int, SCIFIOCell<?>) - Method in class io.scif.img.cell.cache.MapDBCache
 
cache() - Method in class io.scif.SCIFIO
Gets this application context's CacheService.
cacheAll(boolean) - Method in class io.scif.img.cell.cache.AbstractCacheService
 
cacheAll() - Method in class io.scif.img.cell.cache.AbstractCacheService
 
cacheAll(boolean) - Method in interface io.scif.img.cell.cache.CacheService
 
cacheDirectoryListings(boolean) - Method in class io.scif.services.DefaultLocationService
 
cacheDirectoryListings(boolean) - Method in interface io.scif.services.LocationService
Turn cacheing of directory listings on or off.
cacheId(String) - Method in class io.scif.img.DefaultImgUtilityService
Downloads the given URL and caches it to a temporary file, which is deleted upon JVM shutdown.
cacheId(String) - Method in interface io.scif.img.ImgUtilityService
Downloads the given URL and caches it to a temporary file, which is deleted upon JVM shutdown.
cacheOnFinalize(boolean) - Method in class io.scif.img.cell.SCIFIOCell
Sets whether or not this cell tries to cache itself when no references to it remain.
CacheResult - Enum in io.scif.img.cell.cache
List of possible outcomes from the CacheService.cache(String, int, java.io.Serializable) method.
CacheService<T extends Serializable> - Interface in io.scif.img.cell.cache
Interface for caching and retrieving objects.
calcLevels(int, int, int, int, int) - Static method in class io.scif.formats.imaris.ResolutionLevelMaker
 
calcMixedBitDepths(int[], int, int[]) - Static method in class io.scif.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 io.scif.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 io.scif.lifesci.SDTInfo
No of photons.
calcSbParams(SubbandAn, int) - Method in class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
Calculates the parameters of the SubbandAn objects that depend on the Quantizer.
calcSbParams(SubbandAn, int) - Method in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
Calculates the parameters of the SubbandAn objects that depend on the Quantizer.
calibrate(Metadata, int, double[]) - Static method in class io.scif.util.FormatTools
Applies the given scale value, and an origin of 0.0, to each LinearAxis in the provided Metadata.
calibrate(Metadata, int, double[], double[]) - Static method in class io.scif.util.FormatTools
Applies the given scale and origin values to each LinearAxis in the provided Metadata.
calibrate(CalibratedAxis, double, double) - Static method in class io.scif.util.FormatTools
Applies the given scale and origin to the provided CalibratedAxis , if it is a LinearAxis.
calibrate(CalibratedAxis, double, double, String) - Static method in class io.scif.util.FormatTools
As FormatTools.calibrate(CalibratedAxis, double, double) but also sets the unit of the axis.
cameraMode - Variable in class io.scif.formats.MicromanagerFormat.Position
 
cameraRef - Variable in class io.scif.formats.MicromanagerFormat.Position
 
CAN_GROUP - Static variable in class io.scif.util.FormatTools
 
canChangePattern() - Method in class io.scif.filters.FileStitcher
 
canCreatePalette(ImageTypeSpecifier) - Static method in class io.scif.media.imageioimpl.common.PaletteBuilder
Returns true if PaletteBuilder is able to create palette for given image type.
canCreatePalette(RenderedImage) - Static method in class io.scif.media.imageioimpl.common.PaletteBuilder
Returns true if PaletteBuilder is able to create palette for given rendered image.
canDecodeInput(Object) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
canDecodeInput(Object) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
canDecodeInput(Object) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
canDecodeInput(Object) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
canDecodeInput(Object) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
canDecodeInput(Object) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
canDecodeInput(Object) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
canDoQT() - Method in class io.scif.formats.qt.DefaultQTJavaService
 
canDoQT() - Method in interface io.scif.formats.qt.QTJavaService
Whether QuickTime is available to this JVM.
canDoStacks() - Method in class io.scif.AbstractWriter
 
canDoStacks() - Method in class io.scif.formats.APNGFormat.Writer
 
canDoStacks() - Method in class io.scif.formats.AVIFormat.Writer
 
canDoStacks() - Method in class io.scif.formats.ICSFormat.Writer
 
canDoStacks() - Method in class io.scif.formats.JavaFormat.Writer
 
canDoStacks() - Method in class io.scif.formats.JPEG2000Format.Writer
Overridden to indicate that stacks are not supported.
canDoStacks() - Method in class io.scif.formats.qt.LegacyQTFormat.Writer
 
canDoStacks() - Method in class io.scif.formats.qt.NativeQTFormat.Writer
 
canDoStacks() - Method in class io.scif.formats.TIFFFormat.Writer
 
canDoStacks() - Method in class io.scif.ome.formats.OMEXMLFormat.Writer
 
canDoStacks() - Method in interface io.scif.Writer
 
canEncodeImage(ImageWriter, ImageTypeSpecifier) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Checks that the provided ImageWriter can encode the provided ImageTypeSpecifier or not.
canEncodeImage(ImageWriter, ColorModel, SampleModel) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Checks that the provided ImageWriter can encode the provided ColorModel and SampleModel.
canEncodeImage(int, ColorModel, SampleModel) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
canEncodeImage(int, ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
canEncodeImage(ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
canInsertEmpty(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
canInsertImage(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFStreamMetadataFormat
 
CANNOT_GROUP - Static variable in class io.scif.util.FormatTools
 
canOpen(String) - Method in interface io.scif.services.DatasetIOService
Determines whether the given source can be opened as a Dataset using the DatasetIOService.open(String) method.
canOpen(String) - Method in class io.scif.services.DefaultDatasetIOService
 
canOpen(String) - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
canRead() - Method in class io.scif.io.Location
If the underlying location is a URL, this method will return true if the URL exists.
canReadRaster() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
canReadRaster() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
canReadRaster() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
canReadRaster() - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
canReadRaster() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
canReadRaster() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
canReplacePixels(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
canSave(String) - Method in interface io.scif.services.DatasetIOService
Determines whether the given destination can be used to save a Dataset using the DatasetIOService.save(Dataset, String) method.
canSave(String) - Method in class io.scif.services.DefaultDatasetIOService
 
canSave(String) - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
canWrite() - Method in class io.scif.io.Location
If the underlying location is a URL, this method will always return false.
canWriteEmpty() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
canWriteRasters() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
canWriteRasters() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
canWriteRasters() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriter
 
canWriteRasters() - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
canWriteRasters() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
canWriteSequence() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
canWriteSequence() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
CAPTURE_RESOLUTION_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
CaseInsensitiveLocation - Class in io.scif.io
Case insensitive variant of Location.
CaseInsensitiveLocation(Context, String) - Constructor for class io.scif.io.CaseInsensitiveLocation
 
CaseInsensitiveLocation(Context, File) - Constructor for class io.scif.io.CaseInsensitiveLocation
 
CaseInsensitiveLocation(Context, String, String) - Constructor for class io.scif.io.CaseInsensitiveLocation
 
CaseInsensitiveLocation(Context, CaseInsensitiveLocation, String) - Constructor for class io.scif.io.CaseInsensitiveLocation
 
castMeta(Metadata) - Static method in class io.scif.util.SCIFIOMetadataTools
Casts the provided Metadata object to the generic type of this method.
castToTypedPlane(Plane) - Method in class io.scif.AbstractReader
 
castToTypedPlane(Plane) - Method in class io.scif.filters.AbstractReaderFilter
 
castToTypedPlane(Plane) - Method in interface io.scif.Reader
Convenience method for casting Plane implementations to the type associated with this Reader.
cbLength - Variable in class io.scif.jj2000.j2k.codestream.reader.PktInfo
The length of the code-block in this packet (in bytes)
cblk - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Code-blocks belonging to this precinct in each subbands of the resolution level
CBlkCoordInfo - Class in io.scif.jj2000.j2k.codestream
This class is used to store the coordinates of code-blocks.
CBlkCoordInfo() - Constructor for class io.scif.jj2000.j2k.codestream.CBlkCoordInfo
Constructor.
CBlkCoordInfo(int, int) - Constructor for class io.scif.jj2000.j2k.codestream.CBlkCoordInfo
Constructor.
CBlkInfo - Class in io.scif.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 io.scif.jj2000.j2k.codestream.reader.CBlkInfo
Constructs a new instance with specified number of layers and code-block coordinates.
CBlkQuantDataSrcDec - Interface in io.scif.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 io.scif.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 io.scif.jj2000.j2k.entropy.encoder
This class stores coded (compressed) code-blocks with their associated rate-distortion statistics.
CBlkRateDistStats() - Constructor for class io.scif.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 io.scif.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 io.scif.jj2000.j2k.decoder.DecoderSpecs
Code-blocks sizes specification
CBlkSizeSpec - Class in io.scif.jj2000.j2k.entropy
This class extends ModuleSpec class for code-blocks sizes holding purposes.
CBlkSizeSpec(int, int, byte) - Constructor for class io.scif.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 io.scif.jj2000.j2k.entropy.CBlkSizeSpec
Creates a new CBlkSizeSpec object for the specified number of tiles and components and the ParameterList instance.
CBlkWTData - Class in io.scif.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 io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
 
CBlkWTDataFloat - Class in io.scif.jj2000.j2k.wavelet.analysis
This is an implementation of the 'CBlkWTData' abstract class for 32 bit floating point data (float).
CBlkWTDataFloat() - Constructor for class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataFloat
 
CBlkWTDataInt - Class in io.scif.jj2000.j2k.wavelet.analysis
This is an implementation of the 'CBlkWTData' abstract class for signed 32 bit integer data.
CBlkWTDataInt() - Constructor for class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataInt
 
CBlkWTDataSrc - Interface in io.scif.jj2000.j2k.wavelet.analysis
This abstract class defines methods to transfer wavelet data in a code-block by code-block basis.
CBlkWTDataSrcDec - Interface in io.scif.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 io.scif.jj2000.j2k.codestream.reader.PktInfo
The code-block offset in the codestream (for this packet)
CBZip2InputStream - Class in io.scif.io
An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.
CBZip2InputStream(InputStream, LogService) - Constructor for class io.scif.io.CBZip2InputStream
Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.
ccoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
 
ccom - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COM
 
ce - Variable in class io.scif.jj2000.j2k.entropy.Progression
Component index for the end of a progression.
CELL_LENGTH - Static variable in class io.scif.formats.tiff.IFD
 
CELL_WIDTH - Static variable in class io.scif.formats.tiff.IFD
 
cepoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.POC
 
CFA_PATTERN - Static variable in class io.scif.formats.tiff.IFD
 
cfdHF - Variable in class io.scif.lifesci.SDTInfo
 
cfdLH - Variable in class io.scif.lifesci.SDTInfo
 
cfdLL - Variable in class io.scif.lifesci.SDTInfo
 
cfdZC - Variable in class io.scif.lifesci.SDTInfo
 
chan - Variable in class io.scif.lifesci.SDTInfo
Routing channel number.
channel - Variable in class io.scif.formats.imaris.PipelineImage
 
CHANNEL_DEFINITION_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
CHANNEL_NAME - Static variable in class io.scif.util.FormatTools
 
CHANNEL_NUM - Static variable in class io.scif.util.FormatTools
 
ChannelDefinitionBox - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is designed to represent a Channel Definition Box of JPEG JP2 file format.
ChannelDefinitionBox(ColorModel) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Constructs a ChannelDefinitionBox based on the provided ColorModel.
ChannelDefinitionBox(byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Constructs a ChannelDefinitionBox based on the provided content in byte array.
ChannelDefinitionBox(short[], short[], short[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Constructs a ChannelDefinitionBox based on the provided channel definitions.
ChannelDefinitionBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Constructs a ChannelDefinitionBox based on the provided org.w3c.dom.Node.
ChannelFiller - Class in io.scif.filters
For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
ChannelFiller() - Constructor for class io.scif.filters.ChannelFiller
 
ChannelFillerMetadata - Class in io.scif.filters
MetadataWrapper implementation specifically for use with the ChannelFiller.
ChannelFillerMetadata() - Constructor for class io.scif.filters.ChannelFillerMetadata
 
ChannelImageInputStreamSpi - Class in io.scif.media.imageioimpl.stream
 
ChannelImageInputStreamSpi() - Constructor for class io.scif.media.imageioimpl.stream.ChannelImageInputStreamSpi
 
ChannelImageOutputStreamSpi - Class in io.scif.media.imageioimpl.stream
 
ChannelImageOutputStreamSpi() - Constructor for class io.scif.media.imageioimpl.stream.ChannelImageOutputStreamSpi
 
channels - Variable in class io.scif.codec.CodecOptions
Number of channels.
channels - Variable in class io.scif.formats.MicromanagerFormat.Position
 
channels - Variable in class io.scif.lifesci.SDTInfo
 
characterCellHeight - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
characterCellWidth - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
CharArrayLoader - Class in io.scif.img.cell.loaders
SCIFIOArrayLoader implementation for CharArray types.
CharArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.CharArrayLoader
 
checkBufferSize(int, Metadata, int) - Static method in class io.scif.util.FormatTools
Checks that the given buffer length is long enough to hold planes of the specified image index, using the provided Reader.
checkBufferSize(Metadata, int, long[], int) - Static method in class io.scif.util.FormatTools
Checks that the given buffer size is large enough to hold an image with the given planar lengths.
Checker() - Constructor for class io.scif.bf.BioFormatsFormat.Checker
 
Checker - Interface in io.scif
Interface for all SCIFIO Checker components.
Checker() - Constructor for class io.scif.formats.APNGFormat.Checker
 
Checker() - Constructor for class io.scif.formats.AVIFormat.Checker
 
Checker() - Constructor for class io.scif.formats.BMPFormat.Checker
 
Checker() - Constructor for class io.scif.formats.DICOMFormat.Checker
 
Checker() - Constructor for class io.scif.formats.GIFFormat.Checker
 
Checker() - Constructor for class io.scif.formats.JPEG2000Format.Checker
 
Checker() - Constructor for class io.scif.formats.JPEGFormat.Checker
 
Checker() - Constructor for class io.scif.formats.KontronFormat.Checker
 
Checker() - Constructor for class io.scif.formats.MicromanagerFormat.Checker
 
Checker() - Constructor for class io.scif.formats.MinimalTIFFFormat.Checker
 
Checker() - Constructor for class io.scif.formats.MNGFormat.Checker
 
Checker() - Constructor for class io.scif.formats.NRRDFormat.Checker
 
Checker() - Constructor for class io.scif.formats.OBFFormat.Checker
 
Checker() - Constructor for class io.scif.formats.PCXFormat.Checker
 
Checker() - Constructor for class io.scif.formats.PGMFormat.Checker
 
Checker() - Constructor for class io.scif.formats.qt.NativeQTFormat.Checker
 
Checker() - Constructor for class io.scif.formats.ScancoISQFormat.Checker
 
Checker() - Constructor for class io.scif.formats.TextFormat.Checker
 
Checker() - Constructor for class io.scif.ome.formats.OMETIFFFormat.Checker
 
Checker() - Constructor for class io.scif.ome.formats.OMEXMLFormat.Checker
 
checkerIsOpen() - Method in class io.scif.config.SCIFIOConfig
 
checkerSetOpen(boolean) - Method in class io.scif.config.SCIFIOConfig
 
checkHeader(byte[]) - Method in class io.scif.AbstractChecker
 
checkHeader(byte[]) - Method in class io.scif.bf.BioFormatsFormat.Checker
 
checkHeader(byte[]) - Method in interface io.scif.Checker
Checks if the given bytes are a valid header for this Format.
checkHeader() - Method in class io.scif.formats.tiff.TiffParser
Checks the TIFF header.
checkMarkerLength(DataInputStream, String) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Checks that the marker segment length is correct.
checkParams(int, long, byte[], long[], long[]) - Method in class io.scif.AbstractWriter
Ensure that the arguments that are being passed to saveBytes(...) are valid.
checkPlaneForReading(Metadata, int, long, int, long[], long[]) - Static method in class io.scif.util.FormatTools
As FormatTools.checkPlaneForWriting(io.scif.Metadata, int, long, int, long[], long[]) but also asserts that the Metadata has a non-null source attached.
checkPlaneForWriting(Metadata, int, long, int, long[], long[]) - Static method in class io.scif.util.FormatTools
Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given Metadata.
checkPlaneNumber(Metadata, int, long) - Static method in class io.scif.util.FormatTools
Checks that the given plane number is valid for the given reader.
checkPredTerm() - Method in class io.scif.jj2000.j2k.entropy.decoder.MQDecoder
Checks for past errors in the decoding process using the predictable error resilient termination.
checkQTLibrary() - Method in class io.scif.formats.qt.DefaultQTJavaService
 
checkQTLibrary() - Method in interface io.scif.formats.qt.QTJavaService
Checks whether QTJava is available, throwing an exception if not.
checkReadParamBandSettingsWrapper(ImageReadParam, int, int) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
Wrapper for the protected method checkReadParamBandSettings.
checkSuffix(String, String) - Static method in class io.scif.util.FormatTools
Performs suffix matching for the given filename.
checkSuffix(String, String[]) - Static method in class io.scif.util.FormatTools
Performs suffix matching for the given filename.
checkTargetErrors() - Method in class io.scif.jj2000.j2k.util.ThreadPool
Checks that no error or runtime exception in any target have occurred so far.
checkTileSize(Metadata, long[], long[], int) - Static method in class io.scif.util.FormatTools
Checks that the given tile size is valid for the given reader.
checkValidId(String) - Method in class io.scif.services.DefaultLocationService
 
checkValidId(String) - Method in interface io.scif.services.LocationService
Checks that the given id points at a valid data stream.
childCount - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
chksum - Variable in class io.scif.lifesci.SDTInfo
 
CLEAN_FAX_DATA_ERRORS_CORRECTED - Static variable in class io.scif.media.imageio.plugins.tiff.FaxTIFFTagSet
A value to be used with the "CleanFaxData" tag.
CLEAN_FAX_DATA_ERRORS_UNCORRECTED - Static variable in class io.scif.media.imageio.plugins.tiff.FaxTIFFTagSet
A value to be used with the "CleanFaxData" tag.
CLEAN_FAX_DATA_NO_ERRORS - Static variable in class io.scif.media.imageio.plugins.tiff.FaxTIFFTagSet
A value to be used with the "CleanFaxData" tag.
CleaningRef - Interface in io.scif.refs
Interface for Reference subclasses that have some operation that should be performed after they are enqueued in a ReferenceQueue.
cleanRetrieved(String) - Method in interface io.scif.img.cell.cache.CacheService
Start a new thread to remove all previously-retrieved entries for a given cache from disk.
cleanRetrieved(String) - Method in class io.scif.img.cell.cache.MapDBCache
 
cleanStaleCacheEntries() - Method in class io.scif.services.DefaultLocationService
 
cleanStaleCacheEntries() - Method in interface io.scif.services.LocationService
Remove any cached directory listings that have expired.
cleanUp() - Method in class io.scif.filters.AbstractReaderFilter
Helper method that is always called by the AbstractReaderFilter.close(boolean) method, if the fileOnly flag is false.
cleanUp() - Method in class io.scif.filters.ChannelFiller
 
cleanUp() - Method in class io.scif.filters.FileStitcher
 
cleanUp() - Method in class io.scif.filters.PlaneSeparator
 
cleanup() - Method in class io.scif.img.cell.RefMapCleaningProvider.RefMapCleaner
 
cleanup() - Method in class io.scif.img.cell.SCIFIOCellCacheCleaningProvider.SCIFIOCellCacheCleaner
 
cleanup() - Method in class io.scif.img.cell.SCIFIOCellCleaningProvider.SCIFIOCellCleaner
 
cleanup() - Method in class io.scif.img.cell.SCIFIOCellImgCleaningProvider.SCIFIOCellImgCleaner
 
cleanup() - Method in class io.scif.img.ImgPlusCtxCleaningProvider.ImgPlusCtxCleaner
 
cleanup() - Method in interface io.scif.refs.CleaningRef
Hook for cleaning up resources when this reference is removed from a ReferenceQueue.
clear() - Method in class io.scif.codec.ByteVector
 
clearAllCaches() - Method in interface io.scif.img.cell.cache.CacheService
Removes all entries for all caches
clearAllCaches() - Method in class io.scif.img.cell.cache.MapDBCache
 
clearCache(String) - Method in interface io.scif.img.cell.cache.CacheService
Removes all entries from the specified cache.
clearCache(String) - Method in class io.scif.img.cell.cache.MapDBCache
NB: Disables caching on finalize in cleared cells.
clearDestImage() - Method in class io.scif.media.imageioimpl.plugins.raw.RawRenderedImage
 
clearDirectoryListingsCache() - Method in class io.scif.services.DefaultLocationService
 
clearDirectoryListingsCache() - Method in interface io.scif.services.LocationService
Clear the directory listings cache.
ClearTable(int) - Method in class io.scif.media.imageioimpl.common.LZWStringTable
 
clearTargetErrors() - Method in class io.scif.jj2000.j2k.util.ThreadPool
Clears the current target error conditions, if any.
clone() - Method in class io.scif.config.SCIFIOConfig
 
clone() - Method in class io.scif.jj2000.j2k.ModuleSpec
 
clone() - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Clones the directory and all the fields contained therein.
clone() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
clone() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
clone() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
cloneNode(boolean) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
close() - Method in class io.scif.AbstractHasSource
 
close(boolean) - Method in class io.scif.AbstractMetadata
 
close(boolean) - Method in class io.scif.AbstractParser
 
close(boolean) - Method in class io.scif.AbstractReader
 
close(boolean) - Method in class io.scif.AbstractWriter
 
close(boolean) - Method in class io.scif.bf.BioFormatsFormat.Metadata
 
close() - Method in class io.scif.bf.wrapper.RandomAccessInputStreamWrapper
 
close() - Method in class io.scif.codec.JPEGTileDecoder
 
close() - Method in class io.scif.common.RandomAccessInputStreamWrapper
Deprecated.
 
