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A

abort() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
AbstractReaderCommand - Class in io.scif.cli
Abstract superclass for SCIFIOToolCommand implementations that read images.
AbstractReaderCommand() - Constructor for class io.scif.cli.AbstractReaderCommand
 
AbstractSCIFIOToolCommand - Class in io.scif.cli
Abstract SCIFIOToolCommand superclass.
AbstractSCIFIOToolCommand() - Constructor for class io.scif.cli.AbstractSCIFIOToolCommand
 
accumulate - Variable in class io.scif.lifesci.SDTInfo
 
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.
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
 
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.
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.
AddCharString(short, byte) - Method in class io.scif.media.imageioimpl.common.LZWStringTable
 
addComment(String) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
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.
addImage(Object, int, int, int, String) - Method in class io.scif.formats.imaris.ImarisWriter
 
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.
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
 
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.
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
 
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.
APNGOMETranslator() - Constructor for class io.scif.ome.translators.APNGTranslator.APNGOMETranslator
 
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
 
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
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
 
AsciiImage - Class in io.scif.cli.show
A utility class for outputting a BufferedImage as ASCII text.
AsciiImage(BufferedImage) - Constructor for class io.scif.cli.show.AsciiImage
 
asRetrieve(MetadataStore) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
asRetrieve(MetadataStore) - Method in interface io.scif.ome.services.OMEXMLService
 
asStore(MetadataRetrieve) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
asStore(MetadataRetrieve) - Method in interface io.scif.ome.services.OMEXMLService
 
attrInfoMap - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
authenticationCodes - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
available() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
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.
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.
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.
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
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_ENDIAN - Static variable in interface io.scif.jj2000.j2k.io.EndianType
Identifier for big-endian byte ordering (i.e.
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.
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
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
 
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.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.
BLACK - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
The CCITT numerical definition of black.
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).
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
 
BMPConstants - Interface in io.scif.media.imageioimpl.plugins.bmp
 
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.
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
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
buildPalette() - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
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.
byteTable - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
 

C

C_STRING1 - Static variable in class io.scif.lifesci.SDTInfo
 
C_STRING2 - Static variable in class io.scif.lifesci.SDTInfo
 
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.
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
 
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
 
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
 
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
 
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)
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.
cepoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.POC
 
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
 
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.
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.lifesci.SDTInfo
 
characterCellHeight - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
characterCellWidth - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
Checker() - Constructor for class io.scif.bf.BioFormatsFormat.Checker
 
checkHeader(byte[]) - Method in class io.scif.bf.BioFormatsFormat.Checker
 
checkMarkerLength(DataInputStream, String) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Checks that the marker segment length is correct.
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.
checkReadParamBandSettingsWrapper(ImageReadParam, int, int) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
Wrapper for the protected method checkReadParamBandSettings.
checkTargetErrors() - Method in class io.scif.jj2000.j2k.util.ThreadPool
Checks that no error or runtime exception in any target have occurred so far.
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.
clearDestImage() - Method in class io.scif.media.imageioimpl.plugins.raw.RawRenderedImage
 
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.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(boolean) - Method in class io.scif.bf.BioFormatsFormat.Metadata
 
close() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
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.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
 
closeTimePoint() - Method in class io.scif.formats.imaris.TimePoint
 
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
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.
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_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.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 - 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
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.convert.Convert
 
commandName() - Method in class io.scif.cli.help.Help
 
commandName() - Method in class io.scif.cli.info.Info
 
commandName() - Method in interface io.scif.cli.SCIFIOToolCommand
 
commandName() - Method in class io.scif.cli.show.Show
 
commandName() - Method in class io.scif.ome.commands.OMEXMLToolCommand
 
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
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_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[], int, int) - Method in class io.scif.media.imageioimpl.common.LZWCompressor
 
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_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.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_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 - 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
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.
CONTIGUOUS_CODESTREAM_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
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.convert
SCIFIOToolCommand plugin for converting (reading and writing) datasets.
Convert() - Constructor for class io.scif.cli.convert.Convert
 
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
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
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.jj2000.j2k.JJ2KInfo
The copyright message string.
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
 
createArrayForType(int, int) - Static method in class io.scif.media.imageio.plugins.tiff.TIFFField
Creates an array appropriate for the indicated data type.
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.
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
 
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.bf.BioFormatsFormat.Reader
 
createDomainArray() - Method in class io.scif.lifesci.SDTFormat.Reader
 
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.
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.
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.
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.
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.
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
 
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.
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.
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
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).
CUSTOM - Static variable in interface io.scif.jj2000.j2k.wavelet.FilterTypes
User-defined filter: -1
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

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.
DataHandleAdapter - Class in io.scif.bf.wrapper
Adapter class to convert DataHandle to RandomAccessInputStream.
DataHandleAdapter(DataHandle<Location>) - Constructor for class io.scif.bf.wrapper.DataHandleAdapter
 
dataOffs - Variable in class io.scif.lifesci.SDTInfo
Offset of the data block from the beginning of the file.
date - Variable in class io.scif.lifesci.SDTInfo
Date of creation.
dateAndtime - Variable in class io.scif.formats.imaris.PipelineImage
 
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
 
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
 
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_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
 
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
 
delayTime - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
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
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.convert.Convert
 
description() - Method in class io.scif.cli.help.Help
 
description() - Method in class io.scif.cli.info.Info
 
description() - Method in class io.scif.cli.show.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.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.TIFFTranslator.OMETIFFTranslator
 
dest() - Method in class io.scif.ome.translators.TIFFTranslator.TIFFOMETranslator
 
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.
detType - Variable in class io.scif.lifesci.SDTInfo
Detector type (SPC-930 in camera mode).
DICOMOMETranslator() - Constructor for class io.scif.ome.translators.DICOMTranslator.DICOMOMETranslator
 
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
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.
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.
disposalMethod - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
dispose() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
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
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
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
 
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 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.
EOC - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
End of codestream (EOC): 0xFFD9
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
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.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.
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
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.bf.wrapper.DataHandleAdapter
 
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_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_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.
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.
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

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
 
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'.
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.
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.
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_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.
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_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.
fillOrder - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
The logical order of bits within a byte.
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
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.
findPaletteEntry(PaletteBuilder.ColorNode, int, byte[], byte[], byte[]) - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
findString(String...) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
findString(boolean, String...) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
findString(int, String...) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
findString(boolean, int, String...) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
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.
flags - Variable in class io.scif.lifesci.SDTInfo
Scan clocks bits 2-0 (frame, line, pixel), rates_read - bit 15.
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_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_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.
flbckX - Variable in class io.scif.lifesci.SDTInfo
 
flbckY - Variable in class io.scif.lifesci.SDTInfo
 
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 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_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.
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
 
freeTree(PaletteBuilder.ColorNode) - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
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, 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_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.
GeoTIFFTagSet - Class in io.scif.media.imageio.plugins.tiff
A class representing the tags found in a GeoTIFF IFD.
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.
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.
getAlignROI() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets alignROI
getAllowedTagSets() - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageReadParam
Returns a List containing the allowed TIFFTagSet objects.
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.
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
 
getBandSize(SampleModel) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
 
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.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
 
getBlockAligned() - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
This function returns the blockAligned flag
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.
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.
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.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
 
getCachedImageReader() - Method in class io.scif.bf.BioFormatsFormat
Gets a cached ImageReader, suitable for using for format checking or suffix generation.
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.
getChannels() - Method in class io.scif.lifesci.SDTFormat.Metadata
 
getChildNames(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getChildPolicy(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
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
getCodeSegSymbol() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets codeSegSymbol
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
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.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
 
getColorTable(int, long) - Method in class io.scif.bf.BioFormatsFormat.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
 
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.
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.AbstractReaderCommand
 
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
 
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.media.imageio.plugins.tiff.TIFFField
Returns the number of data items present in the field.
getCrop() - Method in class io.scif.cli.AbstractReaderCommand
 
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
 
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.
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.
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.
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
 
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
 
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(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.
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.
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
 
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.
getElementSize(SampleModel) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
 
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
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
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.
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.convert.Convert
 
getExtraArguments() - Method in class io.scif.cli.help.Help
 
getExtraArguments() - Method in class io.scif.cli.info.Info
 
getExtraArguments() - Method in class io.scif.cli.show.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.
getFilePointer() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
getFilter() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets filters.
getFilters() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets filters
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).
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
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.
getFlushedPosition() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
getFormatName() - Method in class io.scif.bf.BioFormatsFormat.Metadata
 
getFormatName() - Method in class io.scif.formats.ImarisFormat
 
getFormatName() - Method in class io.scif.lifesci.SDTFormat
 
getFormatName() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
getGuardBits() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets guardBits
getHeader() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getHeight() - Method in class io.scif.jj2000.j2k.codestream.reader.TagTreeDecoder
Returns the number of leafs along the vertical direction.
getHeight() - Method in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Returns the number of leafs along the vertical direction.
getHeight() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the height of the image.
getHeight(int) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
getHeight() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Returns the height of the image.
getHeight(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getHeight() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getHeight(int) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReader
 
getHeight(int) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
getHeight(int) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
getHeight() - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
getHeight(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getHeight() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getHeight(int) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getHFilters(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterSpec
Returns the horizontal analysis filters to be used in component 'n' and tile 't'.
getHFilters(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterSpec
Returns the horizontal analysis filters to be used in component 'n' and tile 't'.
getHH() - Method in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
Returns the HH child subband of this subband.
getHH() - Method in class io.scif.jj2000.j2k.wavelet.Subband
Returns the HH child subband of this subband.
getHH() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
Returns the HH child subband of this subband.
getHL() - Method in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
Returns the HL (horizontal high-pass) child subband of this subband.
getHL() - Method in class io.scif.jj2000.j2k.wavelet.Subband
Returns the HL (horizontal high-pass) child subband of this subband.
getHL() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
Returns the HL (horizontal high-pass) child subband of this subband.
getHorAnWaveletFilters(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.analysis.ForwWT
Returns the horizontal analysis wavelet filters used in each level, for the specified tile-component.
getHorAnWaveletFilters(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the horizontal analysis wavelet filters used in each level, for the specified component and tile.
getHorizontalResolution() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ResolutionBox
Return the horizontal resolution.
getHorWFilter() - Method in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
This function returns the horizontal wavelet filter relevant to this subband
getHorWFilter() - Method in class io.scif.jj2000.j2k.wavelet.Subband
This function returns the horizontal wavelet filter relevant to this subband
getHorWFilter() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
This function returns the horizontal wavelet filter relevant to this subband
getHPSynthesisFilter() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilter
Returns the time-reversed high-pass synthesis waveform of the filter, which is the high-pass filter.
getHPSynthesisFilter() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the time-reversed high-pass synthesis waveform of the filter, which is the high-pass filter.
getHPSynthesisFilter() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the time-reversed high-pass synthesis waveform of the filter, which is the high-pass filter.
getHPSynWaveForm(float[], float[]) - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilter
Returns the equivalent high-pass synthesis waveform of a cascade of filters, given the syhthesis waveform of the previous stage.
getICCProfile() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
Returns the ICC color profile in this color specification box.
getImageByteDepth() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getImageDimension(int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
Retrieves the dimnsion of the imageIndexth image.
getImageMetadata(int) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
getImageMetadata(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getImageMetadata(int) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReader
 
getImageMetadata(int) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
getImageMetadata(int) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
getImageMetadata(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getImageMetadata(int) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getImageNumBytes() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getImageOffset(int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
Retrieves the image offset of the imageIndexth image.
getImageSizeX() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getImageSizeY() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getImageSizeZ() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getImageType() - Method in class io.scif.media.imageio.stream.RawImageInputStream
Retrieves the image type.
getImageType() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getImageTypes(int) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
getImageTypes(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getImageTypes(int) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReader
 
getImageTypes(int) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
getImageTypes(int) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
getImageTypes(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getImageTypes(int) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getImgHeight(int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the overall height of the image in pixels, for the given resolution level.
getImgHeight() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the image height in the reference grid.
getImgHeight() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the overall height of the image in pixels.
getImgHeight() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the overall height of the image in pixels.
getImgHeight() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the overall height of the image in pixels.
getImgHeight() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the overall height of the image in pixels.
getImgHeight() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the overall height of the image in pixels.
getImgHeight(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the overall height of the image in pixels, for the given resolution level.
getImgHeight(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the overall height of the image in pixels, for the given resolution level.
getImgHeight() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the overall height of the image in pixels.
getImgRes() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the image resolution level to reconstruct from the codestream.
getImgULX(int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the horizontal coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid at the specified resolution level.
getImgULX() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Return the horizontal upper-left coordinate of the image in the reference grid.
getImgULX() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the horizontal coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULX() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the horizontal coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULX() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the horizontal coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULX() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the horizontal coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULX() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the horizontal coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULX() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the horizontal coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULX(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the horizontal coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid at the specified resolution level.
getImgULX(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the horizontal coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid at the specified resolution level.
getImgULX() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the horizontal coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULY(int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the vertical coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid at the specified resolution level.
getImgULY() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Return the vertical upper-left coordinate of the image in the reference grid.
getImgULY() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the vertical coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULY() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the vertical coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULY() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the vertical coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULY() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the vertical coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULY() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the vertical coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULY() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the vertical coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgULY(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the vertical coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid at the specified resolution level.
getImgULY(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the vertical coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid at the specified resolution level.
getImgULY() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the vertical coordinate of the image origin, the top-left corner, in the canvas system, on the reference grid.
getImgWidth(int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the overall width of the image in pixels, for the given (image) resolution level.
getImgWidth() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the image width in the reference grid.
getImgWidth() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the overall width of the image in pixels.
getImgWidth() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the overall width of the image in pixels.
getImgWidth() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the overall width of the image in pixels.
getImgWidth() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the overall width of the image in pixels.
getImgWidth() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the overall width of the image in pixels.
getImgWidth(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the overall width of the image in pixels, for the given resolution level.
getImgWidth(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the overall width of the image in pixels, for the given resolution level.
getImgWidth() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the overall width of the image in pixels.
getImmersion(String) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
getImmersion(String) - Method in interface io.scif.ome.services.OMEMetadataService
Retrieves an Immersion enumeration value for the given String.
getImplementationType(int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the implementation type of this wavelet transform, WT_IMPL_FULL (full-page based transform).
getImplementationType(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTFull
Returns the implementation type of this wavelet transform, WT_IMPL_FULL (full-page based transform).
getImplementationType(int) - Method in interface io.scif.jj2000.j2k.wavelet.WaveletTransform
Returns the implementation type of this wavelet transform (WT_IMPL_LINE or WT_IMPL_FRAME) for the specified component, in the current tile.
getImplType() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the implementation type of this filter, as defined in this class, such as WT_FILTER_INT_LIFT, WT_FILTER_FLOAT_LIFT, WT_FILTER_FLOAT_CONVOL.
getImplType() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the implementation type of this filter, as defined in this class, such as WT_FILTER_INT_LIFT, WT_FILTER_FLOAT_LIFT, WT_FILTER_FLOAT_CONVOL.
getImplType() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns the implementation type of this filter, as defined in this class, such as WT_FILTER_INT_LIFT, WT_FILTER_FLOAT_LIFT, WT_FILTER_FLOAT_CONVOL.
getImplType() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns the implementation type of this filter, as defined in this class, such as WT_FILTER_INT_LIFT, WT_FILTER_FLOAT_LIFT, WT_FILTER_FLOAT_CONVOL.
getImplType() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the implementation type of this filter, as defined in this class, such as WT_FILTER_INT_LIFT, WT_FILTER_FLOAT_LIFT, WT_FILTER_FLOAT_CONVOL.
getIndex() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getIndexColorModel() - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
getIndexedImage() - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
getInstance() - Static method in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Returns a shared instance of a BaselineTIFFTagSet.
getInstance() - Static method in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
Returns a shared instance of an EXIFGPSTagSet.
getInstance() - Static method in class io.scif.media.imageio.plugins.tiff.EXIFInteroperabilityTagSet
Returns the shared instance of EXIFInteroperabilityTagSet.
getInstance() - Static method in class io.scif.media.imageio.plugins.tiff.EXIFParentTIFFTagSet
Returns a shared instance of an EXIFParentTIFFTagSet.
getInstance() - Static method in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
Returns a shared instance of an EXIFTIFFTagSet.
getInstance() - Static method in class io.scif.media.imageio.plugins.tiff.FaxTIFFTagSet
Returns a shared instance of a FaxTIFFTagSet.
getInstance() - Static method in class io.scif.media.imageio.plugins.tiff.GeoTIFFTagSet
Returns a shared instance of a GeoTIFFTagSet.
getInstance() - Static method in class io.scif.media.imageioimpl.common.InvertedCMYKColorSpace
 
getInstance() - Static method in class io.scif.media.imageioimpl.common.SimpleCMYKColorSpace
 
getInstance() - Static method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadataFormat
 
getInstance() - Static method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadataFormat
 
getInstance() - Static method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadataFormat
 
getInstance() - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
getInstance() - Static method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadataFormat
 
getInstance() - Static method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadataFormat
 
getInstance() - Static method in class io.scif.media.imageioimpl.plugins.tiff.TIFFStreamMetadataFormat
 
getIntArrayElementValue(Node) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Gets the integer array from an IIOMetadataNode.
getIntElementValue(Node) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Gets its integer value from an IIOMetadataNode.
getIntellectualProperty() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Returns the IntellectualProperty flag.
getInternCodeBlock(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 reference or copy).
getInternCodeBlock(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 reference or copy).
getInternCodeBlock(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 reference or copy).
getInternCodeBlock(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 reference or copy).
getInternCodeBlock(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 reference or copy).
getInternCompData(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.
getInternCompData(DataBlk, int) - Method in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Apply the component transformation associated with the current tile.
getInternCompData(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' defined in the block given as argument.
getInternCompData(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.
getInternCompData(DataBlk, int) - Method in class io.scif.jj2000.j2k.image.input.ImgReaderPGM
Returns, in the blk argument, the block of image data containing the specifed rectangular area, in the specified component.
getInternCompData(DataBlk, int) - Method in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Apply the inverse component transformation associated with the current tile.
getInternCompData(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.
getInternCompData(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 reference to the internal buffer (see below).
getInternCompData(DataBlk, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns, in the blk argument, the block of image data containing the specifed rectangular area, in the specified component.
getJDKImageReaderWriterSPI(ServiceRegistry, String, boolean) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
 
getKerSpecType(int) - Method in class io.scif.jj2000.j2k.wavelet.WTFilterSpec
Returns the type of specification for the filters in the specified component and tile.
getLaserMedium(String) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
getLaserMedium(String) - Method in interface io.scif.ome.services.OMEMetadataService
Retrieves an LaserMedium enumeration value for the given String.
getLaserType(String) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
getLaserType(String) - Method in interface io.scif.ome.services.OMEMetadataService
Retrieves an LaserType enumeration value for the given String.
getLastBodyBuf() - Method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Returns the buffer of the body of the last encoded packet.
getLastBodyLen() - Method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Returns the length of the body of the last encoded packet, in bytes.
getLastChild() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getLastPosition() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
 
getLatestVersion() - Method in class io.scif.ome.services.DefaultOMEXMLService
 
getLatestVersion() - Method in interface io.scif.ome.services.OMEXMLService
 
getLayers() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets layers
getLeafChildCount() - Method in class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
getLength() - Method in class io.scif.jj2000.j2k.codestream.writer.BitOutputBuffer
Returns the current length of the buffer, in bytes.
getLength() - Method in class io.scif.jj2000.j2k.codestream.writer.CodestreamWriter
Returns the current length of the entire bit stream.
getLength() - Method in class io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
Returns the current length of the entire bit stream.
getLength() - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Returns the length of the header.
getLength() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Returns the box length.
getLength() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getLevels(int) - Method in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
Returns the decomposition number of levels in component 'n' and tile 't'.
getLH() - Method in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
Returns the LH (vertical high-pass) child subband of this subband.
getLH() - Method in class io.scif.jj2000.j2k.wavelet.Subband
Returns the LH (vertical high-pass) child subband of this subband.
getLH() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
Returns the LH (vertical high-pass) child subband of this subband.
getLineWidth() - Method in class io.scif.jj2000.j2k.util.MsgPrinter
Returns the line width that is used for formatting.
getLL() - Method in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
Returns the LL child subband of this subband.
getLL() - Method in class io.scif.jj2000.j2k.wavelet.Subband
Returns the LL child subband of this subband.
getLL() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
Returns the LL child subband of this subband.
getLossless() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets lossless.
getLossless() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets encodingRate
getLPSynthesisFilter() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilter
Returns the time-reversed low-pass synthesis waveform of the filter, which is the low-pass filter.
getLPSynthesisFilter() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the time-reversed low-pass synthesis waveform of the filter, which is the low-pass filter.
getLPSynthesisFilter() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the time-reversed low-pass synthesis waveform of the filter, which is the low-pass filter.
getLPSynWaveForm(float[], float[]) - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilter
Returns the equivalent low-pass synthesis waveform of a cascade of filters, given the syhthesis waveform of the previous stage.
getLUT() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
Return the LUT.
getMainDefDecompType() - Method in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
Returns the main default decomposition type.
getMainDefLevels() - Method in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
Returns the main default decomposition number of levels.
getMap() - Method in class io.scif.cli.AbstractReaderCommand
 
getMax() - Method in class io.scif.jj2000.j2k.IntegerSpec
Get the maximum value of each tile-component
getMaxAvailableBytes() - Method in class io.scif.jj2000.j2k.codestream.writer.CodestreamWriter
Returns the number of bytes remaining available in the bit stream.
getMaxAvailableBytes() - Method in class io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
Returns the number of bytes remaining available in the bit stream.
getMaxCBlkHeight() - Method in class io.scif.jj2000.j2k.entropy.CBlkSizeSpec
Returns the maximum code-block's height
getMaxCBlkWidth() - Method in class io.scif.jj2000.j2k.entropy.CBlkSizeSpec
Returns the maximum code-block's width
getMaxCompHeight() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
getMaxCompImgHeight() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Return the maximum height among all components
getMaxCompImgWidth() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Return the maximum width among all components
getMaxCompWidth() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
getMaxInComp(int) - Method in class io.scif.jj2000.j2k.IntegerSpec
Get the maximum value of each tile for specified component
getMaxInTile(int) - Method in class io.scif.jj2000.j2k.IntegerSpec
Get the maximum value of each component in specified tile
getMaxMagBits(int) - Method in class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
Returns the maximum number of magnitude bits in any subband in the current tile.
getMaxMagBits(int) - Method in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
Returns the maximum number of magnitude bits in any subband of the current tile.
getMaxTileX() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the horizontal index of the rightmost column of tiles.
getMaxTileY() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the vertical index of the bottom row of tiles.
getMaxValue() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
getMaxX() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the X coordinate of the column immediatetely to the right of the rightmost column of the image.
getMaxY() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the Y coordinate of the row immediately below the bottom row of the image.
getMetadata() - Method in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Returns the current IIOMetadata object.
getMetadataStore() - Method in class io.scif.bf.BioFormatsFormat.Metadata
 
getMethod() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
Returns the method to define the color space.
getMethodForMQLengthCalc() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets methodForMQLengthCalc
getMethodForMQTermination() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets methodForMQTermination
getMin() - Method in class io.scif.jj2000.j2k.IntegerSpec
Get the minimum value of each tile-component
getMinInComp(int) - Method in class io.scif.jj2000.j2k.IntegerSpec
Get the minimum value of each tile for specified component
getMinInTile(int) - Method in class io.scif.jj2000.j2k.IntegerSpec
Get the minimum value of each component in specified tile
getMinorVersion() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.FileTypeBox
Returns the minor version of this file type box.
getMinTileX() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the horizontal index of the leftmost column of tiles.
getMinTileX() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getMinTileY() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the vertical index of the uppermost row of tiles.
getMinTileY() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getMinX() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the X coordinate of the leftmost column of the image.
getMinX() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets minX
getMinX() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getMinY() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the X coordinate of the uppermost row of the image.
getMinY() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets minY
getMinY() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getMsgLogger() - Static method in class io.scif.jj2000.j2k.util.FacilityManager
Returns the MsgLogger registered with the current thread (the thread that calls this method).
getMsgLogger(Thread) - Static method in class io.scif.jj2000.j2k.util.FacilityManager
Returns the MsgLogger registered with the thread 't' (the thread that calls this method).
getName() - Method in class io.scif.cli.AbstractSCIFIOToolCommand
 
getName() - Method in class io.scif.cli.convert.Convert
 
getName() - Method in class io.scif.cli.help.Help
 
getName() - Method in class io.scif.cli.info.Info
 
getName() - Method in class io.scif.cli.show.Show
 
getName() - Method in class io.scif.media.imageio.plugins.tiff.TIFFTag
Returns the name of the tag, as it will appear in image metadata.
getName(int) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Returns the XML tag name defined in JP2 XML xsd/dtd for the box with the provided type.
getName() - Method in class io.scif.ome.commands.OMEXMLToolCommand
 
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Creates an IIOMetadataNode from this box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Creates an IIOMetadataNode from this channel definition box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
Creates an IIOMetadataNode from this color specification box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
Creates an IIOMetadataNode from this component mapping box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
Creates an IIOMetadataNode from this data entry URL box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.FileTypeBox
Creates an IIOMetadataNode from this file type box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Creates an IIOMetadataNode from this image header box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
creates an IIOMetadataNode from this palette box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ResolutionBox
Creates an IIOMetadataNode from this resolution box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.SignatureBox
Creates an IIOMetadataNode from this signature box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDBox
Creates an IIOMetadataNode from this UUID box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDListBox
Creates an IIOMetadataNode from this UUID list box.
getNativeNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.XMLBox
Creates an IIOMetadataNode from this XML box.
getNativeNodeForSimpleBox() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Creates an IIOMetadataNode from this box.
getNewCOC() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a new instance of COC
getNewCOD() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a new instance of COD
getNewCOM() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a new instance of COM
getNewCRG() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a new instance of CRG
getNewPOC() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a new instance of POC
getNewQCC() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a new instance of QCC
getNewQCD() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a new instance of QCD
getNewRGN() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a new instance of RGN
getNewSIZ() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a new instance of SIZ
getNewSOT() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns a new instance of SOT
getNextCode() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
getNextCode() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
getNextCodeBlock(int, CBlkRateDistStats) - Method in interface io.scif.jj2000.j2k.entropy.encoder.CodedCBlkDataSrcEnc
Returns the next coded code-block in the current tile for the specified component, as a copy (see below).
getNextCodeBlock(int, CBlkRateDistStats) - Method in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Returns the next coded code-block in the current tile for the specified component, as a copy (see below).
getNextCodeBlock(int, CBlkWTData) - Method in interface io.scif.jj2000.j2k.quantization.quantizer.CBlkQuantDataSrcEnc
Returns the next code-block in the current tile for the specified component, as a copy (see below).
getNextCodeBlock(int, CBlkWTData) - Method in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
Returns the next code-block in the current tile for the specified component, as a copy (see below).
getNextCodeBlock(int, CBlkWTData) - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
This function gets a datablk from the entropy coder.
getNextCodeBlock(int, CBlkWTData) - Method in interface io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataSrc
Returns the next code-block in the current tile for the specified component, as a copy (see below).
getNextCodeBlock(int, CBlkWTData) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the next code-block in the current tile for the specified component, as a copy (see below).
getNextInternCodeBlock(int, CBlkWTData) - Method in interface io.scif.jj2000.j2k.quantization.quantizer.CBlkQuantDataSrcEnc
Returns the next code-block in the current tile for the specified component.
getNextInternCodeBlock(int, CBlkWTData) - Method in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
Returns the next code-block in the current tile for the specified component.
getNextInternCodeBlock(int, CBlkWTData) - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
This function gets a datablk from the entropy coder.
getNextInternCodeBlock(int, CBlkWTData) - Method in interface io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataSrc
Returns the next code-block in the current tile for the specified component.
getNextInternCodeBlock(int, CBlkWTData) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the next code-block in the current tile for the specified component.
getNextResLevel() - Method in class io.scif.jj2000.j2k.wavelet.Subband
Returns the first leaf subband element in the next higher resolution level.
getNextSibling() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getNomRangeBits(int) - Method in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Returns the number of bits, referred to as the "range bits", corresponding to the nominal range of the data in the specified component and in the current tile.
getNomRangeBits(int) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the number of bits, referred to as the "range bits", corresponding to the nominal range of the image data in the specified component.
getNomRangeBits(int) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the number of bits, referred to as the "range bits", corresponding to the nominal range of the image data in the specified component.
getNomRangeBits(int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the number of bits, referred to as the "range bits", corresponding to the nominal range of the data in the specified component.
getNomRangeBits(int) - Method in class io.scif.jj2000.j2k.image.input.ImgReaderPGM
Returns the number of bits corresponding to the nominal range of the data in the specified component.
getNomRangeBits(int) - Method in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Returns the number of bits, referred to as the "range bits", corresponding to the nominal range of the data in the specified component.
getNomRangeBits(int) - Method in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
Returns the number of bits, referred to as the "range bits", corresponding to the nominal range of the data in the specified component.
getNomRangeBits(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.CBlkWTDataSrcDec
Returns the number of bits, referred to as the "range bits", corresponding to the nominal range of the data in the specified component.
getNomRangeBits(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTFull
Returns the number of bits, referred to as the "range bits", corresponding to the nominal range of the data in the specified component.
getNomRangeBits(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the number of bits corresponding to the nominal range of the data in the specified component.
getNomTileHeight() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the nominal tile height
getNomTileHeight() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the nominal width of the tiles in the reference grid.
getNomTileHeight() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the nominal tiles height
getNomTileHeight() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the nominal tiles height
getNomTileHeight() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the nominal tiles height
getNomTileHeight() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the nominal tiles height
getNomTileHeight() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the nominal width of the tiles in the reference grid.
getNomTileHeight() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the nominal height of tiles
getNomTileHeight() - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the nominal tiles height
getNomTileHeight() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the nominal tiles height
getNomTileHeight() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getNomTileWidth() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the nominal tile width
getNomTileWidth() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the nominal width of the tiles in the reference grid.
getNomTileWidth() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the nominal tiles width
getNomTileWidth() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the nominal tiles width
getNomTileWidth() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the nominal tiles width
getNomTileWidth() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the nominal tiles width
getNomTileWidth() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the nominal width of the tiles in the reference grid.
getNomTileWidth() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the nominal width of tiles
getNomTileWidth() - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the nominal tiles width
getNomTileWidth() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the nominal tiles width
getNomTileWidth() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getNOptPoints() - Method in class io.scif.jj2000.j2k.entropy.encoder.LayersInfo
Returns the number of layers to optimize, or optimization points, as specified by this object.
getNoROIDescaling() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava
Gets noROIDescaling
getNumber() - Method in class io.scif.media.imageio.plugins.tiff.TIFFTag
Returns the integer used to represent the tag.
getNumCodedBytes() - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Returns the number of bytes that are necessary from the compressed output stream to decode all the symbols that have been coded this far.
getNumCOM() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns the number of found COM marker segments
getNumComp() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
Return the number of color components.
getNumComponents() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Returns the number of image components.
getNumComponents() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets the number of components
getNumComps() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the number of components in the image.
getNumComps() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the number of components in the image.
getNumComps() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the number of components in the image.
getNumComps() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the number of components in the image.
getNumComps() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the number of components in the image.
getNumComps() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the number of components in the image.
getNumComps() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the number of components in the image.
getNumComps() - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the number of components in the image.
getNumComps() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the number of components in the image.
getNumComps() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the number of components in the image.
getNumCtxts() - Method in class io.scif.jj2000.j2k.entropy.decoder.MQDecoder
Returns the number of contexts in the arithmetic coder.
getNumCtxts() - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Returns the number of contexts in the arithmetic coder.
getNumDecompositionLevels() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets numDecompositionLevels.
getNumEntries() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
Return the number of palette entries.
getNumFoundMarkSeg() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the number of found marker segments in the current header.
getNumGuardBits() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCC
 
getNumGuardBits() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCD
 
getNumGuardBits(int, int) - Method in class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
Returns the number of guard bits used by this quantizer in the given tile-component.
getNumGuardBits(int, int) - Method in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
Returns the number of guard bits used by this quantizer in the given tile-component.
getNumImages() - Method in class io.scif.media.imageio.stream.RawImageInputStream
Retrieves the number of images in the ImageInputStream.
getNumImages(boolean) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
Overrides the method defined in the superclass.
getNumImages(boolean) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
Overrides the method defined in the superclass.
getNumImages(boolean) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReader
 
getNumImages(boolean) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
Overrides the method defined in the superclass.
getNumImages(boolean) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
Overrides the method defined in the superclass.
getNumImages(boolean) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getNumImages(boolean) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
Overrides the method defined in the superclass.
getNumLayers() - Method in class io.scif.jj2000.j2k.entropy.encoder.PostCompRateAllocator
Returns the number of layers that are actually generated.
getNumPrecinct(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.PktDecoder
Gets the number of precincts in a given component and resolution level.
getNumThumbnails(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getNumTIFFFields() - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Returns the number of TIFFFields in this directory.
getNumTileParts(int) - Method in class io.scif.jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
Returns the number of tile-part found for a given tile
getNumTiles() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
getNumTiles(Point) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the number of tiles in the horizontal and vertical directions.
getNumTiles() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the total number of tiles in the image.
getNumTiles() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Return the number of tiles in the image
getNumTiles(Point) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the number of tiles in the horizontal and vertical directions.
getNumTiles() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the total number of tiles in the image.
getNumTiles(Point) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the number of tiles in the horizontal and vertical directions.
getNumTiles() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the total number of tiles in the image.
getNumTiles(Point) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the number of tiles in the horizontal and vertical directions.
getNumTiles() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the total number of tiles in the image.
getNumTiles(Point) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the number of tiles in the horizontal and vertical directions.
getNumTiles() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the total number of tiles in the image.
getNumTiles(Point) - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the number of tiles in the horizontal and vertical directions.
getNumTiles() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the total number of tiles in the image.
getNumTiles(Point) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the number of tiles in the horizontal and vertical directions.
getNumTiles() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the total number of tiles in the image.
getNumTiles(Point) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the number of tiles in the horizontal and vertical directions.
getNumTiles() - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the total number of tiles in the image.
getNumTiles(Point) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the number of tiles in the horizontal and vertical directions.
getNumTiles() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the total number of tiles in the image.
getNumTiles() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets the number of tiles
getNumTiles(Point) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the number of tiles in the horizontal and vertical directions.
getNumTiles() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the total number of tiles in the image.
getNumXTiles() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the number of tiles along the tile grid in the horizontal direction.
getNumXTiles() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getNumYTiles() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the number of tiles along the tile grid in the vertical direction.
getNumYTiles() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getObjectArrayMaxLength(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectArrayMinLength(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectClass(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectDefaultValue(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectEnumerations(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectMaxValue(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectMinValue(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getObjectValueType(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getOffLastROIPkt() - Method in class io.scif.jj2000.j2k.codestream.writer.CodestreamWriter
Gives the offset of the end of last packet containing ROI information
getOffLastROIPkt() - Method in class io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
Gives the offset of the end of last packet containing ROI information
getOMEMetadata(MetadataRetrieve) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
getOMEMetadata(MetadataRetrieve) - Method in interface io.scif.ome.services.OMEXMLService
 
getOMEXML(MetadataRetrieve) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
getOMEXML(MetadataRetrieve) - Method in interface io.scif.ome.services.OMEXMLService
 
getOMEXMLVersion(Object) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
getOMEXMLVersion(Object) - Method in interface io.scif.ome.services.OMEXMLService
 
getOrder() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
getOrigBitDepth(int) - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
getOriginalBitDepth(int) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the original bitdepth of the specified component.
getOriginalMetadata(OMEXMLMetadata) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
getOriginalMetadata(OMEXMLMetadata) - Method in interface io.scif.ome.services.OMEXMLService
 
getPackedBinaryData(Raster, Rectangle) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
For the case of binary data (isBinary() returns true), return the binary data as a packed byte array.
getPackedPktHead(int) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Return the packed packet headers for a given tile.
getPacketPerTilePart() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets packetPerTilePart
getPackPacketHeaderInMain() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets packPacketHeaderInMain
getPackPacketHeaderInTile() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets packPacketHeaderInTile
getParameterInfo() - Static method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the parameters that are used in this class.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.entropy.decoder.EntropyDecoder
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.entropy.encoder.EntropyCoder
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.entropy.encoder.PostCompRateAllocator
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.roi.ROIDeScaler
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilter
Returns the parameters that are used in this class and implementing classes.
getParameterInfo() - Static method in class io.scif.jj2000.j2k.wavelet.analysis.ForwardWT
Returns the parameters that are used in this class and implementing classes.
getParent() - Method in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
Returns the parent of this subband.
getParent() - Method in class io.scif.jj2000.j2k.wavelet.Subband
Returns the parent of this subband.
getParent() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
Returns the parent of this subband.
getParent(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
getParent(String) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadataFormat
 
getParentTag() - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Returns the parent TIFFTag of this directory if one has been defined or null otherwise.
getParsingEnabled() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava
Gets parsingEnabled
getPhotometricInterpretation() - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageWriteParam
Returns the current value that will be written to the Photometricinterpretation tag.
getPos() - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Returns the current offset in the file
getPos() - Method in interface io.scif.jj2000.j2k.io.RandomAccessIO
Returns the current position in the stream, which is the position from where the next byte of data would be read.
getPos() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Returns the current position in the stream, which is the position from where the next byte of data would be read.
getPos() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
Returns the stream position clamped to a maximum of Integer.MAX_VALUE.
getPPX(int, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the precinct partition width for the specified tile-component and (tile-component) resolution level.
getPPX(int, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the precinct partition width for the specified tile-component and resolution level.
getPPX(int, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.PktDecoder
Returns the precinct partition width for the specified component, resolution level and tile.
getPPX(int, int, int) - Method in interface io.scif.jj2000.j2k.entropy.encoder.CodedCBlkDataSrcEnc
Returns the width of a packet for the specified tile- component and resolution level.
getPPX(int, int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Returns the precinct partition width for the specified component, tile and resolution level.
getPPX(int, int, int) - Method in class io.scif.jj2000.j2k.entropy.PrecinctSizeSpec
Returns the precinct partition width in component 'n' and tile 't' at resolution level 'rl'.
getPPY(int, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the precinct partition height for the specified tile-component and (tile-component) resolution level.
getPPY(int, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the precinct partition height for the specified component, tile and resolution level.
getPPY(int, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.PktDecoder
Returns the precinct partition height for the specified component, resolution level and tile.
getPPY(int, int, int) - Method in interface io.scif.jj2000.j2k.entropy.encoder.CodedCBlkDataSrcEnc
Returns the height of a packet for the specified tile- component and resolution level.
getPPY(int, int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Returns the precinct partition height for the specified component, tile and resolution level.
getPPY(int, int, int) - Method in class io.scif.jj2000.j2k.entropy.PrecinctSizeSpec
Returns the precinct partition height in component 'n' and tile 't' at resolution level 'rl'.
getPrecedence() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
Returns Precedence.
getPrecinctPartition() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets precinctPartition
getPrecInfo(int, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.PktDecoder
Get PrecInfo instance of the specified resolution level, component and precinct.
getPrecInfo(int, int, int, int) - Method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Returns information about a given precinct
getPreviousSibling() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
getProgressionName() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets progressionType
getProgressionType() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets progressionType.
getProgressionType() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets progressionType
getProgressWatch() - Static method in class io.scif.jj2000.j2k.util.FacilityManager
Returns the ProgressWatch instance registered with the current thread (the thread that calls this method).
getProperty(String) - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Gets a property from the property set of this image.
getProperty(String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getPropertyNames() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns a list of the properties recognized by this image.
getPropertyNames(String) - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns an array of Strings recognized as names by this property source that begin with the supplied prefix.
getPropertyNames() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getQuantizationStep() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets quantizationStep
getQuantizationType() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets quantizationType
getQuantType() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCC
 
getQuantType() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCD
 
getQuantTypeSpec() - Method in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
Returns the quantization type spec object associated to the quantizer.
getRaw() - Method in class io.scif.media.imageio.plugins.pnm.PNMImageWriteParam
Returns the value of the raw parameter.
getRawImageType() - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Returns an ImageTypeSpecifier describing an image whose underlying data array has the same format as the raw source pixel data.
getRawImageTypeSpecifier(int, int, int, int[], int[], int[], char[]) - Static method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
A utility method that returns an ImageTypeSpecifier suitable for decoding an image with the given parameters.
getReader() - Method in class io.scif.bf.BioFormatsFormat.Metadata
 
getReductionFactorX() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getReductionFactorY() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getReductionFactorZ() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getResetMQ() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets resetMQ
getResolution() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageReadParam
Gets resolution.
getResULX(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the horizontal coordinate of the upper-left corner of the specified resolution in the given component of the current tile.
getResULX(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the horizontal coordinate of the upper-left corner of the specified resolution in the given component of the current tile.
getResULX(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the horizontal coordinate of the upper-left corner of the specified resolution level in the given component of the current tile.
getResULY(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the vertical coordinate of the upper-left corner of the specified component in the given component of the current tile.
getResULY(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the vertical coordinate of the upper-left corner of the specified resolution in the given component of the current tile.
getResULY(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the vertical coordinate of the upper-left corner of the specified resolution in the given component of the current tile.
getRGB() - Method in class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
getROILen() - Method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Gives the length to read in current packet body to get all ROI information
getROIMask(DataBlkInt, Subband, int, int) - Method in class io.scif.jj2000.j2k.roi.encoder.ArbROIMaskGenerator
This functions gets a DataBlk the size of the current code-block an fills this block with the ROI mask.
getROIMask(DataBlkInt, Subband, int, int) - Method in class io.scif.jj2000.j2k.roi.encoder.RectROIMaskGenerator
This functions gets a DataBlk the size of the current code-block and fills this block with the ROI mask.
getROIMask(DataBlkInt, Subband, int, int) - Method in class io.scif.jj2000.j2k.roi.encoder.ROIMaskGenerator
This functions gets a DataBlk with the size of the current code-block and fills it with the ROI mask.
getROIMaskGenerator() - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
This function returns the ROI mask generator.
getROIs() - Method in class io.scif.jj2000.j2k.roi.encoder.ROIMaskGenerator
This function returns the ROIs in the image
getROIs() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets ROIs
getRoot() - Method in class io.scif.ome.OMEMetadata
Returns the root of this Metadata
getRootIFD() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getRootName() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
getSampleModel() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the SampleModel of the image.
getSampleModel() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getSampleModel() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getSDTInfo() - Method in class io.scif.lifesci.SDTFormat.Metadata
 
getSegmentLength() - Method in class io.scif.media.imageio.stream.StreamSegment
Returns the length of the segment.
getShallowClone() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
Returns a TIFFIFD wherein all fields from the BaselineTIFFTagSet are copied by value and all other fields copied by reference.
getShallowClone() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
Returns a TIFFImageMetadata wherein all fields in the root IFD from the BaselineTIFFTagSet are copied by value and all other fields copied by reference.
getShortElementValue(Node) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Gets its short value from an IIOMetadataNode.
getSize(int) - Static method in class io.scif.jj2000.j2k.image.DataBlk
Returns the size in bits, given the data type.
getSize() - Method in class io.scif.jj2000.j2k.util.ThreadPool
Returns the size of the pool.
getSizeOfType(int) - Static method in class io.scif.media.imageio.plugins.tiff.TIFFTag
Returns the number of bytes used to store a value of the given data type.
getSOP() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets SOP.
getSOP() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets SOP
getSources() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
 
getSources() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getSpec(int, int) - Method in class io.scif.jj2000.j2k.ModuleSpec
Gets value of specified tile-component without knowing if a specific tile-component value has been previously entered.
getSpecificationTitle() - Static method in class io.scif.media.imageioimpl.common.PackageUtil
Return the Specification Title string for the package.
getSpecified() - Method in class io.scif.jj2000.j2k.roi.MaxShiftSpec
 
getSpecified() - Method in class io.scif.jj2000.j2k.StringSpec
 
getSpecValType(int, int) - Method in class io.scif.jj2000.j2k.ModuleSpec
Return the spec type of the given tile-component.
getStandardChromaNode() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardChromaNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardChromaNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardChromaNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardChromaNode() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
getStandardChromaNode() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardChromaNode() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
getStandardCompressionNode() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardCompressionNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardCompressionNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardCompressionNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardCompressionNode() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardDataNode() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardDataNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardDataNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardDataNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardDataNode() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
getStandardDataNode() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardDataNode() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
getStandardDimensionNode() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardDimensionNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardDimensionNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardDimensionNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardDimensionNode() - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXMetadata
 
getStandardDimensionNode() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
getStandardDimensionNode() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardDimensionNode() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
getStandardDocumentNode() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardDocumentNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardDocumentNode() - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXMetadata
 
getStandardDocumentNode() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardTextNode() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardTextNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardTextNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardTextNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardTextNode() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
getStandardTextNode() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStandardTransparencyNode() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
getStandardTransparencyNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
getStandardTransparencyNode() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
getStandardTransparencyNode() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
getStandardTransparencyNode() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getStartLevelROI() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets startLevel
getStartPos() - Method in class io.scif.media.imageio.stream.StreamSegment
Returns the starting position of the segment.
getStream() - Method in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Returns the ImageOutputStream that will be written.
getStreamMetadata() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
getStreamMetadata() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getStreamMetadata() - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReader
 
getStreamMetadata() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
getStreamMetadata() - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
getStreamMetadata() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getStreamMetadata(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getStreamMetadata() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getStreamPosition() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
getStreamSegment(long, int) - Method in interface io.scif.media.imageio.stream.StreamSegmentMapper
Returns a StreamSegment object indicating the location of the initial portion of a desired segment in the source stream.
getStreamSegment(long, int, StreamSegment) - Method in interface io.scif.media.imageio.stream.StreamSegmentMapper
Sets the values of a StreamSegment object indicating the location of the initial portion of a desired segment in the source stream.
getString(String, String) - Static method in class io.scif.media.imageioimpl.common.I18NImpl
Returns the message string with the specified key from the "properties" file in the package containing the class with the specified name.
getStringElementValue(Node) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Gets its String value from an IIOMetadataNode.
getStripOrTileByteCountsPosition() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
 
getStripOrTileOffsetsPosition() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
 
getSubband(int, int) - Method in class io.scif.jj2000.j2k.wavelet.Subband
Returns a reference to the Subband element to which the specified point belongs.
getSubbandByIdx(int, int) - Method in class io.scif.jj2000.j2k.wavelet.Subband
Returns a subband element in the tree, given its resolution level and subband index.
getSubbandRectROIMask(int, int) - Method in class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
Returns a reference to the Subband mask element to which the specified point belongs.
getSuffixes() - Method in class io.scif.bf.BioFormatsFormat
 
getSynHighNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the negative support of the high-pass synthesis filter.
getSynHighNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the negative support of the high-pass synthesis filter.
getSynHighNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns the negative support of the high-pass synthesis filter.
getSynHighNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns the negative support of the high-pass synthesis filter.
getSynHighNegSupport() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the negative support of the high-pass synthesis filter.
getSynHighPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the positive support of the high-pass synthesis filter.
getSynHighPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the positive support of the high-pass synthesis filter.
getSynHighPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns the positive support of the high-pass synthesis filter.
getSynHighPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns the positive support of the high-pass synthesis filter.
getSynHighPosSupport() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the positive support of the high-pass synthesis filter.
getSynLowNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the negative support of the low-pass synthesis filter.
getSynLowNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the negative support of the low-pass synthesis filter.
getSynLowNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns the negative support of the low-pass synthesis filter.
getSynLowNegSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns the negative support of the low-pass synthesis filter.
getSynLowNegSupport() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the negative support of the low-pass synthesis filter.
getSynLowPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the positive support of the low-pass synthesis filter.
getSynLowPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the positive support of the low-pass synthesis filter.
getSynLowPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns the positive support of the low-pass synthesis filter.
getSynLowPosSupport() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns the positive support of the low-pass synthesis filter.
getSynLowPosSupport() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the positive support of the low-pass synthesis filter.
getSynSubbandTree(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the subband tree, for the specified tile-component.
getSynSubbandTree(int, int) - Method in class io.scif.jj2000.j2k.entropy.decoder.EntropyDecoder
Returns the subband tree, for the specified tile-component.
getSynSubbandTree(int, int) - Method in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
Returns the subband tree, for the specified tile-component.
getSynSubbandTree(int, int) - Method in class io.scif.jj2000.j2k.roi.ROIDeScaler
Returns the subband tree, for the specified tile-component.
getSynSubbandTree(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the specified synthesis subband tree
getSynSubbandTree(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.InvWTData
Returns the subband tree, for the specified tile-component.
getSynSubbandTree(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the specified synthesis subband tree
getTag(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Returns the TIFFTag which has tag number equal to tagNumber or null if no such tag exists in the TIFFTagSets associated with this directory.
getTag() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Retrieves the tag associated with this field.
getTag(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFTagSet
Returns the TIFFTag from this set that is associated with the given tag number, or null if no tag exists for that number.
getTag(String) - Method in class io.scif.media.imageio.plugins.tiff.TIFFTagSet
Returns the TIFFTag having the given tag name, or null if the named tag does not belong to this tag set.
getTag(int, List) - Static method in class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
 
getTag(String, List) - Static method in class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
 
getTagNames() - Method in class io.scif.media.imageio.plugins.tiff.TIFFTagSet
Retrieves an unmodifiable lexicographically increasing set of tag names.
getTagNumber() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Retrieves the tag number in the range [0, 65535].
getTagNumbers() - Method in class io.scif.media.imageio.plugins.tiff.TIFFTagSet
Retrieves an unmodifiable numerically increasing set of tag numbers.
getTagSet() - Method in class io.scif.media.imageio.plugins.tiff.TIFFTag
Returns the TIFFTagSet of which this tag is a part.
getTagSetList() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
 
getTagSets() - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Returns the TIFFTagSets of which this directory is aware.
getTargetBitrate(int) - Method in class io.scif.jj2000.j2k.entropy.encoder.LayersInfo
Returns the target bitrate of the optmimization point 'n'.
getTargetNbytes() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Return the target number of read bytes.
getTargetRate() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Return the target decoding rate in bits per pixel.
getTBlockSize() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getTerminateOnByte() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Gets terminateOnByte
getThreadConcurrency() - Static method in class io.scif.jj2000.j2k.util.NativeServices
Returns the current concurrency level.
getTIFFCompressor() - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageWriteParam
Returns the TIFFCompressor that is currently set to be used by the ImageWriter to encode each image strip or tile, or null if none has been set.
getTIFFDecompressor() - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageReadParam
Returns the TIFFDecompressor that is currently set to be used by the ImageReader to decode each image strip or tile, or null if none has been set.
getTIFFField(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Retrieves a TIFF field from the directory.
getTIFFField(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
getTIFFFields() - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Retrieves all TIFF fields from the directory.
getTile(Point) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the indexes of the current tile.
getTile(Point) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the indixes of the current tile.
getTile(Point) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the indexes of the current tile.
getTile(Point) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the coordinates of the current tile.
getTile(Point) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the coordinates of the current tile.
getTile(Point) - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the horizontal and vertical indexes of the current tile.
getTile(Point) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the indixes of the current tile.
getTile(Point) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the indexes of the current tile.
getTile(Point) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the indexes of the current tile.
getTile(int, int) - Method in class io.scif.media.imageioimpl.common.SingleTileRenderedImage
Returns the image's Raster as tile (0, 0).
getTile(int, int, WritableRaster) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getTile(int, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
 
getTile(Point) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the coordinates of the current tile.
getTile(int, int) - Method in class io.scif.media.imageioimpl.plugins.raw.RawRenderedImage
 