close(boolean) - Method in class io.scif.filters.AbstractMetadataWrapper
 
close(boolean) - Method in class io.scif.filters.AbstractReaderFilter
 
close() - Method in class io.scif.filters.AbstractReaderFilter
 
close(boolean) - Method in class io.scif.filters.MinMaxFilter
 
close(boolean) - Method in class io.scif.formats.APNGFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.APNGFormat.Reader
 
close(boolean) - Method in class io.scif.formats.APNGFormat.Writer
 
close(boolean) - Method in class io.scif.formats.AVIFormat.Metadata
 
close() - Method in class io.scif.formats.AVIFormat.Writer
 
close(boolean) - Method in class io.scif.formats.BMPFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.DICOMFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.EPSFormat.Metadata
 
close() - Method in class io.scif.formats.FITSFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.GIFFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.ICSFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.ICSFormat.Reader
 
close(int) - Method in class io.scif.formats.ICSFormat.Writer
 
close(boolean) - Method in class io.scif.formats.ImageIOFormat.Metadata
 
close() - Method in class io.scif.formats.imaris.HDFWriter
 
close() - Method in class io.scif.formats.imaris.ImarisWriter
 
close() - Method in class io.scif.formats.ImarisFormat.Writer
 
close() - Method in class io.scif.formats.JavaFormat.Writer
 
close(boolean) - Method in class io.scif.formats.JPEG2000Format.Metadata
 
close(boolean) - Method in class io.scif.formats.JPEGFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.JPEGTileFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.MicromanagerFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.MicromanagerFormat.Reader
 
close(boolean) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.MNGFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.NRRDFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.OBFFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.PCXFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.PGMFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.qt.LegacyQTFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.qt.LegacyQTFormat.Reader
 
close() - Method in class io.scif.formats.qt.LegacyQTFormat.Writer
 
close(boolean) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
 
close() - Method in class io.scif.formats.qt.NativeQTFormat.Writer
 
close(boolean) - Method in class io.scif.formats.qt.PICTFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.TextFormat.Metadata
 
close() - Method in class io.scif.formats.tiff.OnDemandLongArray
 
close(boolean) - Method in class io.scif.formats.TIFFFormat.Metadata
 
close() - Method in class io.scif.formats.TIFFFormat.Writer
 
close(boolean) - Method in class io.scif.formats.ZipFormat.Metadata
 
close(boolean) - Method in class io.scif.formats.ZipFormat.Reader
 
close() - Method in class io.scif.gui.PreviewPane
Closes the underlying image reader.
close(boolean) - Method in interface io.scif.HasSource
Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.
close() - Method in interface io.scif.HasSource
Closes the image source(s) associated with this component and resets the component to its default state.
close() - Method in class io.scif.io.ByteArrayHandle
 
close() - Method in class io.scif.io.CBZip2InputStream
 
close() - Method in class io.scif.io.FileHandle
 
close() - Method in interface io.scif.io.IRandomAccess
Closes this random access stream and releases any system resources associated with the stream.
close() - Method in class io.scif.io.NIOFileHandle
 
close() - Method in class io.scif.io.NIOInputStream
Closes the streams.
close() - Method in class io.scif.io.RandomAccessInputStream
Closes the streams.
close() - Method in class io.scif.io.RandomAccessOutputStream
 
close() - Method in class io.scif.io.StreamHandle
 
close() - Method in class io.scif.io.ZipHandle
 
close() - Method in class io.scif.jj2000.j2k.codestream.writer.CodestreamWriter
Closes the underlying resource (file, stream, network connection, etc.).
close() - Method in class io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
Writes the EOC marker and closes the underlying stream.
close() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Closes the underlying file or network connection from where the image data is being read.
close() - Method in class io.scif.jj2000.j2k.image.input.ImgReaderPGM
Closes the underlying RandomAccessFile from where the image data is being read.
close() - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Closes the buffered random access file
close() - Method in interface io.scif.jj2000.j2k.io.RandomAccessIO
Closes the I/O stream.
close() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Closes this object for reading as well as the wrapped InputStream, if not already closed.
close(boolean) - Method in class io.scif.lifesci.SDTFormat.Metadata
 
close() - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
Invokes the superclass method and sets the internal reference to the source FileChannel to null.
close() - Method in class io.scif.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 io.scif.media.imageio.stream.RawImageInputStream
 
close() - Method in class io.scif.media.imageioimpl.plugins.clib.InputStreamAdapter
 
close() - Method in class io.scif.media.imageioimpl.plugins.clib.OutputStreamAdapter
 
close() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
close() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
close(boolean) - Method in class io.scif.ome.formats.OMETIFFFormat.Metadata
 
close() - Method in class io.scif.ome.formats.OMETIFFFormat.Writer
 
close(boolean) - Method in class io.scif.ome.formats.OMEXMLFormat.Metadata
 
close() - Method in class io.scif.ome.formats.OMEXMLFormat.Writer
 
closeTimePoint() - Method in class io.scif.formats.imaris.TimePoint
 
COBOL - Static variable in class io.scif.common.DateTools
 
COBOL_EPOCH - Static variable in class io.scif.common.DateTools
 
coc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo
Reference to the COC marker segments found in main and first tile-part header.
COC() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
 
COC - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Coding style component (COC): 0xFF53
cod - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo
Reference to the COD marker segments found in main and first tile-part header.
COD() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
COD - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Coding style default (COD): 0xFF52
codeBlockSize - Variable in class io.scif.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 io.scif.codec
This class is an interface for any kind of compression or decompression.
codec() - Method in class io.scif.SCIFIO
Gets this application context's CodecService.
CODEC_ANIMATION - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer
Value indicating Animation codec.
CODEC_CINEPAK - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer
Value indicating Cinepak codec.
CODEC_H_263 - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer
Value indicating H.263 codec.
CODEC_MOTION_JPEG_B - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer
Value indicating Motion JPEG-B codec.
CODEC_MPEG_4 - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer
Value indicating MPEG-4 codec.
CODEC_RAW - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer
Value indicating Raw codec.
CODEC_SORENSON - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer
Value indicating Sorenson codec.
CODEC_SORENSON_3 - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer
Value indicating Sorenson 3 codec.
CodecOptions - Class in io.scif.codec
Options for compressing and decompressing data.
CodecOptions() - Constructor for class io.scif.codec.CodecOptions
Construct a new CodecOptions.
CodecOptions(CodecOptions) - Constructor for class io.scif.codec.CodecOptions
Construct a new CodecOptions using the given CodecOptions.
CodecService - Interface in io.scif.codec
Interface for service which manages available Codecs.
CodedCBlk - Class in io.scif.jj2000.j2k.entropy
This is the generic class to store coded (compressed) code-block.
CodedCBlk() - Constructor for class io.scif.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 io.scif.jj2000.j2k.entropy.CodedCBlk
Creates a new CodedCBlk object with the specified values.
CodedCBlkDataSrcDec - Interface in io.scif.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 io.scif.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.
CodedEnum - Interface in io.scif.enumeration
Enumeration which is coded.
CodestreamManipulator - Class in io.scif.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 io.scif.jj2000.j2k.util.CodestreamManipulator
Instantiates a codestream manipulator..
CodestreamWriter - Class in io.scif.jj2000.j2k.codestream.writer
This is the abstract class for writing to a bit stream.
CodestreamWriter(int) - Constructor for class io.scif.jj2000.j2k.codestream.writer.CodestreamWriter
Allocates this object and initializes the maximum numner of bytes.
codeSymbol(int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
This function performs the arithmetic encoding of one symbol.
codeSymbols(int[], int[], int) - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
This function performs the arithmetic encoding of several symbols together.
COLOR_MAP - Static variable in class io.scif.formats.tiff.IFD
 
COLOR_SPACE - Static variable in class io.scif.formats.tiff.IFD
 
COLOR_SPACE_SRGB - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ColorSpace" tag.
COLOR_SPACE_UNCALIBRATED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ColorSpace" tag.
colorConverter - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
A TIFFColorConverter object describing the color space of the encoded pixel data, or null.
colorCount - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
colorMap - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The value of the ColorMap tag.
colorModel - Variable in class io.scif.codec.CodecOptions
Color model to use when constructing an image (WRITE).
colorModel - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The image's ColorModel.
ColorNode() - Constructor for class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
colorResolution - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
colorsImportant - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
colorSpace - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
ColorSpecificationBox - Class in io.scif.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 io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
Creates a ColorSpecificationBox from the provided data elements.
ColorSpecificationBox(byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
Creates a ColorSpecificationBox from the provided byte array.
ColorSpecificationBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
Constructs a ColorSpecificationBox based on the provided org.w3c.dom.Node.
colorsUsed - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
colorTableSizes - Static variable in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
COLOUR_SPECIFICATION_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
colT - Variable in class io.scif.lifesci.SDTInfo
 
COM - Static variable in class io.scif.codec.LosslessJPEGCodec
 
com - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo
Reference to the COM marker segments found in main and tile-part headers.
COM() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo.COM
 
COM - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Comment (COM): 0xFF64
ComboFileFilter - Class in io.scif.gui
A file filter that recognizes files from a union of other filters.
ComboFileFilter(FileFilter[], String) - Constructor for class io.scif.gui.ComboFileFilter
Constructs a new filter from a list of other filters.
commandName() - Method in class io.scif.cli.AbstractSCIFIOToolCommand
Default command name is a lower-case version of the class name.
commandName() - Method in class io.scif.cli.commands.Convert
 
commandName() - Method in class io.scif.cli.commands.Help
 
commandName() - Method in class io.scif.cli.commands.Info
 
commandName() - Method in class io.scif.cli.commands.Show
 
commandName() - Method in interface io.scif.cli.SCIFIOToolCommand
 
commandName() - Method in class io.scif.ome.commands.OMEXMLToolCommand
 
comment - Variable in class io.scif.formats.MicromanagerFormat.Position
 
comments - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
comments - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
commitBitstreamHeader(HeaderEncoder) - Method in class io.scif.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 io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
Writes the header data in the codestream and actualize ndata with the header length.
comp - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
The components for which the ROI is relevant
COMP_POS_RES_LY_PROG - Static variable in interface io.scif.jj2000.j2k.codestream.ProgressionType
The bit stream is Component/Position/Resolution/Layer progressive : 4
COMPANION_SUFFIXES - Static variable in class io.scif.formats.TIFFFormat
 
compareTo(Object) - Method in class io.scif.formats.tiff.TiffIFDEntry
 
compareTo(TiffRational) - Method in class io.scif.formats.tiff.TiffRational
Compares this object with the specified object for order.
compareTo(Object) - Method in class io.scif.gui.ComboFileFilter
Compares two FileFilter objects alphanumerically.
compareTo(FileFilter) - Method in class io.scif.gui.FormatFileFilter
Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Compares this TIFFField with another TIFFField by comparing the tags.
compDef - Variable in class io.scif.jj2000.j2k.ModuleSpec
The default value for each component.
COMPONENT_MAPPING_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
ComponentMappingBox - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is defined to represent a Color Specification Box of JPEG JP2 file format.
ComponentMappingBox(byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
Constructs a ComponentMappingBox from the provided content byte array.
ComponentMappingBox(short[], byte[], byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
Constructs a ComponentMappingBox from the provided component mapping.
ComponentMappingBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
Constructs a ComponentMappingBox based on the provided org.w3c.dom.Node.
COMPONENTS_CONFIGURATION - Static variable in class io.scif.formats.tiff.IFD
 
COMPONENTS_CONFIGURATION_B - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_CB - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_CR - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_DOES_NOT_EXIST - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_G - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_R - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ComponentsConfiguration" tag.
COMPONENTS_CONFIGURATION_Y - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ComponentsConfiguration" tag.
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Composes the content byte array from the data elements.
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
 
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
 
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
 
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.FileTypeBox
 
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
 
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
 
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ResolutionBox
 
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.SignatureBox
 
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDBox
 
compose() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDListBox
 
composeString(byte[], byte) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
Append newString to the end of oldString.
composeString(byte[], byte) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWUtil
Append newString to the end of oldString.
compress(byte[][], CodecOptions) - Method in class io.scif.codec.AbstractCodec
2D data block encoding default implementation.
compress(byte[], CodecOptions) - Method in class io.scif.codec.Base64Codec
 
compress(byte[], CodecOptions) - Method in interface io.scif.codec.Codec
Compresses a block of data.
compress(byte[][], CodecOptions) - Method in interface io.scif.codec.Codec
Compresses a block of data.
compress(byte[], CodecOptions) - Method in class io.scif.codec.HuffmanCodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.JPEG2000Codec
The CodecOptions parameter should have the following fields set: width height bitsPerSample channels interleaved littleEndian lossless
compress(byte[], CodecOptions) - Method in class io.scif.codec.JPEGCodec
The CodecOptions parameter should have the following fields set: width height channels bitsPerSample interleaved littleEndian signed
compress(byte[], CodecOptions) - Method in class io.scif.codec.LosslessJPEGCodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.LuraWaveCodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.LZWCodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.MJPBCodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.MSRLECodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.MSVideoCodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.NikonCodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.PackbitsCodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.PassthroughCodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.QTRLECodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.RPZACodec
 
compress(byte[], CodecOptions) - Method in class io.scif.codec.ZlibCodec
 
compress(CodecService, byte[], CodecOptions) - Method in enum io.scif.formats.tiff.TiffCompression
Encodes a strip of data.
compress(byte[], int, int) - Method in class io.scif.media.imageioimpl.common.LZWCompressor
 
compressBuffer(int, long, Plane, long[], long[]) - Method in class io.scif.formats.JPEG2000Format.Writer
Compresses the buffer.
COMPRESSED_BITS_PER_PIXEL - Static variable in class io.scif.formats.tiff.IFD
 
COMPRESSION - Static variable in class io.scif.formats.tiff.IFD
 
compression - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The value of the Compression tag.
compression - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
compression - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
COMPRESSION_CCITT_RLE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Compression" tag.
COMPRESSION_CCITT_T_4 - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Compression" tag.
COMPRESSION_CCITT_T_6 - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Compression" tag.
COMPRESSION_DEFLATE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Compression" tag.
COMPRESSION_J2K - Static variable in class io.scif.formats.TIFFFormat.Writer
 
COMPRESSION_J2K_LOSSY - Static variable in class io.scif.formats.TIFFFormat.Writer
 
COMPRESSION_JPEG - Static variable in class io.scif.formats.TIFFFormat.Writer
 
COMPRESSION_JPEG - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Compression" tag.
COMPRESSION_LZW - Static variable in class io.scif.formats.TIFFFormat.Writer
 
COMPRESSION_LZW - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Compression" tag.
COMPRESSION_NONE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Compression" tag.
COMPRESSION_OLD_JPEG - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Compression" tag.
COMPRESSION_PACKBITS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Compression" tag.
COMPRESSION_SUFFIXES - Static variable in class io.scif.util.FormatTools
 
COMPRESSION_UNCOMPRESSED - Static variable in class io.scif.formats.TIFFFormat.Writer
 
COMPRESSION_ZLIB - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Compression" tag.
compressionNumbers - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
Compression tag values for known compression types.
compressionTagValue - Variable in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
The value to be assigned to the TIFF Compression tag in the TIFF image metadata.
CompressionType - Enum in io.scif.codec
An enumeration of compression types.
compressionType - Variable in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
The name of the compression type supported by this compressor.
compressionTypeNames - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
compressionTypes - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
Known TIFF compression types.
CompTransfSpec - Class in io.scif.jj2000.j2k.image
This class extends ModuleSpec class in order to hold tile specifications for component transformation
CompTransfSpec(int, int, byte) - Constructor for class io.scif.jj2000.j2k.image.CompTransfSpec
Constructs an empty 'CompTransfSpec' with specified number of tile and components.
computeRegionsWrapper(ImageReadParam, boolean, int, int, BufferedImage, Rectangle, Rectangle) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
Wrapper for the protected method computeRegions.
computeRegionsWrapper(ImageReadParam, int, int, BufferedImage, Rectangle, Rectangle) - Static method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
Wrapper for the protected method computeRegions.
CONCURRENCY_PROP_NAME - Static variable in class io.scif.jj2000.j2k.util.ThreadPool
The name of the property that sets the concurrency level: io.scif.jj2000.j2k.util.ThreadPool.concurrency
Constants - Class in io.scif.common
Constants that are used within many classes in io.scif.common.
Constants() - Constructor for class io.scif.common.Constants
 
constructImage(int, int, int, int, boolean, boolean, DataBuffer) - Static method in class io.scif.gui.AWTImageTools
Creates an image with the given DataBuffer.
constructImage(int, int, int, int, boolean, boolean, DataBuffer, ColorModel) - Static method in class io.scif.gui.AWTImageTools
Creates an image with the given DataBuffer.
contains(Object) - Method in class io.scif.img.Range
 
containsPoint(int, int) - Method in class io.scif.common.Region
Deprecated.
Returns true if the point specified by the given X and Y coordinates is contained within this region.
containsTIFFField(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Determines whether a TIFF field with the given tag number is contained in this directory.
containsValue(int[], int) - Static method in class io.scif.common.DataTools
Deprecated.
Returns true if the given value is contained in the given array.
CONTIGUOUS_CODESTREAM_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
CONTRAST - Static variable in class io.scif.formats.tiff.IFD
 
CONTRAST_HARD - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Contrast" tag.
CONTRAST_NORMAL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Contrast" tag.
CONTRAST_SOFT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Contrast" tag.
Convert - Class in io.scif.cli.commands
SCIFIOToolCommand plugin for converting (reading and writing) datasets.
Convert() - Constructor for class io.scif.cli.commands.Convert
 
convert(Reader, Writer, String) - Static method in class io.scif.util.FormatTools
Convenience method for writing all of the images and metadata obtained from the specified Reader into the specified Writer.
convert(Reader, Writer, String, SCIFIOConfig) - Static method in class io.scif.util.FormatTools
As FormatTools.convert(Reader, Writer, String), with configuration options.
convertBytes(A, byte[], int) - Method in class io.scif.img.cell.loaders.AbstractArrayLoader
Type-specific conversion method.
convertBytes(ByteArray, byte[], int) - Method in class io.scif.img.cell.loaders.ByteArrayLoader
 
convertBytes(CharArray, byte[], int) - Method in class io.scif.img.cell.loaders.CharArrayLoader
 
convertBytes(DoubleArray, byte[], int) - Method in class io.scif.img.cell.loaders.DoubleArrayLoader
 
convertBytes(FloatArray, byte[], int) - Method in class io.scif.img.cell.loaders.FloatArrayLoader
 
convertBytes(IntArray, byte[], int) - Method in class io.scif.img.cell.loaders.IntArrayLoader
 
convertBytes(LongArray, byte[], int) - Method in class io.scif.img.cell.loaders.LongArrayLoader
 
convertBytes(ShortArray, byte[], int) - Method in class io.scif.img.cell.loaders.ShortArrayLoader
 
convertDate(long, int) - Static method in class io.scif.common.DateTools
Converts the given timestamp into an ISO8601 date.
convertDate(long, int, String) - Static method in class io.scif.common.DateTools
Converts the given timestamp into a date string with the given format.
convertDate(long, int, String, boolean) - Static method in class io.scif.common.DateTools
Converts the given timestamp into a date string with the given format.
convertFactor - Variable in class io.scif.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.
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
Creates a default image metadata object and merges in the supplied metadata.
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriter
 
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriter
 
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
convertImageMetadata(IIOMetadata, ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
convertMetadata(String, MetadataStore) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
convertMetadata(MetadataRetrieve, MetadataStore) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
convertMetadata(String, MetadataStore) - Method in interface io.scif.ome.services.OMEXMLService
 
convertMetadata(MetadataRetrieve, MetadataStore) - Method in interface io.scif.ome.services.OMEXMLService
 
convertObjectToString(Object) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Converts the provided object to String
convertRenderedImage(RenderedImage) - Static method in class io.scif.gui.AWTImageTools
Converts a java.awt.image.RenderedImage into a java.awt.image.BufferedImage.
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
Creates a default stream metadata object and merges in the supplied metadata.
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriter
 
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriter
 
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
convertStreamMetadata(IIOMetadata, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
convertToExpMantissa(float) - Static method in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
Converts the floating point value to its exponent-mantissa representation.
CoordInfo - Class in io.scif.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 io.scif.jj2000.j2k.codestream.CoordInfo
Constructor.
CoordInfo() - Constructor for class io.scif.jj2000.j2k.codestream.CoordInfo
Empty contructor
copy(ImageMetadata) - Method in class io.scif.AbstractImageMetadata
 
copy() - Method in class io.scif.DefaultImageMetadata
 
copy() - Method in interface io.scif.ImageMetadata
 
copy(ImageMetadata) - Method in interface io.scif.ImageMetadata
Populates this ImageMetadata using the provided instance.
copy() - Method in class io.scif.img.cell.SCIFIOCellImg
 
copy() - Method in class io.scif.img.SCIFIOImgPlus
 
copyData(WritableRaster) - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Copies an arbitrary rectangular region of the RenderedImage into a caller-supplied WritableRaster.
copyData(WritableRaster) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
copyInt(byte[], int, int) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Copies that four bytes of an integer into the byte array.
COPYRIGHT - Static variable in class io.scif.formats.tiff.IFD
 
copyright - Static variable in class io.scif.jj2000.j2k.JJ2KInfo
The copyright message string.
copyScaled(BufferedImage, BufferedImage, Object) - Static method in class io.scif.gui.AWTImageTools
Copies the source image into the target, applying scaling.
CorruptedCodestreamException - Exception in io.scif.jj2000.j2k.codestream
Thsi exception is thrown whenever an illegal value is read from a bit stream.
CorruptedCodestreamException() - Constructor for exception io.scif.jj2000.j2k.codestream.CorruptedCodestreamException
Constructs a new CorruptedCodestreamException exception with no detail message.
CorruptedCodestreamException(String) - Constructor for exception io.scif.jj2000.j2k.codestream.CorruptedCodestreamException
Constructs a new CorruptedCodestreamException exception with the specified detail message.
cortime - Variable in class io.scif.lifesci.SDTInfo
Correlation time [ms].
cqcc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCC
 
CRC - Class in io.scif.common
Holds and calculates a CRC for verifying data integrity.
CRC() - Constructor for class io.scif.common.CRC
 
CRC_32_TABLE - Static variable in class io.scif.common.CRC
 
create(long[], T) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
 
create(long[], String, AxisType[], int, boolean, boolean) - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
create(long[], String, AxisType[], int, boolean, boolean, boolean) - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
create(T, long[], String, AxisType[]) - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
create(T, long[], String, AxisType[], boolean) - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
create(ImgFactory<T>, T, long[], String, AxisType[]) - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
create(ImgPlus<T>) - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
create(RandomAccessibleInterval<T>) - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
createArrayForType(int, int) - Static method in class io.scif.media.imageio.plugins.tiff.TIFFField
Creates an array appropriate for the indicated data type.
createAxes(AxisType...) - Static method in class io.scif.util.FormatTools
Creates an array, wrapping all provided AxisTypes as CalibratedAxis with calibration = 1.0.
createAxis(AxisType) - Static method in class io.scif.util.FormatTools
Wraps the provided AxisType in a CalibratedAxis with calibration = 1.0.
createBox(int, Node) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Creates a Box object with the provided type based on the provided Node object based on reflection.
createByteInstance(long[], Fraction) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
 
createCharInstance(long[], Fraction) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
 
createChecker() - Method in class io.scif.AbstractFormat
 
createChecker() - Method in interface io.scif.Format
Create an instance of the Checker associated with this format.
createColorModel(SampleModel) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Creates a ColorModel that may be used with the specified SampleModel.
createColorModel(ColorSpace, SampleModel) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
 
createCompatibleWritableRaster(int, int) - Method in class io.scif.gui.Index16ColorModel
 
createCompatibleWritableRaster(int, int) - Method in class io.scif.gui.SignedColorModel
 
createCompatibleWritableRaster(int, int) - Method in class io.scif.gui.UnsignedIntColorModel
 
createCompressedDataSet(int, String, long[], int, long[]) - Static method in class io.scif.formats.imaris.HDFUtils
 
createDataSet(int, String, long[], int) - Static method in class io.scif.formats.imaris.HDFUtils
 
createDequantizer(CBlkQuantDataSrcDec, int[], DecoderSpecs) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the dequantizer parameters.
createDomainArray() - Method in class io.scif.AbstractReader
Helper method to lazily create the domain array for this reader instance, to avoid constantly re-creating the array.
createDomainArray() - Method in class io.scif.bf.BioFormatsFormat.Reader
 
createDomainArray() - Method in class io.scif.DefaultReader
 
createDomainArray() - Method in class io.scif.formats.APNGFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.AVIFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.BMPFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.DICOMFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.EPSFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.FakeFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.FITSFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.GIFFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.ICSFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.ImageIOFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.JPEG2000Format.Reader
 
createDomainArray() - Method in class io.scif.formats.JPEGTileFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.KontronFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.MicromanagerFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.MinimalTIFFFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.MNGFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.NRRDFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.OBFFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.PCXFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.PGMFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.qt.LegacyQTFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.qt.NativeQTFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.qt.PICTFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.ScancoISQFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.TextFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.TIFFJAIFormat.Reader
 
createDomainArray() - Method in class io.scif.formats.ZipFormat.Reader
 
createDomainArray() - Method in class io.scif.lifesci.SDTFormat.Reader
 
createDomainArray() - Method in class io.scif.ome.formats.OMETIFFFormat.Reader
 
createDomainArray() - Method in class io.scif.ome.formats.OMEXMLFormat.Reader
 
createDoubleInstance(long[], Fraction) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
 
createEntropyDecoder(CodedCBlkDataSrcDec, J2KImageReadParamJava) - Method in class io.scif.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.
createFactory(Metadata, SCIFIOConfig.ImgMode[], T) - Method in class io.scif.img.DefaultImgFactoryHeuristic
 
createFactory(Metadata, SCIFIOConfig.ImgMode[], T) - Method in interface io.scif.img.ImgFactoryHeuristic
 
createFloatInstance(long[], Fraction) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
 
createFromMetadata(IIOMetadata) - Static method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Creates a TIFFDirectory instance from the contents of an image metadata object.
createFromMetadataNode(TIFFTagSet, Node) - Static method in class io.scif.media.imageio.plugins.tiff.TIFFField
Creates a TIFFField from a TIFF native image metadata node.
createImageMetadata(int) - Method in class io.scif.AbstractMetadata
 
createImageMetadata(int) - Method in class io.scif.formats.TIFFFormat.Metadata
 
createImageMetadata(int) - Method in interface io.scif.Metadata
Creates the specified number of blank ImageMetadata.
createImageReader() - Method in class io.scif.bf.BioFormatsFormat
Creates a new Bio-Formats ImageReader.
createIndexColorModel(RenderedImage) - Static method in class io.scif.media.imageioimpl.common.PaletteBuilder
Creates an palette representing colors from given image img.
createIndexedImage(RenderedImage) - Static method in class io.scif.media.imageioimpl.common.PaletteBuilder
Creates an image representing given image src using IndexColorModel.
createIndexMaps(int[][], int[][]) - Static method in class io.scif.formats.FakeFormat.FakeUtils
Populates a mapping between indicies and color values, and the inverse mapping of color values to indicies.
createIndexValueMap(int[][]) - Static method in class io.scif.formats.FakeFormat.FakeUtils
Populates the given array with a random mapping of indices to values.
createInputStreamInstance(Object, boolean, File) - Method in class io.scif.media.imageioimpl.stream.ChannelImageInputStreamSpi
 
createInstance(RandomAccessIO, HeaderDecoder, J2KImageReadParamJava, DecoderSpecs, boolean, HeaderInfo) - Static method in class io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.jj2000.j2k.roi.encoder.ROIScaler
Creates a ROIScaler object.
createInstance(CBlkQuantDataSrcDec, J2KImageReadParamJava, DecoderSpecs) - Static method in class io.scif.jj2000.j2k.roi.ROIDeScaler
Creates a ROIDeScaler object.
createInstance(BlkImgDataSrc, J2KImageWriteParamJava) - Static method in class io.scif.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 io.scif.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.
createIntInstance(long[], Fraction) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
 
createInverseIndexMap(int[][], int[][]) - Static method in class io.scif.formats.FakeFormat.FakeUtils
Populates an array with inverse mapping of values and indices, drawn from a base index:value mapping.
createLongInstance(long[], Fraction) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
 
createLSID(String, int...) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
createLSID(String, int...) - Method in interface io.scif.ome.services.OMEMetadataService
Constructs an LSID, given the object type and indices.
createMetadata() - Method in class io.scif.AbstractFormat
 
createMetadata() - Method in interface io.scif.Format
Create an instance of the Metadata associated with this format.
createNewFile() - Method in class io.scif.io.Location
Creates a new empty file named by this Location's path name iff a file with this name does not already exist.
createOMEXMLMetadata() - Method in class io.scif.ome.services.DefaultOMEXMLService
 
createOMEXMLMetadata(String) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
createOMEXMLMetadata(String, String) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
createOMEXMLMetadata() - Method in interface io.scif.ome.services.OMEXMLService
 
createOMEXMLMetadata(String) - Method in interface io.scif.ome.services.OMEXMLService
 
createOMEXMLMetadata(String, String) - Method in interface io.scif.ome.services.OMEXMLService
 
createOMEXMLRoot(String) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
createOMEXMLRoot(String) - Method in interface io.scif.ome.services.OMEXMLService
 
createOutputStreamInstance(Object, boolean, File) - Method in class io.scif.media.imageioimpl.stream.ChannelImageOutputStreamSpi
 
createParser() - Method in class io.scif.AbstractFormat
 
createParser() - Method in interface io.scif.Format
Create an instance of the Parser associated with this format.
createPlane(long[], long[]) - Method in class io.scif.ByteArrayReader
 
createPlane(ImageMetadata, long[], long[]) - Method in class io.scif.ByteArrayReader
 
createPlane(long[], long[]) - Method in class io.scif.filters.AbstractReaderFilter
 
createPlane(ImageMetadata, long[], long[]) - Method in class io.scif.filters.AbstractReaderFilter
 
createPlane(long[], long[]) - Method in class io.scif.gui.BufferedImageReader
 
createPlane(ImageMetadata, long[], long[]) - Method in class io.scif.gui.BufferedImageReader
 
createPlane(long[], long[]) - Method in interface io.scif.Reader
Creates a blank plane compatible with this reader.
createPlane(ImageMetadata, long[], long[]) - Method in interface io.scif.Reader
Creates a blank plane compatible with this reader.
createPlane(long[], long[]) - Method in interface io.scif.TypedReader
 
createRawImage() - Method in class io.scif.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.
createReader() - Method in class io.scif.AbstractFormat
 
createReader() - Method in interface io.scif.Format
Creates an instance of the Reader associated with this format.
createReaderInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
createReaderInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
createReaderInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
createReaderInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
createReaderInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
createReaderInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
createReaderInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
createROIDeScaler(CBlkQuantDataSrcDec, J2KImageReadParamJava, DecoderSpecs) - Method in class io.scif.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.
createShortInstance(long[], Fraction) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
 
createWriter() - Method in class io.scif.AbstractFormat
 
createWriter() - Method in interface io.scif.Format
Creates an instance of the Writer associated with this format.
createWriterInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
createWriterInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
createWriterInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
createWriterInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
createWriterInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
createWriterInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
createWriterInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
createWriterInstance(Object) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
crg - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo
Reference to the CRG marker segment found in main header
CRG() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo.CRG
 
CRG - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Component registration (CRG): 0xFF63
CRG_FOUND - Static variable in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Flag bit for CRG marker segment found
crgn - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.RGN
 
crossChan - Variable in class io.scif.lifesci.SDTInfo
Cross FCS routing channel number when chan = crossChan and mod == crossMod - Auto FCS otherwise - Cross FCS.
crossMod - Variable in class io.scif.lifesci.SDTInfo
Cross FCS module number.
crossMtResol - Variable in class io.scif.lifesci.SDTInfo
Macro time clock of cross FCS module in 0.1 ns units.
cs - Variable in class io.scif.jj2000.j2k.entropy.Progression
Component index for the start of a progression
CS_2C - Static variable in class io.scif.gui.TwoChannelColorSpace
 
CSB_APPROX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
CSB_ENUM_GREY - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
CSB_ENUM_SRGB - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
CSB_ENUM_YCC - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
CSB_METH - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
Colour Specification Box Fields
CSB_PREC - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
csiz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
cspoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.POC
 
css - Variable in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Causal stripes specifications
ctp - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
The cumulative number of truncation points
cts - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
The component transformation specifications
ctX - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The current tile horizontal index
ctY - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The current tile vertical index
culx - Variable in class io.scif.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 io.scif.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.
curCycle - Variable in class io.scif.lifesci.SDTInfo
Current cycle (accumulation cycle in FLOW mode) - (if multi-cycle measurement).
curPage - Variable in class io.scif.lifesci.SDTInfo
Current measured page.
currLevel - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
currSize - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
curStep - Variable in class io.scif.lifesci.SDTInfo
Current step (if multi-step measurement).
curve - Variable in class io.scif.codec.NikonCodecOptions
 
CUSTOM - Static variable in interface io.scif.jj2000.j2k.wavelet.FilterTypes
User-defined filter: -1
CUSTOM_RENDERED - Static variable in class io.scif.formats.tiff.IFD
 
CUSTOM_RENDERED_CUSTOM - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "CustomRendered" tag.
CUSTOM_RENDERED_NORMAL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "CustomRendered" tag.
cycles - Variable in class io.scif.lifesci.SDTInfo
Cycles (accumulation cycles in FLOW mode).

D

DAC - Static variable in class io.scif.codec.LosslessJPEGCodec
 
data - Variable in class io.scif.jj2000.j2k.entropy.CodedCBlk
The compressed data
data - Variable in class io.scif.jj2000.j2k.image.DataBlkFloat
The array where the data is stored
data - Variable in class io.scif.jj2000.j2k.image.DataBlkInt
The array where the data is stored
data - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataFloat
The array where the data is stored
data - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataInt
The array where the data is stored
data - Variable in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
 
DATA_IDENTIFIER - Static variable in class io.scif.lifesci.SDTInfo
For normal .sdt files (setup + data).
DataBlk - Class in io.scif.jj2000.j2k.image
This is a generic abstract class to store data from a block of an image.
DataBlk() - Constructor for class io.scif.jj2000.j2k.image.DataBlk
 
DataBlkFloat - Class in io.scif.jj2000.j2k.image
This is an implementation of the DataBlk interface for 32 bit floating point data (float).
DataBlkFloat() - Constructor for class io.scif.jj2000.j2k.image.DataBlkFloat
Creates a DataBlkFloat with 0 dimensions and no data array (i.e.
DataBlkFloat(int, int, int, int) - Constructor for class io.scif.jj2000.j2k.image.DataBlkFloat
Creates a DataBlkFloat with the specified dimensions and position.
DataBlkFloat(DataBlkFloat) - Constructor for class io.scif.jj2000.j2k.image.DataBlkFloat
Copy constructor.
DataBlkInt - Class in io.scif.jj2000.j2k.image
This is an implementation of the DataBlk interface for signed 32 bit integral data.
DataBlkInt() - Constructor for class io.scif.jj2000.j2k.image.DataBlkInt
Creates a DataBlkInt with 0 dimensions and no data array (i.e.
DataBlkInt(int, int, int, int) - Constructor for class io.scif.jj2000.j2k.image.DataBlkInt
Creates a DataBlkInt with the specified dimensions and position.
DataBlkInt(DataBlkInt) - Constructor for class io.scif.jj2000.j2k.image.DataBlkInt
Copy constructor.
dataBlockLength - Variable in class io.scif.lifesci.SDTInfo
 
dataBlockOffs - Variable in class io.scif.lifesci.SDTInfo
Offset of the first data block.
DataEntryURLBox - Class in io.scif.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 io.scif.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
Constructs a DataEntryURLBox from its content data.
DataEntryURLBox(byte, byte[], String) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
Constructs a DataEntryURLBox from its data elements.
DataEntryURLBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
Constructs a DataEntryURLBox from a Node.
dataOffs - Variable in class io.scif.lifesci.SDTInfo
Offset of the data block from the beginning of the file.
DataPlane<T> - Interface in io.scif
Extension of the base Plane interface.
datasetIO() - Method in class io.scif.SCIFIO
Gets this application context's DatasetIOService.
DatasetIOPlugin - Class in io.scif.io
I/O plugin for Datasets.
DatasetIOPlugin() - Constructor for class io.scif.io.DatasetIOPlugin
 
DatasetIOService - Interface in io.scif.services
A service for opening and saving Datasets using SCIFIO.
DataTools - Class in io.scif.common
Deprecated.
Use these classes instead: Bytes, StringUtils, ArrayUtils
date - Variable in class io.scif.lifesci.SDTInfo
Date of creation.
DATE_FORMAT - Static variable in class io.scif.formats.MicromanagerFormat.Parser
 
DATE_FORMATS - Static variable in class io.scif.formats.ICSFormat.ICSUtils
 
DATE_FORMATS - Static variable in class io.scif.formats.TIFFFormat.BaseTIFFParser
 
DATE_TIME - Static variable in class io.scif.formats.tiff.IFD
 
DATE_TIME_DIGITIZED - Static variable in class io.scif.formats.tiff.IFD
 
DATE_TIME_ORIGINAL - Static variable in class io.scif.formats.tiff.IFD
 
dateAndtime - Variable in class io.scif.formats.imaris.PipelineImage
 
DateTools - Class in io.scif.common
A utility class with convenience methods for working with dates.
DC_OFFSET - Static variable in class io.scif.jj2000.j2k.image.input.ImgReaderPGM
DC offset value used when reading image
deadTimeComp - Variable in class io.scif.lifesci.SDTInfo
 
debug(String) - Method in class io.scif.cli.AbstractSCIFIOToolCommand
 
DebugTools - Class in io.scif.common
Deprecated.
Use DebugUtils instead.
DEC_SPEC_COMP_DEF - Static variable in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
The identifier for "component default" specified decomposition
DEC_SPEC_MAIN_DEF - Static variable in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
The identifier for "main default" specified decomposition
DEC_SPEC_TILE_COMP - Static variable in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
The identifier for "tile and component specific" specified decomposition
DEC_SPEC_TILE_DEF - Static variable in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
The identifier for "tile specific default" specified decomposition
DecLyrdCBlk - Class in io.scif.jj2000.j2k.entropy.decoder
This class stores coded (compressed) code-blocks that are organized in layers.
DecLyrdCBlk() - Constructor for class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
 
decode() - Method in class io.scif.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 io.scif.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
decode(byte[], int, int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
decode() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFNullDecompressor
 
decode(byte[], int, byte[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFPackBitsDecompressor
 
decode(byte[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFPackBitsUtil
 
decodeNextScanline(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class io.scif.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 io.scif.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 io.scif.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 io.scif.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 io.scif.media.imageioimpl.plugins.tiff.TIFFDeflateDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLSBDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFNullDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFPackBitsDecompressor
 
decodeRaw(byte[], int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
decodeRLE() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
DecoderSpecs - Class in io.scif.jj2000.j2k.decoder
This class holds references to each module specifications used in the decoding chain.
DecoderSpecs(int, int) - Constructor for class io.scif.jj2000.j2k.decoder.DecoderSpecs
Initialize all members with the given number of tiles and components.
decodeSymbol(int) - Method in class io.scif.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 io.scif.jj2000.j2k.entropy.decoder.MQDecoder
This function performs the arithmetic decoding.
decodeT4() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
decodeT6() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int) - Method in interface io.scif.services.LuraWaveService
Wraps com.luratech.lwf.lwfDecoder#decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int) .
decodeToMemoryGray8(byte[], int, int, int) - Method in interface io.scif.services.LuraWaveService
Wraps com.luratech.lwf.lwfDecoder#decodeToMemoryGray8(byte[], int, int, int) .
decodeWord(byte[], int, int, boolean) - Method in class io.scif.img.DefaultImgUtilityService
 
decodeWord(byte[], int, int, boolean) - Method in interface io.scif.img.ImgUtilityService
 
decompress(byte[]) - Method in class io.scif.codec.AbstractCodec
 
decompress(byte[][]) - Method in class io.scif.codec.AbstractCodec
 
decompress(byte[], CodecOptions) - Method in class io.scif.codec.AbstractCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.AbstractCodec
 
decompress(byte[][], CodecOptions) - Method in class io.scif.codec.AbstractCodec
2D data block decoding default implementation.
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.Base64Codec
 
decompress(byte[], CodecOptions) - Method in interface io.scif.codec.Codec
Decompresses a block of data.
decompress(byte[][], CodecOptions) - Method in interface io.scif.codec.Codec
Decompresses a block of data.
decompress(byte[]) - Method in interface io.scif.codec.Codec
Decompresses a block of data.
decompress(byte[][]) - Method in interface io.scif.codec.Codec
Decompresses a block of data.
decompress(RandomAccessInputStream, CodecOptions) - Method in interface io.scif.codec.Codec
Decompresses data from the given RandomAccessInputStream.
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.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 io.scif.codec.JPEG2000Codec
The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(byte[], CodecOptions) - Method in class io.scif.codec.JPEG2000Codec
The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.JPEGCodec
The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.LosslessJPEGCodec
The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.LuraWaveCodec
 
decompress(byte[], CodecOptions) - Method in class io.scif.codec.LuraWaveCodec
The CodecOptions parameter should have the following fields set: maxBytes
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.LZWCodec
The CodecOptions parameter should have the following fields set: maxBytes
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.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 io.scif.codec.MSRLECodec
The CodecOptions parameter should have the following fields set: width height previousImage
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.MSVideoCodec
The CodecOptions parameter should have the following fields set: width height bitsPerSample previousImage
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.NikonCodec
The CodecOptions parameter must be an instance of NikonCodecOptions , and should have the following fields set: vPredictor curve split bitsPerSample maxBytes width height
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.PackbitsCodec
The CodecOptions parameter should have the following fields set: maxBytes
decompress(byte[], CodecOptions) - Method in class io.scif.codec.PassthroughCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.PassthroughCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.QTRLECodec
 
decompress(byte[], CodecOptions) - Method in class io.scif.codec.QTRLECodec
The CodecOptions parameter should have the following fields set: width height bitsPerSample previousImage
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.RPZACodec
The CodecOptions parameter should have the following fields set: width height
decompress(RandomAccessInputStream, CodecOptions) - Method in class io.scif.codec.ZlibCodec
 
decompress(CodecService, byte[], CodecOptions) - Method in enum io.scif.formats.tiff.TiffCompression
Decodes a strip of data.
decSpec - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The decoder specifications
decSpec - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
The decoder specifications
def - Variable in class io.scif.jj2000.j2k.ModuleSpec
Default value for each tile-component
DEF_BUF_LEN - Static variable in class io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
The default buffer length, 1024 bytes
DEF_THREADS_NUM - Static variable in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
The default value for the property in THREADS_PROP_NAME: 0
DEFAULT_BLOCK_SIZE - Static variable in class io.scif.io.RandomAccessInputStream
Block size to use when searching through the stream.
DEFAULT_BYTES_PER_STRIP - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
DEFAULT_DISPLAY_RESOLUTION_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
DEFAULT_KEY - Static variable in class io.scif.formats.APNGFormat.Metadata
 
DefaultChecker - Class in io.scif
Default Checker implementation.
DefaultChecker() - Constructor for class io.scif.DefaultChecker
 
DefaultCodecService - Class in io.scif.codec
Default service for managing available Codecs.
DefaultCodecService() - Constructor for class io.scif.codec.DefaultCodecService
 
DefaultComponent - Interface in io.scif
Marker interface for default class implementations.
DefaultDatasetIOService - Class in io.scif.services
Default DatasetIOService implementation.
DefaultDatasetIOService() - Constructor for class io.scif.services.DefaultDatasetIOService
 
DefaultFilePatternService - Class in io.scif.services
Default FilePatternService implementation.
DefaultFilePatternService() - Constructor for class io.scif.services.DefaultFilePatternService
 
DefaultFormatService - Class in io.scif.services
Default FormatService implementation
DefaultFormatService() - Constructor for class io.scif.services.DefaultFormatService
 
DefaultGUIService - Class in io.scif.gui
Basic GUIService implementation.
DefaultGUIService() - Constructor for class io.scif.gui.DefaultGUIService
 
DefaultImageMetadata - Class in io.scif
Default implementation of ImageMetadata.
DefaultImageMetadata() - Constructor for class io.scif.DefaultImageMetadata
 
DefaultImageMetadata(ImageMetadata) - Constructor for class io.scif.DefaultImageMetadata
 
DefaultImgFactoryHeuristic - Class in io.scif.img
Default ImgFactoryHeuristic implementation.
DefaultImgFactoryHeuristic() - Constructor for class io.scif.img.DefaultImgFactoryHeuristic
 
DefaultImgUtilityService - Class in io.scif.img
Helper methods for converting between SCIFIO and ImgLib2 data structures.
DefaultImgUtilityService() - Constructor for class io.scif.img.DefaultImgUtilityService
 
DefaultInitializeService - Class in io.scif.services
Default InitializeService implementation.
DefaultInitializeService() - Constructor for class io.scif.services.DefaultInitializeService
 
DefaultLocationService - Class in io.scif.services
Default LocationService implementation
DefaultLocationService() - Constructor for class io.scif.services.DefaultLocationService
 
DefaultLocationService.ListingsResult - Class in io.scif.services
 
DefaultMetadata - Class in io.scif
A dummy Metadata implementation.
DefaultMetadata() - Constructor for class io.scif.DefaultMetadata
 
DefaultMetadata(Metadata) - Constructor for class io.scif.DefaultMetadata
 
DefaultMetadata(List<ImageMetadata>) - Constructor for class io.scif.DefaultMetadata
 
DefaultMetadataService - Class in io.scif
Default service for working with SCIFIO metadata.
DefaultMetadataService() - Constructor for class io.scif.DefaultMetadataService
 
DefaultMetaTable - Class in io.scif
Default MetaTable implementation.
DefaultMetaTable() - Constructor for class io.scif.DefaultMetaTable
 
DefaultMetaTable(boolean) - Constructor for class io.scif.DefaultMetaTable
Basic constructor
DefaultMetaTable(Map<String, Object>) - Constructor for class io.scif.DefaultMetaTable
Construct a MetaTable and populate it using an existing map.
defaultMinMax(int) - Static method in class io.scif.util.FormatTools
Get the default range for the specified pixel type.
defaultMinMax(int, boolean) - Static method in class io.scif.util.FormatTools
Get the default range for the specified bits per pixel.
defaultMinMax(int, int) - Static method in class io.scif.util.FormatTools
Helper method to delegate to FormatTools.defaultMinMax(int, boolean) or FormatTools.defaultMinMax(int) based on the given parameters.
defaultMinMax(ImageMetadata) - Static method in class io.scif.util.FormatTools
Helper method to get the default range for the specified ImageMetadata.
DefaultNIOService - Class in io.scif.io
Default service for working with the java.nio package, particularly NIO ByteBuffer objects.
DefaultNIOService() - Constructor for class io.scif.io.DefaultNIOService
 
DefaultOMEMetadataService - Class in io.scif.ome.services
Default implementation of OMEMetadataService.
DefaultOMEMetadataService() - Constructor for class io.scif.ome.services.DefaultOMEMetadataService
 
DefaultOMETranslator - Class in io.scif.ome.translators
Basic translator for OME Metadata.
DefaultOMETranslator() - Constructor for class io.scif.ome.translators.DefaultOMETranslator
 
DefaultOMEXMLService - Class in io.scif.ome.services
Default implementation of OMEXMLService.
DefaultOMEXMLService() - Constructor for class io.scif.ome.services.DefaultOMEXMLService
 
DefaultParser - Class in io.scif
Default Parser implementation.
DefaultParser() - Constructor for class io.scif.DefaultParser
 
DefaultPlaneConverterService - Class in io.scif.img.converters
Default PlaneConverterService implementation.
DefaultPlaneConverterService() - Constructor for class io.scif.img.converters.DefaultPlaneConverterService
 
DefaultQTJavaService - Class in io.scif.formats.qt
Default service for working with QuickTime for Java.
DefaultQTJavaService() - Constructor for class io.scif.formats.qt.DefaultQTJavaService
 
DefaultReader - Class in io.scif
Non-functional default Reader implementation.
DefaultReader() - Constructor for class io.scif.DefaultReader
 
DefaultRefManagerService - Class in io.scif.refs
Default RefManagerService implementation.
DefaultRefManagerService() - Constructor for class io.scif.refs.DefaultRefManagerService
 
DefaultTiffService - Class in io.scif.formats.tiff
Default service for working with TIFF files.
DefaultTiffService() - Constructor for class io.scif.formats.tiff.DefaultTiffService
 
DefaultTranslator - Class in io.scif
Basic Translator implementation.
DefaultTranslator() - Constructor for class io.scif.DefaultTranslator
 
DefaultTranslatorService - Class in io.scif.services
Default TranslatorService implementation.
DefaultTranslatorService() - Constructor for class io.scif.services.DefaultTranslatorService
 
DefaultWriter - Class in io.scif
Non-functional default Writer implementation.
DefaultWriter() - Constructor for class io.scif.DefaultWriter
 