getTile(int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getTileCompHeight(int, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the height in pixels of the specified tile-component for the given (tile-component) resolution level.
getTileCompHeight(int, int) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the height in pixels of the specified tile-component.
getTileCompHeight(int, int) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the height in pixels of the specified tile-component.
getTileCompHeight(int, int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the height in pixels of the specified tile-component.
getTileCompHeight(int, int) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the height in pixels of the specified tile-component.
getTileCompHeight(int, int) - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the height in pixels of the specified tile-component.
getTileCompHeight(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the height in pixels of the specified tile-component.
getTileCompHeight(int, int, int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the height in pixels of the specified tile-component for the given resolution level.
getTileCompHeight(int, int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the height in pixels of the specified tile-component for the given resolution level.
getTileCompHeight(int, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTileCompVal(int, int) - Method in class io.scif.jj2000.j2k.ModuleSpec
Gets value of specified tile-component.
getTileCompWidth(int, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the width in pixels of the specified tile-component for the given (tile-component) resolution level.
getTileCompWidth(int, int) - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the width in pixels of the specified tile-component
getTileCompWidth(int, int) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the width in pixels of the specified tile-component tile.
getTileCompWidth(int, int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the width in pixels of the specified tile-component
getTileCompWidth(int, int) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the width in pixels of the specified tile-component.
getTileCompWidth(int, int) - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the width in pixels of the specified tile-component.
getTileCompWidth(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the width in pixels of the specified tile-component
getTileCompWidth(int, int, int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the width in pixels of the specified tile-component for the given resolution level.
getTileCompWidth(int, int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the width in pixels of the specified tile-component for the given resolution level.
getTileCompWidth(int, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTileDef(int) - Method in class io.scif.jj2000.j2k.ModuleSpec
Gets default value of the specified tile.
getTileGridXOffset() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the X coordinate of the upper-left pixel of tile (0, 0).
getTileGridXOffset(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getTileGridXOffset() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTileGridXOffset() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getTileGridYOffset() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the Y coordinate of the upper-left pixel of tile (0, 0).
getTileGridYOffset(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getTileGridYOffset() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTileGridYOffset() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getTileHeight(int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the overall height of the current tile in pixels, for the given resolution level.
getTileHeight() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the overall height of the current tile in pixels.
getTileHeight() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the overall height of the current tile in pixels.
getTileHeight() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the overall height of the current tile in pixels.
getTileHeight() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the overall height of the current tile in pixels, assuming there is no-tiling.
getTileHeight() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the overall height of the current tile in pixels.
getTileHeight() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the overall height of the current tile in pixels.
getTileHeight(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the overall height of the current tile in pixels, for the given resolution level.
getTileHeight(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the overall height of the current tile in pixels, for the given resolution level.
getTileHeight() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the height of a tile.
getTileHeight(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getTileHeight() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the overall height of the current tile in pixels.
getTileHeight(int) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
getTileHeight(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getTileHeight() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getTileIdx() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the index of the current tile, relative to a standard scan-line order.
getTileIdx() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the index of the current tile, relative to a standard scan-line order.
getTileIdx() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the index of the current tile, relative to a standard scan-line order.
getTileIdx() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the index of the current tile, relative to a standard scan-line order.
getTileIdx() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the index of the current tile, relative to a standard scan-line order.
getTileIdx() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the index of the current tile, relative to a standard scan-line order.
getTileIdx() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the index of the current tile, relative to a standard scan-line order.
getTileIdx() - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the index of the current tile, relative to a standard scan-line order.
getTileIdx() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the index of the current tile, relative to a standard scan-line order.
getTileIdx() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the index of the current tile, relative to a standard scan-line order.
getTileOff(Point, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the horizontal and vertical offset of the upper-left corner of the current tile, in the specified component, relative to the canvas origin, in the component coordinates (not in the reference grid coordinates).
getTilePartULX() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the horizontal offset of tile partition
getTilePartULX() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the horizontal tile partition offset in the reference grid
getTilePartULX() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the horizontal tile partition offset in the reference grid
getTilePartULX() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the horizontal tile partition offset in the reference grid
getTilePartULX() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the horizontal tile partition offset in the reference grid
getTilePartULX() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the horizontal tile partition offset in the reference grid
getTilePartULX() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the horizontal tile partition offset in the reference grid
getTilePartULX() - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the horizontal tile partition offset in the reference grid
getTilePartULX() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the horizontal tile partition offset in the reference grid
getTilePartULX() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTilePartULY() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the vertical offset of tile partition
getTilePartULY() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the vertical tile partition offset in the reference grid
getTilePartULY() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the vertical tile offset in the reference grid
getTilePartULY() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the vertical tile partition offset in the reference grid
getTilePartULY() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the vertical tile partition offset in the reference grid
getTilePartULY() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the vertical tile partition offset in the reference grid
getTilePartULY() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the vertical tile partition offset in the reference grid
getTilePartULY() - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the vertical tile partition offset in the reference grid
getTilePartULY() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the vertical tile partition offset in the reference grid
getTilePartULY() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
getTileSize(SampleModel) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
 
getTileWidth(int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Returns the overall width of the current tile in pixels for the given (tile) resolution level.
getTileWidth() - Method in interface io.scif.jj2000.j2k.image.ImgData
Returns the overall width of the current tile in pixels.
getTileWidth() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Returns the overall width of the current tile in pixels.
getTileWidth() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns the overall width of the current tile in pixels.
getTileWidth() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns the width of the current tile in pixels, assuming there is no-tiling.
getTileWidth() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the overall width of the current tile in pixels.
getTileWidth() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Returns the overall width of the current tile in pixels.
getTileWidth(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Returns the overall width of the current tile in pixels for the given resolution level.
getTileWidth(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Returns the overall width of the current tile in pixels, for the given resolution level.
getTileWidth() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the width of a tile.
getTileWidth(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getTileWidth() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns the width of the current tile in pixels.
getTileWidth(int) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
getTileWidth(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getTileWidth() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getTilingOrigin(Point) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the tiling origin, referred to as '(Px,Py)' in the 'ImgData' interface.
getTilingOrigin(Point) - Method in class io.scif.jj2000.j2k.image.Tiler
Returns the tiling origin, referred to as '(xt0siz,yt0siz)' in the codestream header (SIZ marker segment).
getTimeBase() - Method in class io.scif.lifesci.SDTFormat.Metadata
 
getTimeBins() - Method in class io.scif.lifesci.SDTFormat.Metadata
 
getTotBitrate() - Method in class io.scif.jj2000.j2k.entropy.encoder.LayersInfo
Returns the overall target bitrate for the entire bit stream.
getTotNumLayers() - Method in class io.scif.jj2000.j2k.entropy.encoder.LayersInfo
Returns the total number of layers, according to the layer specification of this object and the overall target bitrate.
getType() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns the type of the data stored in the field.
getType() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Returns the box type.
getTypeByName(String) - Static method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns the data type constant corresponding to the supplied data type name.
getTypeByName(String) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Returns the type String based on the provided name.
getTypeInt(String) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Converts the box type from integer to string.
getTypeName(int) - Static method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns the name of the supplied data type constant.
getTypes() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Returns the channel types.
getTypeString(int) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Converts the box type from integer to string.
getUnknownColorspace() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Returns the UnknowColorspace flag.
getUnpackedBinaryData(Raster, Rectangle) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Returns the binary data unpacked into an array of bytes.
getURL() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
Returns the URL data element.
getUUID() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDBox
Returns the UUID of this box.
getValue(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.TagTreeDecoder
Returns the current value of the specified element in the tag tree.
getValueAsString(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Returns a String containing a human-readable version of the data item.
getValueName(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFTag
Returns the mnemonic name associated with a particular value that this tag's data may take on, or null if no name is present.
getVariant() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
getVariant() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
getVendor() - Static method in class io.scif.media.imageioimpl.common.PackageUtil
Return a vendor string for the package.
getVersion() - Method in class io.scif.media.imageio.plugins.bmp.BMPImageWriteParam
Deprecated. 
getVersion() - Static method in class io.scif.media.imageioimpl.common.PackageUtil
Return a version string for the package.
getVersion() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
Returns the Version data element.
getVertAnWaveletFilters(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.analysis.ForwWT
Returns the vertical analysis wavelet filters used in each level, for the specified tile-component.
getVertAnWaveletFilters(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the vertical analysis wavelet filters used in each level, for the specified component and tile.
getVerticalResolution() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ResolutionBox
Return the vertical resolution.
getVerWFilter() - Method in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
This function returns the vertical wavelet filter relevant to this subband
getVerWFilter() - Method in class io.scif.jj2000.j2k.wavelet.Subband
This function returns the vertical wavelet filter relevant to this subband
getVerWFilter() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
This function returns the vertical wavelet filter relevant to this subband
getVFilters(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterSpec
Returns the vertical analysis filters to be used in component 'n' and tile 't'.
getVFilters(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterSpec
Returns the vertical analysis filters to be used in component 'n' and tile 't'.
getWidth() - Method in class io.scif.jj2000.j2k.codestream.reader.TagTreeDecoder
Returns the number of leafs along the horizontal direction.
getWidth() - Method in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Returns the number of leafs along the horizontal direction.
getWidth() - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Returns the width of the image.
getWidth(int) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
getWidth() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Returns the width of the image.
getWidth(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
getWidth() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
getWidth(int) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReader
 
getWidth(int) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
getWidth(int) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
getWidth() - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
getWidth(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
getWidth() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
getWidth(int) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
getWrappedStream() - Method in class io.scif.media.imageioimpl.plugins.clib.InputStreamAdapter
 
getWriteCodeStreamOnly() - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Gets writeCodeStreamOnly.
getWriter() - Method in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Returns the current ImageWriter.
getWTDataType(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterSpec
Returns the data type used by the filters in this object, as defined in the 'DataBlk' interface for specified tile-component.
getWTDataType(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterSpec
Returns the data type used by the filters in this object, as defined in the 'DataBlk' interface for specified tile-component.
getWTDataType() - Method in class io.scif.jj2000.j2k.wavelet.WTFilterSpec
Returns the data type used by the filters in this object, as defined in the 'DataBlk' interface.
getXBlockSize() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getYBlockSize() - Method in class io.scif.formats.imaris.ResolutionLevel
 
getZBlockSize() - Method in class io.scif.formats.imaris.ResolutionLevel
 
GIFImageMetadata - Class in io.scif.media.imageioimpl.plugins.gif
 
GIFImageMetadata(boolean, String, String, String[], String[]) - Constructor for class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
GIFImageMetadata() - Constructor for class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
GIFImageMetadataFormat - Class in io.scif.media.imageioimpl.plugins.gif
 
GIFImageMetadataFormatResources - Class in io.scif.media.imageioimpl.plugins.gif
 
GIFImageMetadataFormatResources() - Constructor for class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadataFormatResources
 
GIFImageWriter - Class in io.scif.media.imageioimpl.plugins.gif
 
GIFImageWriter(GIFImageWriterSpi) - Constructor for class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
GIFImageWriterSpi - Class in io.scif.media.imageioimpl.plugins.gif
 
GIFImageWriterSpi() - Constructor for class io.scif.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
GIFStreamMetadata - Class in io.scif.media.imageioimpl.plugins.gif
 
GIFStreamMetadata(boolean, String, String, String[], String[]) - Constructor for class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
GIFStreamMetadata() - Constructor for class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
GIFStreamMetadataFormat - Class in io.scif.media.imageioimpl.plugins.gif
 
GIFStreamMetadataFormatResources - Class in io.scif.media.imageioimpl.plugins.gif
 
GIFStreamMetadataFormatResources() - Constructor for class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadataFormatResources
 
globalColorTable - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
GPS_VERSION_2_2 - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
An array of bytes containing the values {'2', '2', '0', '0'} to be used with the "GPSVersionID" tag to indicate GPS version 2.2.
GRAY_RESPONSE_UNIT_HUNDRED_THOUSANDTHS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "GrayResponseUnit" tag.
GRAY_RESPONSE_UNIT_HUNDREDTHS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "GrayResponseUnit" tag.
GRAY_RESPONSE_UNIT_TEN_THOUSANDTHS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "GrayResponseUnit" tag.
GRAY_RESPONSE_UNIT_TENTHS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "GrayResponseUnit" tag.
GRAY_RESPONSE_UNIT_THOUSANDTHS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "GrayResponseUnit" tag.
green - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
green - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
greenMask - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
greenX - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
greenY - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
greenZ - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
GuardBitsSpec - Class in io.scif.jj2000.j2k.quantization
This class extends ModuleSpec class in order to hold specifications about number of guard bits in each tile-component.
GuardBitsSpec(int, int, byte) - Constructor for class io.scif.jj2000.j2k.quantization.GuardBitsSpec
Constructs an empty 'GuardBitsSpec' with specified number of tile and components.
GuardBitsSpec(int, int, byte, J2KImageWriteParamJava, String) - Constructor for class io.scif.jj2000.j2k.quantization.GuardBitsSpec
Constructs a new 'GuardBitsSpec' for the specified number of components and tiles and the arguments of "-Qguard_bits" option.

H

h - Variable in class io.scif.jj2000.j2k.codestream.CoordInfo
Object's height
h - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Precinct height in the corresponding resolution level
h - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
Height of the code-block
h - Variable in class io.scif.jj2000.j2k.codestream.reader.TagTreeDecoder
The vertical dimensions of the base level
h - Variable in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
The vertical dimensions of the base level
h - Variable in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
The height of the code-block
h - Variable in class io.scif.jj2000.j2k.image.DataBlk
The height of the block, in pixels.
h - Variable in class io.scif.jj2000.j2k.image.input.ImgReader
The height of the image
h - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
height of rectangular ROI
h - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
Height of the subband mask
h - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The height of the code-block
h - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The height of the subband
handleException(Throwable) - Static method in class io.scif.jj2000.j2k.JJ2KExceptionHandler
Handles the exception.
hasChildNodes() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
hasExtendedMeasureInfo - Variable in class io.scif.lifesci.SDTInfo
 
Hash(short, byte) - Static method in class io.scif.media.imageioimpl.common.LZWStringTable
 
hasJPEGTables - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
hasMeasFCSInfo - Variable in class io.scif.lifesci.SDTInfo
 
hasMeasHISTInfo - Variable in class io.scif.lifesci.SDTInfo
 
hasMeasStopInfo - Variable in class io.scif.lifesci.SDTInfo
 
hasMeasureInfo - Variable in class io.scif.lifesci.SDTInfo
 
hasPlainTextExtension - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
hasThumbnails(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
hasValueNames() - Method in class io.scif.media.imageio.plugins.tiff.TIFFTag
Returns true if there are mnemonic names associated with the set of legal values for the data associated with this tag.
hbuf - Variable in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
The DataOutputStream to store header data.
hd - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The decoded bit stream header
HDFPreprocessor - Class in io.scif.formats.imaris
 
HDFPreprocessor(int, int, int, ResolutionLevel[]) - Constructor for class io.scif.formats.imaris.HDFPreprocessor
 
HDFUtils - Class in io.scif.formats.imaris
 
HDFUtils() - Constructor for class io.scif.formats.imaris.HDFUtils
 
HDFWriter - Class in io.scif.formats.imaris
 
HDFWriter(String, int, int, int, int, double, double, Color[], int, int, ResolutionLevel[]) - Constructor for class io.scif.formats.imaris.HDFWriter
 
HeaderBox - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is defined to represent an Image Header Box of JPEG JP2 file format.
HeaderBox(int, int, int, int, int, int, int) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Create an Image Header Box from the element values.
HeaderBox(byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Create an Image Header Box using the content data.
HeaderBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Constructs an Image Header Box from a Node.
HeaderDecoder - Class in io.scif.jj2000.j2k.codestream.reader
This class reads Main and Tile-part headers from the codestream.
HeaderDecoder(RandomAccessIO, J2KImageReadParamJava, HeaderInfo) - Constructor for class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Creates a HeaderDecoder instance and read in two passes the main header of the codestream.
HeaderEncoder - Class in io.scif.jj2000.j2k.codestream.writer
This class writes almost of the markers and marker segments in main header and in tile-part headers.
HeaderEncoder(ImgData, boolean[], ForwardWT, Tiler, J2KImageWriteParamJava, ROIScaler, PostCompRateAllocator) - Constructor for class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Initializes the header writer with the references to the coding chain.
HeaderInfo - Class in io.scif.jj2000.j2k.codestream
Classe that holds information found in the marker segments of the main and tile-part headers.
HeaderInfo() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo
 
HeaderInfo.COC - Class in io.scif.jj2000.j2k.codestream
Internal class holding information found in the COC marker segments
HeaderInfo.COD - Class in io.scif.jj2000.j2k.codestream
Internal class holding information found in the COD marker segments
HeaderInfo.COM - Class in io.scif.jj2000.j2k.codestream
Internal class holding information found in the COM marker segments
HeaderInfo.CRG - Class in io.scif.jj2000.j2k.codestream
Internal class holding information found in the CRG marker segment
HeaderInfo.POC - Class in io.scif.jj2000.j2k.codestream
Internal class holding information found in the POC marker segments
HeaderInfo.QCC - Class in io.scif.jj2000.j2k.codestream
Internal class holding information found in the QCC marker segments
HeaderInfo.QCD - Class in io.scif.jj2000.j2k.codestream
Internal class holding information found in the QCD marker segments
HeaderInfo.RGN - Class in io.scif.jj2000.j2k.codestream
Internal class holding information found in the RGN marker segments
HeaderInfo.SIZ - Class in io.scif.jj2000.j2k.codestream
Internal class holding information found in the SIZ marker segment
HeaderInfo.SOT - Class in io.scif.jj2000.j2k.codestream
Internal class holding information found in the SOt marker segments
headerValid - Variable in class io.scif.lifesci.SDTInfo
 
height - Variable in class io.scif.lifesci.SDTInfo
 
height - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The image's height in pixels.
height - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
height - Variable in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
Help - Class in io.scif.cli.help
Alternate invocation for getting help information on a command.
Help() - Constructor for class io.scif.cli.help.Help
 
hFilter - Variable in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
The horizontal analysis filter used to decompose this subband.
hFilter - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
The horizontal analysis filter used to recompose this subband, from its childs.
hh - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
The subband masks of the child HH
histograms - Variable in class io.scif.formats.imaris.PipelineImage
 
hl - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
The subband masks of the child HL
horz - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Black and white horizontal mode table.
horzMode - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Horizontal mode table.

I

I18NImpl - Class in io.scif.media.imageioimpl.common
Class to simplify use of internationalization message strings.
I18NImpl() - Constructor for class io.scif.media.imageioimpl.common.I18NImpl
 
iccs - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
ICC Profiling specifications
ICSOMETranslator() - Constructor for class io.scif.ome.translators.ICSTranslator.ICSOMETranslator
 
ICSTranslator - Class in io.scif.ome.translators
Container class for to and from ICS/OME formats
ICSTranslator() - Constructor for class io.scif.ome.translators.ICSTranslator
 
ICSTranslator.ICSOMETranslator - Class in io.scif.ome.translators
Translator class from ICSFormat.Metadata to OMEMetadata.
ICSTranslator.OMEICSTranslator - Class in io.scif.ome.translators
Translator class from ICSFormat.Metadata to OMEMetadata.
idx - Variable in class io.scif.jj2000.j2k.codestream.CBlkCoordInfo
The code-block horizontal and vertical indexes
IISRandomAccessIO - Class in io.scif.media.imageioimpl.plugins.jpeg2000
A wrapper for converting an ImageInputStream into a RandomAccessIO.
IISRandomAccessIO(ImageInputStream) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
Creates a RandomAccessIO instance from the supplied ImageInputStream.
image - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The final destination image.
IMAGE_HEADER_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
JP2 Header boxes
IMAGE_METADATA_NAME - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
imageHeight - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
ImageInputStreamWrapper - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is designed to wrap a ImageInputStream into a InputStream.
ImageInputStreamWrapper(ImageInputStream) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
Constructs an ImageInputStreamWrapper from the provided ImageInputStream.
imageIsContiguous(RenderedImage) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Returns whether the image has contiguous data across rows.
imageLeftPosition - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
imageRX - Variable in class io.scif.lifesci.SDTInfo
 
imageRY - Variable in class io.scif.lifesci.SDTInfo
 
imageSize - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
imageTopPosition - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
ImageUtil - Class in io.scif.media.imageioimpl.common
 
ImageUtil() - Constructor for class io.scif.media.imageioimpl.common.ImageUtil
 
imageWidth - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
imageX - Variable in class io.scif.lifesci.SDTInfo
4 subsequent fields valid only for Camera mode or FIFO_IMAGE mode.
imageY - Variable in class io.scif.lifesci.SDTInfo
 
ImarisFormat - Class in io.scif.formats
SCIFIO Format supporting the writer for Imaris 5.5 files
ImarisFormat() - Constructor for class io.scif.formats.ImarisFormat
 
ImarisFormat.Writer - Class in io.scif.formats
 
ImarisWriter - Class in io.scif.formats.imaris
 
ImarisWriter(String, long, long, long, long, long, double, double, int, Color[]) - Constructor for class io.scif.formats.imaris.ImarisWriter
 
IMB_C - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
IMB_IPR - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
IMB_UnkC - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
IMB_VERS - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
Image Header Box Fields
ImgData - Interface in io.scif.jj2000.j2k.image
This interface defines methods to access image attributes (width, height, number of components, etc.).
ImgDataAdapter - Class in io.scif.jj2000.j2k.image
This class provides a default implementation of the methods in the 'ImgData' interface.
ImgDataAdapter(ImgData) - Constructor for class io.scif.jj2000.j2k.image.ImgDataAdapter
Instantiates the ImgDataAdapter object specifying the ImgData source.
ImgDataConverter - Class in io.scif.jj2000.j2k.image
This class is responsible of all data type conversions.
ImgDataConverter(BlkImgDataSrc, int) - Constructor for class io.scif.jj2000.j2k.image.ImgDataConverter
Constructs a new ImgDataConverter object that operates on the specified source of image data.
ImgDataConverter(BlkImgDataSrc) - Constructor for class io.scif.jj2000.j2k.image.ImgDataConverter
Constructs a new ImgDataConverter object that operates on the specified source of image data.
ImgDataJoiner - Class in io.scif.jj2000.j2k.image
This class implements the ImgData interface and allows to obtain data from different sources.
ImgDataJoiner(BlkImgDataSrc[], int[]) - Constructor for class io.scif.jj2000.j2k.image.ImgDataJoiner
Class constructor.
imgdatasrc - Variable in class io.scif.jj2000.j2k.image.ImgDataAdapter
The ImgData source
imgH - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The image width on the hi-res reference grid
ImgReader - Class in io.scif.jj2000.j2k.image.input
This is the generic interface to be implemented by all image file (or other resource) readers for different image file formats.
ImgReader() - Constructor for class io.scif.jj2000.j2k.image.input.ImgReader
 
ImgReaderPGM - Class in io.scif.jj2000.j2k.image.input
This class implements the ImgData interface for reading 8 bit unsigned data from a binary PGM file.
ImgReaderPGM(File) - Constructor for class io.scif.jj2000.j2k.image.input.ImgReaderPGM
Creates a new PGM file reader from the specified file.
ImgReaderPGM(String) - Constructor for class io.scif.jj2000.j2k.image.input.ImgReaderPGM
Creates a new PGM file reader from the specified file name.
ImgReaderPGM(RandomAccessFile) - Constructor for class io.scif.jj2000.j2k.image.input.ImgReaderPGM
Creates a new PGM file reader from the specified RandomAccessFile object.
imgW - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The image width on the hi-res reference grid
incr - Variable in class io.scif.lifesci.SDTInfo
 
info(String) - Method in class io.scif.cli.AbstractSCIFIOToolCommand
 
Info - Class in io.scif.cli.info
Parses and prints the metadata for a given dataset.
Info() - Constructor for class io.scif.cli.info.Info
 
INFO - Static variable in interface io.scif.jj2000.j2k.util.MsgLogger
Severity of message.
info - Variable in class io.scif.lifesci.SDTInfo
 
infoLength - Variable in class io.scif.lifesci.SDTInfo
Length of the info part.
infoOffs - Variable in class io.scif.lifesci.SDTInfo
Offset of the info part which contains general text information (Title, date, time, contents etc.).
INIT_EL_COPYING - Static variable in class io.scif.jj2000.j2k.util.ArrayUtil
The number of elements to copy initially in an optimized array copy
initBitBuf() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Initialize bit buffer machinery.
initChilds() - Method in class io.scif.jj2000.j2k.wavelet.Subband
Initializes the childs of this node with the correct values.
initialize(int, long, Interval) - Method in class io.scif.formats.ImarisFormat.Writer
 
initialize() - Method in class io.scif.jj2000.j2k.entropy.encoder.EBCOTRateAllocator
Initializes the layers array.
initialize() - Method in class io.scif.jj2000.j2k.entropy.encoder.PostCompRateAllocator
Initializes the rate allocation points, taking into account header overhead and such.
initialize(ImageInputStream, boolean) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
 
initializeFromStream(ImageInputStream, boolean) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
initializeStringTable() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
Initialize the string table.
initializeStringTable() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWUtil
Initialize the string table.
initJPEGWriter(boolean, boolean) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
Initializes the JPEGWriter and JPEGParam instance variables.
initProgressWatch(int, int, String) - Method in interface io.scif.jj2000.j2k.util.ProgressWatch
Initialize the progress watching process
initSubbandsFields(int, SubbandSyn) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Initialises subbands fields, such as code-blocks dimension and number of magnitude bits, in the subband tree.
initTileComp(int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Load options, length calculation type and termination type for each tile-component.
INK_SET_CMYK - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "InkSet" tag.
INK_SET_NOT_CMYK - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "InkSet" tag.
InputStreamAdapter - Class in io.scif.media.imageioimpl.plugins.clib
 
InputStreamAdapter(ImageInputStream) - Constructor for class io.scif.media.imageioimpl.plugins.clib.InputStreamAdapter
 
insertBefore(Node, Node) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
insertNode(PaletteBuilder.ColorNode, Color, int) - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
intArraySet(int[], int) - Static method in class io.scif.jj2000.j2k.util.ArrayUtil
Reinitializes an int array to the given value in an optimized way.
IntegerSpec - Class in io.scif.jj2000.j2k
This class extends ModuleSpec and is responsible of Integer specifications for each tile-component.
IntegerSpec(int, int, byte) - Constructor for class io.scif.jj2000.j2k.IntegerSpec
Constructs a new 'IntegerSpec' for the specified number of tiles and components and with allowed type of specifications.
IntegerSpec(int, int, byte, J2KImageWriteParamJava, String, String) - Constructor for class io.scif.jj2000.j2k.IntegerSpec
Constructs a new 'IntegerSpec' for the specified number of tiles and components, the allowed specifications type instance.
INTELLECTUAL_PROPERTY_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
intent - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
interlaceFlag - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
INTEROPERABILITY_INDEX_R98 - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFInteroperabilityTagSet
A value to be used with the "InteroperabilityIndex" tag.
INTEROPERABILITY_INDEX_THM - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFInteroperabilityTagSet
A value to be used with the "InteroperabilityIndex" tag.
INV_ICT - Static variable in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Identifier for the Inverse Irreversible Component Transformation (INV_ICT).
INV_RCT - Static variable in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Identifier for the Inverse Reversible Component Transformation (INV_RCT).
InvCompTransf - Class in io.scif.jj2000.j2k.image.invcomptransf
This class apply inverse component transformations to the tiles depending on specification read from the codestream header.
InvCompTransf(BlkImgDataSrc, DecoderSpecs, int[]) - Constructor for class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Constructs a new ForwCompTransf object that operates on the specified source of image data.
inverseFill - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Whether bits are inserted in reverse order (TIFF FillOrder 2).
InverseWT - Class in io.scif.jj2000.j2k.wavelet.synthesis
This abstract class extends the WaveletTransform one with the specifics of inverse wavelet transforms.
InverseWT(MultiResImgData, DecoderSpecs) - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.InverseWT
Initializes this object with the given source of wavelet coefficients.
InvertedCMYKColorSpace - Class in io.scif.media.imageioimpl.common
Singleton class representing a simple, mathematically defined inverted CMYK color space.
InvWT - Interface in io.scif.jj2000.j2k.wavelet.synthesis
This interface extends the WaveletTransform with the specifics of inverse wavelet transforms.
InvWTAdapter - Class in io.scif.jj2000.j2k.wavelet.synthesis
This class provides default implementation of the methods in the 'InvWT' interface.
InvWTAdapter(MultiResImgData, DecoderSpecs) - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Instantiates the 'InvWTAdapter' object using the specified 'MultiResImgData' source.
InvWTData - Interface in io.scif.jj2000.j2k.wavelet.synthesis
This interface extends the MultiResImgData interface with the methods that are necessary for inverse wavelet data (i.e.
InvWTFull - Class in io.scif.jj2000.j2k.wavelet.synthesis
This class implements the InverseWT with the full-page approach for int and float data.
InvWTFull(CBlkWTDataSrcDec, DecoderSpecs) - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.InvWTFull
Initializes this object with the given source of wavelet coefficients.
io.scif.bf - package io.scif.bf
Contains Bio-Formats format, wrapping Bio-Formats proprietary readers as a SCIFIO Format.
io.scif.bf.ome - package io.scif.bf.ome
Contains translators from BioFormatsFormat to OME-XML.
io.scif.bf.wrapper - package io.scif.bf.wrapper
Contains wrapping and utility classes needed for BF <-> SCIFIO conversion.
io.scif.cli - package io.scif.cli
 
io.scif.cli.convert - package io.scif.cli.convert
 
io.scif.cli.help - package io.scif.cli.help
 
io.scif.cli.info - package io.scif.cli.info
 
io.scif.cli.show - package io.scif.cli.show
 
io.scif.formats - package io.scif.formats
 
io.scif.formats.imaris - package io.scif.formats.imaris
 
io.scif.jj2000.j2k - package io.scif.jj2000.j2k
 
io.scif.jj2000.j2k.codestream - package io.scif.jj2000.j2k.codestream
 
io.scif.jj2000.j2k.codestream.reader - package io.scif.jj2000.j2k.codestream.reader
 
io.scif.jj2000.j2k.codestream.writer - package io.scif.jj2000.j2k.codestream.writer
 
io.scif.jj2000.j2k.decoder - package io.scif.jj2000.j2k.decoder
 
io.scif.jj2000.j2k.entropy - package io.scif.jj2000.j2k.entropy
 
io.scif.jj2000.j2k.entropy.decoder - package io.scif.jj2000.j2k.entropy.decoder
 
io.scif.jj2000.j2k.entropy.encoder - package io.scif.jj2000.j2k.entropy.encoder
 
io.scif.jj2000.j2k.fileformat - package io.scif.jj2000.j2k.fileformat
 
io.scif.jj2000.j2k.fileformat.reader - package io.scif.jj2000.j2k.fileformat.reader
 
io.scif.jj2000.j2k.fileformat.writer - package io.scif.jj2000.j2k.fileformat.writer
 
io.scif.jj2000.j2k.image - package io.scif.jj2000.j2k.image
 
io.scif.jj2000.j2k.image.forwcomptransf - package io.scif.jj2000.j2k.image.forwcomptransf
 
io.scif.jj2000.j2k.image.input - package io.scif.jj2000.j2k.image.input
 
io.scif.jj2000.j2k.image.invcomptransf - package io.scif.jj2000.j2k.image.invcomptransf
 
io.scif.jj2000.j2k.io - package io.scif.jj2000.j2k.io
 
io.scif.jj2000.j2k.quantization - package io.scif.jj2000.j2k.quantization
 
io.scif.jj2000.j2k.quantization.dequantizer - package io.scif.jj2000.j2k.quantization.dequantizer
 
io.scif.jj2000.j2k.quantization.quantizer - package io.scif.jj2000.j2k.quantization.quantizer
 
io.scif.jj2000.j2k.roi - package io.scif.jj2000.j2k.roi
 
io.scif.jj2000.j2k.roi.encoder - package io.scif.jj2000.j2k.roi.encoder
 
io.scif.jj2000.j2k.util - package io.scif.jj2000.j2k.util
 
io.scif.jj2000.j2k.wavelet - package io.scif.jj2000.j2k.wavelet
 
io.scif.jj2000.j2k.wavelet.analysis - package io.scif.jj2000.j2k.wavelet.analysis
 
io.scif.jj2000.j2k.wavelet.synthesis - package io.scif.jj2000.j2k.wavelet.synthesis
 
io.scif.lifesci - package io.scif.lifesci
 
io.scif.media.imageio.plugins.bmp - package io.scif.media.imageio.plugins.bmp
Package containing the public classes used by the Sun BMP plug-in for the Image I/O Framework.
io.scif.media.imageio.plugins.jpeg2000 - package io.scif.media.imageio.plugins.jpeg2000
Package containing the public classes used by the Sun JPEG 2000 plug-in for the Image I/O Framework.
io.scif.media.imageio.plugins.pnm - package io.scif.media.imageio.plugins.pnm
Package containing the public classes used by the Sun PNM plug-in for the Image I/O Framework.
io.scif.media.imageio.plugins.tiff - package io.scif.media.imageio.plugins.tiff
Package containing the public classes used by the TIFF plug-in for the Image I/O Framework.
io.scif.media.imageio.stream - package io.scif.media.imageio.stream
Provides ImageInputStream and ImageOutputStream classes for use with the Java Image I/O Framework.
io.scif.media.imageioimpl.common - package io.scif.media.imageioimpl.common
 
io.scif.media.imageioimpl.plugins.bmp - package io.scif.media.imageioimpl.plugins.bmp
 
io.scif.media.imageioimpl.plugins.clib - package io.scif.media.imageioimpl.plugins.clib
 
io.scif.media.imageioimpl.plugins.gif - package io.scif.media.imageioimpl.plugins.gif
 
io.scif.media.imageioimpl.plugins.jpeg - package io.scif.media.imageioimpl.plugins.jpeg
 
io.scif.media.imageioimpl.plugins.jpeg2000 - package io.scif.media.imageioimpl.plugins.jpeg2000
 
io.scif.media.imageioimpl.plugins.pcx - package io.scif.media.imageioimpl.plugins.pcx
 
io.scif.media.imageioimpl.plugins.png - package io.scif.media.imageioimpl.plugins.png
 
io.scif.media.imageioimpl.plugins.pnm - package io.scif.media.imageioimpl.plugins.pnm
 
io.scif.media.imageioimpl.plugins.raw - package io.scif.media.imageioimpl.plugins.raw
 
io.scif.media.imageioimpl.plugins.tiff - package io.scif.media.imageioimpl.plugins.tiff
 
io.scif.media.imageioimpl.plugins.wbmp - package io.scif.media.imageioimpl.plugins.wbmp
 
io.scif.media.imageioimpl.stream - package io.scif.media.imageioimpl.stream
 
io.scif.media.jai.imageioimpl - package io.scif.media.jai.imageioimpl
 
io.scif.media.jai.operator - package io.scif.media.jai.operator
Provides JAI operations which read and write images using the Java Image I/O Framework.
io.scif.ome - package io.scif.ome
 
io.scif.ome.commands - package io.scif.ome.commands
 
io.scif.ome.services - package io.scif.ome.services
 
io.scif.ome.translators - package io.scif.ome.translators
 
isAttributeRequired(String, String) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
isBinary(SampleModel) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
 
isCached() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
isCachedFile() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
isCachedMemory() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
isCompressionLossless - Variable in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Whether the compression is lossless.
isCompressionLossless() - Method in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Retrieves a value indicating whether the compression is lossless.
isCompressionLossless() - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageWriteParam
 
isCompressionLossless - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
Lossless flag for known compression types.
isCompSpecified(int) - Method in class io.scif.jj2000.j2k.ModuleSpec
Whether or not specifications have been entered for the given component.
isCompTransfUsed() - Method in class io.scif.jj2000.j2k.image.CompTransfSpec
Check if component transformation is used in any of the tiles.
isDataTypeOK(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFTag
Returns true if the given data type may be used for the data associated with this tag.
isDerived(int, int) - Method in class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
Returns true if the quantizer of given tile-component uses derived quantization step sizes.
isDerived(int, int) - Method in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
Returns true if given tile-component uses derived quantization step sizes.
isDerived(int, int) - Method in class io.scif.jj2000.j2k.quantization.QuantTypeSpec
Returns true if given tile-component uses derived quantization step size.
isEOFInBuffer - Variable in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Whether the end of the file is in the current buffer or not
isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in interface io.scif.ome.services.OMEXMLService
 
isFormat(Location) - Method in class io.scif.bf.BioFormatsFormat.Checker
 
isFormat(Location, SCIFIOConfig) - Method in class io.scif.bf.BioFormatsFormat.Checker
 
isFormat(DataHandle<Location>) - Method in class io.scif.bf.BioFormatsFormat.Checker
 
isFullyNonReversible() - Method in class io.scif.jj2000.j2k.quantization.QuantTypeSpec
Check the irreversibility of the whole image.
isFullyReversible() - Method in class io.scif.jj2000.j2k.quantization.QuantTypeSpec
Check the reversibility of the whole image.
isGrayscaleMapping(IndexColorModel) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Tests whether the color indices represent a gray-scale image with the indicated number of bits over the color component range [0,255].
isIFDPointer() - Method in class io.scif.media.imageio.plugins.tiff.TIFFTag
Returns true if this tag is used to point to an IFD structure containing additional tags.
isImageTiled(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
isImageTiled(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
isIndicesForGrayscale(byte[], byte[], byte[]) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Tests whether the color indices represent a gray-scale image.
isInitialized(int, long) - Method in class io.scif.formats.ImarisFormat.Writer
 
isIntegral() - Method in class io.scif.media.imageio.plugins.tiff.TIFFField
Indicates whether the value associated with the field is of integral data type.
isLeaf - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
isLeaf(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
isLittleEndian() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
isNode - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
Flag indicating whether this subband mask is a node or not
isNode - Variable in class io.scif.jj2000.j2k.wavelet.Subband
True if it is a node in the tree, false if it is a leaf.
isNonStandardICCColorSpace(ColorSpace) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Returns true if the given ColorSpace object is an instance of ICC_ColorSpace but is not one of the standard ColorSpaces returned by ColorSpace.getInstance().
isOMEXMLMetadata(Object) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
isOMEXMLMetadata(Object) - Method in interface io.scif.ome.services.OMEXMLService
 
isOMEXMLRoot(Object) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
isOMEXMLRoot(Object) - Method in interface io.scif.ome.services.OMEXMLService
 
isOriginalSigned(int) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns true if the original data of the specified component was signed.
isOrigSig - Variable in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
An array specifying, for each component,if the data was signed or not
isOrigSigned(int) - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
isOrigSigned(int) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Returns true if the data read was originally signed in the specified component, false if not.
isOrigSigned(int) - Method in class io.scif.jj2000.j2k.image.input.ImgReaderPGM
Returns true if the data read was originally signed in the specified component, false if not.
isOrigSigned(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Returns true if the data read was originally signed in the specified component, false if not.
isot - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SOT
 
isPacketWritable() - Method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Returns true if the current packet is writable i.e.
isRandomAccessEasy(int) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
isRandomAccessEasy(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
isRandomAccessEasy(int) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
isRandomAccessEasy(int) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
isRandomAccessEasy(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
isRandomAccessEasy(int) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
ISRandomAccessIO - Class in io.scif.jj2000.j2k.util
This class implements a wrapper to turn an InputStream into a RandomAccessIO.
ISRandomAccessIO(InputStream, int, int, int) - Constructor for class io.scif.jj2000.j2k.util.ISRandomAccessIO
Creates a new RandomAccessIO wrapper for the given InputStream 'is'.
ISRandomAccessIO(InputStream) - Constructor for class io.scif.jj2000.j2k.util.ISRandomAccessIO
Creates a new RandomAccessIO wrapper for the given InputStream 'is'.
isReadOnly() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
isReadOnly() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
isReadOnly() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
isReadOnly() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
isReadOnly() - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXMetadata
 
isReadOnly() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
isReadOnly() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
isReadOnly() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
isReadOnly() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
isReversible(int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.EntropyCoder
Returns the reversibility of the tile-component data that is provided by the object.
isReversible() - Method in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Returns true if this transform is reversible in current tile.
isReversible() - Method in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Returns true if this transform is reversible in current tile.
isReversible(int, int) - Method in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
Returns true if the quantized data is reversible, for the specified tile-component.
isReversible(int, int) - Method in class io.scif.jj2000.j2k.quantization.QuantTypeSpec
Check the reversibility of the given tile-component.
isReversible(int, int) - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
Since ROI scaling is always a reversible operation, it calls isReversible() method of it source (the quantizer module).
isReversible() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns the reversibility of the filter.
isReversible() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns the reversibility of the filter.
isReversible(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterSpec
Check the reversibility of filters contained is the given tile-component.
isReversible(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.analysis.ForwWTDataProps
Returns the reversibility of the given tile-component.
isReversible(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Returns the reversibility of the wavelet transform for the specified component and tile.
isReversible(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTFull
Returns the reversibility of the wavelet transform for the specified component, in the current tile.
isReversible() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns the reversibility of the filter.
isReversible() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns the reversibility of the filter.
isReversible(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterSpec
Check the reversibility of filters contained is the given tile-component.
isReversible() - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns the reversibility of the filter.
isReversible(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.WaveletTransform
Returns the reversibility of the wavelet transform for the specified component and tile.
isROIinPkt() - Method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Tells if there was ROI information in the last written packet
isSameAsFullWT(int, int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Returns true if the wavelet filter computes or uses the same "inner" subband coefficient as the full frame wavelet transform, and false otherwise.
isSameAsFullWT(int, int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Returns true if the wavelet filter computes or uses the same "inner" subband coefficient as the full frame wavelet transform, and false otherwise.
isSameAsFullWT(int, int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns true if the wavelet filter computes or uses the same "inner" subband coefficient as the full frame wavelet transform, and false otherwise.
isSameAsFullWT(int, int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns true if the wavelet filter computes or uses the same "inner" subband coefficient as the full frame wavelet transform, and false otherwise.
isSameAsFullWT(int, int, int) - Method in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
Returns true if the wavelet filter computes or uses the same "inner" subband coefficient as the full frame wavelet transform, and false otherwise.
isTermPass - Variable in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
Array of flags indicating terminated passes (valid or non-valid truncation points).
isTileCompSpecified(int, int) - Method in class io.scif.jj2000.j2k.ModuleSpec
Whether or not a tile-component specification has been defined
isTileSpecified(int) - Method in class io.scif.jj2000.j2k.ModuleSpec
Whether or not specifications have been entered for the given tile.
isTopDown() - Method in class io.scif.media.imageio.plugins.bmp.BMPImageWriteParam
Returns the value of the topDown parameter.
iterator() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
Returns an Iterator over the TIFF fields.

J

J2KImageReader - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is the Java Image IO plugin reader for JPEG 2000 JP2 image file format.
J2KImageReader(ImageReaderSpi) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
Constructs J2KImageReader from the provided ImageReaderSpi.
J2KImageReaderResources - Class in io.scif.media.imageioimpl.plugins.jpeg2000
 
J2KImageReaderResources() - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReaderResources
 
J2KImageReaderSpi - Class in io.scif.media.imageioimpl.plugins.jpeg2000
 
J2KImageReaderSpi() - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
J2KImageReadParam - Class in io.scif.media.imageio.plugins.jpeg2000
A subclass of ImageReadParam for reading images in the JPEG 2000 format.
J2KImageReadParam() - Constructor for class io.scif.media.imageio.plugins.jpeg2000.J2KImageReadParam
Constructs a default instance of J2KImageReadParam.
J2KImageReadParamJava - Class in io.scif.media.imageioimpl.plugins.jpeg2000
A subclass of ImageReadParam for reading images in the JPEG 2000 format.
J2KImageReadParamJava() - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava
Constructs a default instance of J2KImageReadParamJava.
J2KImageReadParamJava(ImageReadParam) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava
 
J2KImageWriteParam - Class in io.scif.media.imageio.plugins.jpeg2000
A subclass of ImageWriteParam for writing images in the JPEG 2000 format.
J2KImageWriteParam(Locale) - Constructor for class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Constructor which sets the Locale.
J2KImageWriteParam() - Constructor for class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Constructs a J2KImageWriteParam object with default values for all parameters.
J2KImageWriteParamJava - Class in io.scif.media.imageioimpl.plugins.jpeg2000
A subclass of ImageWriteParam for writing images in the JPEG 2000 format.
J2KImageWriteParamJava(RenderedImage, Locale) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Constructor to set locales.
J2KImageWriteParamJava(IIOImage, ImageWriteParam) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Constructor to set locales.
J2KImageWriteParamJava() - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Constructs a J2KImageWriteParamJava object with default values for all parameters.
J2KImageWriteParamJava(RenderedImage) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Constructs a J2KImageWriteParamJava object with default values for all parameters.
J2KImageWriteParamJava(Raster) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Constructs a J2KImageWriteParamJava object with default values for all parameters.
J2KImageWriter - Class in io.scif.media.imageioimpl.plugins.jpeg2000
The Java Image IO plugin writer for encoding a RenderedImage into a JPEG 2000 part 1 file (JP2) format.
J2KImageWriter(ImageWriterSpi) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
Constructs J2KImageWriter based on the provided ImageWriterSpi.
J2KImageWriterResources - Class in io.scif.media.imageioimpl.plugins.jpeg2000
 
J2KImageWriterResources() - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriterResources
 
J2KImageWriterSpi - Class in io.scif.media.imageioimpl.plugins.jpeg2000
 
J2KImageWriterSpi() - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
J2KMetadata - Class in io.scif.media.imageioimpl.plugins.jpeg2000
Metadata for the J2K plug-in.
J2KMetadata() - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
Constructor containing code shared by other constructors.
J2KMetadata(ImageInputStream, J2KImageReader) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
J2KMetadata(ImageWriteParam, ImageWriter) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
Constructs a default stream J2KMetadata object appropriate for the given write parameters.
J2KMetadata(ImageTypeSpecifier, ImageWriteParam, ImageWriter) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
Constructs a default image J2KMetadata object appropriate for the given image type and write parameters.
J2KMetadata(ColorModel, SampleModel, int, int, ImageWriteParam, ImageWriter) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
Constructs a default image J2KMetadata object appropriate for the given image type and write parameters.
J2KMetadataFormat - Class in io.scif.media.imageioimpl.plugins.jpeg2000
 
J2KMetadataFormatResources - Class in io.scif.media.imageioimpl.plugins.jpeg2000
 
J2KMetadataFormatResources() - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormatResources
 
J2KReadState - Class in io.scif.media.imageioimpl.plugins.jpeg2000
 
J2KReadState(ImageInputStream, J2KImageReadParamJava, J2KMetadata, J2KImageReader) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
Constructs J2KReadState.
J2KReadState(ImageInputStream, J2KImageReadParamJava, J2KImageReader) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
Constructs J2KReadState.
J2KRenderedImage - Class in io.scif.media.imageioimpl.plugins.jpeg2000
 
J2KRenderedImage(ImageInputStream, J2KImageReadParamJava, J2KMetadata, J2KImageReader) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
 
J2KRenderedImage(ImageInputStream, J2KImageReadParamJava, J2KImageReader) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
 
J2KRenderedImage(J2KReadState) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.J2KRenderedImage
 
JJ2KExceptionHandler - Class in io.scif.jj2000.j2k
This class handles exceptions.
JJ2KExceptionHandler() - Constructor for class io.scif.jj2000.j2k.JJ2KExceptionHandler
 
JJ2KInfo - Class in io.scif.jj2000.j2k
This class holds general JJ2000 information, such as the version number, copyright, contact address, etc.
JJ2KInfo() - Constructor for class io.scif.jj2000.j2k.JJ2KInfo
 
JP2_HEADER_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
JP2_SIGNATURE_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
Main boxes
JPEG_PROC_BASELINE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "JPEGProc" tag.
JPEG_PROC_LOSSLESS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "JPEGProc" tag.
JPEGParam - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
ImageWriteParam for JPEG writer.
JPEGParam - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
JPEGReader - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
JPEGStreamMetadata - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
Stream metadata equivalent to a tables-only stream such as in the JPEGTables.
JPEGWriter - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
The JPEG writer.

K

KH - Static variable in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
The value of the high-pass subband normalization factor
KH - Static variable in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
The value of the high-pass subband normalization factor
KL - Static variable in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
The value of the low-pass subband normalization factor
KL - Static variable in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
The value of the low-pass subband normalization factor

L

l2Norm - Variable in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
The L2-norm of the synthesis basis waveform of this subband, applicable to "leafs" only.
LATITUDE_REF_NORTH - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSLatitudeRef" and "GPSDestLatitudeRef" tags.
LATITUDE_REF_SOUTH - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSLatitudeRef" and "GPSDestLatitudeRef" tags.
layerIdx - Variable in class io.scif.jj2000.j2k.codestream.reader.PktInfo
The layer associated with the current code-block in this packet.
LayersInfo - Class in io.scif.jj2000.j2k.entropy.encoder
This class stores the specification of a layer distribution in the bit stream.
LayersInfo(float) - Constructor for class io.scif.jj2000.j2k.entropy.encoder.LayersInfo
Creates a new LayersInfo object.
lblockNo - Variable in class io.scif.lifesci.SDTInfo
Long blockNo - see remarks below.
lcm(int, int) - Static method in class io.scif.jj2000.j2k.util.MathUtil
Method that calculates the Least Common Multiple (LCM) of two strictly positive integer numbers.
lcm(int[]) - Static method in class io.scif.jj2000.j2k.util.MathUtil
Method that calculates the Least Common Multiple (LCM) of several positive integer numbers.
lcoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
 
lcod - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
lcom - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COM
 
lcrg - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.CRG
 
lcs - Variable in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
The length calculation specifications
LCS_CALIBRATED_RGB - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
LCS_sRGB - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
LCS_WINDOWS_COLOR_SPACE - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
len - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
Length of each piece of code-block's codewords
length() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
length() - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Returns the current length of the stream, in bytes, taking into account any buffering.
length() - Method in interface io.scif.jj2000.j2k.io.RandomAccessIO
Returns the current length of the stream, in bytes, taking into account any buffering.
length() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Returns the length of the stream.
length() - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
Returns the number of bytes currently in the FileChannel.
length() - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
Returns the number of bytes currently in the FileChannel.
length() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
length() - Method in class io.scif.media.imageio.stream.SegmentedImageInputStream
 
length - Variable in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Box length, extra length, type and content data array
length() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
Returns the length of the data stream.
LENGTH_LAZY - Static variable in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Identifier for the lazy length calculation.
LENGTH_LAZY_GOOD - Static variable in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Identifier for a very simple length calculation.
LENGTH_NEAR_OPT - Static variable in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Identifier for the near optimal length calculation.
level - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The level in the tree to which this subband belongs, which is the number of wavelet decompositions performed to produce this subband.
level - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
lh - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
The subband masks of the child LH
LIGHT_SOURCE_CLOUDY_WEATHER - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_COOL_WHITE_FLUORESCENT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_D50 - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_D55 - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_D65 - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_D75 - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_DAY_WHITE_FLUORESCENT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_DAYLIGHT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_DAYLIGHT_FLUORESCENT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_FINE_WEATHER - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_FLASH - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_FLUORESCENT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_ISO_STUDIO_TUNGSTEN - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_OTHER - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_SHADE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_STANDARD_LIGHT_A - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_STANDARD_LIGHT_B - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_STANDARD_LIGHT_C - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_TUNGSTEN - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_UNKNOWN - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
LIGHT_SOURCE_WHITE_FLUORESCENT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "LightSource" tag.
linediv - Variable in class io.scif.lifesci.SDTInfo
Line predivider = 2 ** (linediv).
LITTLE_ENDIAN - Static variable in interface io.scif.jj2000.j2k.io.EndianType
Identifier for little-endian byte ordering (i.e.
ll - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
The subband masks of the child LL
loadLibrary() - Static method in class io.scif.jj2000.j2k.util.NativeServices
Loads the shared library implementing the native methods of this class and returns true on success.
localColorTable - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
location(String) - Method in class io.scif.cli.AbstractSCIFIOToolCommand
 
LOG - Static variable in interface io.scif.jj2000.j2k.util.MsgLogger
Severity of message.
log2(int) - Static method in class io.scif.jj2000.j2k.util.MathUtil
Method that calculates the floor of the log, base 2, of 'x'.
logicalScreenHeight - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
logicalScreenWidth - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
LongArrayOptionHandler - Class in io.scif.cli
OptionHandler implementation for setting long array fields.
LongArrayOptionHandler(CmdLineParser, OptionDef, Setter<Long>) - Constructor for class io.scif.cli.LongArrayOptionHandler
 
LONGITUDE_REF_EAST - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSLongitudeRef" and "GPSDestLongitudeRef" tags.
LONGITUDE_REF_WEST - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSLongitudeRef" and "GPSDestLongitudeRef" tags.
lpoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.POC
 
lqcc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCC
 
lqcd - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCD
 
lrgn - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.RGN
 
lrxs - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandRectROIMask
The lower right x coordinates of the applicable ROIs
lrys - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandRectROIMask
The lower right y coordinates of the applicable ROIs
lsiz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
lsot - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SOT
 
lvls - Variable in class io.scif.jj2000.j2k.codestream.reader.TagTreeDecoder
The number of levels in the tag tree
lvls - Variable in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
The number of levels in the tag tree
lw - Variable in class io.scif.jj2000.j2k.util.MsgPrinter
The line width to use
LY_RES_COMP_POS_PROG - Static variable in interface io.scif.jj2000.j2k.codestream.ProgressionType
The bit stream is Layer/Resolution/Component/Position progressive : 0
lye - Variable in class io.scif.jj2000.j2k.entropy.Progression
The index of the last layer.
lyepoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.POC
 
LZWCompressor - Class in io.scif.media.imageioimpl.common
Modified from original LZWCompressor to change interface to passing a buffer of data to be compressed.
LZWCompressor(ImageOutputStream, int, boolean) - Constructor for class io.scif.media.imageioimpl.common.LZWCompressor
 
LZWStringTable - Class in io.scif.media.imageioimpl.common
General purpose LZW String Table.
LZWStringTable() - Constructor for class io.scif.media.imageioimpl.common.LZWStringTable
Constructor allocate memory for string store data