DefaultXMLService - Class in io.scif.xml
Default service for working with XML.
DefaultXMLService() - Constructor for class io.scif.xml.DefaultXMLService
 
delayTime - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
delete() - Method in class io.scif.io.Location
Deletes this file.
deleteOnExit() - Method in class io.scif.io.Location
Request that this file be deleted when the JVM terminates.
DELTA - Static variable in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
The value of the fourth lifting step coefficient
DELTA - Static variable in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
The value of the fourth lifting step coefficient
DependencyException - Exception in io.scif
Exception thrown when there is an object instantiation error or error processing dependencies.
DependencyException(String) - Constructor for exception io.scif.DependencyException
Default constructor.
DependencyException(String, Class<? extends Service>) - Constructor for exception io.scif.DependencyException
Default constructor.
DependencyException(String, Class<? extends Service>, Throwable) - Constructor for exception io.scif.DependencyException
Default constructor.
DependencyException(Throwable) - Constructor for exception io.scif.DependencyException
Default constructor.
Dequantizer - Class in io.scif.jj2000.j2k.quantization.dequantizer
This is the abstract class from which all dequantizers must inherit.
Dequantizer(CBlkQuantDataSrcDec, int[], DecoderSpecs) - Constructor for class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
Initializes the source of compressed data.
DequantizerParams - Class in io.scif.jj2000.j2k.quantization.dequantizer
This is the generic ineterface for dequantization parameters.
DequantizerParams() - Constructor for class io.scif.jj2000.j2k.quantization.dequantizer.DequantizerParams
 
derived - Variable in class io.scif.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).
description() - Method in class io.scif.cli.AbstractSCIFIOToolCommand
 
description() - Method in class io.scif.cli.commands.Convert
 
description() - Method in class io.scif.cli.commands.Help
 
description() - Method in class io.scif.cli.commands.Info
 
description() - Method in class io.scif.cli.commands.Show
 
description() - Method in class io.scif.ome.commands.OMEXMLToolCommand
 
dest() - Method in class io.scif.bf.ome.BioFormatsTranslator.BioFormatsOMETranslator
 
dest() - Method in class io.scif.DefaultTranslator
 
dest() - Method in class io.scif.formats.APNGFormat.APNGTranslator
 
dest() - Method in class io.scif.formats.AVIFormat.Translator
 
dest() - Method in class io.scif.formats.EPSFormat.EPSTranslator
 
dest() - Method in class io.scif.formats.FakeFormat.FakeTranslator
 
dest() - Method in class io.scif.formats.ICSFormat.ICSTranslator
 
dest() - Method in class io.scif.formats.ImageIOFormat.ImageIOTranslator
 
dest() - Method in class io.scif.formats.MicromanagerFormat.MicromanagerTranslator
 
dest() - Method in class io.scif.formats.qt.LegacyQTFormat.LegacyQTTranslator
 
dest() - Method in class io.scif.formats.qt.NativeQTFormat.NativeQTTranslator
 
dest() - Method in class io.scif.formats.TIFFFormat.TIFFTranslator
 
dest() - Method in class io.scif.ome.formats.OMETIFFFormat.OMETIFFTranslator
 
dest() - Method in class io.scif.ome.formats.OMEXMLFormat.OMETranslator
 
dest() - Method in class io.scif.ome.formats.OMEXMLFormat.OMEXMLTranslator
 
dest() - Method in class io.scif.ome.translators.APNGTranslator.APNGOMETranslator
 
dest() - Method in class io.scif.ome.translators.APNGTranslator.OMEAPNGTranslator
 
dest() - Method in class io.scif.ome.translators.BMPTranslator.BMPOMETranslator
 
dest() - Method in class io.scif.ome.translators.DefaultOMETranslator
 
dest() - Method in class io.scif.ome.translators.DICOMTranslator.DICOMOMETranslator
 
dest() - Method in class io.scif.ome.translators.EPSTranslator.OMEEPSTranslator
 
dest() - Method in class io.scif.ome.translators.ICSTranslator.ICSOMETranslator
 
dest() - Method in class io.scif.ome.translators.ICSTranslator.OMEICSTranslator
 
dest() - Method in class io.scif.ome.translators.MicromanagerTranslator.MicromanagerOMETranslator
 
dest() - Method in class io.scif.ome.translators.NRRDTranslator.NRRDOMETranslator
 
dest() - Method in class io.scif.ome.translators.OBFTranslator.OBFOMETranslator
 
dest() - Method in class io.scif.ome.translators.OMETIFFTranslator.OMETIFFtoOMETranslator
 
dest() - Method in class io.scif.ome.translators.OMETIFFTranslator.OMEtoOMETIFFTranslator
 
dest() - Method in class io.scif.ome.translators.TIFFTranslator.OMETIFFTranslator
 
dest() - Method in class io.scif.ome.translators.TIFFTranslator.TIFFOMETranslator
 
dest() - Method in interface io.scif.Translator
 
DEST_DISTANCE_REF_KILOMETERS - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSDestDistanceRef" tag.
DEST_DISTANCE_REF_KNOTS - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSDestDistanceRef" tag.
DEST_DISTANCE_REF_MILES - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSDestDistanceRef" tag.
destinationBands - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The sequence of destination bands to receive the source data.
detectorID - Variable in class io.scif.formats.MicromanagerFormat.Position
 
detectorManufacturer - Variable in class io.scif.formats.MicromanagerFormat.Position
 
detectorModel - Variable in class io.scif.formats.MicromanagerFormat.Position
 
detType - Variable in class io.scif.lifesci.SDTInfo
Detector type (SPC-930 in camera mode).
DHP - Static variable in class io.scif.codec.LosslessJPEGCodec
 
DHT - Static variable in class io.scif.codec.LosslessJPEGCodec
 
DICOM_MAGIC_STRING - Static variable in class io.scif.formats.DICOMFormat
 
DICOMDictionary - Class in io.scif.formats.dicom
Data dictionary of DICOM types.
DICOMDictionary() - Constructor for class io.scif.formats.dicom.DICOMDictionary
 
DICOMFormat - Class in io.scif.formats
DICOMReader is the file format reader for DICOM files.
DICOMFormat() - Constructor for class io.scif.formats.DICOMFormat
 
DICOMFormat.Checker - Class in io.scif.formats
 
DICOMFormat.DICOMTag - Class in io.scif.formats
 
DICOMFormat.Metadata - Class in io.scif.formats
 
DICOMFormat.Parser - Class in io.scif.formats
 
DICOMFormat.Reader - Class in io.scif.formats
 
DICOMOMETranslator() - Constructor for class io.scif.ome.translators.DICOMTranslator.DICOMOMETranslator
 
DICOMTag() - Constructor for class io.scif.formats.DICOMFormat.DICOMTag
 
DICOMTranslator - Class in io.scif.ome.translators
Container class for translators between OME and DICOM formats.
DICOMTranslator() - Constructor for class io.scif.ome.translators.DICOMTranslator
 
DICOMTranslator.DICOMOMETranslator - Class in io.scif.ome.translators
Translator class from DICOMFormat.Metadata to OMEMetadata
difference(byte[], IFD) - Method in class io.scif.formats.tiff.DefaultTiffService
 
difference(byte[], IFD) - Method in interface io.scif.formats.tiff.TiffService
Performs in-place differencing according to the given predictor value.
DIFFERENTIAL_CORRECTION_APPLIED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSDifferential" tag.
DIFFERENTIAL_CORRECTION_NONE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSDifferential" tag.
DIGITAL_ZOOM_RATIO - Static variable in class io.scif.formats.tiff.IFD
 
dimCount() - Method in class io.scif.img.cell.SCIFIOCell
 
DimensionSwapper - Class in io.scif.filters
Handles swapping the dimension order of an image series.
DimensionSwapper() - Constructor for class io.scif.filters.DimensionSwapper
 
DimensionSwapperMetadata - Class in io.scif.filters
MetadataWrapper implementation specifically for use with the DimensionSwapper.
DimensionSwapperMetadata() - Constructor for class io.scif.filters.DimensionSwapperMetadata
 
DIRECTION_REF_MAGNETIC - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSTrackRef", "GPSImgDirectionRef", and "GPSDestBearingRef" tags.
DIRECTION_REF_TRUE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSTrackRef", "GPSImgDirectionRef", and "GPSDestBearingRef" tags.
dirty() - Method in class io.scif.img.cell.SCIFIOCell
 
disable(Class<? extends Filter>) - Method in interface io.scif.filters.MasterFilter
Removes the specified filter from the filter stack, if present.
disable(Class<? extends Filter>) - Method in class io.scif.filters.MasterFilterHelper
 
disable(Class<? extends Filter>) - Method in class io.scif.filters.ReaderFilter
 
diskFull() - Method in class io.scif.img.cell.cache.AbstractCacheService
 
diskIsFull(boolean) - Method in class io.scif.img.cell.cache.AbstractCacheService
 
disposalMethod - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
dispose() - Method in class io.scif.img.cell.cache.MapDBCache
 
dispose() - Method in class io.scif.img.cell.SCIFIOCellImg
 
dispose() - Method in class io.scif.img.SCIFIOImgPlus
 
dispose() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
dispose() - Method in class io.scif.refs.DefaultRefManagerService
Signal to any active RefCleaner that this service has been disposed.
dither - Variable in class io.scif.lifesci.SDTInfo
 
dl - Variable in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
The coded (compressed) data length.
DLL_DATA_IDENTIFIER - Static variable in class io.scif.lifesci.SDTInfo
For .sdt files created using DLL function SPC_save_data_to_sdtfile (no setup, only data).
dls - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
Number of decomposition levels specifications
DNL - Static variable in class io.scif.codec.LosslessJPEGCodec
 
DO_NOT_CONVERT - Static variable in class io.scif.bf.BioFormatsFormat
List of classes already converted to SCIFIO.
doCodestreamManipulation() - Method in class io.scif.jj2000.j2k.util.CodestreamManipulator
This method performs the actual manipulation of the codestream which is the reparsing for tile parts and packed packet headers
DOCUMENT_NAME - Static variable in class io.scif.formats.tiff.IFD
 
DOT_RANGE - Static variable in class io.scif.formats.tiff.IFD
 
DOUBLE - Static variable in class io.scif.util.FormatTools
Identifies the DOUBLE data type used to store pixel values.
DoubleArrayLoader - Class in io.scif.img.cell.loaders
SCIFIOArrayLoader implementation for DoubleArray types.
DoubleArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.DoubleArrayLoader
 
doublesToBytes(double[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates an array of double values into an array of byte values.
doubleToBytes(double, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates the double value into an array of eight bytes.
doubleValue() - Method in class io.scif.formats.tiff.TiffRational
Returns the value of the specified number as a double.
DQT - Static variable in class io.scif.codec.LosslessJPEGCodec
 
DRI - Static variable in class io.scif.codec.LosslessJPEGCodec
 
dropCache(String) - Method in interface io.scif.img.cell.cache.CacheService
Closes and removes the specified cache.
dropCache(String) - Method in class io.scif.img.cell.cache.MapDBCache
 
dstHeight - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The height of the region of the destination image to be written.
dstMinX - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The X coordinate of the upper left pixel to be written in the destination image.
dstMinY - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The Y coordinate of the upper left pixel to be written in the destination image.
dstWidth - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The width of the region of the destination image to be written.
dstXOffset - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The horizontal destination offset used, along with sourceXOffset and subsampleX, to map between horizontal source and destination pixel coordinates.
dstYOffset - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The vertical destination offset used, along with sourceYOffset and subsampleY, to map between horizontal source and destination pixel coordinates.
dump(PrintStream) - Method in class io.scif.media.imageioimpl.common.LZWCompressor
 
dump(PrintStream) - Method in class io.scif.media.imageioimpl.common.LZWStringTable
 
dwt - Variable in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Reference to the DWT module

E

ealDE - Variable in class io.scif.lifesci.SDTInfo
 
EBCOTRateAllocator - Class in io.scif.jj2000.j2k.entropy.encoder
This implements the EBCOT post compression rate allocation algorithm.
EBCOTRateAllocator(CodedCBlkDataSrcEnc, LayersInfo, CodestreamWriter, J2KImageWriteParamJava) - Constructor for class io.scif.jj2000.j2k.entropy.encoder.EBCOTRateAllocator
Initializes the EBCOT rate allocator of entropy coded data.
ecopts - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
The Entropy decoder options specifications
ECS_GRAY - Static variable in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
ECS_sRGB - Static variable in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
The enumerated color space defined in JP2 file format.
ECS_YCC - Static variable in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
elementInfoMap - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
EM_DOMAIN - Static variable in class io.scif.util.FormatTools
Identifies the electron microscopy domain.
emptyArray(int) - Method in class io.scif.img.cell.loaders.ByteArrayLoader
 
emptyArray(int) - Method in class io.scif.img.cell.loaders.CharArrayLoader
 
emptyArray(int) - Method in class io.scif.img.cell.loaders.DoubleArrayLoader
 
emptyArray(int) - Method in class io.scif.img.cell.loaders.FloatArrayLoader
 
emptyArray(int) - Method in class io.scif.img.cell.loaders.IntArrayLoader
 
emptyArray(int) - Method in class io.scif.img.cell.loaders.LongArrayLoader
 
emptyArray(int) - Method in interface io.scif.img.cell.loaders.SCIFIOArrayLoader
 
emptyArray(int) - Method in class io.scif.img.cell.loaders.ShortArrayLoader
 
enable(Class<F>) - Method in interface io.scif.filters.MasterFilter
Inserts an instance of the indicated filter class into the filter stack.
enable(Class<F>) - Method in class io.scif.filters.MasterFilterHelper
 
enable(Class<F>) - Method in class io.scif.filters.ReaderFilter
 
enable(boolean) - Method in class io.scif.img.cell.cache.AbstractCacheService
 
enable(boolean) - Method in interface io.scif.img.cell.cache.CacheService
 
enabled() - Method in class io.scif.img.cell.cache.AbstractCacheService
 
enabled() - Method in interface io.scif.img.cell.cache.CacheService
 
enabledDefault() - Method in class io.scif.filters.AbstractFilter
 
enabledDefault() - Method in interface io.scif.filters.Filter
 
encode(int, int, int, BitOutputBuffer) - Method in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Encodes information for the specified element of the tree, given the threshold and sends it to the 'out' stream.
encode(byte[], int, int, int, int[], int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Encodes the supplied image data, writing to the currently set ImageOutputStream.
encode(byte[], int, int, int, int[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
encode(byte[], int, int, int, int[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFDeflater
 
encode(byte[], int, int, int, int[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLSBCompressor
 
encode(byte[], int, int, int, int[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWCompressor
 
encode(byte[], int, int, int, int[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFNullCompressor
 
encode(byte[], int, int, int, int[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFPackBitsCompressor
 
encode(byte[], int, int, int, int[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRLECompressor
 
encode(byte[], int, int, int, int[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFT4Compressor
 
encode(byte[], int, int, int, int[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFT6Compressor
 
encode1D(byte[], int, int, int, byte[], int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
One-dimensionally encode a row of data using CCITT Huffman compression.
encodeMainHeader() - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Write main header.
encodePacket(int, int, int, int, CBlkRateDistStats[][], int[][], BitOutputBuffer, byte[], int) - Method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Encodes a packet and returns the buffer containing the encoded packet header.
encodeRLE(byte[], int, int, int, byte[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRLECompressor
Encode a row of data using Modified Huffman Compression also known as CCITT RLE (Run Lenth Encoding).
encodeT4(boolean, boolean, byte[], int, int, int, int, byte[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFT4Compressor
Encode a buffer of data using CCITT T.4 Compression also known as Group 3 facsimile compression.
encodeT6(byte[], int, int, int, int, byte[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFT6Compressor
Encode a buffer of data using CCITT T.6 Compression also known as Group 4 facsimile compression.
encodeTilePartHeader(int, int) - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Writes tile-part header.
ENCODING - Static variable in class io.scif.common.Constants
 
ENCODING - Static variable in interface io.scif.media.imageioimpl.plugins.pcx.PCXConstants
 
EndianType - Interface in io.scif.jj2000.j2k.io
This interface defines constants for the two types of byte ordering: little- and big-endian.
endInsertEmpty() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
endReplacePixels() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
endTime - Variable in class io.scif.lifesci.SDTInfo
Macro time of the last photon.
endWriteEmpty() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
endWriteSequence() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
endWriteSequence() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
EntropyCoder - Class in io.scif.jj2000.j2k.entropy.encoder
This abstract class provides the general interface for block-based entropy encoders.
EntropyCoder(CBlkQuantDataSrcEnc) - Constructor for class io.scif.jj2000.j2k.entropy.encoder.EntropyCoder
Initializes the source of quantized wavelet coefficients.
EntropyDecoder - Class in io.scif.jj2000.j2k.entropy.decoder
This is the abstract class from which all entropy decoders must inherit.
EntropyDecoder(CodedCBlkDataSrcDec) - Constructor for class io.scif.jj2000.j2k.entropy.decoder.EntropyDecoder
Initializes the source of compressed data.
EnumException - Exception in io.scif.enumeration
 
EnumException() - Constructor for exception io.scif.enumeration.EnumException
 
EnumException(String) - Constructor for exception io.scif.enumeration.EnumException
 
EnumException(String, Throwable) - Constructor for exception io.scif.enumeration.EnumException
 
EnumException(Throwable) - Constructor for exception io.scif.enumeration.EnumException
 
EOC - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
End of codestream (EOC): 0xFFD9
EOF_ERROR_MSG - Static variable in class io.scif.io.AbstractNIOHandle
Error message to be used when instantiating an EOFException.
EOI - Static variable in class io.scif.codec.LosslessJPEGCodec
 
EOI - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
EPH - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
End of packet header (EPH): 0xFF92
EPH_LENGTH - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Length of EPH marker (in bytes)
ephs - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
The End of Packet Headers (EPH) markers specifications
EPSFormat - Class in io.scif.formats
Reader is the file format reader for Encapsulated PostScript (EPS) files.
EPSFormat() - Constructor for class io.scif.formats.EPSFormat
 
EPSFormat.EPSTranslator - Class in io.scif.formats
Necessary dummy translator, so that an EPS-OMEXML translator can be used.
EPSFormat.Metadata - Class in io.scif.formats
 
EPSFormat.Parser - Class in io.scif.formats
 
EPSFormat.Reader - Class in io.scif.formats
 
EPSFormat.Writer - Class in io.scif.formats
 
EPSTranslator() - Constructor for class io.scif.formats.EPSFormat.EPSTranslator
 
EPSTranslator - Class in io.scif.ome.translators
Container class for translators between OME and EPS formats.
EPSTranslator() - Constructor for class io.scif.ome.translators.EPSTranslator
 
EPSTranslator.OMEEPSTranslator - Class in io.scif.ome.translators
Translator class from EPSFormat.Metadata to OMEMetadata.
epxDiv - Variable in class io.scif.lifesci.SDTInfo
 
equals(Object) - Method in class io.scif.common.Region
Deprecated.
 
equals(Object) - Method in class io.scif.formats.tiff.TiffRational
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class io.scif.img.cell.SCIFIOCell
Two SCIFIOCells are equal iff they come from the same cache, with the same index, and have the same data state.
equals(Object) - Method in class io.scif.io.Location
 
equals(Object) - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Tests if the 'obj' object is the same filter as this one.
equals(Object) - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Tests if the 'obj' object is the same filter as this one.
equals(Object) - Method in class io.scif.media.imageioimpl.common.InvertedCMYKColorSpace
 
equals(Object) - Method in class io.scif.media.imageioimpl.common.SimpleCMYKColorSpace
 
err(String) - Method in class io.scif.cli.AbstractSCIFIOToolCommand
 
ERROR - Static variable in interface io.scif.jj2000.j2k.util.MsgLogger
Severity of message.
error(SAXParseException) - Method in class io.scif.xml.ParserErrorHandler
 
error(SAXParseException) - Method in class io.scif.xml.ValidationErrorHandler
 
ers - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
The error resilience specifications concerning the entropy decoder
ERS_SEG_SYMBOLS - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
The "segmentation symbols used" flag within Sers: 2
ERS_SOP - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
The "SOP marker segments used" flag within Sers: 1
escapeXML(String) - Method in class io.scif.xml.DefaultXMLService
 
escapeXML(String) - Method in interface io.scif.xml.XMLService
Escape special characters.
exec(String) - Method in class io.scif.common.ReflectedUniverse
Deprecated.
Executes a command in the universe.
EXIF - Static variable in class io.scif.formats.tiff.IFD
 
EXIF_VERSION - Static variable in class io.scif.formats.tiff.IFD
 
EXIF_VERSION_2_1 - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
An array of bytes containing the values {'0', '2', '1', '0'} to be used with the "EXIFVersion" tag to indicate EXIF version 2.1.
EXIF_VERSION_2_2 - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
An array of bytes containing the values {'0', '2', '2', '0'} to be used with the "EXIFVersion" tag to indicate EXIF version 2.2.
EXIFGPSTagSet - Class in io.scif.media.imageio.plugins.tiff
A class representing the tags found in an EXIF GPS Info IFD.
EXIFInteroperabilityTagSet - Class in io.scif.media.imageio.plugins.tiff
A class representing the tags found in an EXIF Interoperability IFD.
EXIFParentTIFFTagSet - Class in io.scif.media.imageio.plugins.tiff
A class containing the TIFF tags used to reference the EXIF and GPS IFDs.
EXIFTIFFTagSet - Class in io.scif.media.imageio.plugins.tiff
A class representing the tags found in an EXIF IFD.
exists() - Method in class io.scif.io.Location
Returns whether or not the pathname exists.
EXP - Static variable in class io.scif.codec.LosslessJPEGCodec
 
exp - Variable in class io.scif.jj2000.j2k.quantization.dequantizer.StdDequantizerParams
The quantization step "exponent" value, for each resolution level and subband, as it appears in the codestream.
expandCode(byte[], int, short, int) - Method in class io.scif.media.imageioimpl.common.LZWStringTable
If expanded data doesnt fit into array only what will fit is written to buf and the return value indicates how much of the expanded code has been written to the buf.
EXPOSURE_BIAS_VALUE - Static variable in class io.scif.formats.tiff.IFD
 
EXPOSURE_INDEX - Static variable in class io.scif.formats.tiff.IFD
 
EXPOSURE_MODE - Static variable in class io.scif.formats.tiff.IFD
 
EXPOSURE_MODE_AUTO_BRACKET - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureMode" tag.
EXPOSURE_MODE_AUTO_EXPOSURE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureMode" tag.
EXPOSURE_MODE_MANUAL_EXPOSURE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureMode" tag.
EXPOSURE_PROGRAM - Static variable in class io.scif.formats.tiff.IFD
 
EXPOSURE_PROGRAM_ACTION_PROGRAM - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureProgram" tag.
EXPOSURE_PROGRAM_APERTURE_PRIORITY - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureProgram" tag.
EXPOSURE_PROGRAM_CREATIVE_PROGRAM - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureProgram" tag.
EXPOSURE_PROGRAM_LANDSCAPE_MODE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureProgram" tag.
EXPOSURE_PROGRAM_MANUAL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureProgram" tag.
EXPOSURE_PROGRAM_MAX_RESERVED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureProgram" tag.
EXPOSURE_PROGRAM_NORMAL_PROGRAM - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureProgram" tag.
EXPOSURE_PROGRAM_NOT_DEFINED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureProgram" tag.
EXPOSURE_PROGRAM_PORTRAIT_MODE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureProgram" tag.
EXPOSURE_PROGRAM_SHUTTER_PRIORITY - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "ExposureProgram" tag.
EXPOSURE_TIME - Static variable in class io.scif.formats.tiff.IFD
EXIF tags.
exposureTime - Variable in class io.scif.formats.MicromanagerFormat.Position
 
EXTRA_SAMPLES - Static variable in class io.scif.formats.tiff.IFD
 
EXTRA_SAMPLES_ASSOCIATED_ALPHA - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "ExtraSamples" tag.
EXTRA_SAMPLES_UNASSOCIATED_ALPHA - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "ExtraSamples" tag.
EXTRA_SAMPLES_UNSPECIFIED - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "ExtraSamples" tag.
extractFakeInfo(MetadataService, String) - Static method in class io.scif.formats.FakeFormat.FakeUtils
Parses the provided path and returns a mapping of all known key/value pairs that were discovered.
extractTilePartMarkSeg(short, RandomAccessIO, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
This method extracts a marker segment in a tile-part header and stores it into a byte buffer for the second pass.
extraLength - Variable in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
 
extraSamples - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The value of the ExtraSamples tag.