M

m - Variable in class io.scif.jj2000.j2k.entropy.CodedCBlk
The vertical index of the code-block, within the subband.
m - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The vertical index of the code-block, within the subband
magbits - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The number of magnitude bits in the integer representation.
magbits - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
The number of magnitude bits
main(String[]) - Static method in class io.scif.cli.SCIFIOTools
 
mainHeadOff - Variable in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
The offset of the main header in the input stream
makeCompressionTypes() - Method in class io.scif.formats.ImarisFormat.Writer
 
makeMask(Subband, int, int) - Method in class io.scif.jj2000.j2k.roi.encoder.ArbROIMaskGenerator
This function generates the ROI mask for one tile-component.
makeMask(Subband, int, int) - Method in class io.scif.jj2000.j2k.roi.encoder.RectROIMaskGenerator
This function generates the ROI mask for the entire tile.
makeMask(Subband, int, int) - Method in class io.scif.jj2000.j2k.roi.encoder.ROIMaskGenerator
This function generates the ROI mask for the entire tile.
makeRange(long[], long[], long[], ImageMetadata, List<CalibratedAxis>) - Method in class io.scif.cli.AbstractReaderCommand
Convenience method to split a single list of values to a set of offset/length values.
makeReader(String) - Method in class io.scif.cli.AbstractReaderCommand
Helper method to initialize a reader given the current command parameters.
makeSaneDimensionOrder(String) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
makeSaneDimensionOrder(String) - Method in interface io.scif.ome.services.OMEMetadataService
Adjusts the given dimension order as needed so that it contains exactly one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.
makeSuffixArray() - Method in class io.scif.bf.BioFormatsFormat
 
makeSuffixArray() - Method in class io.scif.formats.ImarisFormat
 
makeSuffixArray() - Method in class io.scif.lifesci.SDTFormat
 
makeupCodes - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Black and white make-up code table.
makeupCodesBlack - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Make-up codes for black runs.
makeupCodesWhite - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Make-up codes for white runs.
MANUFACTURER - Static variable in interface io.scif.media.imageioimpl.plugins.pcx.PCXConstants
 
mark(int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
mark() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
mark(int) - Method in class io.scif.media.imageioimpl.plugins.clib.InputStreamAdapter
 
mark(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
Markers - Interface in io.scif.jj2000.j2k.codestream
This interface defines the values of the different markers in the JPEG 2000 codestream.
markSupported() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
markSupported() - Method in class io.scif.media.imageioimpl.plugins.clib.InputStreamAdapter
 
markSupported() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
maskPGM - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
ImgReaderPGM object with the arbrtrary ROI
masterClock - Variable in class io.scif.lifesci.SDTInfo
Use or not Master Clock (SPC140 multi-module).
MathUtil - Class in io.scif.jj2000.j2k.util
This class contains a collection of utility methods fro mathematical operations.
MathUtil() - Constructor for class io.scif.jj2000.j2k.util.MathUtil
 
MAX_CB_AREA - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The maximum code-block area (width x height).
MAX_CB_DIM - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The maximum code-block dimension.
MAX_COMP_BITDEPTH - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
The maximum number of component bitdepth
MAX_DATATYPE - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
The numerically largest constant representing a TIFF data type.
MAX_EL_COPYING - Static variable in class io.scif.jj2000.j2k.util.ArrayUtil
The maximum array size to do element by element copying, larger arrays are copyied in a n optimized way.
MAX_INT - Static variable in class io.scif.jj2000.j2k.IntegerSpec
The largest value of type int
MAX_LPPM - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Maximum length of PPM marker segment
MAX_LPPT - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Maximum length of PPT marker segment
maxAdcRate - Variable in class io.scif.lifesci.SDTInfo
 
maxByte - Variable in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
The maximum number of bytes that can be read from the buffer
maxBytes - Variable in class io.scif.jj2000.j2k.codestream.writer.CodestreamWriter
The maximum number of bytes that can be written to the bit stream
maxCfdRate - Variable in class io.scif.lifesci.SDTInfo
(-1.0 - not set).
maxImgRes - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
The maximum available image resolution level
MAXLEVEL - Static variable in class io.scif.media.imageioimpl.common.PaletteBuilder
maximum of tree depth
maxNodes - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
MaxShiftSpec - Class in io.scif.jj2000.j2k.roi
This class contains the maxshift scaling value for each tile-component.
MaxShiftSpec(int, int, byte, String) - Constructor for class io.scif.jj2000.j2k.roi.MaxShiftSpec
Constructs a 'ModuleSpec' object, initializing all the components and tiles to the 'SPEC_DEF' spec type, for the specified number of components and tiles.
maxSyncRate - Variable in class io.scif.lifesci.SDTInfo
Maximum rates during the measurement.
maxTacRate - Variable in class io.scif.lifesci.SDTInfo
 
mcsPoints - Variable in class io.scif.lifesci.SDTInfo
No of MCS values.
mcsTime - Variable in class io.scif.lifesci.SDTInfo
Interval time [ms] for MCS histogram.
mdl - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The maximum number of decompostion levels for each component of the current tile.
measDescBlockLength - Variable in class io.scif.lifesci.SDTInfo
 
measDescBlockNo - Variable in class io.scif.lifesci.SDTInfo
Number of the measurement description block corresponding to this data block.
measDescBlockOffs - Variable in class io.scif.lifesci.SDTInfo
 
measMode - Variable in class io.scif.lifesci.SDTInfo
 
MEASURE_MODE_2D - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSMeasureMode" tag.
MEASURE_MODE_3D - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSMeasureMode" tag.
memBank - Variable in class io.scif.lifesci.SDTInfo
 
mergeIntensity() - Method in class io.scif.lifesci.SDTFormat.Metadata
 
mergeIntensity() - Method in class io.scif.lifesci.SDTFormat.Parser
 
mergeNativeTree(Node) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
mergeNativeTree(Node) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
mergeStandardTree(Node) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
mergeStandardTree(Node) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
mergeTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
mergeTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
mergeTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXMetadata
 
mergeTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
mergeTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
mergeTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
mergeTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
Metadata() - Constructor for class io.scif.bf.BioFormatsFormat.Metadata
 
Metadata() - Constructor for class io.scif.lifesci.SDTFormat.Metadata
 
metadata - Variable in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
The IIOMetadata object containing metadata for the current image.
metadata - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The IIOMetadata object containing metadata for the current image.
METERING_MODE_AVERAGE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "MeteringMode" tag.
METERING_MODE_CENTER_WEIGHTED_AVERAGE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "MeteringMode" tag.
METERING_MODE_MAX_RESERVED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "MeteringMode" tag.
METERING_MODE_MIN_RESERVED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "MeteringMode" tag.
METERING_MODE_MULTI_SPOT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "MeteringMode" tag.
METERING_MODE_OTHER - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "MeteringMode" tag.
METERING_MODE_PARTIAL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "MeteringMode" tag.
METERING_MODE_PATTERN - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "MeteringMode" tag.
METERING_MODE_SPOT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "MeteringMode" tag.
METERING_MODE_UNKNOWN - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "MeteringMode" tag.
MicromanagerOMETranslator() - Constructor for class io.scif.ome.translators.MicromanagerTranslator.MicromanagerOMETranslator
 
MicromanagerTranslator - Class in io.scif.ome.translators
Container class for translators between OME and Micromanager formats.
MicromanagerTranslator() - Constructor for class io.scif.ome.translators.MicromanagerTranslator
 
MicromanagerTranslator.MicromanagerOMETranslator - Class in io.scif.ome.translators
Translator class from OMEMetadata to MicromanagerFormat.Metadata.
MIN_CB_DIM - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The minimum code-block dimension.
MIN_DATATYPE - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
The numerically smallest constant representing a TIFF data type.
minAdcRate - Variable in class io.scif.lifesci.SDTInfo
 
minCfdRate - Variable in class io.scif.lifesci.SDTInfo
(-1.0 - not set).
minSyncRate - Variable in class io.scif.lifesci.SDTInfo
Minimum rates during the measurement.
minTacRate - Variable in class io.scif.lifesci.SDTInfo
 
minX - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The X coordinate of the image's upper-left pixel.
minY - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The Y coordinate of the image's upper-left pixel.
mod - Variable in class io.scif.lifesci.SDTInfo
Module number.
modFpgaVer - Variable in class io.scif.lifesci.SDTInfo
New in v.8.4.
modSerNo - Variable in class io.scif.lifesci.SDTInfo
Serial number of the module.
modType - Variable in class io.scif.lifesci.SDTInfo
Module type.
modTypeCode - Variable in class io.scif.lifesci.SDTInfo
 
ModuleSpec - Class in io.scif.jj2000.j2k
This generic class is used to handle values to be used by a module for each tile and component.
ModuleSpec(int, int, byte) - Constructor for class io.scif.jj2000.j2k.ModuleSpec
Constructs a 'ModuleSpec' object, initializing all the components and tiles to the 'SPEC_DEF' spec val type, for the specified number of components and tiles.
MQCoder - Class in io.scif.jj2000.j2k.entropy.encoder
This class implements the MQ arithmetic coder.
MQCoder(ByteOutputBuffer, int, int[]) - Constructor for class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Instantiates a new MQ-coder, with the specified number of contexts and initial states.
MQDecoder - Class in io.scif.jj2000.j2k.entropy.decoder
This class implements the MQ arithmetic decoder.
MQDecoder(ByteInputBuffer, int, int[]) - Constructor for class io.scif.jj2000.j2k.entropy.decoder.MQDecoder
Instantiates a new MQ-decoder, with the specified number of contexts and initial states.
mqrs - Variable in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
MQ reset specifications
mReserved1 - Variable in class io.scif.lifesci.SDTInfo
 
mReserved2 - Variable in class io.scif.lifesci.SDTInfo
 
mressrc - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
The 'MultiResImgData' source
mressrc - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
The MultiResImgData source
msbSkipped - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
The number of most significant bits which are skipped for this code-block (= Mb-1-bitDepth).
MsgLogger - Interface in io.scif.jj2000.j2k.util
This class provides a simple common abstraction of a facility that logs and/or displays messages or simple strings.
MsgPrinter - Class in io.scif.jj2000.j2k.util
This utility class formats messages to the specified line width, by inserting line-breaks between words, and printing the resulting lines.
MsgPrinter(int) - Constructor for class io.scif.jj2000.j2k.util.MsgPrinter
Creates a new message printer with the specified line width and with the default locale.
mtResol - Variable in class io.scif.lifesci.SDTInfo
Macro time clock in 0.1 ns units.
MultiResImgData - Interface in io.scif.jj2000.j2k.wavelet.synthesis
This interface defines methods to access image attributes (width, height, number of components, etc.) of multiresolution images, such as those resulting from an inverse wavelet transform.
MultiResImgDataAdapter - Class in io.scif.jj2000.j2k.wavelet.synthesis
This class provides a default implementation for the methods of the 'MultiResImgData' interface.
MultiResImgDataAdapter(MultiResImgData) - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Instantiates the MultiResImgDataAdapter object specifying the MultiResImgData source.

N

n - Variable in class io.scif.jj2000.j2k.entropy.CodedCBlk
The horizontal index of the code-block, within the subband.
n - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The horizontal index of the code-block, within the subband
nativeMetadataFormatClassName - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
nativeMetadataFormatName - Static variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
nativeMetadataFormatName - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
nativeMetadataFormatName - Static variable in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
NativeServices - Class in io.scif.jj2000.j2k.util
This class presents a collection of static methods that allow access to some native methods.
nblk - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Number of code-blocks in each subband belonging to this precinct
nc - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The number of components
nc - Variable in class io.scif.jj2000.j2k.image.input.ImgReader
The number of components in the image
nComp - Variable in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
The number of components in the image
nComp - Variable in class io.scif.jj2000.j2k.ModuleSpec
The number of components
ncx - Variable in class io.scif.lifesci.SDTInfo
 
ncy - Variable in class io.scif.lifesci.SDTInfo
 
ndata - Variable in class io.scif.jj2000.j2k.codestream.writer.CodestreamWriter
The number of bytes already written to the bit stream
ndex - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Number of bits in the output bit buffer.
NEW_SUBFILE_TYPE_REDUCED_RESOLUTION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A mask to be used with the "NewSubfileType" tag.
NEW_SUBFILE_TYPE_SINGLE_PAGE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A mask to be used with the "NewSubfileType" tag.
NEW_SUBFILE_TYPE_TRANSPARENCY - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A mask to be used with the "NewSubfileType" tag.
nextBlockOffs - Variable in class io.scif.lifesci.SDTInfo
Offset to the data block header of the next data block.
nextSegment(byte[], int, int) - Method in class io.scif.jj2000.j2k.entropy.decoder.MQDecoder
Resets the MQ decoder to start a new segment.
nextState(byte[], int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Return min of maxOffset or offset of first pixel different from pixel at bitOffset.
nextSubband() - Method in class io.scif.jj2000.j2k.wavelet.Subband
Returns the next subband in the same resolution level, following the subband index order.
nextTile() - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in interface io.scif.jj2000.j2k.image.ImgData
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.image.Tiler
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTFull
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Advances to the next tile, in standard scan-line order (by rows then columns).
nextTile() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Advances to the next tile, in standard scan-line order (by rows then columns).
nl - Variable in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
The number of layers in the coded data.
nls - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
Number of layers specifications
nomCBlkH - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The nominal code-block height
nomCBlkW - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The nominal code-block width
NONE - Static variable in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Identifier for no component transformation.
NONE - Static variable in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Identifier for no component transformation.
NoNextElementException - Exception in io.scif.jj2000.j2k
This exception is thrown whenever a next???? method is called and there is no next element to return.
NoNextElementException() - Constructor for exception io.scif.jj2000.j2k.NoNextElementException
Constructs a new NoNextElementException exception with no detail message.
NoNextElementException(String) - Constructor for exception io.scif.jj2000.j2k.NoNextElementException
Constructs a new NoNextElementException exception with the specified detail message.
noOfDataBlocks - Variable in class io.scif.lifesci.SDTInfo
no_of_data_blocks valid only when in 0 ..
noOfMeasDescBlocks - Variable in class io.scif.lifesci.SDTInfo
 
NotImplementedError - Error in io.scif.jj2000.j2k
This exception is thrown whenever a feature or functionality that has not been implemented is calle.
NotImplementedError() - Constructor for error io.scif.jj2000.j2k.NotImplementedError
Constructs a new NotImplementedError exception with the default detail message.
NotImplementedError(String) - Constructor for error io.scif.jj2000.j2k.NotImplementedError
Constructs a new NotImplementedError exception with the specified detail message m.
nrc - Variable in class io.scif.jj2000.j2k.roi.encoder.ROIMaskGenerator
Number of components
nROIbp - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
Number of ROI magnitude bit-planes
nROIcoeff - Variable in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
The number of ROI coefficients in the code-block
nROIcoeff - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
Number of ROI coefficients in the code-block
nROIcp - Variable in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
Number of ROI coding passes
NRRDOMETranslator() - Constructor for class io.scif.ome.translators.NRRDTranslator.NRRDOMETranslator
 
NRRDTranslator - Class in io.scif.ome.translators
Container class for translators between OME and NRRD formats.
NRRDTranslator() - Constructor for class io.scif.ome.translators.NRRDTranslator
 
NRRDTranslator.NRRDOMETranslator - Class in io.scif.ome.translators
Translator class from NRRDFormat.Metadata to OMEMetadata
nStep - Variable in class io.scif.jj2000.j2k.quantization.dequantizer.StdDequantizerParams
The quantization step for non-reversible systems, normalized to a dynamic range of 1, for each resolution level and subband, as derived from the exponent-mantissa representation in the codestream.
nt - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The total number of tiles.
ntH - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The nominal tile height, in the hi-res reference grid
nTileParts - Variable in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
The number of tile parts per tile
nTiles - Variable in class io.scif.jj2000.j2k.ModuleSpec
The number of tiles
nTotTrunc - Variable in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
The total number of truncation points
ntp - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
The number of truncation point for each layer
nTrunc - Variable in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
The total number of truncation points from layer 1 to the last one in this object.
ntW - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The nominal tile width, in the hi-res reference grid
ntX - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The number of tile in the horizontal direction
ntY - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The number of tiles in the vertical direction
NUM_EMPTY_PASSES_IN_MS_BP - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The number of empty passes in the most significant bit-plane.
NUM_NON_BYPASS_MS_BP - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The number of most significant bit-planes where bypass mode is not to be used, even if bypass mode is on: 4.
NUM_PASSES - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The number of coding passes per bit-plane.
numCb - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The number of code-blocks (in both directions) contained in this subband.
numLayers - Variable in class io.scif.jj2000.j2k.entropy.encoder.PostCompRateAllocator
The number of layers.
numNodes - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
numTruncPnts - Variable in class io.scif.jj2000.j2k.codestream.reader.PktInfo
The number of truncation points that appear in this packet, and all previous packets, for this code-block.
nVldTrunc - Variable in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
The number of valid truncation points

O

OBFOMETranslator() - Constructor for class io.scif.ome.translators.OBFTranslator.OBFOMETranslator
 
OBFTranslator - Class in io.scif.ome.translators
Container class for translators between OME and OBF formats.
OBFTranslator() - Constructor for class io.scif.ome.translators.OBFTranslator
 
OBFTranslator.OBFOMETranslator - Class in io.scif.ome.translators
Translator class from OBFFormat.Metadata to OMEMetadata
off - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
Offset of each piece of code-block's codewords in the file
offset - Variable in class io.scif.jj2000.j2k.image.DataBlk
The offset in the array of the top-left coefficient
offset - Variable in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
The current offset of the buffer (which will differ from the offset of the file)
offset - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The offset in the array of the top-left coefficient
offset - Variable in class io.scif.lifesci.SDTInfo
 
offset - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The offset in the source ImageInputStream of the start of the data to be decompressed.
offX - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The horizontal offsets of the upper-left corner of the current tile (not active tile) with respect to the canvas origin, in the component hi-res grid, for each component.
offY - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The vertical offsets of the upper-left corner of the current tile (not active tile) with respect to the canvas origin, in the component hi-res grid, for each component.
OMEAPNGTranslator() - Constructor for class io.scif.ome.translators.APNGTranslator.OMEAPNGTranslator
 
OMEEPSTranslator() - Constructor for class io.scif.ome.translators.EPSTranslator.OMEEPSTranslator
 
OMEICSTranslator() - Constructor for class io.scif.ome.translators.ICSTranslator.OMEICSTranslator
 
OMEMetadata - Class in io.scif.ome
io.scif.Metadata class wrapping an OME-XML root.
OMEMetadata(Context) - Constructor for class io.scif.ome.OMEMetadata
 
OMEMetadata(Context, OMEXMLMetadata) - Constructor for class io.scif.ome.OMEMetadata
 
OMEMetadataService - Interface in io.scif.ome.services
A utility class for working with OME metadata objects, including MetadataStore and MetadataRetrieve.
OMETIFFTranslator() - Constructor for class io.scif.ome.translators.TIFFTranslator.OMETIFFTranslator
 
OMETranslator<M extends Metadata,N extends Metadata> - Class in io.scif.ome.translators
Abstract base class for all Translator implementations that operate on OMEMetadata.
OMETranslator() - Constructor for class io.scif.ome.translators.OMETranslator
 
OMEXMLService - Interface in io.scif.ome.services
SCIFIO service wrapper for OMEXMLService.
OMEXMLToolCommand - Class in io.scif.ome.commands
SCIFIOToolCommand plugin for printing OME-XML.
OMEXMLToolCommand() - Constructor for class io.scif.ome.commands.OMEXMLToolCommand
 
oneD - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
Coding dimensionality: 1 for 2-dimensional, 0 for 1-dimensional.
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
onRegistration(ServiceRegistry, Class) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.bf.BioFormatsFormat.Reader
 
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.lifesci.SDTFormat.Reader
 
OPT_BYPASS - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The flag bit to indicate that selective arithmetic coding bypass should be used.
OPT_PRED_TERM - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The flag bit to indicate that error resilience info is embedded on MQ termination.
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The prefix for bit stream reader options: 'B'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
The prefix for header decoder options: 'H'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
The prefix for packet encoding options: 'P'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.entropy.decoder.EntropyDecoder
The prefix for entropy decoder optiojns: 'C'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.entropy.encoder.EntropyCoder
The prefix for entropy coder options: 'C'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.entropy.encoder.PostCompRateAllocator
The prefix for rate allocation options: 'A'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
The prefix for component transformation type: 'M'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
The prefix for inverse component transformation options: 'M'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
The prefix for dequantizer options: 'Q'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
The prefix for quantizer options: 'Q'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
The prefix for ROI Scaler options: 'R'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.roi.ROIDeScaler
The prefix for ROI decoder options: 'R'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilter
The prefix for wavelet filter options: 'F'
OPT_PREFIX - Static variable in class io.scif.jj2000.j2k.wavelet.analysis.ForwardWT
The prefix for wavelet transform options: 'W'
OPT_RESET_MQ - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The flag bit to indicate that the MQ states for all contexts should be reset at the end of each non-bypass coding pass.
OPT_SEG_SYMBOLS - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The flag bit to indicate that a segmentation marker is to be inserted at the end of each normalization coding pass.
OPT_TERM_PASS - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The flag bit to indicate that regular termination should be used.
OPT_VERT_STR_CAUSAL - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The flag bit to indicate the vertically stripe-causal context formation should be used.
order(boolean) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
orientation - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The orientation of this subband (WT_ORIENT_LL, WT_ORIENT_HL, WT_ORIENT_LH, WT_ORIENT_HH).
ORIENTATION_ROW_0_BOTTOM_COLUMN_0_LEFT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Orientation" tag.
ORIENTATION_ROW_0_BOTTOM_COLUMN_0_RIGHT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Orientation" tag.
ORIENTATION_ROW_0_LEFT_COLUMN_0_BOTTOM - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Orientation" tag.
ORIENTATION_ROW_0_LEFT_COLUMN_0_TOP - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Orientation" tag.
ORIENTATION_ROW_0_RIGHT_COLUMN_0_BOTTOM - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Orientation" tag.
ORIENTATION_ROW_0_RIGHT_COLUMN_0_TOP - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Orientation" tag.
ORIENTATION_ROW_0_TOP_COLUMN_0_LEFT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Orientation" tag.
ORIENTATION_ROW_0_TOP_COLUMN_0_RIGHT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Orientation" tag.
origSrc - Variable in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
The image data reader.
OutputStreamAdapter - Class in io.scif.media.imageioimpl.plugins.clib
 
OutputStreamAdapter(ImageOutputStream) - Constructor for class io.scif.media.imageioimpl.plugins.clib.OutputStreamAdapter
 
overfl - Variable in class io.scif.lifesci.SDTInfo
 
overflowCorrFactor - Variable in class io.scif.lifesci.SDTInfo
 
overruns - Variable in class io.scif.lifesci.SDTInfo
No of Fifo overruns when > 0 fcs curve & endTime are not valid.

P

PackageUtil - Class in io.scif.media.imageioimpl.common
 
PackageUtil() - Constructor for class io.scif.media.imageioimpl.common.PackageUtil
 
packetIdx - Variable in class io.scif.jj2000.j2k.codestream.reader.PktInfo
Index of the packet
page - Variable in class io.scif.lifesci.SDTInfo
 
palette - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
palette - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
PALETTE_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
PALETTE_COLOR - Static variable in interface io.scif.media.imageioimpl.plugins.pcx.PCXConstants
 
PALETTE_GRAYSCALE - Static variable in interface io.scif.media.imageioimpl.plugins.pcx.PCXConstants
 
PaletteBox - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is designed to represent a palette box for JPEG 2000 JP2 file format.
PaletteBox(IndexColorModel) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
Constructs a PlatteBox from an IndexColorModel.
PaletteBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
Constructs a PlatteBox from an org.w3c.dom.Node.
PaletteBox(int, byte[], byte[][]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
Constructs a PlatteBox from the provided length, bit depths of the color components and the LUT.
PaletteBox(byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
Constructs a PlatteBox from the provided byte array.
PaletteBuilder - Class in io.scif.media.imageioimpl.common
This class implements the octree quantization method as it is described in the "Graphics Gems" (ISBN 0-12-286166-3, Chapter 4, pages 297-293)
PaletteBuilder(RenderedImage) - Constructor for class io.scif.media.imageioimpl.common.PaletteBuilder
 
PaletteBuilder(RenderedImage, int) - Constructor for class io.scif.media.imageioimpl.common.PaletteBuilder
 
PaletteBuilder.ColorNode - Class in io.scif.media.imageioimpl.common
The node of color tree.
paletteIndex - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
paletteSize - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
params - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Dequantization parameters of all subbands and all components in the current tile.
parent - Variable in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
The reference to the parent of this subband.
parent - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
The reference to the parent of this subband.
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Parses the data elements from the byte array.
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Parse the channel definitions from the content data array.
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ComponentMappingBox
Parse the component mapping from the provided content data array.
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.DataEntryURLBox
Parses the content of this box from its content byte array.
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.FileTypeBox
 
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.HeaderBox
Parse the data elements from the byte array of the content.
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.PaletteBox
 
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ResolutionBox
Parse the data elements from the provided content data array.
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDBox
Parses the data elements from the provided data array.
parse(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDListBox
Parses the data elements from the provided content data array.
parseArguments(Parameters) - Method in class io.scif.cli.LongArrayOptionHandler
 
parseByteArray(String) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Parses the byte array expressed by a string.
parseIdx(String, int) - Static method in class io.scif.jj2000.j2k.ModuleSpec
This method is responsible of parsing tile indexes set and component indexes set for an option.
parseIFD(Node) - Static method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
parseIntArray(String) - Static method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Parses the integer array expressed a string.
Parser() - Constructor for class io.scif.bf.BioFormatsFormat.Parser
 
Parser() - Constructor for class io.scif.lifesci.SDTFormat.Parser
 
parseROIs(String, int, Vector) - Static method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
This function parses the values given for the ROIs with the argument -Rroi.
pass - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Black and white pass mode table.
passMode - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Pass mode table.
pcs - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
The progression changes specifications
PCXConstants - Interface in io.scif.media.imageioimpl.plugins.pcx
 
PCXImageReader - Class in io.scif.media.imageioimpl.plugins.pcx
 
PCXImageReader(PCXImageReaderSpi) - Constructor for class io.scif.media.imageioimpl.plugins.pcx.PCXImageReader
 
PCXImageReaderSpi - Class in io.scif.media.imageioimpl.plugins.pcx
 
PCXImageReaderSpi() - Constructor for class io.scif.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
PCXImageWriter - Class in io.scif.media.imageioimpl.plugins.pcx
 
PCXImageWriter(PCXImageWriterSpi) - Constructor for class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriter
 
PCXImageWriterSpi - Class in io.scif.media.imageioimpl.plugins.pcx
 
PCXImageWriterSpi() - Constructor for class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
PCXMetadata - Class in io.scif.media.imageioimpl.plugins.pcx
 
PHOTOMETRIC_INTERPRETATION_BLACK_IS_ZERO - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PhotometricInterpretation" tag.
PHOTOMETRIC_INTERPRETATION_CIELAB - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PhotometricInterpretation" tag.
PHOTOMETRIC_INTERPRETATION_CMYK - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PhotometricInterpretation" tag.
PHOTOMETRIC_INTERPRETATION_ICCLAB - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PhotometricInterpretation" tag.
PHOTOMETRIC_INTERPRETATION_PALETTE_COLOR - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PhotometricInterpretation" tag.
PHOTOMETRIC_INTERPRETATION_RGB - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PhotometricInterpretation" tag.
PHOTOMETRIC_INTERPRETATION_TRANSPARENCY_MASK - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PhotometricInterpretation" tag.
PHOTOMETRIC_INTERPRETATION_WHITE_IS_ZERO - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PhotometricInterpretation" tag.
PHOTOMETRIC_INTERPRETATION_Y_CB_CR - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PhotometricInterpretation" tag.
photometricInterpretation - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The value of the PhotometricInterpretation tag.
PipelineImage - Class in io.scif.formats.imaris
 
PipelineImage(Object, int, int, int, String) - Constructor for class io.scif.formats.imaris.PipelineImage
 
pixClk - Variable in class io.scif.lifesci.SDTInfo
 
pixelAspectRatio - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
pixels - Variable in class io.scif.formats.imaris.PipelineImage
 
pixTime - Variable in class io.scif.lifesci.SDTInfo
 
pktDec - Variable in class io.scif.jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
Reference to the PktDecoder instance
PktDecoder - Class in io.scif.jj2000.j2k.codestream.reader
This class is used to read packet's head and body.
PktDecoder(DecoderSpecs, HeaderDecoder, RandomAccessIO, BitstreamReaderAgent, boolean, int) - Constructor for class io.scif.jj2000.j2k.codestream.reader.PktDecoder
Creates an empty PktDecoder object associated with given decoder specifications and HeaderDecoder.
PktEncoder - Class in io.scif.jj2000.j2k.codestream.writer
This class builds packets and keeps the state information of packet interdependencies.
PktEncoder(CodedCBlkDataSrcEnc, J2KImageWriteParamJava, Point[][][]) - Constructor for class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Creates a new packet header encoder, using the information from the 'infoSrc' object.
pktIdx - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
Index of the packet where each layer has been found
PktInfo - Class in io.scif.jj2000.j2k.codestream.reader
This class defines an object used to countain informations about a packet to which the current code-block belongs.
PktInfo(int, int) - Constructor for class io.scif.jj2000.j2k.codestream.reader.PktInfo
Classe's constructor.
planar - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
true if the image is encoded using separate planes.
PLANAR_CONFIGURATION_CHUNKY - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PlanarConfiguration" tag.
PLANAR_CONFIGURATION_PLANAR - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "PlanarConfiguration" tag.
PLM - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Packet length, main header (PLM): 0xFF57
PLT - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Packet length, tile-part header (PLT): 0xFF58
PNMImageReader - Class in io.scif.media.imageioimpl.plugins.pnm
This class is the Java Image IO plugin reader for PNM images.
PNMImageReader(ImageReaderSpi) - Constructor for class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
Constructs PNMImageReader from the provided ImageReaderSpi.
PNMImageReaderSpi - Class in io.scif.media.imageioimpl.plugins.pnm
 
PNMImageReaderSpi() - Constructor for class io.scif.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
PNMImageWriteParam - Class in io.scif.media.imageio.plugins.pnm
A subclass of ImageWriteParam for writing images in the PNM format.
PNMImageWriteParam() - Constructor for class io.scif.media.imageio.plugins.pnm.PNMImageWriteParam
Constructs a PNMImageWriteParam object with default values for parameters.
PNMImageWriter - Class in io.scif.media.imageioimpl.plugins.pnm
The Java Image IO plugin writer for encoding a binary RenderedImage into a PNM format.
PNMImageWriter(ImageWriterSpi) - Constructor for class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriter
Constructs PNMImageWriter based on the provided ImageWriterSpi.
PNMImageWriterSpi - Class in io.scif.media.imageioimpl.plugins.pnm
 
PNMImageWriterSpi() - Constructor for class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
PNMMetadata - Class in io.scif.media.imageioimpl.plugins.pnm
Metadata for the PNM plug-in.
PNMMetadata(IIOMetadata) - Constructor for class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
PNMMetadataFormat - Class in io.scif.media.imageioimpl.plugins.pnm
 
PNMMetadataFormatResources - Class in io.scif.media.imageioimpl.plugins.pnm
 
PNMMetadataFormatResources() - Constructor for class io.scif.media.imageioimpl.plugins.pnm.PNMMetadataFormatResources
 
poc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo
Reference to the POC marker segments found in main and first tile-part header.
POC() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo.POC
 
POC - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
 
polarityF - Variable in class io.scif.lifesci.SDTInfo
 
polarityL - Variable in class io.scif.lifesci.SDTInfo
2 = disabled line markers.
polarityP - Variable in class io.scif.lifesci.SDTInfo
 
populateImageMetadata() - Method in class io.scif.bf.BioFormatsFormat.Metadata
 
populateImageMetadata() - Method in class io.scif.lifesci.SDTFormat.Metadata
 
populateImageMetadata() - Method in class io.scif.ome.OMEMetadata
 
populateImageMetadata(MetadataRetrieve, int, ImageMetadata) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populateImageMetadata(MetadataRetrieve, int, ImageMetadata) - Method in interface io.scif.ome.services.OMEMetadataService
Populates the provided ImageMetadata object using the specified image index into the MetadataRetrieve.
populateMetadata(MetadataStore, int, String, boolean, String, String, int, int, int, int, int, double, double, double, double, double, int) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populateMetadata(MetadataStore, int, String, Metadata) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populateMetadata(MetadataStore, int, String, ImageMetadata) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populateMetadata(MetadataStore, String, int, String, boolean, String, String, int, int, int, int, int, double, double, double, double, double, int) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populateMetadata(MetadataRetrieve, Metadata) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populateMetadata(MetadataStore, int, String, boolean, String, String, int, int, int, int, int, double, double, double, double, double, int) - Method in interface io.scif.ome.services.OMEMetadataService
Populates the given MetadataStore, for the specified imageIndex, using the provided values.
populateMetadata(MetadataStore, int, String, Metadata) - Method in interface io.scif.ome.services.OMEMetadataService
Populates the given MetadataStore, for the specified imageIndex, using the values from the provided Metadata.
populateMetadata(MetadataStore, int, String, ImageMetadata) - Method in interface io.scif.ome.services.OMEMetadataService
Populates the given MetadataStore, for the specified imageIndex, using the values from the provided ImageMetadata.
populateMetadata(MetadataStore, String, int, String, boolean, String, String, int, int, int, int, int, double, double, double, double, double, int) - Method in interface io.scif.ome.services.OMEMetadataService
Populates the given MetadataStore, for the specified imageIndex, using the provided values.
populateMetadata(MetadataRetrieve, Metadata) - Method in interface io.scif.ome.services.OMEMetadataService
Uses the provided MetadataRetrieve to populate the format-agnostic image information in the provided Metadata object (that is, the ImageMetadata).
populateOriginalMetadata(OMEMetadata, Hashtable<String, Object>) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
populateOriginalMetadata(OMEMetadata, String, String) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
populateOriginalMetadata(OMEMetadata, Hashtable<String, Object>) - Method in interface io.scif.ome.services.OMEXMLService
 
populateOriginalMetadata(OMEMetadata, String, String) - Method in interface io.scif.ome.services.OMEXMLService
 
populatePixels(MetadataStore, Metadata) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populatePixels(MetadataStore, Metadata, boolean) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populatePixels(MetadataStore, Metadata, boolean, boolean) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populatePixels(MetadataStore, List<ImageMetadata>, boolean, String) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populatePixels(MetadataStore, Metadata) - Method in interface io.scif.ome.services.OMEMetadataService
Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.
populatePixels(MetadataStore, Metadata, boolean) - Method in interface io.scif.ome.services.OMEMetadataService
Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.
populatePixels(MetadataStore, Metadata, boolean, boolean) - Method in interface io.scif.ome.services.OMEMetadataService
Populates the 'pixels' element of the given metadata store, using core metadata from the given metadata.
populatePixels(MetadataStore, List<ImageMetadata>, boolean, String) - Method in interface io.scif.ome.services.OMEMetadataService
Populates the 'pixels' element of the given metadata store, using the provided ImageMetadata.
populatePixelsOnly(MetadataStore, Reader) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populatePixelsOnly(MetadataStore, int, boolean, String, String, int, int, int, int, int, double, double, double, double, double, int) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
populatePixelsOnly(MetadataStore, Reader) - Method in interface io.scif.ome.services.OMEMetadataService
 
populatePixelsOnly(MetadataStore, int, boolean, String, String, int, int, int, int, int, double, double, double, double, double, int) - Method in interface io.scif.ome.services.OMEMetadataService
 
pos - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
Progression order specifications
pos - Variable in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
The current position in the byte-buffer
POS_COMP_RES_LY_PROG - Static variable in interface io.scif.jj2000.j2k.codestream.ProgressionType
The bit stream is Position/Component/Resolution/Layer progressive : 3
PostCompRateAllocator - Class in io.scif.jj2000.j2k.entropy.encoder
This is the abstract class from which post-compression rate allocators which generate layers should inherit.
PostCompRateAllocator(CodedCBlkDataSrcEnc, int, CodestreamWriter, J2KImageWriteParamJava) - Constructor for class io.scif.jj2000.j2k.entropy.encoder.PostCompRateAllocator
Initializes the source of entropy coded data.
pphs - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
Packed packet header specifications
PPM - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Packed packet headers, main header (PPM): 0xFF60
PPM_FOUND - Static variable in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Flag bit for SOD marker segment found
ppoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.POC
 
PPT - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Packed packet headers, tile-part header (PPT): 0xFF61
PPT_FOUND - Static variable in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Flag bit for SOD marker segment found
PrecCoordInfo - Class in io.scif.jj2000.j2k.codestream
This class is used to store the coordinates of precincts.
PrecCoordInfo(int, int, int, int, int, int) - Constructor for class io.scif.jj2000.j2k.codestream.PrecCoordInfo
Constructor.
PrecCoordInfo() - Constructor for class io.scif.jj2000.j2k.codestream.PrecCoordInfo
Empty Constructor.
PRECINCT_PARTITION_DEF_SIZE - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
The default size exponent of the precincts
precinctPartitionUsed() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Returns the boolean used to know if the precinct partition is used
precinctPartitionUsed(int, int) - Method in interface io.scif.jj2000.j2k.entropy.encoder.CodedCBlkDataSrcEnc
Returns true if the precinct partition is used for the specified component and tile, returns false otherwise
precinctPartitionUsed(int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Returns true if precinct partition is used for the specified component and tile, returns false otherwise.
PrecinctSizeSpec - Class in io.scif.jj2000.j2k.entropy
This class extends ModuleSpec class for precinct partition sizes holding purposes.
PrecinctSizeSpec(int, int, byte, IntegerSpec) - Constructor for class io.scif.jj2000.j2k.entropy.PrecinctSizeSpec
Creates a new PrecinctSizeSpec object for the specified number of tiles and components.
PrecinctSizeSpec(int, int, byte, BlkImgDataSrc, IntegerSpec, J2KImageWriteParamJava, String) - Constructor for class io.scif.jj2000.j2k.entropy.PrecinctSizeSpec
Creates a new PrecinctSizeSpec object for the specified number of tiles and components and the J2KImageWriteParamJava instance.
PrecInfo - Class in io.scif.jj2000.j2k.codestream
Class that holds precinct coordinates and references to contained code-blocks in each subband.
PrecInfo(int, int, int, int, int, int, int, int, int) - Constructor for class io.scif.jj2000.j2k.codestream.PrecInfo
Class constructor.
PREDICTOR_HORIZONTAL_DIFFERENCING - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Predictor" tag.
PREDICTOR_NONE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Predictor" tag.
prepareInsertEmpty(int, ImageTypeSpecifier, int, int, IIOMetadata, List, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
prepareReplacePixels(int, Rectangle) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
prepareWriteEmpty(IIOMetadata, ImageTypeSpecifier, int, int, IIOMetadata, List, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
prepareWriteSequence(IIOMetadata) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
prepareWriteSequence(IIOMetadata) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
print(PrintWriter, int, int, String) - Method in class io.scif.jj2000.j2k.util.MsgPrinter
Formats the message to print in the current line width, by breaking the message into lines between words.
println(String, int, int) - Method in interface io.scif.jj2000.j2k.util.MsgLogger
Prints the string 'str' to the output device, appending a line return.
println(String, int, int) - Method in class io.scif.jj2000.j2k.util.StreamMsgLogger
Prints the string 'str' to the 'out' stream, appending a newline.
println(String, int, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
printmsg(int, String) - Method in interface io.scif.jj2000.j2k.util.MsgLogger
Prints the message 'msg' to the output device, appending a newline, with severity 'sev'.
printmsg(int, String) - Method in class io.scif.jj2000.j2k.util.StreamMsgLogger
Prints the message 'msg' to the output device, appending a newline, with severity 'sev'.
printmsg(int, String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
PRIORITY - Static variable in class io.scif.ome.translators.TIFFTranslator
 
process(LinkedList<PipelineImage>) - Method in class io.scif.formats.imaris.HDFPreprocessor
 
processImageProgressWrapper(float) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
Wrapper for the protected method processImageProgress So it can be access from the classes which are not in ImageReader hierarchy.
processImageProgressWrapper(float) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
Wrapper for the protected method processImageProgress So it can be access from the classes which are not in ImageWriter hierachy.
processImageProgressWrapper(float) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
Wrapper for the protected method processImageProgress So it can be access from the classes which are not in ImageReader hierachy.
processImageUpdateWrapper(BufferedImage, int, int, int, int, int, int, int[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
Wrapper for the protected method processImageUpdate So it can be access from the classes which are not in ImageReader hierarchy.
processImageUpdateWrapper(BufferedImage, int, int, int, int, int, int, int[]) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
Wrapper for the protected method processImageUpdate So it can be access from the classes which are not in ImageReader hierachy.
processOnRegistration(ServiceRegistry, Class, String, ImageReaderWriterSpi, int, int) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
 
processPlane(Reader, Plane, int, long, long, Interval) - Method in class io.scif.cli.AbstractReaderCommand
Helper method to open the specified region of the specified plane and perform any command-specific operations.
processPlane(Reader, Plane, int, long, long, Interval) - Method in class io.scif.cli.convert.Convert
 
processPlane(Reader, Plane, int, long, long, Interval) - Method in class io.scif.cli.show.Show
 
PROFILE_EMBEDDED - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
PROFILE_LINKED - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
prog - Variable in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
The progressive flag, false by default (see above).
Progression - Class in io.scif.jj2000.j2k.entropy
This class holds one of the different progression orders defined in the bit stream.
Progression(int, int, int, int, int, int) - Constructor for class io.scif.jj2000.j2k.entropy.Progression
Constructor.
ProgressionSpec - Class in io.scif.jj2000.j2k.entropy
This class extends ModuleSpec class for progression type(s) and progression order changes holding purposes.
ProgressionSpec(int, int, byte) - Constructor for class io.scif.jj2000.j2k.entropy.ProgressionSpec
Creates a new ProgressionSpec object for the specified number of tiles and components.
ProgressionSpec(int, int, int, IntegerSpec, byte, J2KImageWriteParamJava, String) - Constructor for class io.scif.jj2000.j2k.entropy.ProgressionSpec
Creates a new ProgressionSpec object for the specified number of tiles, components and the J2KImageWriteParamJava instance.
ProgressionType - Interface in io.scif.jj2000.j2k.codestream
This interface defines the identifiers for the different bit stream profiles and progression types.
progressive - Variable in class io.scif.jj2000.j2k.image.DataBlk
The progressive attribute (false by default)
ProgressWatch - Interface in io.scif.jj2000.j2k.util
 
properties - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
A Hashtable containing the image properties.
psot - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SOT
 
pss - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
Precinct partition specifications
px - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The horizontal coordinate of the tiling origin in the canvas system, on the reference grid.
py - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The vertical coordinate of the tiling origin in the canvas system, on the reference grid.

Q

Q_TYPE_SCALAR_DZ - Static variable in interface io.scif.jj2000.j2k.quantization.QuantizationType
The ID of the scalar deadzone dequantizer
qcc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo
Reference to the QCC marker segments found in main and first tile-part header.
QCC() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo.QCC
 
QCC - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Quantization component (QCC): 0xFF5D
qcd - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo
Reference to the QCD marker segments found in main and first tile-part header.
QCD() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo.QCD
 
QCD - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Quantization default (QCD): 0xFF5C
qsss - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
Quantization normalized base step size specifications
QSTEP_EXPONENT_BITS - Static variable in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
The number of exponent bits for the quantization steps
QSTEP_MANTISSA_BITS - Static variable in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
The number of mantissa bits for the quantization steps
QSTEP_MAX_EXPONENT - Static variable in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
The maximum value of the exponent for the quantization steps
QSTEP_MAX_MANTISSA - Static variable in class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
The maximum value of the mantissa for the quantization steps
qts - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
Quantization type specifications
QuantizationType - Interface in io.scif.jj2000.j2k.quantization
This interface defines the IDs of the possible quantization types.
Quantizer - Class in io.scif.jj2000.j2k.quantization.quantizer
This abstract class provides the general interface for quantizers.
Quantizer(CBlkWTDataSrc) - Constructor for class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
Initializes the source of wavelet transform coefficients.
QuantStepSizeSpec - Class in io.scif.jj2000.j2k.quantization
This class extends ModuleSpec class in order to hold specifications about the quantization base normalized step size to use in each tile-component.
QuantStepSizeSpec(int, int, byte) - Constructor for class io.scif.jj2000.j2k.quantization.QuantStepSizeSpec
Constructs an empty 'QuantStepSizeSpec' with specified number of tile and components.
QuantStepSizeSpec(int, int, byte, J2KImageWriteParamJava, String) - Constructor for class io.scif.jj2000.j2k.quantization.QuantStepSizeSpec
Constructs a new 'QuantStepSizeSpec' for the specified number of components and tiles and the arguments of "-Qstep" option.
QuantTypeSpec - Class in io.scif.jj2000.j2k.quantization
This class extends ModuleSpec class in order to hold specifications about the quantization type to use in each tile-component.
QuantTypeSpec(int, int, byte) - Constructor for class io.scif.jj2000.j2k.quantization.QuantTypeSpec
Constructs an empty 'QuantTypeSpec' with specified number of tile and components.
QuantTypeSpec(int, int, byte, J2KImageWriteParamJava, String) - Constructor for class io.scif.jj2000.j2k.quantization.QuantTypeSpec
Constructs a new 'QuantTypeSpec' for the specified number of components and tiles and the arguments of "-Qtype" option.

R

r - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Resolution level index
r - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
radius of circular ROI
ralloc - Variable in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Reference to the rate allocator
RandomAccessIO - Interface in io.scif.jj2000.j2k.io
This abstract class defines the interface to perform random access I/O.
rawImage - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
A BufferedImage for the decodeRaw method to write into.
RawImageInputStream - Class in io.scif.media.imageio.stream
This class defines the content of the ImageInputStream containing several raw images with the same image type: the number of the images, the image type, the offset for the first sample of each image, and the image size information.
RawImageInputStream(ImageInputStream, ImageTypeSpecifier, long[], Dimension[]) - Constructor for class io.scif.media.imageio.stream.RawImageInputStream
Constructor.
RawImageInputStream(ImageInputStream, SampleModel, long[], Dimension[]) - Constructor for class io.scif.media.imageio.stream.RawImageInputStream
Constructor.
RawImageInputStream(ImageInputStream, InputSource) - Constructor for class io.scif.media.imageio.stream.RawImageInputStream
Constructor.
RawImageReader - Class in io.scif.media.imageioimpl.plugins.raw
This class is the Java Image IO plugin reader for Raw images.
RawImageReader(ImageReaderSpi) - Constructor for class io.scif.media.imageioimpl.plugins.raw.RawImageReader
Constructs RawImageReader from the provided ImageReaderSpi.
RawImageReaderSpi - Class in io.scif.media.imageioimpl.plugins.raw
 
RawImageReaderSpi() - Constructor for class io.scif.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
RawImageWriteParam - Class in io.scif.media.imageioimpl.plugins.raw
A subclass of ImageWriteParam for writing images in the RAW format.
RawImageWriteParam(Locale) - Constructor for class io.scif.media.imageioimpl.plugins.raw.RawImageWriteParam
Constructor to set locales.
RawImageWriter - Class in io.scif.media.imageioimpl.plugins.raw
The Java Image IO plugin writer for encoding a binary RenderedImage into a Raw format.
RawImageWriter(ImageWriterSpi) - Constructor for class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
Constructs RawImageWriter based on the provided ImageWriterSpi.
RawImageWriterSpi - Class in io.scif.media.imageioimpl.plugins.raw
 
RawImageWriterSpi() - Constructor for class io.scif.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
RawRenderedImage - Class in io.scif.media.imageioimpl.plugins.raw
 
RawRenderedImage(RawImageInputStream, RawImageReader, ImageReadParam, int) - Constructor for class io.scif.media.imageioimpl.plugins.raw.RawRenderedImage
 
rb - Variable in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
The "range bits" for each transformed component
rcom - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COM
 
RCOM_GEN_USE - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
General use registration value (COM): 0x0001
re - Variable in class io.scif.jj2000.j2k.entropy.Progression
Resolution index for the end of a progression.
read(byte[]) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
read(byte[], int, int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
read(ByteBuffer) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
read(ByteBuffer, int, int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
read() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
read(Reader) - Method in class io.scif.cli.AbstractReaderCommand
Intermediate read method.
read() - Method in class io.scif.jj2000.j2k.entropy.decoder.ByteInputBuffer
Reads the next byte of data from this input stream.
read() - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Reads an unsigned byte of data from the stream.
read() - Method in interface io.scif.jj2000.j2k.io.RandomAccessIO
Reads a byte of data from the stream.
read() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads a byte of data from the stream.
read() - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
 
read(byte[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
 
read() - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
read(byte[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
read() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
read(byte[]) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
read(byte[], int, int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
read() - Method in class io.scif.media.imageio.stream.SegmentedImageInputStream
Reads the next byte of data from the input stream.
read(byte[], int, int) - Method in class io.scif.media.imageio.stream.SegmentedImageInputStream
Reads up to len bytes of data from the input stream into an array of bytes.
read(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
read() - Method in class io.scif.media.imageioimpl.plugins.clib.InputStreamAdapter
 
read(byte[], int, int) - Method in class io.scif.media.imageioimpl.plugins.clib.InputStreamAdapter
 
read(ImageInputStream, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Reads a box from the ImageInputStream
read() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
read() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
read(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
read(byte[], int, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
read(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
read(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReader
 
read(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
read(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
read(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
read(Rectangle) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
read(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
readAsRaster() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
readAsRaster(WritableRaster) - Method in class io.scif.media.imageioimpl.plugins.raw.RawRenderedImage
 
readAsRenderedImage(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
readAsRenderedImage(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
readAsRenderedImage(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
readBit() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readBits(int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readBitsPerComponentBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
Read the bits per component.
readBlockHeader(DataHandle<Location>) - Method in class io.scif.lifesci.SDTInfo
Convenience method for reading from a block header section of an SDT header stream.
readBoolean() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readBoolean() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readBufferedImage() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
readByte() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readByte() - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Should read a signed byte (i.e., 8 bit) from the input.
readByte() - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Reads a signed byte (i.e., 8 bit) from the input.
readByte() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads a signed byte (8 bit) from the input.
readByte() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readByte() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readBytes(IIOByteBuffer, int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readChannelDefinitionBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method reads the Channel Definition box
readChar() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readChar() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readChecked() - Method in class io.scif.jj2000.j2k.entropy.decoder.ByteInputBuffer
Reads the next byte of data from this input stream.
readColourSpecificationBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
Read the color specifications.
readComponentMappingBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
Read the component mapping channel.
readContiguousCodeStreamBox(int, long) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method skips the Contiguous codestream box and adds position of contiguous codestream to a vector
readCString() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readDouble() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readDouble() - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Reads an IEEE double precision (i.e., 64 bit) floating-point number from the input.
readDouble() - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Should read an IEEE double precision (i.e., 64 bit) floating-point number from the input.
readDouble() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads an IEEE double precision (i.e., 64 bit) floating-point number from the input.
readDouble() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readDouble() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readEPHMarker(PktHeaderBitReader) - Method in class io.scif.jj2000.j2k.codestream.reader.PktDecoder
Try to read an EPH marker.
Reader() - Constructor for class io.scif.bf.BioFormatsFormat.Reader
 
Reader() - Constructor for class io.scif.lifesci.SDTFormat.Reader
 
reader - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The ImageReader calling this TIFFDecompressor.
readFileFormat() - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method checks whether the given RandomAccessIO is a valid JP2 file and if so finds the first codestream in the file.
readFileTypeBox(int, long) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method reads the File Type box
readFloat() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readFloat() - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Reads an IEEE single precision (i.e., 32 bit) floating-point number from the input.
readFloat() - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Should read an IEEE single precision (i.e., 32 bit) floating-point number from the input.
readFloat() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads an IEEE single precision (i.e., 32 bit) floating-point number from the input.
readFloat() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readFloat() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readFoundTilePartMarkSeg(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Return the DecoderSpecs instance filled when reading the headers
readFully(byte[]) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readFully(byte[], int, int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readFully(byte[], int, int) - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Reads up to len bytes of data from this file into an array of bytes.
readFully(byte[], int, int) - Method in interface io.scif.jj2000.j2k.io.RandomAccessIO
Reads up to len bytes of data from this file into an array of bytes.
readFully(byte[], int, int) - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads 'len' bytes of data from this file into an array of bytes.
readFully(char[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
 
readFully(short[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
 
readFully(int[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
 
readFully(long[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
 
readFully(float[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
 
readFully(double[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
 
readFully(char[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
readFully(short[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
readFully(int[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
readFully(long[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
readFully(float[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
readFully(double[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
readFully(byte[], int, int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readFully(byte[]) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readFully(short[], int, int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readFully(char[], int, int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readFully(int[], int, int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readFully(long[], int, int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readFully(float[], int, int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readFully(double[], int, int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readFully(byte[], int, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readHeader() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
readHeader() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
readHeader() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
readHeader() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
readImageHeaderBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method reads the Image Header box
readInt() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readInt() - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Reads a signed int (i.e., 32 bit) from the input.
readInt() - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Should read a signed int (i.e., 32 bit) from the input.
readInt() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads a signed int (32 bit) from the input.
readInt() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readInt() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readIntPropertyBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method reads the contents of the Intellectual property box
readJP2HeaderBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method reads the JP2Header box
readLine() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readLine() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readLong() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readLong() - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Reads a signed long (i.e., 64 bit) from the input.
readLong() - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Should read a signed long (i.e., 64 bit) from the input.
readLong() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads a signed long (64 bit) from the input.
readLong() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readLong() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readMultiByteInteger(ImageInputStream) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
 
readNewBuffer(int) - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Reads a new buffer from the file.
readPaletteBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method reads the content of the palette box
readPktBody(int, int, int, int, CBlkInfo[][][], int[]) - Method in class io.scif.jj2000.j2k.codestream.reader.PktDecoder
Reads specificied packet body in order to find offset of each code-block's piece of codeword.
readPktHead(int, int, int, int, CBlkInfo[][][], int[]) - Method in class io.scif.jj2000.j2k.codestream.reader.PktDecoder
Read specified packet head and found length of each code-block's piece of codewords as well as number of skipped most significant bit-planes.
readRaster(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
readRaster(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
readRaster(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
readRaster(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
readRaster(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
readRaster(int, ImageReadParam) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
readResolutionBox(int, int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
Read the resolution.
readShort() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readShort() - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Reads a signed short (i.e., 16 bit) from the input.
readShort() - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Should read a signed short (i.e., 16 bit) from the input.
readShort() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads a signed short (16 bit) from the input.
readShort() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readShort() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readSOPMarker(int[], int, int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.PktDecoder
Try to read a SOP marker and check that its sequence number if not out of sequence.
readString(String) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readString(int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readSupportsThumbnails() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
readTile(int, int, int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
readUnsignedByte() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readUnsignedByte() - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Should read an unsigned byte (i.e., 8 bit) from the input.
readUnsignedByte() - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Reads an unsigned byte (i.e., 8 bit) from the input.
readUnsignedByte() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads an unsigned byte (8 bit) from the input.
readUnsignedByte() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readUnsignedByte() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readUnsignedInt() - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Reads an unsigned int (i.e., 32 bit) from the input.
readUnsignedInt() - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Should read an unsigned int (i.e., 32 bit) from the input.
readUnsignedInt() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads a unsigned int (32 bit) from the input.
readUnsignedInt() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readUnsignedInt() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readUnsignedShort() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readUnsignedShort() - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Reads an unsigned short (i.e., 16 bit) from the input.
readUnsignedShort() - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Should read an unsigned short (i.e., 16 bit) from the input.
readUnsignedShort() - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Reads an unsigned short (16 bit) from the input.
readUnsignedShort() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readUnsignedShort() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
readURLBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method reads the contents of the XML box
readUTF() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
readUTF() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
readUUIDBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method reads the contents of the Intellectual property box
readUUIDListBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method reads the contents of the UUID List box
readXMLBox(int) - Method in class io.scif.jj2000.j2k.fileformat.reader.FileFormatReader
This method reads the contents of the XML box
rect - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
Flag indicating whether the ROI is rectangular or not
RectROIMaskGenerator - Class in io.scif.jj2000.j2k.roi.encoder
This class generates the ROI masks when there are only rectangular ROIs in the image.
RectROIMaskGenerator(ROI[], int) - Constructor for class io.scif.jj2000.j2k.roi.encoder.RectROIMaskGenerator
The constructor of the mask generator.
red - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder.ColorNode
 
red - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
redMask - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
reduceList - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
reduceTree() - Method in class io.scif.media.imageioimpl.common.PaletteBuilder
 
redX - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
redY - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
redZ - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
registerMsgLogger(Thread, MsgLogger) - Static method in class io.scif.jj2000.j2k.util.FacilityManager
Registers the MsgLogger 'ml' as the logging facility of the thread 't'.
registerProgressWatch(Thread, ProgressWatch) - Static method in class io.scif.jj2000.j2k.util.FacilityManager
 
removeAllowedTagSet(TIFFTagSet) - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageReadParam
Removes a TIFFTagSet object from the list of allowed tag sets.
removeBinData(OMEXMLMetadata) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
removeBinData(OMEXMLMetadata) - Method in interface io.scif.ome.services.OMEXMLService
 
removeChannels(OMEXMLMetadata, int, int) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
removeChannels(OMEXMLMetadata, int, int) - Method in interface io.scif.ome.services.OMEXMLService
 
removeChild(Node) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
removeTagSet(TIFFTagSet) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Removes an element from the group of TIFFTagSets of which this directory is aware.
removeTIFFField(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Removes a TIFF field from the directory.
removeTIFFField(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
removeTIFFFields() - Method in class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Removes all TIFF fields from the directory.
RenderedImageSrc - Class in io.scif.media.imageioimpl.plugins.jpeg2000
 