F

F_NUMBER - Static variable in class io.scif.formats.tiff.IFD
 
FacilityManager - Class in io.scif.jj2000.j2k.util
This class manages common facilities for mutithreading environments, It can register different facilities for each thread, and also a default one, so that they can be referred by static methods, while possibly having different ones for different threads.
FacilityManager() - Constructor for class io.scif.jj2000.j2k.util.FacilityManager
 
factory() - Method in class io.scif.img.cell.SCIFIOCellImg
 
FakeFormat - Class in io.scif.formats
FakeFormat is the file format reader for faking input data.
FakeFormat() - Constructor for class io.scif.formats.FakeFormat
 
FakeFormat.FakeTranslator - Class in io.scif.formats
Translator from Metadata to FakeFormat$Metadata.
FakeFormat.FakeUtils - Class in io.scif.formats
Helper methods for the Fake file format.
FakeFormat.Metadata - Class in io.scif.formats
Metadata class for Fake format.
FakeFormat.Parser - Class in io.scif.formats
Parser for Fake file format.
FakeFormat.Reader - Class in io.scif.formats
Reader for the Fake file format.
FakeTranslator() - Constructor for class io.scif.formats.FakeFormat.FakeTranslator
 
FakeUtils() - Constructor for class io.scif.formats.FakeFormat.FakeUtils
 
fastCodeSymbols(int, int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
This method performs the coding of the symbol 'bit', using context 'ctxt', 'n' times, using the MQ-coder speedup mode if possible.
fastDecodeSymbols(int[], int, int) - Method in class io.scif.jj2000.j2k.entropy.decoder.MQDecoder
Decodes 'n' symbols from the bit stream using the same context 'ctxt'.
fatalError(SAXParseException) - Method in class io.scif.xml.ParserErrorHandler
 
fatalError(SAXParseException) - Method in class io.scif.xml.ValidationErrorHandler
 
FaxTIFFTagSet - Class in io.scif.media.imageio.plugins.tiff
A class representing the extra tags found in a TIFF-F (RFC 2036) file.
FCS_DATA_IDENTIFIER - Static variable in class io.scif.lifesci.SDTInfo
For .sdt files created in FIFO mode (setup, data blocks = Decay, FCS, FIDA, FILDA & MCS curves for each used routing channel).
fcsDecayCalc - Variable in class io.scif.lifesci.SDTInfo
Bit 0 = 1 - decay curve calculated.
fcsPoints - Variable in class io.scif.lifesci.SDTInfo
No of FCS values.
fcsType - Variable in class io.scif.lifesci.SDTInfo
0 - linear FCS with log binning (100 bins/log) when bit 15 = 1 (0x8000) - Multi-Tau FCS where bits 14-0 = ktau parameter.
FCTLChunk() - Constructor for class io.scif.formats.APNGFormat.FCTLChunk
 
FDATChunk() - Constructor for class io.scif.formats.APNGFormat.FDATChunk
 
fidaPoints - Variable in class io.scif.lifesci.SDTInfo
No of FIDA values.
fidaTime - Variable in class io.scif.lifesci.SDTInfo
Interval time [ms] for FIDA histogram.
Field - Annotation Type in io.scif
Field annotation.
FieldPrinter - Class in io.scif
This class can be used as a flag to ensure all SCIFIO components are printed in a consistent manner via their toString methods.
FieldPrinter(Object) - Constructor for class io.scif.FieldPrinter
 
FIFO_IMAGE_MODE - Static variable in class io.scif.lifesci.SDTInfo
 
fifoTyp - Variable in class io.scif.lifesci.SDTInfo
 
fildaPoints - Variable in class io.scif.lifesci.SDTInfo
No of FILDA values.
fildaTime - Variable in class io.scif.lifesci.SDTInfo
Interval time [ms] for FILDA histogram.
FILE_SOURCE - Static variable in class io.scif.formats.tiff.IFD
 
FILE_SOURCE_DSC - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "FileSource" tag.
FILE_TYPE_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
FileBitstreamReaderAgent - Class in io.scif.jj2000.j2k.codestream.reader
This class reads the bit stream (with the help of HeaderDecoder for tile headers and PktDecoder for packets header and body) and retrives location of all code-block's codewords.
FileBitstreamReaderAgent(HeaderDecoder, RandomAccessIO, DecoderSpecs, J2KImageReadParamJava, boolean, HeaderInfo) - Constructor for class io.scif.jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
Reads all tiles headers and keep offset of their first packet.
FileChannelImageInputStream - Class in io.scif.media.imageio.stream
A class which implements ImageInputStream using a FileChannel as the eventual data source.
FileChannelImageInputStream(FileChannel) - Constructor for class io.scif.media.imageio.stream.FileChannelImageInputStream
Constructs a FileChannelImageInputStream from a FileChannel.
FileChannelImageOutputStream - Class in io.scif.media.imageio.stream
A class which implements ImageOutputStream using a FileChannel as the eventual data destination.
FileChannelImageOutputStream(FileChannel) - Constructor for class io.scif.media.imageio.stream.FileChannelImageOutputStream
Constructs a FileChannelImageOutputStream from a FileChannel.
FileCodestreamWriter - Class in io.scif.jj2000.j2k.codestream.writer
This class implements a CodestreamWriter for Java streams.
FileCodestreamWriter(File, int) - Constructor for class io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
Opens the file 'file' for writing the bit stream, using the 'he' header encoder.
FileCodestreamWriter(String, int) - Constructor for class io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
Opens the file named 'fname' for writing the bit stream, using the 'he' header encoder.
FileCodestreamWriter(OutputStream, int) - Constructor for class io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
Uses the output stream 'os' for writing the bit stream, using the 'he' header encoder.
FileFormatBoxes - Interface in io.scif.jj2000.j2k.fileformat
This class contains all the markers used in the JPEG 2000 Part I file format
FileFormatReader - Class in io.scif.jj2000.j2k.fileformat.reader
This class reads the file format wrapper that may or may not exist around a valid JPEG 2000 codestream.
FileFormatReader(RandomAccessIO, J2KMetadata) - Constructor for class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
The constructor of the FileFormatReader
FileFormatWriter - Class in io.scif.jj2000.j2k.fileformat.writer
This class writes the file format wrapper that may or may not exist around a valid JPEG 2000 codestream.
FileFormatWriter(File, ImageOutputStream, int, int, int, int[], int, ColorModel, SampleModel, J2KMetadata) - Constructor for class io.scif.jj2000.j2k.fileformat.writer.FileFormatWriter
The constructor of the FileFormatWriter.
fileGroupOption(String) - Method in class io.scif.AbstractGroupable
 
fileGroupOption(String) - Method in class io.scif.filters.AbstractReaderFilter
 
fileGroupOption(String) - Method in class io.scif.formats.DICOMFormat.Parser
 
fileGroupOption(String) - Method in class io.scif.formats.MicromanagerFormat.Parser
 
fileGroupOption(String) - Method in class io.scif.formats.NRRDFormat.Parser
 
fileGroupOption(String) - Method in class io.scif.formats.NRRDFormat.Reader
 
fileGroupOption(String) - Method in interface io.scif.Groupable
Returns an int indicating that we cannot, must, or might group the files in a given dataset.
fileGroupOption(String) - Method in class io.scif.ome.formats.OMETIFFFormat.Parser
 
FileHandle - Class in io.scif.io
A wrapper for RandomAccessFile that implements the IRandomAccess interface.
FileHandle(File, String) - Constructor for class io.scif.io.FileHandle
Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.
FileHandle(String, String) - Constructor for class io.scif.io.FileHandle
Creates a random access file stream to read from, and optionally to write to, a file with the specified name.
FileInfo - Class in io.scif
Encompasses basic metadata about a file.
FileInfo() - Constructor for class io.scif.FileInfo
 
filename - Variable in class io.scif.FileInfo
Absolute path to this file.
fileNameMap - Variable in class io.scif.formats.MicromanagerFormat.Position
 
FilePattern - Class in io.scif
FilePattern is a collection of methods for handling file patterns, a way of succinctly representing a collection of files meant to be part of the same data series.
FilePattern(Context, Location) - Constructor for class io.scif.FilePattern
Creates a pattern object using the given file as a template.
FilePattern(Context, String, String) - Constructor for class io.scif.FilePattern
Creates a pattern object using the given filename and directory path as a template.
FilePattern(Context, String) - Constructor for class io.scif.FilePattern
Creates a pattern object for files with the given pattern string.
filePattern() - Method in class io.scif.SCIFIO
Gets this application context's FilePatternService.
FilePatternBlock - Class in io.scif
FilePatternBlock represents a single block in a FilePattern.
FilePatternBlock(String) - Constructor for class io.scif.FilePatternBlock
 
FilePatternService - Interface in io.scif.services
A collection of utility methods to facilitate FilePattern use.
FileStitcher - Class in io.scif.filters
Logic to stitch together files with similar names.
FileStitcher() - Constructor for class io.scif.filters.FileStitcher
Constructs a FileStitcher around a new image reader.
FileStitcher(boolean) - Constructor for class io.scif.filters.FileStitcher
Constructs a FileStitcher with the given reader.
FileTypeBox - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is defined to represent a File Type Box of JPEG JP2 file format.
FileTypeBox(int, int, int[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.FileTypeBox
Constructs a FileTypeBox from the provided brand, minor version and compatibility list.
FileTypeBox(byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.FileTypeBox
Constructs a FileTypeBox from the provided byte array.
FileTypeBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.FileTypeBox
Constructs a FileTypeBox from org.w3c.dom.Node.
FILL_ORDER - Static variable in class io.scif.formats.tiff.IFD
 
FILL_ORDER_LEFT_TO_RIGHT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "FillOrder" tag.
FILL_ORDER_RIGHT_TO_LEFT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "FillOrder" tag.
fillBasedOnBands(int, boolean, short[], short[], short[]) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Fills the channel definitions into the arrays based on the number of components and isPremultiplied.
fillBits - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
EOL padding flag: 1 if fill bits have been added before an EOL such that the EOL ends on a byte boundary, 0 otherwise.
fillInIFD(IFD) - Method in class io.scif.formats.tiff.TiffParser
Fill in IFD entries that are stored at an arbitrary offset.
FillOrder - Enum in io.scif.formats.tiff
Utility class for working with TIFF fill orders.
fillOrder - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
The logical order of bits within a byte.
Filter - Interface in io.scif.filters
Interface for modifying object behavior.
FILTER_53 - Static variable in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
The filter for lossless compression.
FILTER_97 - Static variable in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
The filter for lossy compression.
FILTER_SPEC_COMP_DEF - Static variable in class io.scif.jj2000.j2k.wavelet.WTFilterSpec
The identifier for "component default" specified filters
FILTER_SPEC_MAIN_DEF - Static variable in class io.scif.jj2000.j2k.wavelet.WTFilterSpec
The identifier for "main default" specified filters
FILTER_SPEC_TILE_COMP - Static variable in class io.scif.jj2000.j2k.wavelet.WTFilterSpec
The identifier for "tile and component specific" specified filters
FILTER_SPEC_TILE_DEF - Static variable in class io.scif.jj2000.j2k.wavelet.WTFilterSpec
The identifier for "tile specific default" specified filters
filterType() - Method in class io.scif.filters.ChannelFillerMetadata
 
filterType() - Method in class io.scif.filters.DimensionSwapperMetadata
 
filterType() - Method in interface io.scif.filters.MetadataWrapper
 
filterType() - Method in class io.scif.filters.PlaneSeparatorMetadata
 
FilterTypes - Interface in io.scif.jj2000.j2k.wavelet
This interface defines the identifiers for the different types of filters that are supported.
finalize() - Method in class io.scif.jj2000.j2k.entropy.decoder.StdEntropyDecoder
Prints the timing information, if collected, and calls 'finalize' on the super class.
finalize() - Method in class io.scif.jj2000.j2k.entropy.encoder.EBCOTRateAllocator
Prints the timing information, if collected, and calls 'finalize' on the super class.
finalize() - Method in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Prints the timing information, if collected, and calls 'finalize' on the super class.
finalize() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
finalize() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
finalize() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
FindCharString(short, byte) - Method in class io.scif.media.imageioimpl.common.LZWStringTable
 
findColorIndex(PaletteBuilder.ColorNode, Color) - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
findDimensionList(String) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
findDimensionList(String) - Method in interface io.scif.ome.services.OMEMetadataService
Converts the given String to a list of AxisTypes suitable for Metadata construction.
findDimensionOrder(Metadata, int) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
findDimensionOrder(ImageMetadata) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
findDimensionOrder(Metadata, int) - Method in interface io.scif.ome.services.OMEMetadataService
Extracts a standard 5-D dimension order from an N-dimensional ImageMetadata object.
findDimensionOrder(ImageMetadata) - Method in interface io.scif.ome.services.OMEMetadataService
Extracts a standard 5-D dimension order from an N-dimensional ImageMetadata object.
findImagePatterns(String) - Method in class io.scif.services.DefaultFilePatternService
 
findImagePatterns(String, String, String[]) - Method in class io.scif.services.DefaultFilePatternService
 
findImagePatterns(String) - Method in interface io.scif.services.FilePatternService
Finds the list of names matching the provided base and generates all patterns that match the list.
findImagePatterns(String, String, String[]) - Method in interface io.scif.services.FilePatternService
Generates a list of all the patterns that match the provided list of file names.
findPaletteEntry(PaletteBuilder.ColorNode, int, byte[], byte[], byte[]) - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
findPattern(String) - Method in class io.scif.filters.FileStitcher
Constructs a new FilePattern around the pattern extracted from the given id.
findPattern(String) - Method in class io.scif.services.DefaultFilePatternService
 
findPattern(Location) - Method in class io.scif.services.DefaultFilePatternService
 
findPattern(File) - Method in class io.scif.services.DefaultFilePatternService
 
findPattern(String, String) - Method in class io.scif.services.DefaultFilePatternService
 
findPattern(String, String, String[]) - Method in class io.scif.services.DefaultFilePatternService
 
findPattern(String, String, String[], int[]) - Method in class io.scif.services.DefaultFilePatternService
 
findPattern(String[]) - Method in class io.scif.services.DefaultFilePatternService
 
findPattern(String) - Method in interface io.scif.services.FilePatternService
Identifies the group pattern from a given file within that group.
findPattern(Location) - Method in interface io.scif.services.FilePatternService
Identifies the group pattern from a given file within that group.
findPattern(File) - Method in interface io.scif.services.FilePatternService
Identifies the group pattern from a given file within that group.
findPattern(String, String) - Method in interface io.scif.services.FilePatternService
Identifies the group pattern from a given file within that group.
findPattern(String, String, String[]) - Method in interface io.scif.services.FilePatternService
Identifies the group pattern from a given file within that group.
findPattern(String, String, String[], int[]) - Method in interface io.scif.services.FilePatternService
Identifies the group pattern from a given file within that group.
findPattern(String[]) - Method in interface io.scif.services.FilePatternService
Generate a pattern from a list of file names.
findPatterns(String) - Method in class io.scif.filters.FileStitcher
Finds the file pattern for the given ID, based on the state of the file stitcher.
findString(String...) - Method in class io.scif.bf.wrapper.RandomAccessInputStreamWrapper
 
findString(boolean, String...) - Method in class io.scif.bf.wrapper.RandomAccessInputStreamWrapper
 
findString(int, String...) - Method in class io.scif.bf.wrapper.RandomAccessInputStreamWrapper
 
findString(boolean, int, String...) - Method in class io.scif.bf.wrapper.RandomAccessInputStreamWrapper
 
findString(String...) - Method in class io.scif.common.RandomAccessInputStreamWrapper
Deprecated.
 
findString(boolean, String...) - Method in class io.scif.common.RandomAccessInputStreamWrapper
Deprecated.
 
findString(int, String...) - Method in class io.scif.common.RandomAccessInputStreamWrapper
Deprecated.
 
findString(boolean, int, String...) - Method in class io.scif.common.RandomAccessInputStreamWrapper
Deprecated.
 
findString(String...) - Method in class io.scif.io.NIOInputStream
Reads a string ending with one of the given terminating substrings.
findString(boolean, String...) - Method in class io.scif.io.NIOInputStream
Reads or skips a string ending with one of the given terminating substrings.
findString(int, String...) - Method in class io.scif.io.NIOInputStream
Reads a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(boolean, int, String...) - Method in class io.scif.io.NIOInputStream
Reads or skips a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(String...) - Method in class io.scif.io.RandomAccessInputStream
Reads a string ending with one of the given terminating substrings.
findString(boolean, String...) - Method in class io.scif.io.RandomAccessInputStream
Reads or skips a string ending with one of the given terminating substrings.
findString(int, String...) - Method in class io.scif.io.RandomAccessInputStream
Reads a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(boolean, int, String...) - Method in class io.scif.io.RandomAccessInputStream
Reads or skips a string ending with one of the given terminating substrings, using the specified block size for buffering.
findTranslator(Metadata, Metadata, boolean) - Method in class io.scif.services.DefaultTranslatorService
 
findTranslator(Class<? extends Metadata>, Class<? extends Metadata>, boolean) - Method in class io.scif.services.DefaultTranslatorService
 
findTranslator(Metadata, Metadata, boolean) - Method in interface io.scif.services.TranslatorService
Returns a translator capable of translating from the source Metadata to the dest Metadata type, or null if no such Translator exists.
findTranslator(Class<? extends Metadata>, Class<? extends Metadata>, boolean) - Method in interface io.scif.services.TranslatorService
Returns a translator capable of translating from the source Metadata to the dest Metadata type, or null if no such Translator exists.
finishLengthCalculation(int[], int) - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Terminates the calculation of the required length for each coding pass.
FIRST_BYPASS_PASS_IDX - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The index of the first "raw" pass, if bypass mode is on.
FITSFormat - Class in io.scif.formats
FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
FITSFormat() - Constructor for class io.scif.formats.FITSFormat
 
FITSFormat.Metadata - Class in io.scif.formats
 
FITSFormat.Parser - Class in io.scif.formats
 
FITSFormat.Reader - Class in io.scif.formats
 
flags - Variable in class io.scif.lifesci.SDTInfo
Scan clocks bits 2-0 (frame, line, pixel), rates_read - bit 15.
FLASH - Static variable in class io.scif.formats.tiff.IFD
 
FLASH_DID_NOT_FIRE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Flash" tag, indicating that the flash did not fire.
FLASH_ENERGY - Static variable in class io.scif.formats.tiff.IFD
 
FLASH_FIRED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Flash" tag, indicating that the flash fired, but the strobe return status is unknown.
FLASH_MASK_FIRED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A mask to be used with the "Flash" tag, indicating that the flash fired.
FLASH_MASK_FUNCTION_NOT_PRESENT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A mask to be used with the "Flash" tag, indicating no flash function present.
FLASH_MASK_MODE_AUTO - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A mask to be used with the "Flash" tag, indicating auto mode.
FLASH_MASK_MODE_FLASH_FIRING - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A mask to be used with the "Flash" tag, indicating compulsory flash firing mode.
FLASH_MASK_MODE_FLASH_SUPPRESSION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A mask to be used with the "Flash" tag, indicating compulsory flash suppression mode.
FLASH_MASK_RED_EYE_REDUCTION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A mask to be used with the "Flash" tag, indicating red-eye reduction supported.
FLASH_MASK_RETURN_DETECTED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A mask to be used with the "Flash" tag, indicating strobe return light detected.
FLASH_MASK_RETURN_NOT_DETECTED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A mask to be used with the "Flash" tag, indicating strobe return light not detected.
FLASH_PIX_VERSION - Static variable in class io.scif.formats.tiff.IFD
 
FLASH_STROBE_RETURN_LIGHT_DETECTED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Flash" tag, indicating that the flash fired, and the strobe return light was detected.
FLASH_STROBE_RETURN_LIGHT_NOT_DETECTED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Flash" tag, indicating that the flash fired, but the strobe return light was not detected.
flattenIntoHashMap() - Method in class io.scif.common.IniList
Flattens all of the INI tables into a single HashMap whose keys are of the format "[table name] table key".
flbckX - Variable in class io.scif.lifesci.SDTInfo
 
flbckY - Variable in class io.scif.lifesci.SDTInfo
 
FLIM_DOMAIN - Static variable in class io.scif.util.FormatTools
Identifies the fluorescence-lifetime domain.
FLOAT - Static variable in class io.scif.util.FormatTools
Identifies the FLOAT data type used to store pixel values.
FloatArrayLoader - Class in io.scif.img.cell.loaders
SCIFIOArrayLoader implementation for FloatArray types.
FloatArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.FloatArrayLoader
 
floatsToBytes(float[], boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates an array of float values into an array of byte values.
floatToBytes(float, boolean) - Static method in class io.scif.common.DataTools
Deprecated.
Translates the float value into an array of four bytes.
floatValue() - Method in class io.scif.formats.tiff.TiffRational
Returns the value of the specified number as a float.
FLOW_DATA_IDENTIFIER - Static variable in class io.scif.lifesci.SDTInfo
For .sdt files created automatically in Continuous Flow mode measurement (no setup, only data).
flush() - Method in class io.scif.io.RandomAccessOutputStream
 
flush() - Method in interface io.scif.jj2000.j2k.io.BinaryDataOutput
Any data that has been buffered must be written, and the stream should be realigned at the byte level.
flush() - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Any data that has been buffered must be written (including buffering at the bit level), and the stream should be realigned at the byte level.
flush() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Does nothing since this class does not implement data output.
flush() - Method in interface io.scif.jj2000.j2k.util.MsgLogger
Writes any buffered data from the println() method to the device.
flush() - Method in class io.scif.jj2000.j2k.util.StreamMsgLogger
Writes any buffered data from the print() and println() methods to the device.
flush() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
flush() - Method in class io.scif.media.imageioimpl.common.BitFile
 
flush() - Method in class io.scif.media.imageioimpl.common.LZWCompressor
Indicate to compressor that no more data to go so write out any remaining buffered data.
flush() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
A null operation as writing is not supported.
flush() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
flushBefore(long) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
FOCAL_LENGTH - Static variable in class io.scif.formats.tiff.IFD
 
FOCAL_LENGTH_35MM_FILM - Static variable in class io.scif.formats.tiff.IFD
 
FOCAL_PLANE_RESOLUTION_UNIT - Static variable in class io.scif.formats.tiff.IFD
 
FOCAL_PLANE_RESOLUTION_UNIT_CENTIMETER - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "FocalPlaneXResolution" tag.
FOCAL_PLANE_RESOLUTION_UNIT_INCH - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "FocalPlaneXResolution" tag.
FOCAL_PLANE_RESOLUTION_UNIT_NONE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "FocalPlaneResolutionUnit" tag.
FOCAL_PLANE_X_RESOLUTION - Static variable in class io.scif.formats.tiff.IFD
 
FOCAL_PLANE_Y_RESOLUTION - Static variable in class io.scif.formats.tiff.IFD
 
Format - Interface in io.scif
Interface for all SCIFIO formats.
format() - Method in class io.scif.SCIFIO
Gets this application context's FormatService.
formatDate(String, String) - Static method in class io.scif.common.DateTools
Formats the given date as an ISO 8601 date.
formatDate(String, String, boolean) - Static method in class io.scif.common.DateTools
Formats the given date as an ISO 8601 date.
formatDate(String, String[]) - Static method in class io.scif.common.DateTools
Formats the given date as an ISO 8601 date.
formatDate(String, String[], boolean) - Static method in class io.scif.common.DateTools
Formats the given date as an ISO 8601 date.
FormatException - Exception in io.scif
FormatException is the exception thrown when something goes wrong performing a file format operation.
FormatException() - Constructor for exception io.scif.FormatException
 
FormatException(String) - Constructor for exception io.scif.FormatException
 
FormatException(String, Throwable) - Constructor for exception io.scif.FormatException
 
FormatException(Throwable) - Constructor for exception io.scif.FormatException
 
FormatFileFilter - Class in io.scif.gui
A file filter for identifying the files supported by an associated Formats.
FormatFileFilter(Format) - Constructor for class io.scif.gui.FormatFileFilter
Constructs a new filter that accepts files of the given format's type.
FormatService - Interface in io.scif.services
A collection of methods for finding Format instances given a child class, discovering available formats, and managing the list of available formats.
FormatTools - Class in io.scif.util
A collection of constants and utility methods applicable for all cycles of image processing within SCIFIO.
FORW_ICT - Static variable in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Identifier for the Forward Irreversible Component Transformation (FORW_ICT).
FORW_RCT - Static variable in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Identifier for the Forward Reversible Component Transformation (FORW_RCT).
ForwardWT - Class in io.scif.jj2000.j2k.wavelet.analysis
This abstract class represents the forward wavelet transform functional block.
ForwardWT(ImgData) - Constructor for class io.scif.jj2000.j2k.wavelet.analysis.ForwardWT
Initializes this object for the specified number of tiles 'nt' and components 'nc'.
ForwCompTransf - Class in io.scif.jj2000.j2k.image.forwcomptransf
This class apply component transformations to the tiles depending on user specifications.
ForwCompTransf(BlkImgDataSrc, J2KImageWriteParamJava) - Constructor for class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Constructs a new ForwCompTransf object that operates on the specified source of image data.
ForwCompTransfSpec - Class in io.scif.jj2000.j2k.image.forwcomptransf
This class extends CompTransfSpec class in order to hold encoder specific aspects of CompTransfSpec.
ForwCompTransfSpec(int, int, byte, AnWTFilterSpec, J2KImageWriteParamJava, String) - Constructor for class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransfSpec
Constructs a new 'ForwCompTransfSpec' for the specified number of components and tiles and the arguments of optName option.
ForwWT - Interface in io.scif.jj2000.j2k.wavelet.analysis
This interface extends the WaveletTransform with the specifics of forward wavelet transforms.
ForwWTDataProps - Interface in io.scif.jj2000.j2k.wavelet.analysis
This interface extends the ImgData interface with methods that are necessary for forward wavelet data (i.e.
ForwWTFull - Class in io.scif.jj2000.j2k.wavelet.analysis
This class implements the ForwardWT with the full-page approach to be used either with integer or floating-point filters
ForwWTFull(BlkImgDataSrc, J2KImageWriteParamJava, int, int) - Constructor for class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Initializes this object with the given source of image data and with all the decompositon parameters
frame - Variable in class io.scif.formats.imaris.PipelineImage
 