RenderedImageSrc(Raster, J2KImageWriteParamJava, J2KImageWriter) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Creates RenderedImageSrc for encoding a Raster.
RenderedImageSrc(RenderedImage, J2KImageWriteParamJava, J2KImageWriter) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Creates RenderedImageSrc for encoding a RenderedImage.
replaceChild(Node, Node) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
replacePixels(RenderedImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
replacePixels(Raster, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
repoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.POC
 
repT - Variable in class io.scif.lifesci.SDTInfo
 
requiredSize - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
RES_LY_COMP_POS_PROG - Static variable in interface io.scif.jj2000.j2k.codestream.ProgressionType
The bit stream is Resolution/Layer/Component/Position progressive : 1
RES_POS_COMP_LY_PROG - Static variable in interface io.scif.jj2000.j2k.codestream.ProgressionType
The bit stream is Resolution/Position/Component/Layer progressive : 2
reserved1 - Variable in class io.scif.lifesci.SDTInfo
 
reserved2 - Variable in class io.scif.lifesci.SDTInfo
 
reset() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
reset() - Method in class io.scif.jj2000.j2k.codestream.writer.BitOutputBuffer
Resets the buffer.
reset() - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Resets the contents of this HeaderEncoder to its initial state.
reset() - Method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Resets the state of the object to the initial state, as if the object was just created.
reset() - Method in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Resets the tree values and state.
reset(int[]) - Method in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Resets the tree values and state.
reset() - Method in class io.scif.jj2000.j2k.entropy.encoder.ByteOutputBuffer
Discards all the buffered data, by resetting the counter of written bytes to 0.
reset() - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Reinitializes the MQ coder and the underlying 'ByteOutputBuffer' buffer as if a new object was instantaited.
reset() - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
reset() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
 
reset() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
reset() - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
reset() - Method in class io.scif.media.imageioimpl.plugins.clib.InputStreamAdapter
 
reset() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
reset() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
reset() - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
reset() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
reset() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
reset() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
reset() - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
reset() - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXMetadata
 
reset() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
 
reset() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriter
 
reset() - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
reset() - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
 
reset() - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
reset() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
reset() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
reset() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
reset() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
reset() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
reset() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
reset() - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
resetCtxt(int) - Method in class io.scif.jj2000.j2k.entropy.decoder.MQDecoder
Resets a context to the original probability distribution.
resetCtxt(int) - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Resets a context to the original probability distribution, and sets its more probable symbol to 0.
resetCtxts() - Method in class io.scif.jj2000.j2k.entropy.decoder.MQDecoder
Resets a context to the original probability distribution.
resetCtxts() - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Resets all contexts to their original probability distribution and sets all more probable symbols to 0.
resetHeaderMarkers() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Method that resets members indicating which markers have already been found
resetLocal() - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
resLvl - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The resolution level to which this subband contributes.
reslvl - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
The resquested image resolution level for reconstruction.
RESOLUTION_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
RESOLUTION_UNIT_CENTIMETER - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "ResolutionUnit" tag.
RESOLUTION_UNIT_INCH - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "ResolutionUnit" tag.
RESOLUTION_UNIT_NONE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "ResolutionUnit" tag.
ResolutionBox - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is defined to represent a Resolution Box of JPEG JP2 file format.
ResolutionBox(int, byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ResolutionBox
Constructs a ResolutionBox from the provided type and content data array.
ResolutionBox(int, float, float) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ResolutionBox
Constructs a ResolutionBox from the provided type and horizontal/vertical resolutions.
ResolutionBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.ResolutionBox
Constructs a ResolutionBox based on the provided org.w3c.dom.Node.
ResolutionLevel - Class in io.scif.formats.imaris
 
ResolutionLevel(int, int, int, int, int, int, int, int, int) - Constructor for class io.scif.formats.imaris.ResolutionLevel
 
ResolutionLevelMaker - Class in io.scif.formats.imaris
 
ResolutionLevelMaker() - Constructor for class io.scif.formats.imaris.ResolutionLevelMaker
 
resourceBaseName - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
restart(int, int[], int, CBlkInfo[][][][][], boolean, ByteArrayInputStream) - Method in class io.scif.jj2000.j2k.codestream.reader.PktDecoder
Re-initialize the PktDecoder instance at the beginning of a new tile.
restore() - Method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Restores the last saved state of this object.
restore() - Method in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Restores the saved values and state of the tree.
revision - Variable in class io.scif.lifesci.SDTInfo
Software revision number (lower 4 bits >= 10(decimal)).
rgh - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Precinct height reported in the reference grid
rgn - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo
Reference to the RGN marker segments found in main and first tile-part header.
RGN() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo.RGN
 
RGN - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Region-of-interest (RGN): 0xFF5E
rgulx - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Precinct horizontal upper-left coordinate in the reference grid
rguly - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Precinct vertical upper-left coordinate in the reference grid
rgw - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Precinct width reported in the reference grid
ROI - Class in io.scif.jj2000.j2k.roi.encoder
This class contains the shape of a single ROI.
ROI(int, ImgReaderPGM) - Constructor for class io.scif.jj2000.j2k.roi.encoder.ROI
Constructor for ROI with arbitrary shape
ROI(int, int, int, int, int) - Constructor for class io.scif.jj2000.j2k.roi.encoder.ROI
Constructor for rectangular ROIs
ROI(int, int, int, int) - Constructor for class io.scif.jj2000.j2k.roi.encoder.ROI
Constructor for circular ROIs
ROIDeScaler - Class in io.scif.jj2000.j2k.roi
This class takes care of the de-scaling of ROI coefficients.
ROIDeScaler(CBlkQuantDataSrcDec, MaxShiftSpec) - Constructor for class io.scif.jj2000.j2k.roi.ROIDeScaler
Constructor of the ROI descaler, takes EntropyDEcoder as source of data to de-scale.
roiInTile - Variable in class io.scif.jj2000.j2k.roi.encoder.ROIMaskGenerator
 
ROIMaskGenerator - Class in io.scif.jj2000.j2k.roi.encoder
This class generates the ROI masks for the ROIScaler.It gives the scaler the ROI mask for the current code-block.
ROIMaskGenerator(ROI[], int) - Constructor for class io.scif.jj2000.j2k.roi.encoder.ROIMaskGenerator
The constructor of the mask generator
rois - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
ROI maxshift value specifications
rois - Variable in class io.scif.jj2000.j2k.roi.encoder.ROIMaskGenerator
Array containing the ROIs
roiSc - Variable in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Reference to the ROI module
ROIScaler - Class in io.scif.jj2000.j2k.roi.encoder
This class deals with the ROI functionality.
ROIScaler(Quantizer, ROIMaskGenerator, boolean, int, boolean, J2KImageWriteParamJava) - Constructor for class io.scif.jj2000.j2k.roi.encoder.ROIScaler
Constructor of the ROI scaler, takes a Quantizer as source of data to scale.
root - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
root - Variable in class io.scif.ome.OMEMetadata
OME core
rootName - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
rotate90(Point) - Method in class io.scif.jj2000.j2k.ModuleSpec
Rotate the ModuleSpec instance by 90 degrees (this modifies only tile and tile-component specifications).
rs - Variable in class io.scif.jj2000.j2k.entropy.Progression
Resolution index for the start of a progression
rsiz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
RSIZ_BASELINE - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
No special capabilities (baseline) in codestream, in Rsiz field of SIZ marker: 0x00.
RSIZ_ER_FLAG - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Error resilience marker flag bit in Rsiz field in SIZ marker: 0x01
RSIZ_ROI - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
ROI present marker flag bit in Rsiz field in SIZ marker: 0x02
rspoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.POC
 
rts - Variable in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Regular termination specifications
run() - Method in class io.scif.cli.AbstractSCIFIOToolCommand
Performs the actual tool operations.
run() - Method in class io.scif.cli.convert.Convert
 
run() - Method in class io.scif.cli.help.Help
 
run() - Method in class io.scif.cli.info.Info
 
run(String...) - Static method in class io.scif.cli.SCIFIOTools
Entry point for running SCIFIO commands.
run() - Method in class io.scif.cli.show.Show
 
run() - Method in class io.scif.ome.commands.OMEXMLToolCommand
 
runAndWrite() - Method in class io.scif.jj2000.j2k.entropy.encoder.EBCOTRateAllocator
Runs the rate allocation algorithm and writes the data to the bit stream writer object provided to the constructor.
runAndWrite() - Method in class io.scif.jj2000.j2k.entropy.encoder.PostCompRateAllocator
Runs the rate allocation algorithm and writes the data to the bit stream.
runCommand(String...) - Method in class io.scif.cli.AbstractSCIFIOToolCommand
 
runCommand(String...) - Method in interface io.scif.cli.SCIFIOToolCommand
Executes this command with the given arguments.
runTarget(Runnable, Object) - Method in class io.scif.jj2000.j2k.util.ThreadPool
Runs the run method of the specified target in an idle thread of this pool.
runTarget(Runnable, Object, boolean) - Method in class io.scif.jj2000.j2k.util.ThreadPool
Runs the run method of the specified target in an idle thread of this pool.
runTarget(Runnable, Object, boolean, boolean) - Method in class io.scif.jj2000.j2k.util.ThreadPool
Runs the run method of the specified target in an idle thread of this pool.

S

SAMPLE_FORMAT_FLOATING_POINT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "SampleFormat" tag.
SAMPLE_FORMAT_SIGNED_INTEGER - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "SampleFormat" tag.
SAMPLE_FORMAT_UNDEFINED - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "SampleFormat" tag.
SAMPLE_FORMAT_UNSIGNED_INTEGER - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "SampleFormat" tag.
sampleFormat - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The value of the SampleFormat tag.
sampleModel - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The image's SampleModel.
samplesPerPixel - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The value of the SamplesPerPixel tag.
SATURATION_HIGH - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Saturation" tag.
SATURATION_LOW - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Saturation" tag.
SATURATION_NORMAL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Saturation" tag.
save() - Method in class io.scif.jj2000.j2k.codestream.writer.PktEncoder
Saves the current state of this object.
save() - Method in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Saves the current values and state of the tree.
saved - Variable in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
The saved state.
savePlane(int, long, Plane) - Method in class io.scif.formats.ImarisFormat.Writer
 
sb - Variable in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
The subband to which the code-block belongs
sb - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The subband in which this code-block is found
sbandIdx - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The subband index within its resolution level.
scanRX - Variable in class io.scif.lifesci.SDTInfo
 
scanRY - Variable in class io.scif.lifesci.SDTInfo
 
scanw - Variable in class io.scif.jj2000.j2k.image.DataBlk
The width of the scanlines used to store the data in the array
scanw - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The width of the scanlines used to store the data in the array
scanX - Variable in class io.scif.lifesci.SDTInfo
 
scanY - Variable in class io.scif.lifesci.SDTInfo
 
SCENE_CAPTURE_TYPE_LANDSCAPE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SceneCaptureType" tag.
SCENE_CAPTURE_TYPE_NIGHT_SCENE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SceneCaptureType" tag.
SCENE_CAPTURE_TYPE_PORTRAIT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SceneCaptureType" tag.
SCENE_CAPTURE_TYPE_STANDARD - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SceneCaptureType" tag.
SCENE_TYPE_DSC - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SceneType" tag.
SCIFIOToolCommand - Interface in io.scif.cli
Base interface for all SCIFIOTools commands.
SCIFIOTools - Class in io.scif.cli
Entry point for all SCIFIO commands.
scoc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
 
scod - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
SCOX_HOR_CB_PART - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Horizontal code-block partition origin is at x=1
SCOX_PRECINCT_PARTITION - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Precinct used flag
SCOX_USE_EPH - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Use end of packet header marker
SCOX_USE_SOP - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Use start of packet marker
SCOX_VER_CB_PART - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Vertical code-block partition origin is at y=1
SDTFormat - Class in io.scif.lifesci
SDTReader is the file format reader for Becker & Hickl SPC-Image SDT files.
SDTFormat() - Constructor for class io.scif.lifesci.SDTFormat
 
SDTFormat.Metadata - Class in io.scif.lifesci
 
SDTFormat.Parser - Class in io.scif.lifesci
 
SDTFormat.Reader - Class in io.scif.lifesci
 
SDTInfo - Class in io.scif.lifesci
SDTInfo encapsulates the header information for Becker & Hickl SPC-Image SDT files.
SDTInfo(DataHandle<Location>, MetaTable) - Constructor for class io.scif.lifesci.SDTInfo
Constructs a new SDT header by reading values from the given input source, populating the given metadata table.
seek(long) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
seek(int) - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Moves the current position to the given offset at which the next read or write occurs.
seek(int) - Method in interface io.scif.jj2000.j2k.io.RandomAccessIO
Moves the current position for the next read or write operation to offset.
seek(int) - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Moves the current position for the next read operation to offset.
seek(long) - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
Invokes the superclass method and sets the position within the memory mapped buffer.
seek(long) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
Invokes the superclass method, writes any unwritten data, and sets the channel position to the supplied parameter.
seek(long) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
seek(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
segLen - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
The length of each segment (used with regular termination or in selective arithmetic bypass coding mode)
segLengths - Variable in class io.scif.jj2000.j2k.codestream.reader.PktInfo
The length of each terminated segment in the packet.
SegmentedImageInputStream - Class in io.scif.media.imageio.stream
A SegmentedImageInputStream provides a view of a subset of another ImageInputStream consiting of a series of segments with given starting positions in the source stream and lengths.
SegmentedImageInputStream(ImageInputStream, StreamSegmentMapper) - Constructor for class io.scif.media.imageio.stream.SegmentedImageInputStream
Constructs a SegmentedImageInputStream given a ImageInputStream as input and an instance of StreamSegmentMapper.
SegmentedImageInputStream(ImageInputStream, long[], int[]) - Constructor for class io.scif.media.imageio.stream.SegmentedImageInputStream
Constructs a SegmentedImageInputStream given a ImageInputStream as input and a list of the starting positions and lengths of the segments of the source stream.
SegmentedImageInputStream(ImageInputStream, long[], int, int) - Constructor for class io.scif.media.imageio.stream.SegmentedImageInputStream
Constructs a SegmentedImageInputStream given a ImageInputStream as input, a list of the starting positions of the segments of the source stream, the common length of each segment, and the total length of the segments.
selectConvexHull(int[], double[], boolean[], int, boolean) - Method in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
Compute the rate-distorsion slopes and selects those that lie in a convex hull.
SENSING_METHOD_COLOR_SEQUENTIAL_AREA_SENSOR - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SensingMethod" tag.
SENSING_METHOD_COLOR_SEQUENTIAL_LINEAR_SENSOR - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SensingMethod" tag.
SENSING_METHOD_NOT_DEFINED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SensingMethod" tag.
SENSING_METHOD_ONE_CHIP_COLOR_AREA_SENSOR - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SensingMethod" tag.
SENSING_METHOD_THREE_CHIP_COLOR_AREA_SENSOR - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SensingMethod" tag.
SENSING_METHOD_TRILINEAR_SENSOR - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SensingMethod" tag.
SENSING_METHOD_TWO_CHIP_COLOR_AREA_SENSOR - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SensingMethod" tag.
setActiveSrcHeight(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the activeSrcHeight field.
setActiveSrcHeight(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setActiveSrcMinX(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the activeSrcMinX field.
setActiveSrcMinX(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setActiveSrcMinY(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the activeSrcMinY field.
setActiveSrcMinY(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setActiveSrcWidth(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the activeSrcWidth field.
setActiveSrcWidth(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setAlignROI(boolean) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets alignROI
setBinOffset(int) - Method in class io.scif.lifesci.SDTFormat.Metadata
 
setBitOffset(int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
setBitsPerSample(int[]) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the bitsPerSample field.
setBitsPerSample(int[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setBypass(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets bypass
setByteArray(byte[], int, int) - Method in class io.scif.jj2000.j2k.entropy.decoder.ByteInputBuffer
Sets the underlying buffer byte array to the given one, with the given offset and length.
setByteCount(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the byteCount field.
setByteCount(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setByteOrder(ByteOrder) - Method in class io.scif.media.imageio.stream.FileChannelImageInputStream
 
setByteOrder(ByteOrder) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
setByteOrder(ByteOrder) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
setCausalCXInfo(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets causalCXInfo
setChannels(int) - Method in class io.scif.lifesci.SDTFormat.Metadata
 
setCodeBlockSize(int[]) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Sets codeBlockSize.
setCodeBlockSize(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets codeBlockSize
setCodeSegSymbol(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets codeSegSymbol
setColorConverter(TIFFColorConverter) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the TIFFColorConverter object describing the color space of the encoded data in the input stream.
setColorConverter(TIFFColorConverter) - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageReadParam
Sets the TIFFColorConverter object for the pixel data being read.
setColorConverter(TIFFColorConverter, int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageWriteParam
Sets the TIFFColorConverter object describing the color space to which the input data should be converted for storage in the input stream.
setColorMap(char[]) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the colorMap field.
setColorMap(char[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setCompDef(int, Object) - Method in class io.scif.jj2000.j2k.entropy.CBlkSizeSpec
Sets default value for specified component and specValType tag if allowed by its priority.
setCompDef(int, Object) - Method in class io.scif.jj2000.j2k.ModuleSpec
Sets default value for specified component and specValType tag if allowed by its priority.
setComponentTransformation(boolean) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Sets componentTransformation.
setComponentTransformation(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets componentTransformation
setCompression(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the compression field.
setCompression(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setCompressionType(String) - Method in class io.scif.media.imageio.plugins.bmp.BMPImageWriteParam
Sets the compression type to one of the values indicated by getCompressionTypes.
setContent(byte[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Sets the box content.
setCrop(long[]) - Method in class io.scif.cli.AbstractReaderCommand
 
setData(Object) - Method in class io.scif.jj2000.j2k.image.DataBlk
Sets the data array to the specified one.
setData(Object) - Method in class io.scif.jj2000.j2k.image.DataBlkFloat
Sets the data array to the specified one.
setData(Object) - Method in class io.scif.jj2000.j2k.image.DataBlkInt
Sets the data array to the specified one.
setData(Object) - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
Sets the data array to the specified one.
setData(Object) - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataFloat
Sets the data array to the specified one.
setData(Object) - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataInt
Sets the data array to the specified one.
setDataFloat(float[]) - Method in class io.scif.jj2000.j2k.image.DataBlkFloat
Sets the data array to the specified one.
setDataFloat(float[]) - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataFloat
Sets the data array to the specified one.
setDataInt(int[]) - Method in class io.scif.jj2000.j2k.image.DataBlkInt
Sets the data array to the specified one.
setDataInt(int[]) - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTDataInt
Sets the data array to the specified one.
setDecodingRate(double) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageReadParam
Sets decodingRate.
setDecompositionLevel(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets decompositionLevel
setDefault(Object) - Method in class io.scif.jj2000.j2k.entropy.CBlkSizeSpec
Sets default value for this module
setDefault(Object) - Method in class io.scif.jj2000.j2k.ModuleSpec
Sets default value for this module
setDefaultAttributes(IIOMetadataNode) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Sets the default attributes, "Length", "Type", and "ExtraLength", to the provided IIOMetadataNode.
setDefaultCreationDate(MetadataStore, String, int) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
setDefaultCreationDate(MetadataStore, String, int) - Method in interface io.scif.ome.services.OMEMetadataService
Sets a default creation date.
setDefaultDateEnabled(boolean) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
setDefaultDateEnabled(boolean) - Method in interface io.scif.ome.services.OMEMetadataService
Disables the setting of a default creation date.
setDest(Location, int, SCIFIOConfig) - Method in class io.scif.formats.ImarisFormat.Writer
 
setDest(DataHandle<Location>, int, SCIFIOConfig) - Method in class io.scif.formats.ImarisFormat.Writer
 
setDestImage(BufferedImage) - Method in class io.scif.media.imageioimpl.plugins.raw.RawRenderedImage
 
setDestinationBands(int[]) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the destinationBands field.
setDestinationBands(int[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstHeight(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the dstHeight field.
setDstHeight(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstMinX(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the dstMinX field.
setDstMinX(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstMinY(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the dstMinY field.
setDstMinY(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstWidth(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the dstWidth field.
setDstWidth(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstXOffset(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the dstXOffset field.
setDstXOffset(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setDstYOffset(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the dstYOffset field.
setDstYOffset(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setEncoding(String) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
setEncodingRate(double) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Sets encodingRate.
setEncodingRate(double) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets encodingRate
setEPH(boolean) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Sets EPH.
setEPH(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets EPH
setExtraLength(long) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Sets the box extra length length to the provided value.
setExtraSamples(int[]) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the extraSamples field.
setExtraSamples(int[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setFilter(String) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Sets filter.
setFilters(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets filters
setFromTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
setFromTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
setFromTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
setFromTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
setFromTree(String, Node) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
setGuardBits(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets guardBits
setHeaderEncoder(HeaderEncoder) - Method in class io.scif.jj2000.j2k.entropy.encoder.PostCompRateAllocator
Keep a reference to the header encoder.
setHeight(int) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
setImage(BufferedImage) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the image field.
setImage(BufferedImage) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setImgResLevel(int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.InvWT
Sets the image reconstruction resolution level.
setImgResLevel(int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Sets the image reconstruction resolution level.
setInput(Object, boolean, boolean) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageReader
Overrides the method defined in the superclass.
setInput(Object, boolean, boolean) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReader
Overrides the method defined in the superclass.
setInput(Object, boolean, boolean) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageReader
 
setInput(Object, boolean, boolean) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageReader
Overrides the method defined in the superclass.
setInput(Object, boolean, boolean) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageReader
Overrides the method defined in the superclass.
setInput(Object, boolean, boolean) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
setInput(Object, boolean, boolean) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
Overrides the method defined in the superclass.
setLayers(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets the layers
setLenCalcType(int) - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Set the length calculation type to the specified type
setLength(long) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
setLength(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Sets the box length to the provided value.
setLineWidth(int) - Method in class io.scif.jj2000.j2k.util.MsgPrinter
Sets the line width to the specified value.
setLossless(boolean) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Sets lossless.
setLossless(boolean) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets lossless
setMainCompDefDecompType(int, int, int) - Method in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
Sets the "component main default" decomposition type and number of levels for the specified component.
setMap(String) - Method in class io.scif.cli.AbstractReaderCommand
 
setMaxBitDepth(int) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
Set the maximum sample size and maximum sample value.
setMergeIntensity(boolean) - Method in class io.scif.lifesci.SDTFormat.Metadata
 
setMergeIntensity(boolean) - Method in class io.scif.lifesci.SDTFormat.Parser
 
setMetadata(Metadata) - Method in class io.scif.formats.ImarisFormat.Writer
 
setMetadata(IIOMetadata) - Method in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Sets the value of the metadata field.
setMetadata(IIOMetadata) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the metadata field.
setMetadata(IIOMetadata) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFEXIFJPEGCompressor
 
setMetadata(IIOMetadata) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Sets the value of the metadata field.
setMetadata(IIOMetadata) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGCompressor
Sets the value of the metadata field.
setMetadata(IIOMetadata) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFT4Compressor
Sets the value of the metadata field.
setMetadata(IIOMetadata) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setMethodForMQLengthCalc(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets methodForMQLengthCalc
setMethodForMQTermination(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets methodForMQTermination
setMinX(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets minX
setMinY(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets minY
setNoROIDescaling(boolean) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava
Sets noROIDescaling
setNumDecompositionLevels(int) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Sets numDecompositionLevels.
setOffset(long) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the offset field.
setOffset(long) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setOrder(ByteOrder) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
setOutput(Object) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
setOutput(Object) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
setOutput(Object) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
setOutput(Object) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriter
 