FREE_BYTE_COUNTS - Static variable in class io.scif.formats.tiff.IFD
 
FREE_OFFSETS - Static variable in class io.scif.formats.tiff.IFD
 
freeTree(PaletteBuilder.ColorNode) - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
FREQUENCY - Static variable in class io.scif.img.axes.SCIFIOAxes
Identifies the Frequency dimensional type, representing a dimension consisting of frequencies.
fromCIEXYZ(float[]) - Method in class io.scif.gui.TwoChannelColorSpace
 
fromCIEXYZ(float[]) - Method in class io.scif.media.imageioimpl.common.BogusColorSpace
 
fromCIEXYZ(float[]) - Method in class io.scif.media.imageioimpl.common.InvertedCMYKColorSpace
 
fromCIEXYZ(float[]) - Method in class io.scif.media.imageioimpl.common.SimpleCMYKColorSpace
 
FromOMETranslator<M extends Metadata> - Class in io.scif.ome.translators
Abstract base class for all io.scif.Translators that translate from an OMEMetadata object.
FromOMETranslator() - Constructor for class io.scif.ome.translators.FromOMETranslator
 
fromRGB(float[]) - Method in class io.scif.gui.TwoChannelColorSpace
 
fromRGB(float, float, float, float[]) - Method in class io.scif.media.imageio.plugins.tiff.TIFFColorConverter
Converts an RGB triple into the native color space of this TIFFColorConverter, and stores the result in the first three entries of the result array.
fromRGB(float[]) - Method in class io.scif.media.imageioimpl.common.BogusColorSpace
 
fromRGB(float[]) - Method in class io.scif.media.imageioimpl.common.InvertedCMYKColorSpace
 
fromRGB(float[]) - Method in class io.scif.media.imageioimpl.common.SimpleCMYKColorSpace
 
fromRGB(float, float, float, float[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFCIELabColorConverter
 
fromRGB(float, float, float, float[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
FT_BR - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
File Type Fields
ftpIdx - Variable in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
The index of the first truncation point returned

G

gain - Variable in class io.scif.formats.MicromanagerFormat.Position
 
GAIN_CONTROL - Static variable in class io.scif.formats.tiff.IFD
 
GAIN_CONTROL_HIGH_GAIN_DOWN - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "GainControl" tag.
GAIN_CONTROL_HIGH_GAIN_UP - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "GainControl" tag.
GAIN_CONTROL_LOW_GAIN_DOWN - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "GainControl" tag.
GAIN_CONTROL_LOW_GAIN_UP - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "GainControl" tag.
GAIN_CONTROL_NONE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "GainControl" tag.
GAMMA - Static variable in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
The value of the third lifting step coefficient
GAMMA - Static variable in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
The value of the third lifting step coefficient
gammaBlue - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
gammaGreen - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
gammaRed - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
gb - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Number of guard bits off all component in the current tile.
gbs - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
Number of guard bits specifications
gcd(int, int) - Static method in class io.scif.jj2000.j2k.util.MathUtil
Method that calculates the Greatest Common Divisor (GCD) of two positive integer numbers.
gcd(int[]) - Static method in class io.scif.jj2000.j2k.util.MathUtil
Method that calculates the Greatest Common Divisor (GCD) of several positive integer numbers.
GEL_DOMAIN - Static variable in class io.scif.util.FormatTools
Identifies the gel and blot imaging domain.
GeoTIFFTagSet - Class in io.scif.media.imageio.plugins.tiff
A class representing the tags found in a GeoTIFF IFD.
get(int) - Method in class io.scif.AbstractMetadata
 
get(int) - Method in class io.scif.codec.ByteVector
 
get(int) - Static method in enum io.scif.codec.CompressionType
Retrieves the compression by reverse lookup of its "code".
get(int) - Static method in enum io.scif.codec.JPEG2000BoxType
Retrieves the box type by reverse lookup of its "code".
get(int) - Static method in enum io.scif.codec.JPEG2000SegmentMarker
Retrieves the segment marker by reverse lookup of its "code".
get() - Method in class io.scif.formats.DICOMFormat.DICOMTag
 
get(String) - Method in class io.scif.formats.ICSFormat.Metadata
Convenience method to directly access the hashtable.
get(int) - Static method in enum io.scif.formats.tiff.FillOrder
Retrieves a fill order by reverse lookup of its "code".
get(int) - Static method in enum io.scif.formats.tiff.IFDType
Retrieves a IFD type by reverse lookup of its "code".
get(int) - Method in class io.scif.formats.tiff.OnDemandLongArray
 
get(int) - Static method in enum io.scif.formats.tiff.PhotoInterp
Retrieves a photometric interpretation by reverse lookup of its "code".
get(int) - Static method in enum io.scif.formats.tiff.ResolutionUnit
Retrieves a resolution unit by reverse lookup of its "code".
get(int) - Static method in enum io.scif.formats.tiff.TiffCompression
Retrieves a TIFF compression instance by code.
get(int) - Method in class io.scif.img.cell.SCIFIOCellCache
Returns the SCIFIOCell at the specified index from this cache, or null if index has not been loaded yet.
get(int) - Method in interface io.scif.Metadata
Returns the ImageMetadata at the specified image within this dataset.
get8BitLookupTable(ColorModel) - Static method in class io.scif.gui.AWTImageTools
Converts an IndexColorModel to a 2D byte array.
getAbortRequest() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
This method wraps the protected method abortRequested to allow the abortions be monitored by J2KReadState.
getAbortRequest() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
This method wraps the protected method abortRequested to allow the abortions be monitored by J2KRenderedImage.
getAbortRequest() - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
This method wraps the protected method abortRequested to allow the abortions be monitored by J2KReadState.
getAbsoluteFile() - Method in class io.scif.io.Location
 
getAbsolutePath() - Method in class io.scif.io.Location
 
getAct() - Method in class io.scif.formats.GIFFormat.Metadata
 
getActl() - Method in class io.scif.formats.APNGFormat.Metadata
 
getActualNbytes() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Return the actual number of read bytes.
getActualRate() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Return the actual decoding rate in bits per pixel.
getAdjustedOrder() - Method in class io.scif.AxisGuesser
Gets the adjusted dimension order.
getAdvancedImageUsedFiles(int, boolean) - Method in class io.scif.AbstractParser
 
getAdvancedImageUsedFiles(int, boolean) - Method in interface io.scif.Parser
Returns an array of FileInfo objects representing the files needed to open the current series.
getAdvancedUsedFiles(boolean) - Method in class io.scif.AbstractParser
 
getAdvancedUsedFiles(boolean) - Method in interface io.scif.Parser
Returns an array of FileInfo objects representing the files needed to open this dataset.
getAlignROI() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets alignROI
getAll() - Method in class io.scif.AbstractMetadata
 
getAll() - Method in interface io.scif.Metadata
Returns the list of ImageMetadata associated with this dataset.
getAllFormats() - Method in class io.scif.services.DefaultFormatService
 
getAllFormats() - Method in interface io.scif.services.FormatService
Returns a list of all Formats within this context.
getAllowedTagSets() - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageReadParam
Returns a List containing the allowed TIFFTagSet objects.
getAlpha(int) - Method in class io.scif.gui.Index16ColorModel
 
getAlpha(int) - Method in class io.scif.gui.SignedColorModel
 
getAlpha(Object) - Method in class io.scif.gui.SignedColorModel
 
getAlpha(int) - Method in class io.scif.gui.UnsignedIntColorModel
 
getAlpha(Object) - Method in class io.scif.gui.UnsignedIntColorModel
 
getAlphas() - Method in class io.scif.gui.Index16ColorModel
Return the array of alpha color components.
getAltCodec() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
 
getAltPlanes() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
 
getAnHighNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the negative support of the high-pass analysis filter.
getAnHighNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the negative support of the high-pass analysis filter.
getAnHighNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns the negative support of the high-pass analysis filter.
getAnHighNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns the negative support of the high-pass analysis filter.
getAnHighNegSupport() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the negative support of the high-pass analysis filter.
getAnHighPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the positive support of the high-pass analysis filter.
getAnHighPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the positive support of the high-pass analysis filter.
getAnHighPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns the positive support of the high-pass analysis filter.
getAnHighPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns the positive support of the high-pass analysis filter.
getAnHighPosSupport() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the positive support of the high-pass analysis filter.
getAnLowNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the negative support of the low-pass analysis filter.
getAnLowNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the negative support of the low-pass analysis filter.
getAnLowNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns the negative support of the low-pass analysis filter.
getAnLowNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns the negative support of the low-pass analysis filter.
getAnLowNegSupport() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the negative support of the low-pass analysis filter.
getAnLowPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the positive support of the low-pass analysis filter.
getAnLowPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the positive support of the low-pass analysis filter.
getAnLowPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns the positive support of the low-pass analysis filter.
getAnLowPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns the positive support of the low-pass analysis filter.
getAnLowPosSupport() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the positive support of the low-pass analysis filter.
getAnSubbandTree(int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.EntropyCoder
Returns a reference to the root of subband tree structure representing the subband decomposition for the specified tile-component.
getAnSubbandTree(int, int) - Method in class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
Returns a reference to the subband tree structure representing the subband decomposition for the specified tile-component.
getAnSubbandTree(int, int) - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
Returns a reference to the subband tree structure representing the subband decomposition for the specified tile-component.
getAnSubbandTree(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.analysis.ForwWTDataProps
Returns a reference to the root of subband tree structure representing the subband decomposition for the specified tile-component.
getAnSubbandTree(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns a reference to the subband tree structure representing the subband decomposition for the specified tile-component of the source.
getApproximationAccuracy() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
Returns ApproximationAccuracy.
getArrayAccess(ImgPlus<?>) - Method in class io.scif.img.DefaultImgUtilityService
Obtains array access instance backing the given img, if any.
getArrayAccess(ImgPlus<?>) - Method in interface io.scif.img.ImgUtilityService
Obtains array access instance backing the given img, if any.
getArrayConverter() - Method in class io.scif.img.converters.DefaultPlaneConverterService
 
getArrayConverter() - Method in interface io.scif.img.converters.PlaneConverterService
 
getArtifactId() - Method in class io.scif.app.SCIFIOApp
 
getAsBytes() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns the data as an uninterpreted array of bytes.
getAsChars() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns TIFFTag.TIFF_SHORT data as an array of chars (unsigned 16-bit integers).
getAsDouble(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns data in any format as a double.
getAsDoubles() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns TIFFTag.TIFF_DOUBLE data as an array of doubles (64-bit floating-point values).
getAsFloat(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns data in any format as a float.
getAsFloats() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns TIFFTag.TIFF_FLOAT data as an array of floats (32-bit floating-point values).
getAsInt(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns data in any format as an int.
getAsInts() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns TIFFTag.TIFF_SLONG data as an array of ints (signed 32-bit integers).
getAsLong(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns data in any format as a long.
getAsLongs() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns TIFFTag.TIFF_LONG or TIFF_IFD_POINTER data as an array of longs (signed 64-bit integers).
getAsMetadata() - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Converts the directory to a metadata object.
getAsNativeNode() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns the TIFFField as a node named either "TIFFField" or "TIFFIFD" as described in the TIFF native image metadata specification.
getAsRational(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns a TIFFTag.TIFF_RATIONAL data item as a two-element array of ints.
getAsRationals() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns TIFFTag.TIFF_RATIONAL data as an array of 2-element arrays of longs.
getAsShorts() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns TIFFTag.TIFF_SSHORT data as an array of shorts (signed 16-bit integers).
getAssociation() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Returns the association which associates a color channel to a color component in the color space of the image.
getAsSRational(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns a TIFFTag.TIFF_SRATIONAL data item as a two-element array of ints.
getAsSRationals() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns TIFFTag.TIFF_SRATIONAL data as an array of 2-element arrays of ints.
getAsString(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns a TIFFTag.TIFF_ASCII value as a String.
getAsTree(String) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
getAsTree(String) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getAsTree(String) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getAsTree(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getAsTree(String) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXMetadata
 
getAsTree(String) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
getAsTree(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getAsTree(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
getAsTree(String) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
getAttribute(Node, String) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Extracts the value of the attribute from name.
getAttribute(Node, String) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
getAttributeDataType(String, String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeDefaultValue(String, String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeDescription(String, String, Locale) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeEnumerations(String, String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeListMaxLength(String, String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeListMinLength(String, String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeMaxValue(String, String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeMinValue(String, String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeNames(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAttributeValueType(String, String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getAuthorLastName() - Method in class io.scif.formats.ICSFormat.Metadata
 
getAxes() - Method in class io.scif.AbstractImageMetadata
 
getAxes() - Method in class io.scif.formats.ICSFormat.Metadata
 
getAxes() - Method in interface io.scif.ImageMetadata
Returns an array of the types for axes associated with the specified image index.
getAxesLengths() - Method in class io.scif.AbstractImageMetadata
 
getAxesLengths(List<CalibratedAxis>) - Method in class io.scif.AbstractImageMetadata
 
getAxesLengths() - Method in interface io.scif.ImageMetadata
Returns an array of the lengths for axes associated with the specified image index.
getAxesLengths(List<CalibratedAxis>) - Method in interface io.scif.ImageMetadata
Returns an array of the lengths for axes in the provided AxisType list.
getAxesLengthsNonPlanar() - Method in class io.scif.AbstractImageMetadata
 
getAxesLengthsNonPlanar() - Method in interface io.scif.ImageMetadata
Returns an array of the lengths for the non-planar axes in this image.
getAxesLengthsPlanar() - Method in class io.scif.AbstractImageMetadata
 
getAxesLengthsPlanar() - Method in interface io.scif.ImageMetadata
Returns an array of the lengths for the planar axes in this image.
getAxesNonPlanar() - Method in class io.scif.AbstractImageMetadata
 
getAxesNonPlanar() - Method in interface io.scif.ImageMetadata
Returns an array of the AxisTypes that define the number of planes in the dataset.
getAxesPlanar() - Method in class io.scif.AbstractImageMetadata
 
getAxesPlanar() - Method in interface io.scif.ImageMetadata
Returns an array of the AxisTypes that, together, define the bounds of a single plane in the dataset.
getAxesSizes() - Method in class io.scif.formats.ICSFormat.Metadata
 
getAxis(AxisType) - Method in class io.scif.AbstractImageMetadata
 
getAxis(int) - Method in class io.scif.AbstractImageMetadata
 
getAxis(AxisType) - Method in interface io.scif.ImageMetadata
Returns the CalibratedAxis associated with the given type.
getAxis(int) - Method in interface io.scif.ImageMetadata
Gets the axis of the (zero-indexed) specified plane.
getAxisCount(int) - Method in class io.scif.AxisGuesser
Gets the number of axes in the pattern of the given type.
getAxisCountC() - Method in class io.scif.AxisGuesser
Gets the number of C axes in the pattern.
getAxisCountS() - Method in class io.scif.AxisGuesser
Gets the number of S axes in the pattern.
getAxisCountT() - Method in class io.scif.AxisGuesser
Gets the number of T axes in the pattern.
getAxisCountZ() - Method in class io.scif.AxisGuesser
Gets the number of Z axes in the pattern.
getAxisGlobalMaximum(int, AxisType, int) - Method in class io.scif.filters.MinMaxFilter
Retrieves a specified planar axis's global maximum.
getAxisGlobalMinimum(int, AxisType, int) - Method in class io.scif.filters.MinMaxFilter
Retrieves a specified planar axis's global minimum.
getAxisIndex(CalibratedAxis) - Method in class io.scif.AbstractImageMetadata
 
getAxisIndex(AxisType) - Method in class io.scif.AbstractImageMetadata
 
getAxisIndex(CalibratedAxis) - Method in interface io.scif.ImageMetadata
Returns the array index for the specified CalibratedAxis.
getAxisIndex(AxisType) - Method in interface io.scif.ImageMetadata
As ImageMetadata.getAxisIndex(CalibratedAxis) but only requires the AxisType of the desired axis.
getAxisKnownMaximum(int, AxisType, int) - Method in class io.scif.filters.MinMaxFilter
Retrieves the specified planar axis's maximum based on the images that have been read.
getAxisKnownMinimum(int, AxisType, int) - Method in class io.scif.filters.MinMaxFilter
Retrieves the specified planar axis's minimum based on the images that have been read.
getAxisLength(int) - Method in class io.scif.AbstractImageMetadata
 
getAxisLength(CalibratedAxis) - Method in class io.scif.AbstractImageMetadata
 
getAxisLength(AxisType) - Method in class io.scif.AbstractImageMetadata
 
getAxisLength(int) - Method in interface io.scif.ImageMetadata
Gets the length of the (zero-indexed) specified plane.
getAxisLength(CalibratedAxis) - Method in interface io.scif.ImageMetadata
A convenience method for looking up the length of an axis based on its type.
getAxisLength(AxisType) - Method in interface io.scif.ImageMetadata
As ImageMetadata.getAxisLength(CalibratedAxis) but only requires the AxisType of the desired axis.
getAxisType(String) - Static method in class io.scif.AxisGuesser
Returns a best guess of the given label's axis type.
getAxisTypes() - Method in class io.scif.AxisGuesser
Gets the guessed axis type for each dimensional block.
getBandSize(SampleModel) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
 
getBinData() - Method in class io.scif.ome.formats.OMEXMLFormat.Metadata
 
getBinDataOffsets() - Method in class io.scif.ome.formats.OMEXMLFormat.Metadata
 
getBinning(String) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
getBinning(String) - Method in interface io.scif.ome.services.OMEMetadataService
Retrieves an Binning enumeration value for the given String.
getBinOffset() - Method in class io.scif.lifesci.SDTFormat.Metadata
 
getBitDepth() - Method in class io.scif.formats.APNGFormat.IHDRChunk
 
getBitDepth() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.BitsPerComponentBox
Returns the bit depths for all the image components.
getBitDepth() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Returns the bit depth for all the image components.
getBitDepths() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
Return the bit depths for all the color components.
getBitOffset() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
getBits(int) - Method in class io.scif.codec.BitBuffer
Returns an int value representing the value of the bits read from the byte array, from the current position.
getBitsPerElement() - Method in class io.scif.img.cell.loaders.ByteArrayLoader
 
getBitsPerElement() - Method in class io.scif.img.cell.loaders.CharArrayLoader
 
getBitsPerElement() - Method in class io.scif.img.cell.loaders.DoubleArrayLoader
 
getBitsPerElement() - Method in class io.scif.img.cell.loaders.FloatArrayLoader
 
getBitsPerElement() - Method in class io.scif.img.cell.loaders.IntArrayLoader
 
getBitsPerElement() - Method in class io.scif.img.cell.loaders.LongArrayLoader
 
getBitsPerElement() - Method in interface io.scif.img.cell.loaders.SCIFIOArrayLoader
 
getBitsPerElement() - Method in class io.scif.img.cell.loaders.ShortArrayLoader
 
getBitsPerPixel() - Method in class io.scif.AbstractImageMetadata
 
getBitsPerPixel() - Method in class io.scif.formats.ICSFormat.Metadata
 
getBitsPerPixel() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
 
getBitsPerPixel() - Method in interface io.scif.ImageMetadata
Returns the number of valid bits per pixel.
getBitsPerPixel(int) - Static method in class io.scif.util.FormatTools
Retrieves how many bytes per pixel the current plane or section has.
getBitsPerSample() - Method in class io.scif.formats.tiff.IFD
Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given TIFF IFD.
getBlendOp() - Method in class io.scif.formats.APNGFormat.FCTLChunk
 
getBlock(int) - Method in class io.scif.FilePattern
Gets the specified numerical block.
getBlock() - Method in class io.scif.FilePatternBlock
 
getBlockAligned() - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
This function returns the blockAligned flag
getBlocks() - Method in class io.scif.FilePattern
Gets each numerical block.
getBlockSize() - Method in class io.scif.formats.GIFFormat.Metadata
 
getBlue() - Method in class io.scif.formats.APNGFormat.PLTEChunk
 
getBlue(int) - Method in class io.scif.gui.Index16ColorModel
 
getBlue(int) - Method in class io.scif.gui.SignedColorModel
 
getBlue(Object) - Method in class io.scif.gui.SignedColorModel
 
getBlue(int) - Method in class io.scif.gui.UnsignedIntColorModel
 
getBlue(Object) - Method in class io.scif.gui.UnsignedIntColorModel
 
getBlues() - Method in class io.scif.gui.Index16ColorModel
Return the array of blue color components.
getBmpBitsPerPixel() - Method in class io.scif.formats.AVIFormat.Metadata
 
getBmpColorsUsed() - Method in class io.scif.formats.AVIFormat.Metadata
 
getBmpCompression() - Method in class io.scif.formats.AVIFormat.Metadata
 
getBmpScanLineSize() - Method in class io.scif.formats.AVIFormat.Metadata
 
getBmpWidth() - Method in class io.scif.formats.AVIFormat.Metadata
 
getBounds() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns a Rectangle indicating the image bounds.
getBoxClass(int) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Returns the Box class for the box with the provided type.
getBranchIndex(Color, int) - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
getBrand() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.FileTypeBox
Returns the brand of this file type box.
getBuffer() - Method in class io.scif.jj2000.j2k.codestream.writer.BitOutputBuffer
Returns the byte buffer.
getBuffer() - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Returns the byte-buffer used to store the codestream header.
getBufferLength() - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Returns the number of bytes used in the codestream header's buffer.
getBufferSize() - Method in class io.scif.io.NIOFileHandle
Gets the current buffer size.
getBypass() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets bypass
getByte(int) - Method in class io.scif.jj2000.j2k.entropy.encoder.ByteOutputBuffer
Returns the byte buffered at the given position in the buffer.
getByteArrayElementValue(Node) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Gets the byte array from an IIOMetadataNode.
getByteBuffer() - Method in class io.scif.io.ByteArrayHandle
Gets the byte buffer backing this handle.
getByteElementValue(Node) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Gets its byte value from an IIOMetadataNode.
getByteInputBuffer() - Method in class io.scif.jj2000.j2k.entropy.decoder.MQDecoder
Returns the underlying 'ByteInputBuffer' from where the MQ coded input bytes are read.
getByteOrder() - Method in class io.scif.formats.ICSFormat.Metadata
 
getByteOrder() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
getByteOrdering() - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Returns the endianess (i.e., byte ordering) of the implementing class.
getByteOrdering() - Method in interface io.scif.jj2000.j2k.io.BinaryDataOutput
Returns the endianness (i.e., byte ordering) of the implementing class.
getByteOrdering() - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Returns the endianess (i.e., byte ordering) of the implementing class.
getByteOrdering() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Returns the endianess (i.e., byte ordering) of multi-byte I/O operations.
getByteOrdering() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
getBytes() - Method in class io.scif.BufferedImagePlane
Standardizes this plane's BufferedImage to a byte[].
getBytes() - Method in class io.scif.ByteArrayPlane
 
getBytes(BufferedImage) - Static method in class io.scif.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(WritableRaster) - Static method in class io.scif.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(WritableRaster, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(BufferedImage, boolean) - Static method in class io.scif.gui.AWTImageTools
Get the bytes from an image, merging the channels as necessary.
getBytes() - Method in class io.scif.io.ByteArrayHandle
Gets the byte array backing this FileHandle.
getBytes() - Method in interface io.scif.Plane
Gets this plane's standardized pixel data.
getBytesPerElement() - Method in enum io.scif.formats.tiff.IFDType
Retrieves the number of bytes per element.
getBytesPerLine() - Method in class io.scif.formats.PCXFormat.Metadata
 
getBytesPerPixel(int) - Static method in class io.scif.util.FormatTools
Retrieves how many bytes per pixel the current plane or section has.
getBytesPerPixel(String) - Static method in class io.scif.util.FormatTools
Retrieves the number of bytes per pixel in the current plane.
getBytesPerPlane() - Method in class io.scif.formats.AVIFormat.Metadata
 
getBytesPerSample() - Method in class io.scif.formats.tiff.IFD
Retrieves the image's bytes per sample (derived from tag BitsPerSample) from this IFD.
getCachedImageReader() - Method in class io.scif.bf.BioFormatsFormat
Gets a cached ImageReader, suitable for using for format checking or suffix generation.
getCachedListing(String) - Method in class io.scif.services.DefaultLocationService
 
getCachedListing(String) - Method in interface io.scif.services.LocationService
Returns the set of listings for the provided key.
getCacheId() - Method in class io.scif.img.cell.SCIFIOCell
 
getCacheId() - Method in class io.scif.img.cell.SCIFIOCellCache
 
getCalibrationUnit() - Method in class io.scif.formats.TIFFFormat.Metadata
 
getCanonicalFile() - Method in class io.scif.io.Location
 
getCanonicalPath() - Method in class io.scif.io.Location
Returns the canonical path to this file.
getCausalCXInfo() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets causalCXInfo
getCBlkHeight(byte, int, int) - Method in class io.scif.jj2000.j2k.entropy.CBlkSizeSpec
Returns the code-block height: for the specified tile/component for the specified tile for the specified component default value The value returned depends on the value of the variable 'type' which can take the following values : SPEC_DEF -> Default value is returned.
getCBlkHeight(int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.EntropyCoder
Returns the code-block height for the specified tile and component.
getCBlkHeight(int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Returns the code-block height for the specified tile and component.
getCBlkInfo() - Method in class io.scif.jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
Gets the reference to the CBlkInfo array
getCBlkWidth(byte, int, int) - Method in class io.scif.jj2000.j2k.entropy.CBlkSizeSpec
Returns the code-block width : for the specified tile/component for the specified tile for the specified component default value The value returned depends on the value of the variable 'type' which can take the following values :
SPEC_DEF -> Default value is returned.
getCBlkWidth(int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.EntropyCoder
Returns the code-block width for the specified tile and component.
getCBlkWidth(int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Returns the code-block width for the specified tile and component.
getCbULX() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the vertical code-block partition origin.
getCbULX() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the horizontal code-block partition origin.Allowable values are 0 and 1, nothing else.
getCbULX() - Method in class io.scif.jj2000.j2k.entropy.decoder.EntropyDecoder
Returns the horizontal code-block partition origin.
getCbULX() - Method in class io.scif.jj2000.j2k.entropy.encoder.EntropyCoder
Returns the horizontal offset of the code-block partition.
getCbULX() - Method in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
Returns the horizontal code-block partition origin.
getCbULX() - Method in class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
Returns the horizontal offset of the code-block partition.
getCbULX() - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
Returns the horizontal offset of the code-block partition.
getCbULX() - Method in class io.scif.jj2000.j2k.roi.ROIDeScaler
Returns the horizontal code-block partition origin.
getCbULX() - Method in interface io.scif.jj2000.j2k.wavelet.analysis.ForwWTDataProps
Returns the horizontal offset of the code-block partition.
getCbULX() - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the horizontal offset of the code-block partition.
getCbULX() - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.InvWTData
Returns the horizontal code-block partition origin.
getCbULY() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the vertical code-block partition origin.
getCbULY() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the vertical code-block partition origin.
getCbULY() - Method in class io.scif.jj2000.j2k.entropy.decoder.EntropyDecoder
Returns the vertical code-block partition origin.
getCbULY() - Method in class io.scif.jj2000.j2k.entropy.encoder.EntropyCoder
Returns the vertical offset of the code-block partition.
getCbULY() - Method in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
Returns the vertical code-block partition origin.
getCbULY() - Method in class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
Returns the vertical offset of the code-block partition.
getCbULY() - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
Returns the vertical offset of the code-block partition.
getCbULY() - Method in class io.scif.jj2000.j2k.roi.ROIDeScaler
Returns the vertical code-block partition origin.
getCbULY() - Method in interface io.scif.jj2000.j2k.wavelet.analysis.ForwWTDataProps
Returns the vertical offset of the code-block partition.
getCbULY() - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the vertical offset of the code-block partition.
getCbULY() - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.InvWTData
Returns the vertical code-block partition origin Allowable values are 0 and 1, nothing else.
getChannel() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Returns the defined channels.
getChannelNames() - Method in class io.scif.formats.ICSFormat.Metadata
 
getChannels() - Method in class io.scif.formats.TextFormat.Metadata
 
getChannels() - Method in class io.scif.lifesci.SDTFormat.Metadata
 
getCheckerClass() - Method in class io.scif.AbstractFormat
 
getCheckerClass() - Method in interface io.scif.Format
 
getChildNames(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getChildPolicy(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getCHUNK_SIGNATURE() - Method in class io.scif.formats.APNGFormat.APNGChunk
 
getChunkSizes() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
 
getCleanHash() - Method in class io.scif.img.cell.SCIFIOCell
 
getCode() - Method in enum io.scif.codec.CompressionType
Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum io.scif.codec.JPEG2000BoxType
Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum io.scif.codec.JPEG2000SegmentMarker
Implemented as specified by the CodedEnum I/F.
getCode() - Method in interface io.scif.enumeration.CodedEnum
Retrieves the integer "code" for this enumeration.
getCode() - Method in enum io.scif.formats.tiff.FillOrder
 
getCode() - Method in enum io.scif.formats.tiff.IFDType
 
getCode() - Method in enum io.scif.formats.tiff.PhotoInterp
 
getCode() - Method in enum io.scif.formats.tiff.ResolutionUnit
 
getCode() - Method in enum io.scif.formats.tiff.TiffCompression
 
getCodeBlock(int, int, int, SubbandSyn, int, int, DecLyrdCBlk) - Method in class io.scif.jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
Returns the specified coded code-block, for the specified component, in the current tile.
getCodeBlock(int, int, int, SubbandSyn, int, int, DecLyrdCBlk) - Method in interface io.scif.jj2000.j2k.entropy.decoder.CodedCBlkDataSrcDec
Returns the specified coded code-block, for the specified component, in the current tile.
getCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in class io.scif.jj2000.j2k.entropy.decoder.StdEntropyDecoder
Returns the specified code-block in the current tile for the specified component, as a copy (see below).
getCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in interface io.scif.jj2000.j2k.quantization.dequantizer.CBlkQuantDataSrcDec
Returns the specified code-block in the current tile for the specified component, as a copy (see below).
getCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in class io.scif.jj2000.j2k.quantization.dequantizer.StdDequantizer
Returns the specified code-block in the current tile for the specified component, as a copy (see below).
getCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in class io.scif.jj2000.j2k.roi.ROIDeScaler
Returns the specified code-block in the current tile for the specified component, as a copy (see below).
getCodeBlock(int, int, int, SubbandSyn, DataBlk) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.CBlkWTDataSrcDec
Returns the specified code-block in the current tile for the specified component, as a copy (see below).
getCodeBlockSize() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets codeBlockSize.
getCodeBlockSize() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets codeBlockSize
getCodec(Class<C>) - Method in interface io.scif.codec.CodecService
 
getCodec(Class<C>) - Method in class io.scif.codec.DefaultCodecService
 
getCodec() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
 
getCodecName() - Method in enum io.scif.formats.tiff.TiffCompression
Retrieves the name of the TIFF compression codec.
getCodecOptions() - Method in class io.scif.AbstractWriter
 
getCodecOptions() - Method in class io.scif.formats.tiff.TiffParser
Retrieves the current set of codec options being used to decompress pixel data.
getCodecOptions() - Method in interface io.scif.Writer
 
getCodeSegSymbol() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets codeSegSymbol
getCodestreamOffset() - Method in class io.scif.formats.JPEG2000Format.Parser
Retrieves the offset to the first contiguous codestream.
getCodestreamPixelType() - Method in class io.scif.formats.JPEG2000Format.Parser
Returns the pixel type as specified in the header.
getCodeStreamPos() - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method creates and returns an array of positions to contiguous codestreams in the file
getCodestreamSizeC() - Method in class io.scif.formats.JPEG2000Format.Parser
Returns the number of channels the image has as specified in the header.
getCodestreamSizeX() - Method in class io.scif.formats.JPEG2000Format.Parser
Returns the width of the image as specified in the header.
getCodestreamSizeY() - Method in class io.scif.formats.JPEG2000Format.Parser
Returns the height of the image as specified in the header.
getColorConverter() - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageReadParam
Returns the currently set TIFFColorConverter object, or null if none is set.
getColorConverter() - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageWriteParam
Returns the current TIFFColorConverter object that will be used to perform color conversion when writing the image, or null if none is set.
getColorModel() - Method in class io.scif.AbstractWriter
 
getColorModel() - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
Returns the color model created from the palette box.
getColorModel() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the ColorModel of the image.
getColorModel() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getColorModel() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getColorModel() - Method in interface io.scif.Writer
Gets the color model.
getColorTable() - Method in class io.scif.AbstractPlane
 
getColorTable(int, long) - Method in class io.scif.bf.BioFormatsFormat.Metadata
 
getColorTable(int, long) - Method in class io.scif.formats.AVIFormat.Metadata
 
getColorTable(int, long) - Method in class io.scif.formats.BMPFormat.Metadata
 
getColorTable(int, long) - Method in class io.scif.formats.DICOMFormat.Metadata
 
getColorTable(int, long) - Method in class io.scif.formats.FakeFormat.Metadata
Returns the current color table for this dataset
getColorTable(int, long) - Method in class io.scif.formats.GIFFormat.Metadata
 
getColorTable(int, long) - Method in class io.scif.formats.JPEG2000Format.Metadata
 
getColorTable(int, long) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
 
getColorTable(int, long) - Method in class io.scif.formats.PCXFormat.Metadata
 
getColorTable(int, long) - Method in class io.scif.formats.qt.PICTFormat.Metadata
 
getColorTable(int, long) - Method in class io.scif.formats.TIFFFormat.Metadata
 
getColorTable(int, long) - Method in class io.scif.formats.ZipFormat.Metadata
 
getColorTable(int, long) - Method in interface io.scif.HasColorTable
 
getColorTable(int, int) - Method in class io.scif.img.cell.SCIFIOCellImg
Returns the ColorTable of the specified image and plane index.
getColorTable(int) - Method in class io.scif.img.SCIFIOImgPlus
 
getColorTable(int, int) - Method in class io.scif.img.SCIFIOImgPlus
 
getColorTable(int, long) - Method in class io.scif.ome.formats.OMETIFFFormat.Metadata
 
getColorTable() - Method in interface io.scif.Plane
Gets this plane's ColorTable.
getColorTables() - Method in class io.scif.formats.GIFFormat.Metadata
 
getColourType() - Method in class io.scif.formats.APNGFormat.IHDRChunk
 
getComment() - Method in class io.scif.formats.tiff.IFD
Convenience method for obtaining the ImageDescription from this IFD.
getComment() - Method in class io.scif.formats.tiff.TiffParser
Convenience method for obtaining a stream's first ImageDescription.
getComments() - Method in class io.scif.formats.JPEG2000Format.Parser
Retrieves the list of comments stored in the file.
getCompanionFile() - Method in class io.scif.formats.TIFFFormat.Metadata
 
getCompanionFiles() - Method in class io.scif.formats.DICOMFormat.Metadata
 
getCompatibilityList() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.FileTypeBox
Returns the compatibilty list of this file type box.
getCompData(DataBlk, int) - Method in interface io.scif.jj2000.j2k.image.BlkImgDataSrc
Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component.
getCompData(DataBlk, int) - Method in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Apply forward component transformation associated with the current tile.
getCompData(DataBlk, int) - Method in class io.scif.jj2000.j2k.image.ImgDataConverter
Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component, using the 'transfer type' specified in the block given as argument.
getCompData(DataBlk, int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component.
getCompData(DataBlk, int) - Method in class io.scif.jj2000.j2k.image.input.ImgReaderPGM
Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component.
getCompData(DataBlk, int) - Method in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Apply inverse component transformation associated with the current tile.
getCompData(DataBlk, int) - Method in class io.scif.jj2000.j2k.image.Tiler
Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component.
getCompData(DataBlk, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTFull
Returns a block of image data containing the specifed rectangular area, in the specified component, as a copy (see below).
getCompData(DataBlk, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component.
getCompDef(int) - Method in class io.scif.jj2000.j2k.ModuleSpec
Gets default value of the specified component.
getCompHeight(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the height in pixels of the specified component in the current tile.
getCompImgHeight(int) - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
getCompImgHeight(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the height in pixels of the specified component in the overall image, for the given (component) resolution level.
getCompImgHeight(int) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the height in pixels of the specified component in the overall image.
getCompImgHeight(int) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the height in pixels of the specified component in the overall image.
getCompImgHeight(int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the height in pixels of the specified component in the overall image.
getCompImgHeight(int) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the height in pixels of the specified component in the overall image.
getCompImgHeight(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the height in pixels of the specified component in the overall image.
getCompImgHeight(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the height in pixels of the specified component in the overall image, for the given resolution level.
getCompImgHeight(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the height in pixels of the specified component in the overall image, for the given resolution level.
getCompImgHeight(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the height in pixels of the specified component in the overall image.
getCompImgWidth(int) - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
Width of the specified tile-component
getCompImgWidth(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the width in pixels of the specified component in the overall image, for the given (component) resolution level.
getCompImgWidth(int) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the width in pixels of the specified component in the overall image.
getCompImgWidth(int) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the width in pixels of the specified component in the overall image.
getCompImgWidth(int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the width in pixels of the specified component in the overall image.
getCompImgWidth(int) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the width in pixels of the specified component in the overall image.
getCompImgWidth(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the width in pixels of the specified component in the overall image.
getCompImgWidth(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the width in pixels of the specified component in the overall image, for the given resolution level.
getCompImgWidth(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the width in pixels of the specified component in the overall image, for the given resolution level.
getCompImgWidth(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the width in pixels of the specified component in the overall image.
getComponent() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
 
getComponentAssociation() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
 
getComponentTransformation() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets componentTransformation.
getComponentTransformation() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets componentTransformation
getComponentType() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
 
getCompression() - Method in class io.scif.AbstractWriter
 
getCompression() - Method in enum io.scif.codec.CompressionType
Returns the compression.
getCompression() - Method in class io.scif.formats.BMPFormat.Metadata
 
getCompression() - Method in class io.scif.formats.ICSFormat.Metadata
 
getCompression() - Method in class io.scif.formats.tiff.IFD
Retrieves the image's compression type (TIFF tag Compression) from this IFD.
getCompression() - Method in class io.scif.ome.formats.OMEXMLFormat.Metadata
 
getCompression() - Method in interface io.scif.Writer
 
getCompressionCodecOptions(IFD) - Method in enum io.scif.formats.tiff.TiffCompression
Creates a set of codec options for compression.
getCompressionCodecOptions(IFD, CodecOptions) - Method in enum io.scif.formats.tiff.TiffCompression
Creates a set of codec options for compression.
getCompressionMethod() - Method in class io.scif.formats.APNGFormat.IHDRChunk
 
getCompressionTagValue() - Method in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Retrieve the value to be assigned to the TIFF Compression tag in the TIFF image metadata.
getCompressionType() - Method in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Retrieve the name of the compression type supported by this compressor.
getCompressionType() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Returns the compression type.
getCompressionTypes() - Method in class io.scif.AbstractWriter
 
getCompressionTypes() - Method in interface io.scif.Writer
Gets the available compression types.
getCompSubsX(int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the component subsampling factor in the horizontal direction, for the specified component.
getCompSubsX(int) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the component sub-sampling factor, with respect to the reference grid, along the horizontal direction for the specified component.
getCompSubsX(int) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the component subsampling factor in the horizontal direction, for the specified component.
getCompSubsX(int) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the component subsampling factor in the horizontal direction, for the specified component.
getCompSubsX(int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the component subsampling factor in the horizontal direction, for the specified component.
getCompSubsX(int) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the component subsampling factor in the horizontal direction, for the specified component.
getCompSubsX(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the component subsampling factor in the horizontal direction, for the specified component.
getCompSubsX(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the component subsampling factor in the horizontal direction, for the specified component.
getCompSubsX(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the component subsampling factor in the horizontal direction, for the specified component.
getCompSubsX(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the component subsampling factor in the horizontal direction, for the specified component.
getCompSubsY(int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the component subsampling factor in the vertical direction, for the specified component.
getCompSubsY(int) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the component sub-sampling factor, with respect to the reference grid, along the vertical direction for the specified component.
getCompSubsY(int) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the component subsampling factor in the vertical direction, for the specified component.
getCompSubsY(int) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the component subsampling factor in the vertical direction, for the specified component.
getCompSubsY(int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the component subsampling factor in the vertical direction, for the specified component.
getCompSubsY(int) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the component subsampling factor in the vertical direction, for the specified component.
getCompSubsY(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the component subsampling factor in the vertical direction, for the specified component.
getCompSubsY(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the component subsampling factor in the vertical direction, for the specified component.
getCompSubsY(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the component subsampling factor in the vertical direction, for the specified component.
getCompSubsY(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the component subsampling factor in the vertical direction, for the specified component.
getCompULX(int) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the horizontal coordinate of the upper-left corner of the specified component in the current tile.
getCompULX(int) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the horizontal coordinate of the upper-left corner of the specified component in the current tile.
getCompULX(int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the horizontal coordinate of the upper-left corner of the specified component in the current tile.
getCompULX(int) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the horizontal coordinate of the upper-left corner of the specified component in the current tile.
getCompULX(int) - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the horizontal coordinate of the upper-left corner of the specified component in the current tile.
getCompULX(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the horizontal coordinate of the upper-left corner of the specified component in the current tile.
getCompULX(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the horizontal coordinate of the upper-left corner of the active tile, with respect to the canvas origin, in the component coordinates, for the specified component.
getCompULY(int) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the vertical coordinate of the upper-left corner of the specified component in the current tile.
getCompULY(int) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the vertical coordinate of the upper-left corner of the specified component in the current tile.
getCompULY(int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the vertical coordinate of the upper-left corner of the specified component in the current tile.
getCompULY(int) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the vertical coordinate of the upper-left corner of the specified component in the current tile.
getCompULY(int) - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the vertical coordinate of the upper-left corner of the specified component in the current tile.
getCompULY(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the vertical coordinate of the upper-left corner of the specified component in the current tile.
getCompULY(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the vertical coordinate of the upper-left corner of the active tile, with respect to the canvas origin, in the component coordinates, for the specified component.
getCompWidth(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the width in pixels of the specified component in the current tile.
getConfig() - Method in class io.scif.cli.commands.AbstractReaderCommand
 
getConstrainedLengths(Metadata, int, SCIFIOConfig) - Method in class io.scif.img.DefaultImgUtilityService
 
getConstrainedLengths(Metadata, int, SCIFIOConfig) - Method in interface io.scif.img.ImgUtilityService
Returns an N-dimensional list of axis lengths from the given Metadata, constrained by the provided SubRegion (if present)
getContainerSizeX() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getContainerSizeY() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getContainerSizeZ() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getContent() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Returns the box content in byte array.
getContents() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadataFormatResources
 
getContents() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadataFormatResources
 
getContents() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadataFormatResources
 
getContents() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReaderResources
 
getContents() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriterResources
 
getContents() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormatResources
 
getContents() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadataFormatResources
 
getContents() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadataFormatResources
 
getContents() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFStreamMetadataFormatResources
 
getContext() - Method in class io.scif.filters.AbstractReaderFilter
 
getCopy() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
getCopy(int) - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a copy of this object
getCopy() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
getCopy() - Method in class io.scif.jj2000.j2k.decoder.DecoderSpecs
Returns a copy of the current object.
getCopy() - Method in class io.scif.jj2000.j2k.ModuleSpec
 
getCorrection(String) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
getCorrection(String) - Method in interface io.scif.ome.services.OMEMetadataService
Retrieves an Correction enumeration value for the given String.
getCount() - Method in class io.scif.FilePattern
 
getCount() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns the number of data items present in the field.
getCreationDate() - Method in class io.scif.formats.ScancoISQFormat.Metadata
 
getCreationDate() - Method in class io.scif.formats.TIFFFormat.Metadata
 
getCrop() - Method in class io.scif.cli.commands.AbstractReaderCommand
 
getCurrentFile() - Method in class io.scif.AbstractReader
 
getCurrentFile() - Method in class io.scif.filters.AbstractReaderFilter
 
getCurrentFile() - Method in interface io.scif.Reader
Returns the current file.
getCurrentHash() - Method in class io.scif.img.cell.SCIFIOCell
 
getCurrentInflatedFrame() - Method in class io.scif.formats.OBFFormat.Metadata
 
getData() - Method in class io.scif.AbstractPlane
 
getData() - Method in interface io.scif.DataPlane
Gets this plane's type-specific pixel data.
getData() - Method in class io.scif.formats.TextFormat.Metadata
 
getData() - Method in class io.scif.gui.SignedByteBuffer
 
getData(int) - Method in class io.scif.gui.SignedByteBuffer
 
getData() - Method in class io.scif.gui.SignedShortBuffer
 
getData(int) - Method in class io.scif.gui.SignedShortBuffer
 
getData() - Method in class io.scif.gui.UnsignedIntBuffer
 
getData(int) - Method in class io.scif.gui.UnsignedIntBuffer
 
getData() - Method in class io.scif.jj2000.j2k.image.DataBlk
Returns the array containing the data, or null if there is no data.
getData() - Method in class io.scif.jj2000.j2k.image.DataBlkFloat
Returns the array containing the data, or null if there is no data array.
getData() - Method in class io.scif.jj2000.j2k.image.DataBlkInt
Returns the array containing the data, or null if there is no data array.
getData() - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
Returns the array containing the data, or null if there is no data.
getData() - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataFloat
Returns the array containing the data, or null if there is no data array.
getData() - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataInt
Returns the array containing the data, or null if there is no data array.
getData() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns a reference to the data object associated with the field.
getData() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the entire image in a single Raster.
getData(Rectangle) - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns an arbitrary rectangular region of the RenderedImage in a Raster.
getData() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDBox
Returns the UUID data of this box.
getData() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getData(Rectangle) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getDataElements(int, Object) - Method in class io.scif.gui.Index16ColorModel
 
getDataElements(int, Object) - Method in class io.scif.gui.SignedColorModel
 
getDataElements(int, Object) - Method in class io.scif.gui.UnsignedIntColorModel
 
getDataFile() - Method in class io.scif.formats.NRRDFormat.Metadata
 
getDataFloat() - Method in class io.scif.jj2000.j2k.image.DataBlkFloat
Returns the array containing the data, or null if there is no data array.
getDataFloat() - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataFloat
Returns the array containing the data, or null if there is no data array.
getDataInt() - Method in class io.scif.jj2000.j2k.image.DataBlkInt
Returns the array containing the data, or null if there is no data array.
getDataInt() - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataInt
Returns the array containing the data, or null if there is no data array.
getDataOffset() - Method in class io.scif.formats.ScancoISQFormat.Metadata
 
getDatasetInfo() - Method in class io.scif.formats.MNGFormat.Metadata
 
getDatasetName() - Method in class io.scif.AbstractMetadata
 
getDatasetName() - Method in interface io.scif.Metadata
Returns a String representation of this Dataset's name
getDatasets() - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
getDatasets(ImageDisplay) - Method in class io.scif.services.SCIFIODatasetService
Deprecated.
 
getDatasetSize() - Method in class io.scif.AbstractMetadata
 
getDatasetSize() - Method in interface io.scif.Metadata
Returns the size, in bytes, of the current dataset.
getDataType() - Method in class io.scif.io.DatasetIOPlugin
 
getDataType() - Method in class io.scif.jj2000.j2k.image.DataBlk
Returns the data type of the DataBlk object, as defined in this class.
getDataType() - Method in class io.scif.jj2000.j2k.image.DataBlkFloat
Returns the identifier of this data type, TYPE_FLOAT, as defined in DataBlk.
getDataType() - Method in class io.scif.jj2000.j2k.image.DataBlkInt
Returns the identifier of this data type, TYPE_INT, as defined in DataBlk.
getDataType() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloat
Returns the type of data on which this filter works, as defined in the DataBlk interface, which is always TYPE_FLOAT for this class.
getDataType() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterInt
Returns the type of data on which this filter works, as defined in the DataBlk interface, which is always TYPE_INT for this class.
getDataType() - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
Returns the data type of the CBlkWTData object, as defined in the DataBlk class.
getDataType() - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataFloat
Returns the identifier of this data type, TYPE_FLOAT, as defined in DataBlk.
getDataType() - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataInt
Returns the data type of this object, always DataBlk.TYPE_INT.
getDataType(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataSrc
Return the data type of this CBlkWTDataSrc for the given component in the current tile.
getDataType(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Return the data type of this CBlkWTDataSrc.
getDataType() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloat
Returns the type of data on which this filter works, as defined in the DataBlk interface, which is always TYPE_FLOAT for this class.
getDataType() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterInt
Returns the type of data on which this filter works, as defined in the DataBlk interface, which is always TYPE_INT for this class.
getDataType() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the type of data on which this filter works, as defined in the DataBlk interface.
getDataTypes() - Method in class io.scif.media.imageio.plugins.tiff.TIFFTag
Returns a bit mask indicating the set of data types that may be used to store the data associated with the tag.
getDate() - Method in class io.scif.formats.DICOMFormat.Metadata
 
getDate() - Method in class io.scif.formats.ICSFormat.Metadata
 
getdBlock() - Method in class io.scif.formats.GIFFormat.Metadata
 
getDecoder() - Method in class io.scif.formats.JPEGTileFormat.Metadata
 
getDecoderSpecs() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Return the DecoderSpecs instance filled when reading the headers
getDecodingRate() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageReadParam
Gets decodingRate.
getDecomp(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.analysis.ForwWT
Returns the wavelet tree decomposition.
getDecomp(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the wavelet tree decomposition.
getDecompLevels(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.analysis.ForwWT
Returns the number of decomposition levels that are applied to obtain the LL band, in the specified tile-component.
getDecompLevels(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the number of decomposition levels that are applied to the LL band, in the specified tile-component.
getDecompositionLevel() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets decompositionLevel
getDecompType(int) - Method in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
Returns the decomposition type to be used in component 'n' and tile 't'.
getDecSpecType(int) - Method in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
Returns the type of specification for the decomposition in the specified component and tile.
getDefault() - Method in class io.scif.jj2000.j2k.ModuleSpec
Gets default value for this module.
getDefaultConfiguration() - Static method in class io.scif.gui.AWTImageTools
Gets the default graphics configuration for the environment.
getDefaultConverter() - Method in class io.scif.img.converters.DefaultPlaneConverterService
 
getDefaultConverter() - Method in interface io.scif.img.converters.PlaneConverterService
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
getDefaultImageMetadata(ImageTypeSpecifier, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
getDefaultMetaVariable() - Method in class io.scif.cli.LongArrayOptionHandler
 
getDefaultOptions() - Static method in class io.scif.codec.CodecOptions
Return CodecOptions with reasonable default values.
getDefaultOptions() - Static method in class io.scif.codec.JPEG2000CodecOptions
Return JPEG2000CodecOptions with reasonable default values.
getDefaultOptions(CodecOptions) - Static method in class io.scif.codec.JPEG2000CodecOptions
Return JPEG2000CodecOptions using the given CodecOptions as the default.
getDefaultReadParam() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
getDefaultReadParam() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getDefaultReadParam() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
getDefaultReadParam() - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
getDefaultReadParam() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getDefaultReadParam() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
getDefaultStreamMetadata(ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
getDefaultWriteParam() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
getDefaultWriteParam() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
getDefaultWriteParam() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
getDefaultWriteParam() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriter
 
getDefaultWriteParam() - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
getDefaultWriteParam() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
getDelayDen() - Method in class io.scif.formats.APNGFormat.FCTLChunk
 
getDelayNum() - Method in class io.scif.formats.APNGFormat.FCTLChunk
 
getDenominator() - Method in class io.scif.formats.tiff.TiffRational
Gets this number's denominator.
getDequantizerType() - Method in class io.scif.jj2000.j2k.quantization.dequantizer.DequantizerParams
Returns the type of the dequantizer for which the parameters are.
getDequantizerType() - Method in class io.scif.jj2000.j2k.quantization.dequantizer.StdDequantizerParams
Returns the type of the dequantizer for which the parameters are.
getDescription() - Method in class io.scif.formats.ICSFormat.Metadata
 
getDescription() - Method in class io.scif.formats.TIFFFormat.Metadata
 
getDescription() - Method in class io.scif.gui.ComboFileFilter
Returns the filter's description.
getDescription() - Method in class io.scif.gui.FormatFileFilter
Gets the filter's description.
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.stream.ChannelImageInputStreamSpi
 
getDescription(Locale) - Method in class io.scif.media.imageioimpl.stream.ChannelImageOutputStreamSpi
 
getDestination(ImageReadParam, Iterator, int, int) - Static method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getDestinationRegion() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getDestinationType(ImageReadParam, Iterator) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Gets the destination image type.
getDetectorManufacturer() - Method in class io.scif.formats.ICSFormat.Metadata
 
getDetectorModel() - Method in class io.scif.formats.ICSFormat.Metadata
 
getDetectorType(String) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
getDetectorType(String) - Method in interface io.scif.ome.services.OMEMetadataService
Retrieves an DetectorType enumeration value for the given String.
getDichroicModel() - Method in class io.scif.formats.ICSFormat.Metadata
 
getDimensionOrder(int) - Method in class io.scif.filters.DimensionSwapper
Returns the (potentially swapped) output order of the AxisTypes.
getDimLengths(Metadata, int, SCIFIOConfig) - Method in class io.scif.img.DefaultImgUtilityService
Compiles an N-dimensional list of axis lengths from the given reader.
getDimLengths(Metadata, int, SCIFIOConfig) - Method in interface io.scif.img.ImgUtilityService
Compiles an N-dimensional list of axis lengths from the given Metadata.
getDispose() - Method in class io.scif.formats.GIFFormat.Metadata
 
getDisposeOp() - Method in class io.scif.formats.APNGFormat.FCTLChunk
 
getDomains() - Method in class io.scif.AbstractReader
 
getDomains() - Method in class io.scif.filters.AbstractReaderFilter
 
getDomains() - Method in class io.scif.formats.ICSFormat.Reader
 
getDomains() - Method in class io.scif.ome.formats.OMETIFFFormat.Reader
 
getDomains() - Method in class io.scif.ome.formats.OMEXMLFormat.Reader
 
getDomains() - Method in interface io.scif.Reader
Returns the list of domains represented by the current file.
getDoubles(BufferedImage) - Static method in class io.scif.gui.AWTImageTools
Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster) - Static method in class io.scif.gui.AWTImageTools
Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools
Extracts pixel data as arrays of doubles, one per channel.
getElem(int) - Method in class io.scif.gui.SignedByteBuffer
 
getElem(int, int) - Method in class io.scif.gui.SignedByteBuffer
 
getElem(int, int) - Method in class io.scif.gui.SignedShortBuffer
 
getElem(int) - Method in class io.scif.gui.UnsignedIntBuffer
 
getElem(int, int) - Method in class io.scif.gui.UnsignedIntBuffer
 
getElemDouble(int) - Method in class io.scif.gui.UnsignedIntBuffer
 
getElemDouble(int, int) - Method in class io.scif.gui.UnsignedIntBuffer
 
getElement(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getElementDescription(String, Locale) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getElementLength() - Method in class io.scif.formats.DICOMFormat.DICOMTag
 
getElementMaxChildren(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getElementMinChildren(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getElementNames() - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
This method will be called by the getNativeNodeForSimpleBox of the class Box to get the element names.
getElementNames() - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
This method will be called by the getNativeNodeForSimpleBox of the class Box to get the element names.
getElementNames() - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.FileTypeBox
This method will be called by the getNativeNodeForSimpleBox of the class Box to get the element names.
getElementNames() - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
This method will be called by the getNativeNodeForSimpleBox of the class Box to get the element names.
getElementNames() - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDBox
This method will be called by the getNativeNodeForSimpleBox of the class Box to get the element names.
getElementNames() - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.XMLBox
This method will be called by the getNativeNodeForSimpleBox of the class Box to get the element names.
getElements() - Method in class io.scif.FilePattern
 
getElements() - Method in class io.scif.FilePatternBlock
 
getElementSize() - Method in class io.scif.img.cell.SCIFIOCell
 
getElementSize(SampleModel) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
 
getElemFloat(int) - Method in class io.scif.gui.UnsignedIntBuffer
 
getElemFloat(int, int) - Method in class io.scif.gui.UnsignedIntBuffer
 
getEmissionModel() - Method in class io.scif.formats.ICSFormat.Metadata
 
getEMSingleton() - Method in class io.scif.formats.ICSFormat.Metadata
 
getEMWaves() - Method in class io.scif.formats.ICSFormat.Metadata
 
getEncoding() - Method in class io.scif.formats.NRRDFormat.Metadata
 
getEncodingRate() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets encodingRate.
getEncodingRate() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets encodingRate
getEnergy() - Method in class io.scif.formats.ScancoISQFormat.Metadata
 
getEntryCount() - Method in class io.scif.io.ZipHandle
Deprecated.
The value returned by this method is inconsistent, and not used internally at all, either.
getEntryName() - Method in class io.scif.io.ZipHandle
Get the name of the backing Zip entry.
getEnumeratedColorSpace() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
Returns the enumerated color space.
getEPH() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets EPH.
getEPH() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets EPH
getErrorCount() - Method in class io.scif.xml.ValidationErrorHandler
 
getErrorMessage() - Method in class io.scif.FilePattern
Gets the file pattern error message, if any.
getESizeArray() - Method in class io.scif.img.cell.SCIFIOCell
 
getExcitationModel() - Method in class io.scif.formats.ICSFormat.Metadata
 
getExifIFDs() - Method in class io.scif.formats.tiff.TiffParser
Returns EXIF IFDs.
getExifTagName(int) - Static method in class io.scif.formats.TIFFFormat.BaseTIFFParser
 
getExperimenterEmail() - Method in class io.scif.formats.TIFFFormat.Metadata
 
getExperimenterFirstName() - Method in class io.scif.formats.TIFFFormat.Metadata
 
getExperimenterLastName() - Method in class io.scif.formats.TIFFFormat.Metadata
 
getExperimentType() - Method in class io.scif.formats.ICSFormat.Metadata
 
getExperimentType(String) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
getExperimentType(String) - Method in interface io.scif.ome.services.OMEMetadataService
Retrieves an ExperimentType enumeration value for the given String.
getExposureTime() - Method in class io.scif.formats.ICSFormat.Metadata
 
getEXSingleton() - Method in class io.scif.formats.ICSFormat.Metadata
 
getExtraArguments() - Method in class io.scif.cli.AbstractSCIFIOToolCommand
Each SCIFIOToolCommand implementation should have a List<String> Argument field which is multiValued = true and with an index putting it at the end of the argument list.
getExtraArguments() - Method in class io.scif.cli.commands.Convert
 
getExtraArguments() - Method in class io.scif.cli.commands.Help
 
getExtraArguments() - Method in class io.scif.cli.commands.Info
 
getExtraArguments() - Method in class io.scif.cli.commands.Show
 
getExtraArguments() - Method in class io.scif.ome.commands.OMEXMLToolCommand
 
getExtraLayers(int) - Method in class io.scif.jj2000.j2k.entropy.encoder.LayersInfo
Returns the number of extra layers to add after the optimization point 'n', but before optimization point 'n+1'.
getExtraLength() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Returns the box extra length.
getEXWaves() - Method in class io.scif.formats.ICSFormat.Metadata
 
getFailureClass() - Method in exception io.scif.DependencyException
Returns the class that was used during a failed instantiation.
getFctl() - Method in class io.scif.formats.APNGFormat.Metadata
 
getFdatChunks() - Method in class io.scif.formats.APNGFormat.FCTLChunk
 
getFieldName(Class<?>, int) - Static method in class io.scif.common.DebugTools
Deprecated.
This method uses reflection to scan the values of the given class's static fields, returning the first matching field's name.
getFieldName(int) - Static method in class io.scif.formats.tiff.IFD
Deprecated.
getFile(MicromanagerFormat.Metadata, int, long) - Method in class io.scif.formats.MicromanagerFormat.Position
 
getFile() - Method in class io.scif.io.StreamHandle
 
getFileChannel() - Method in class io.scif.io.NIOFileHandle
Gets the FileChannel from this FileHandle.
getFileList() - Method in class io.scif.formats.DICOMFormat.Metadata
 
getFileName() - Method in class io.scif.io.RandomAccessInputStream
 
getFilename(int, int, Reader, String) - Static method in class io.scif.util.FormatTools
 
getFilenames(String, Reader) - Static method in class io.scif.util.FormatTools
 
getFilePattern() - Method in class io.scif.AxisGuesser
Gets the file pattern.
getFilePattern() - Method in class io.scif.filters.FileStitcher
Gets the file pattern object used to build the list of files.
getFilePointer() - Method in class io.scif.bf.wrapper.RandomAccessInputStreamWrapper
 
getFilePointer() - Method in class io.scif.common.RandomAccessInputStreamWrapper
Deprecated.
 
getFilePointer() - Method in class io.scif.io.ByteArrayHandle
 
getFilePointer() - Method in class io.scif.io.FileHandle
 
getFilePointer() - Method in interface io.scif.io.IRandomAccess
Returns the current offset in this stream.
getFilePointer() - Method in class io.scif.io.NIOFileHandle
 
getFilePointer() - Method in class io.scif.io.NIOInputStream
Gets the current (absolute) file pointer.
getFilePointer() - Method in class io.scif.io.RandomAccessInputStream
Gets the current (absolute) file pointer.
getFilePointer() - Method in class io.scif.io.RandomAccessOutputStream
Returns the current offset within the stream.
getFilePointer() - Method in class io.scif.io.StreamHandle
 
getFiles() - Method in class io.scif.FilePattern
Gets a listing of all files matching the given file pattern.
getFillOrder() - Method in class io.scif.formats.tiff.IFD
Retrieves the image's fill order (TIFF tag FillOrder) from this IFD.
getFilter() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets filters.
getFilterClasses() - Method in interface io.scif.filters.MasterFilter
Returns a list of all filter classes this MasterFilter can enable/disable.
getFilterClasses() - Method in class io.scif.filters.MasterFilterHelper
 
getFilterClasses() - Method in class io.scif.filters.ReaderFilter
 
getFilterMethod() - Method in class io.scif.formats.APNGFormat.IHDRChunk
 
getFilters() - Method in class io.scif.gui.ComboFileFilter
Gets the list of file filters forming this filter combination.
getFilters() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets filters
getFilterSetModel() - Method in class io.scif.formats.ICSFormat.Metadata
 
getFilterType() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilter
Returns the type of filter used according to the FilterTypes interface.
getFilterType() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the type of filter used according to the FilterTypes interface(W9x7).
getFilterType() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the type of filter used according to the FilterTypes interface (W5x3).
getFinalCRC() - Method in class io.scif.common.CRC
 
getFirst() - Method in class io.scif.FilePattern
 
getFirst() - Method in class io.scif.FilePatternBlock
 
getFirstChild() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getFirstCodeStreamLength() - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method returns the length of the first contiguous codestreams in the file
getFirstCodeStreamPos() - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method returns the position of the first contiguous codestreams in the file
getFirstIFD() - Method in class io.scif.formats.tiff.TiffParser
Gets the first IFD within the TIFF file, or null if the input source is not a valid TIFF file.
getFirstIFD() - Method in class io.scif.ome.formats.OMETIFFFormat.Metadata
 
getFirstIFDEntry(int) - Method in class io.scif.formats.tiff.TiffParser
Retrieve a given entry from the first IFD in the stream.
getFirstOffset() - Method in class io.scif.formats.tiff.TiffParser
Gets offset to the first IFD, or -1 if stream is not TIFF.
getFirstSlicePosition() - Method in class io.scif.formats.ScancoISQFormat.Metadata
 
getFixedPoint(int) - Method in interface io.scif.jj2000.j2k.image.BlkImgDataSrc
Returns the position of the fixed point in the specified component, or equivalently the number of fractional bits.
getFixedPoint(int) - Method in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Returns the position of the fixed point in the specified component.
getFixedPoint(int) - Method in class io.scif.jj2000.j2k.image.ImgDataConverter
Returns the position of the fixed point in the specified component.
getFixedPoint(int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the position of the fixed point in the specified component.
getFixedPoint(int) - Method in class io.scif.jj2000.j2k.image.input.ImgReaderPGM
Returns the position of the fixed point in the specified component (i.e.
getFixedPoint(int) - Method in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Returns the position of the fixed point in the specified component.
getFixedPoint(int) - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the position of the fixed point in the specified component.
getFixedPoint(int) - Method in class io.scif.jj2000.j2k.quantization.dequantizer.StdDequantizer
Returns the position of the fixed point in the output data for the specified component.
getFixedPoint(int) - Method in interface io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataSrc
Returns the position of the fixed point in the specified component, or equivalently the number of fractional bits.
getFixedPoint(int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the position of the fixed point in the specified component.
getFixedPoint(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.CBlkWTDataSrcDec
Returns the position of the fixed point in the specified component, or equivalently the number of fractional bits.
getFixedPoint(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTFull
Returns the position of the fixed point in the specified component.
getFixedPoint(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the position of the fixed point in the specified component (i.e.
getFlags() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
Returns the Flags data element.
getFloats(BufferedImage) - Static method in class io.scif.gui.AWTImageTools
Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster) - Static method in class io.scif.gui.AWTImageTools
Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools
Extracts pixel data as arrays of floats, one per channel.
getFlushedPosition() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
getFormat() - Method in class io.scif.AbstractHasFormat
 
getFormat() - Method in class io.scif.DefaultChecker
 
getFormat() - Method in class io.scif.DefaultMetadata
 
getFormat() - Method in class io.scif.DefaultParser
 
getFormat() - Method in class io.scif.DefaultReader
 
getFormat() - Method in class io.scif.DefaultWriter
 
getFormat() - Method in class io.scif.filters.AbstractMetadataWrapper
 
getFormat() - Method in class io.scif.filters.AbstractReaderFilter
 
getFormat() - Method in class io.scif.gui.FormatFileFilter
Returns the filter's format.
getFormat() - Method in interface io.scif.HasFormat
Provides a link back to the format associated with this component.
getFormat(String) - Method in class io.scif.services.DefaultFormatService
Returns the first Format known to be compatible with the source provided.
getFormat(String, SCIFIOConfig) - Method in class io.scif.services.DefaultFormatService
 
getFormat(RandomAccessInputStream) - Method in class io.scif.services.DefaultFormatService
 
getFormat(RandomAccessInputStream, SCIFIOConfig) - Method in class io.scif.services.DefaultFormatService
 
getFormat(String) - Method in interface io.scif.services.FormatService
Returns the first Format known to be compatible with the source provided.
getFormat(String, SCIFIOConfig) - Method in interface io.scif.services.FormatService
Returns the first Format known to be compatible with the source provided.
getFormat(RandomAccessInputStream) - Method in interface io.scif.services.FormatService
getFormat(RandomAccessInputStream, SCIFIOConfig) - Method in interface io.scif.services.FormatService
getFormatFromChecker(Class<C>) - Method in class io.scif.services.DefaultFormatService
 
getFormatFromChecker(Class<C>) - Method in interface io.scif.services.FormatService
Format lookup method using the Checker component.
getFormatFromClass(Class<F>) - Method in class io.scif.services.DefaultFormatService
 
getFormatFromClass(Class<F>) - Method in interface io.scif.services.FormatService
Lookup method for the Format map.
getFormatFromComponent(Class<?>) - Method in class io.scif.services.DefaultFormatService
 
getFormatFromComponent(Class<?>) - Method in interface io.scif.services.FormatService
Returns the Format compatible with this component class, or null if no matching Format can be found.
getFormatFromMetadata(Class<M>) - Method in class io.scif.services.DefaultFormatService
 
getFormatFromMetadata(Class<M>) - Method in interface io.scif.services.FormatService
Format lookup method using the Metadata component.
getFormatFromParser(Class<P>) - Method in class io.scif.services.DefaultFormatService
 
getFormatFromParser(Class<P>) - Method in interface io.scif.services.FormatService
Format lookup method using the Parser component.
getFormatFromReader(Class<R>) - Method in class io.scif.services.DefaultFormatService
 
getFormatFromReader(Class<R>) - Method in interface io.scif.services.FormatService
Format lookup method using the Reader component
getFormatFromWriter(Class<W>) - Method in class io.scif.services.DefaultFormatService
 
getFormatFromWriter(Class<W>) - Method in interface io.scif.services.FormatService
Format lookup method using the Writer component.
getFormatList(String) - Method in class io.scif.services.DefaultFormatService
 
getFormatList(String, SCIFIOConfig, boolean) - Method in class io.scif.services.DefaultFormatService
 
getFormatList(RandomAccessInputStream) - Method in class io.scif.services.DefaultFormatService
 
getFormatList(RandomAccessInputStream, SCIFIOConfig, boolean) - Method in class io.scif.services.DefaultFormatService
 
getFormatList(String) - Method in interface io.scif.services.FormatService
Returns a list of all formats that are compatible with the source provided, ordered by their priority.
getFormatList(String, SCIFIOConfig, boolean) - Method in interface io.scif.services.FormatService
Returns a list of all formats that are compatible with the source provided, ordered by their priority.
getFormatList(RandomAccessInputStream) - Method in interface io.scif.services.FormatService
getFormatList(RandomAccessInputStream, SCIFIOConfig, boolean) - Method in interface io.scif.services.FormatService
getFormatName() - Method in class io.scif.AbstractFormat
 
getFormatName() - Method in class io.scif.AbstractHasFormat
 
getFormatName() - Method in class io.scif.bf.BioFormatsFormat.Metadata
 
getFormatName() - Method in class io.scif.filters.AbstractMetadataWrapper
 
getFormatName() - Method in class io.scif.filters.AbstractReaderFilter
 
getFormatName() - Method in interface io.scif.Format
Gets the name of this file format.
getFormatName() - Method in class io.scif.formats.ImarisFormat
 
getFormatName() - Method in interface io.scif.HasFormat
Helper method for accessing Format.getFormatName().
getFormatName() - Method in class io.scif.lifesci.SDTFormat
 
getFormatName() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
getFormatName() - Method in class io.scif.ome.formats.OMETIFFFormat
 
getFormatName() - Method in class io.scif.ome.formats.OMEXMLFormat
 
getFp() - Method in class io.scif.io.StreamHandle
 
getFrameCoordinates() - Method in class io.scif.formats.APNGFormat.APNGChunk
 
getFrameCoordinates() - Method in class io.scif.formats.APNGFormat.FCTLChunk
 
getFramesPerSecond() - Method in class io.scif.AbstractWriter
 
getFramesPerSecond() - Method in interface io.scif.Writer
 
getGains() - Method in class io.scif.formats.ICSFormat.Metadata
 
getGct() - Method in class io.scif.formats.GIFFormat.Metadata
 
getGlobal() - Method in class io.scif.formats.BMPFormat.Metadata
 
getGlobalCRC() - Method in class io.scif.common.CRC
 
getGreen() - Method in class io.scif.formats.APNGFormat.PLTEChunk
 
getGreen(int) - Method in class io.scif.gui.Index16ColorModel
 
getGreen(int) - Method in class io.scif.gui.SignedColorModel
 
getGreen(Object) - Method in class io.scif.gui.SignedColorModel
 
getGreen(int) - Method in class io.scif.gui.UnsignedIntColorModel
 
getGreen(Object) - Method in class io.scif.gui.UnsignedIntColorModel
 
getGreens() - Method in class io.scif.gui.Index16ColorModel
Return the array of green color components.
getGroupId() - Method in class io.scif.app.SCIFIOApp
 
getGuardBits() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets guardBits
getHandle(String) - Method in class io.scif.services.DefaultLocationService
 
getHandle(String, boolean) - Method in class io.scif.services.DefaultLocationService
 
getHandle(String, boolean, boolean) - Method in class io.scif.services.DefaultLocationService
 
getHandle(String) - Method in interface io.scif.services.LocationService
Gets an IRandomAccess object that can read from the given file.
getHandle(String, boolean) - Method in interface io.scif.services.LocationService
Gets an IRandomAccess object that can read from or write to the given file.
getHandle(String, boolean, boolean) - Method in interface io.scif.services.LocationService
Gets an IRandomAccess object that can read from or write to the given file.
getHashes() - Method in class io.scif.img.cell.SCIFIOCell
 
getHeader() - Method in class io.s