setOutput(Object) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriter
 
setOutput(Object) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
setOutput(Object) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
setOutput(Object) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
setPackedBinaryData(byte[], WritableRaster, Rectangle) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Sets the supplied Raster's data from an array of packed binary data of the form returned by getPackedBinaryData().
setPacketPerTilePart(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets packetPerTilePart
setPackPacketHeaderInMain(boolean) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets packPacketHeaderInMain
setPackPacketHeaderInTile(boolean) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets packPacketHeaderInTile
setParsingEnabled(boolean) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReadParamJava
Sets parsingEnabled
setPhotometricInterpretation(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the photometricInterpretation field.
setPhotometricInterpretation(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setPlanar(boolean) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the planar field.
setPlanar(boolean) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setPrecinctPartition(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets precinctPartition
setProgressionName(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets progressionName
setProgressionType(String) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Sets progressionType.
setProgressionType(LayersInfo, String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets progressionType
setQuantizationStep(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets quantizationStep
setQuantizationType(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets quantizationType
setRaw(boolean) - Method in class io.scif.media.imageio.plugins.pnm.PNMImageWriteParam
Sets the representation to be used.
setReader(IFormatReader) - Method in class io.scif.bf.BioFormatsFormat.Metadata
 
setReader(ImageReader) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the reader field.
setReader(ImageReader) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setResetMQ(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets resetMQ
setResolution(int) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageReadParam
Sets resolution.
setROIs(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets ROIs
setRoot(OMEXMLMetadata) - Method in class io.scif.ome.OMEMetadata
Sets the root for this Metadata
setSampleFormat(int[]) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the sampleFormat field.
setSampleFormat(int[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSamplesPerPixel(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the samplesPerPixel field.
setSamplesPerPixel(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSDTInfo(SDTInfo) - Method in class io.scif.lifesci.SDTFormat.Metadata
 
setSegmentLength(int) - Method in class io.scif.media.imageio.stream.StreamSegment
Sets the length of the segment.
setSOP(boolean) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Sets SOP.
setSOP(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets SOP
setSourceBands(int[]) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the sourceBands field.
setSourceBands(int[]) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Override the method setSourceBands in the super class.
setSourceBands(int[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSourceSubsampling(int, int, int, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Override the method setSourceSubsampling in the super class.
setSourceXOffset(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the sourceXOffset field.
setSourceXOffset(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSourceYOffset(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the sourceYOffset.
setSourceYOffset(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSrcHeight(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the srcHeight field.
setSrcHeight(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSrcMinX(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the srcMinX field.
setSrcMinX(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSrcMinY(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the srcMinY field.
setSrcMinY(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSrcWidth(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the srcWidth field.
setSrcWidth(int) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setStartLevelROI(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets the startLevelROI
setStartPos(long) - Method in class io.scif.media.imageio.stream.StreamSegment
Sets the starting position of the segment.
setStream(ImageOutputStream) - Method in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Sets the ImageOutputStream to be written.
setStream(ImageInputStream) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the stream field.
setStream(ImageOutputStream) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWCompressor
 
setStream(ImageInputStream) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
setSubsampleX(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the subsampleX field.
setSubsampleY(int) - Method in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
Sets the value of the subsampleY field.
setTerminateOnByte(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Sets terminateOnByte
setTermType(int) - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
Set termination type to the specified type
setThreadConcurrency(int) - Static method in class io.scif.jj2000.j2k.util.NativeServices
Sets the concurrency level of the threading system of the Java Virtual Machine (JVM) to the specified level.
setTIFFCompressor(TIFFCompressor) - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageWriteParam
Sets the TIFFCompressor object to be used by the ImageWriter to encode each image strip or tile.
setTIFFDecompressor(TIFFDecompressor) - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageReadParam
Sets the TIFFDecompressor object to be used by the ImageReader to decode each image strip or tile.
setTile(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Changes the current tile, given the new indexes.
setTile(int, int) - Method in class io.scif.jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
Changes the current tile, given the new indexes.
setTile(int, int) - Method in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Changes the current tile, given the new indexes.
setTile(int, int) - Method in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Changes the current tile, given the new indexes.
setTile(int, int) - Method in interface io.scif.jj2000.j2k.image.ImgData
Changes the current tile, given the new indices.
setTile(int, int) - Method in class io.scif.jj2000.j2k.image.ImgDataAdapter
Changes the current tile, given the new indexes.
setTile(int, int) - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Changes the current tile, given the new coordinates.
setTile(int, int) - Method in class io.scif.jj2000.j2k.image.input.ImgReader
Changes the current tile, given the new coordinates.
setTile(int, int) - Method in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Changes the current tile, given the new indexes.
setTile(int, int) - Method in class io.scif.jj2000.j2k.image.Tiler
Changes the current tile, given the new tile indexes.
setTile(int, int) - Method in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
Changes the current tile, given the new indexes.
setTile(int, int) - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
Changes the current tile, given the new indexes.
setTile(int, int) - Method in class io.scif.jj2000.j2k.wavelet.analysis.ForwWTFull
Changes the current tile, given the new coordinates.
setTile(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTAdapter
Changes the current tile, given the new indices.
setTile(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.InvWTFull
Changes the current tile, given the new indexes.
setTile(int, int) - Method in interface io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgData
Changes the current tile, given the new indexes.
setTile(int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Changes the current tile, given the new indexes.
setTile(int, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Changes the current tile, given the new coordinates.
setTileCompVal(int, int, Object) - Method in class io.scif.jj2000.j2k.entropy.CBlkSizeSpec
Sets value for specified tile-component.
setTileCompVal(int, int, Object) - Method in class io.scif.jj2000.j2k.ModuleSpec
Sets value for specified tile-component.
setTileDef(int, Object) - Method in class io.scif.jj2000.j2k.entropy.CBlkSizeSpec
Sets default value for specified tile and specValType tag if allowed by its priority.
setTileDef(int, Object) - Method in class io.scif.jj2000.j2k.ModuleSpec
Sets default value for specified tile and specValType tag if allowed by its priority.
setTileOfTileParts(int) - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Sets the tile of each tile part in order.
setTiling(int, int, int, int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Override the method setTiling in the super class.
setTimeBase(double) - Method in class io.scif.lifesci.SDTFormat.Metadata
 
setTimeBins(int) - Method in class io.scif.lifesci.SDTFormat.Metadata
 
setTopDown(boolean) - Method in class io.scif.media.imageio.plugins.bmp.BMPImageWriteParam
If set, the data will be written out in a top-down manner, the first scanline being written first.
setUnpackedBinaryData(byte[], WritableRaster, Rectangle) - Static method in class io.scif.media.imageioimpl.common.ImageUtil
Copies data into the packed array of the Raster from an array of unpacked data of the form returned by getUnpackedBinaryData().
setup - Variable in class io.scif.lifesci.SDTInfo
 
SETUP_IDENTIFIER - Static variable in class io.scif.lifesci.SDTInfo
For .set files (setup only).
setupLength - Variable in class io.scif.lifesci.SDTInfo
Length of the setup data.
setupOffs - Variable in class io.scif.lifesci.SDTInfo
Offset of the setup text data (system parameters, display parameters, trace parameters etc.).
setValue(int, int, int) - Method in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Changes the value of a leaf in the tag tree.
setValues(int[]) - Method in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Sets the values of the leafs to the new set of values and updates the tag tree accordingly.
setVariant(int) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
Sets the variant: '1' - '6'.
setWidth(int) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMMetadata
 
setWriteCodeStreamOnly(boolean) - Method in class io.scif.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Sets writeCodeStreamOnly.
setWriter(ImageWriter) - Method in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Sets the value of the writer field.
sgcod_mct - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
sgcod_nl - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
sgcod_po - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
SHARPNESS_HARD - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Sharpness" tag.
SHARPNESS_NORMAL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Sharpness" tag.
SHARPNESS_SOFT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "Sharpness" tag.
SHLIB_NAME - Static variable in class io.scif.jj2000.j2k.util.NativeServices
The name of the shared library containing the implementation of the native methods: 'jj2000'.
Show - Class in io.scif.cli.show
Opens a dataset for viewing.
Show() - Constructor for class io.scif.cli.show.Show
 
SignatureBox - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is defined to represent a Signature Box of JPEG JP2 file format.
SignatureBox() - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.SignatureBox
Constructs a SignatureBox.
SignatureBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.SignatureBox
Constructs a SignatureBox based on the provided org.w3c.dom.Node.
SignatureBox(byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.SignatureBox
Constructs a SignatureBox based on the provided byte array.
SimpleCMYKColorSpace - Class in io.scif.media.imageioimpl.common
Singleton class representing a simple, mathematically defined CMYK color space.
SimpleRenderedImage - Class in io.scif.media.imageioimpl.common
 
SimpleRenderedImage() - Constructor for class io.scif.media.imageioimpl.common.SimpleRenderedImage
 
singleInstance(String) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
SingleTileRenderedImage - Class in io.scif.media.imageioimpl.common
A simple class that provides RenderedImage functionality given a Raster and a ColorModel.
SingleTileRenderedImage(Raster, ColorModel) - Constructor for class io.scif.media.imageioimpl.common.SingleTileRenderedImage
Constructs a SingleTileRenderedImage based on a Raster and a ColorModel.
siz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo
Reference to the SIZ marker segment found in main header
SIZ() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
SIZ - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
SIZ marker (Image and tile size): 0xFF51
size() - Method in class io.scif.jj2000.j2k.entropy.encoder.ByteOutputBuffer
Returns the number of valid bytes in the output buffer (count class variable).
skip(long) - Method in class io.scif.media.imageioimpl.plugins.clib.InputStreamAdapter
 
skip(long) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
skipBytes(int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
skipBytes(int) - Method in interface io.scif.jj2000.j2k.io.BinaryDataInput
Skips n bytes from the input.
skipBytes(int) - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Skips n bytes from the input.
skipBytes(int) - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Skips 'n' bytes from the input.
skipBytes(int) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
skipBytes(long) - Method in class io.scif.media.imageio.stream.RawImageInputStream
 
skipBytes(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
skipMSBP - Variable in class io.scif.jj2000.j2k.entropy.CodedCBlk
The number of skipped most significant bit-planes.
slice - Variable in class io.scif.formats.imaris.PipelineImage
 
SOC - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Start of codestream (SOC): 0xFF4F
SOD - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Start of data (SOD): 0xFF93
SOD_FOUND - Static variable in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Flag bit for SOD marker segment found
SOI - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
SOP - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Start pf packet (SOP): 0xFF91
SOP_LENGTH - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Length of SOP marker (in bytes)
sops - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
The Start Of Packet (SOP) markers specifications
sortFlag - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
sortFlag - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
sot - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo
Reference to the SOT marker segments found in tile-part headers.
SOT() - Constructor for class io.scif.jj2000.j2k.codestream.HeaderInfo.SOT
 
SOT - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Start of tile-part (SOT): 0xFF90
source() - Method in class io.scif.bf.ome.BioFormatsTranslator.BioFormatsOMETranslator
 
source() - Method in class io.scif.ome.translators.APNGTranslator.APNGOMETranslator
 
source() - Method in class io.scif.ome.translators.APNGTranslator.OMEAPNGTranslator
 
source() - Method in class io.scif.ome.translators.BMPTranslator.BMPOMETranslator
 
source() - Method in class io.scif.ome.translators.DefaultOMETranslator
 
source() - Method in class io.scif.ome.translators.DICOMTranslator.DICOMOMETranslator
 
source() - Method in class io.scif.ome.translators.EPSTranslator.OMEEPSTranslator
 
source() - Method in class io.scif.ome.translators.ICSTranslator.ICSOMETranslator
 
source() - Method in class io.scif.ome.translators.ICSTranslator.OMEICSTranslator
 
source() - Method in class io.scif.ome.translators.MicromanagerTranslator.MicromanagerOMETranslator
 
source() - Method in class io.scif.ome.translators.NRRDTranslator.NRRDOMETranslator
 
source() - Method in class io.scif.ome.translators.OBFTranslator.OBFOMETranslator
 
source() - Method in class io.scif.ome.translators.TIFFTranslator.OMETIFFTranslator
 
source() - Method in class io.scif.ome.translators.TIFFTranslator.TIFFOMETranslator
 
sourceBands - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The sequence of source bands that are to be copied into the destination.
sources - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The image's sources, stored in a Vector.
sourceXOffset - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The source X offset used, along with dstXOffset and subsampleX, to map between horizontal source and destination pixel coordinates.
sourceYOffset - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The source Y offset used, along with dstYOffset and subsampleY, to map between vertical source and destination pixel coordinates.
spcoc_ch - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
 
spcoc_cs - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
 
spcoc_cw - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
 
spcoc_ndl - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
 
spcoc_ps - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
 
spcoc_t - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
 
spcod_ch - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
spcod_cs - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
spcod_cw - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
spcod_ndl - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
spcod_ps - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
spcod_t - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
 
SPEC_COMP_DEF - Static variable in class io.scif.jj2000.j2k.ModuleSpec
The identifier for "component default" specification
SPEC_DEF - Static variable in class io.scif.jj2000.j2k.ModuleSpec
The identifier for default specification
SPEC_TILE_COMP - Static variable in class io.scif.jj2000.j2k.ModuleSpec
The identifier for a "tile-component" specification
SPEC_TILE_DEF - Static variable in class io.scif.jj2000.j2k.ModuleSpec
The identifier for "tile default" specification
SPEC_TYPE_COMP - Static variable in class io.scif.jj2000.j2k.ModuleSpec
The identifier for a specification module that applies only to components
SPEC_TYPE_TILE - Static variable in class io.scif.jj2000.j2k.ModuleSpec
The identifier for a specification module that applies only to tiles
SPEC_TYPE_TILE_COMP - Static variable in class io.scif.jj2000.j2k.ModuleSpec
The identifier for a specification module that applies both to tiles and components
specified - Variable in class io.scif.jj2000.j2k.ModuleSpec
The specified value in string format
specType - Variable in class io.scif.jj2000.j2k.ModuleSpec
The type of the specification module
specValType - Variable in class io.scif.jj2000.j2k.ModuleSpec
The spec type for each tile-component.
specValType - Variable in class io.scif.jj2000.j2k.wavelet.WTFilterSpec
The spec type for each tile and component.
SPEED_REF_KILOMETERS_PER_HOUR - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSSpeedRef" tag.
SPEED_REF_KNOTS - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSSpeedRef" tag.
SPEED_REF_MILES_PER_HOUR - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSSpeedRef" tag.
split(WaveletFilter, WaveletFilter) - Method in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
Splits the current subband in its four subbands.
split(WaveletFilter, WaveletFilter) - Method in class io.scif.jj2000.j2k.wavelet.Subband
Splits the current subband in its four subbands.
split(WaveletFilter, WaveletFilter) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
Splits the current subband in its four subbands.
spqcc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCC
 
spqcd - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCD
 
sprgn - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.RGN
 
sqcc - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCC
 
sqcd - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCD
 
SQCX_EXP_MASK - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Exponent bitmask in SPQCX when no quantization: 3
SQCX_EXP_SHIFT - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Exponent shift in SPQCX when no quantization: 3
SQCX_GB_MSK - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Guard bits mask in SQCX field: 7
SQCX_GB_SHIFT - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Guard bits shift in SQCX field: 5
SQCX_NO_QUANTIZATION - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
No quantization (i.e.
SQCX_SCALAR_DERIVED - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Scalar derived (i.e.
SQCX_SCALAR_EXPOUNDED - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Scalar expounded (i.e.
src - Variable in class io.scif.jj2000.j2k.entropy.decoder.EntropyDecoder
The bit stream transport from where to get the compressed data (the source)
src - Variable in class io.scif.jj2000.j2k.entropy.encoder.EntropyCoder
The source of quantized wavelet coefficients
src - Variable in class io.scif.jj2000.j2k.entropy.encoder.PostCompRateAllocator
The source of entropy coded data
src - Variable in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
The entropy decoder from where to get the quantized data (the source).
src - Variable in class io.scif.jj2000.j2k.quantization.quantizer.Quantizer
The source of wavelet transform coefficients
src - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
srcColorModel - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
srcHeight - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The height of the source region being decoded from the source stream.
srcMinX - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The X coordinate of the upper-left pixel of the source region being decoded from the source stream.
srcMinY - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The Y coordinate of the upper-left pixel of the source region being decoded from the source stream.
srcRaster - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
srcWidth - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The width of the source region being decoded from the source stream.
srgn - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.RGN
 
SRGN_IMPLICIT - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Implicit (i.e.
ssiz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
SSIZ_DEPTH_BITS - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Component bitdepth bits in Ssiz field in SIZ marker: 7
sss - Variable in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Error resilience segment symbol use specifications
status - Variable in class io.scif.lifesci.SDTInfo
Last SPC_test_state return value (status).
STATUS_MEASUREMENT_IN_PROGRESS - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSStatus" tag.
STATUS_MEASUREMENT_INTEROPERABILITY - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSStatus" tag.
StdDequantizer - Class in io.scif.jj2000.j2k.quantization.dequantizer
This class implements a scalar dequantizer with deadzone.
StdDequantizer(CBlkQuantDataSrcDec, int[], DecoderSpecs) - Constructor for class io.scif.jj2000.j2k.quantization.dequantizer.StdDequantizer
Initializes the source of compressed data.
StdDequantizerParams - Class in io.scif.jj2000.j2k.quantization.dequantizer
This class holds the parameters for the scalar deadzone dequantizer (StdDequantizer class) for the current tile.
StdDequantizerParams() - Constructor for class io.scif.jj2000.j2k.quantization.dequantizer.StdDequantizerParams
 
StdEntropyCoder - Class in io.scif.jj2000.j2k.entropy.encoder
This class implements the JPEG 2000 entropy coder, which codes stripes in code-blocks.
StdEntropyCoder(CBlkQuantDataSrcEnc, CBlkSizeSpec, PrecinctSizeSpec, StringSpec, StringSpec, StringSpec, StringSpec, StringSpec, StringSpec, StringSpec) - Constructor for class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
Instantiates a new entropy coder engine, with the specified source of data, nominal block width and height.
StdEntropyCoderOptions - Interface in io.scif.jj2000.j2k.entropy
This interface define the constants that identify the possible options for the entropy coder, as well some fixed parameters of the JPEG 2000 entropy coder.
StdEntropyDecoder - Class in io.scif.jj2000.j2k.entropy.decoder
This class implements the JPEG 2000 entropy decoder, which codes stripes in code-blocks.
StdEntropyDecoder(CodedCBlkDataSrcDec, DecoderSpecs, boolean, boolean, int) - Constructor for class io.scif.jj2000.j2k.entropy.decoder.StdEntropyDecoder
Instantiates a new entropy decoder engine, with the specified source of data, nominal block width and height.
StdQuantizer - Class in io.scif.jj2000.j2k.quantization.quantizer
This class implements scalar quantization of integer or floating-point valued source data.
StdQuantizer(CBlkWTDataSrc, J2KImageWriteParamJava) - Constructor for class io.scif.jj2000.j2k.quantization.quantizer.StdQuantizer
Initializes the source of wavelet transform coefficients.
steps - Variable in class io.scif.lifesci.SDTInfo
 
stepSize - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The quantization step size of the code-block.
stepWMSE - Variable in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
The contribution to the MSE or WMSE error that would result in the image if there was an error of exactly one quantization step size in the sample of the subband.
stopt - Variable in class io.scif.lifesci.SDTInfo
 
stopTime - Variable in class io.scif.lifesci.SDTInfo
Time from start to - disarm (simple measurement) - or to the end of the cycle (for complex measurement).
stream - Variable in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
The ImageOutputStream to be written.
stream - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The ImageInputStream containing the TIFF source data.
STREAM_METADATA_NAME - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
StreamMsgLogger - Class in io.scif.jj2000.j2k.util
This class implements the MsgLogger interface for streams.
StreamMsgLogger(OutputStream, OutputStream, int) - Constructor for class io.scif.jj2000.j2k.util.StreamMsgLogger
Constructs a StreamMsgLogger that uses 'outstr' as the 'out' stream, and 'errstr' as the 'err' stream.
StreamMsgLogger(Writer, Writer, int) - Constructor for class io.scif.jj2000.j2k.util.StreamMsgLogger
Constructs a StreamMsgLogger that uses 'outstr' as the 'out' stream, and 'errstr' as the 'err' stream.
StreamMsgLogger(PrintWriter, PrintWriter, int) - Constructor for class io.scif.jj2000.j2k.util.StreamMsgLogger
Constructs a StreamMsgLogger that uses 'outstr' as the 'out' stream, and 'errstr' as the 'err' stream.
StreamSegment - Class in io.scif.media.imageio.stream
A utility class representing a segment within a stream as a long starting position and an int length.
StreamSegment() - Constructor for class io.scif.media.imageio.stream.StreamSegment
Constructs a StreamSegment.
StreamSegment(long, int) - Constructor for class io.scif.media.imageio.stream.StreamSegment
Constructs a StreamSegment with a given starting position and length.
StreamSegmentMapper - Interface in io.scif.media.imageio.stream
An interface for use with the SegmentedImageInputStream class.
StringFormatException - Exception in io.scif.jj2000.j2k.util
Thrown to indicate that the application has attempted to parse a badly formatted string.
StringFormatException() - Constructor for exception io.scif.jj2000.j2k.util.StringFormatException
Creates the exception with an empty messgage.
StringFormatException(String) - Constructor for exception io.scif.jj2000.j2k.util.StringFormatException
Creates the exception with the specified detail message.
StringSpec - Class in io.scif.jj2000.j2k
This class extends ModuleSpec class in order to hold tile-component specifications using Strings.
StringSpec(int, int, byte) - Constructor for class io.scif.jj2000.j2k.StringSpec
Constructs an empty 'StringSpec' with specified number of tile and components.
StringSpec(int, int, byte, String, String[], J2KImageWriteParamJava, String) - Constructor for class io.scif.jj2000.j2k.StringSpec
Constructs a new 'StringSpec' for the specified number of components:tiles and the arguments of optName option.
STRIPE_HEIGHT - Static variable in interface io.scif.jj2000.j2k.entropy.StdEntropyCoderOptions
The stripe height.
subb_HH - Variable in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
The reference to the HH subband resulting from the decomposition of this subband.
subb_HH - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
The reference to the HH subband resulting from the decomposition of this subband.
subb_HL - Variable in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
The reference to the HL subband (horizontal high-pass) resulting from the decomposition of this subband.
subb_HL - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
The reference to the HL subband (horizontal high-pass) resulting from the decomposition of this subband.
subb_LH - Variable in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
The reference to the LH subband (vertical high-pass) resulting from the decomposition of this subband.
subb_LH - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
The reference to the LH subband (vertical high-pass) resulting from the decomposition of this subband.
subb_LL - Variable in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
The reference to the LL subband resulting from the decomposition of this subband.
subb_LL - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
The reference to the LL subband resulting from the decomposition of this subband.
Subband - Class in io.scif.jj2000.j2k.wavelet
This abstract class represents a subband in a bidirectional tree structure that describes the subband decomposition for a wavelet transform.
Subband() - Constructor for class io.scif.jj2000.j2k.wavelet.Subband
Creates a Subband element with all the default values.
Subband(int, int, int, int, int, WaveletFilter[], WaveletFilter[]) - Constructor for class io.scif.jj2000.j2k.wavelet.Subband
Creates the top-level node and the entire subband tree, with the top-level dimensions, the number of decompositions, and the decomposition tree as specified.
SubbandAn - Class in io.scif.jj2000.j2k.wavelet.analysis
This class represents a subband in a bidirectional tree structure that describes the subband decomposition for a wavelet transform, specifically for the analysis side.
SubbandAn() - Constructor for class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
Creates a SubbandAn element with all the default values.
SubbandAn(int, int, int, int, int, WaveletFilter[], WaveletFilter[]) - Constructor for class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
Creates the top-level node and the entire subband tree, with the top-level dimensions, the number of decompositions, and the decomposition tree as specified.
SubbandRectROIMask - Class in io.scif.jj2000.j2k.roi.encoder
This class describes the ROI mask for a single subband.
SubbandRectROIMask(Subband, int[], int[], int[], int[], int) - Constructor for class io.scif.jj2000.j2k.roi.encoder.SubbandRectROIMask
The constructor of the SubbandROIMask takes the dimensions of the subband as parameters.
SubbandROIMask - Class in io.scif.jj2000.j2k.roi.encoder
This abstract class describes the ROI mask for a single subband.
SubbandROIMask(int, int, int, int) - Constructor for class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
The constructor of the SubbandROIMask takes the dimensions of the subband as parameters
SubbandSyn - Class in io.scif.jj2000.j2k.wavelet.synthesis
This class represents a subband in a tree structure that describes the subband decomposition for a wavelet transform, specifically for the syhthesis side.
SubbandSyn() - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
Creates a SubbandSyn element with all the default values.
SubbandSyn(int, int, int, int, int, WaveletFilter[], WaveletFilter[]) - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
Creates the top-level node and the entire subband tree, with the top-level dimensions, the number of decompositions, and the decomposition tree as specified.
subbTrees - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
The subband trees for each component in the current tile.
SUBFILE_TYPE_FULL_RESOLUTION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "SubfileType" tag.
SUBFILE_TYPE_REDUCED_RESOLUTION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "SubfileType" tag.
SUBFILE_TYPE_SINGLE_PAGE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "SubfileType" tag.
SUBJECT_DISTANCE_RANGE_CLOSE_VIEW - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SubjectDistanceRange" tag.
SUBJECT_DISTANCE_RANGE_DISTANT_VIEW - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SubjectDistanceRange" tag.
SUBJECT_DISTANCE_RANGE_MACRO - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SubjectDistanceRange" tag.
SUBJECT_DISTANCE_RANGE_UNKNOWN - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "SubjectDistanceRange" tag.
subsampleX - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The horizontal subsampling factor.
subsampleY - Variable in class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
The vertical subsampling factor.
suffixSufficient() - Method in class io.scif.bf.BioFormatsFormat.Checker
 
synFD - Variable in class io.scif.lifesci.SDTInfo
 
synHF - Variable in class io.scif.lifesci.SDTInfo
 
synTH - Variable in class io.scif.lifesci.SDTInfo
 
synthetize_hpf(Object, int, int, int, Object, int, int, int, Object, int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilter
Reconstructs the output signal by the synthesis filter, recomposing the low-pass and high-pass input signals in one output signal.
synthetize_hpf(float[], int, int, int, float[], int, int, int, float[], int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloat
A specific version of the synthetize_hpf() method that works on float data.
synthetize_hpf(Object, int, int, int, Object, int, int, int, Object, int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloat
The general version of the synthetize_hpf() method, it just calls the specialized version.
synthetize_hpf(float[], int, int, int, float[], int, int, int, float[], int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
An implementation of the synthetize_hpf() method that works on int data, for the inverse 9x7 wavelet transform using the lifting scheme.
synthetize_hpf(int[], int, int, int, int[], int, int, int, int[], int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterInt
A specific version of the synthetize_hpf() method that works on int data.
synthetize_hpf(Object, int, int, int, Object, int, int, int, Object, int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterInt
The general version of the synthetize_hpf() method, it just calls the specialized version.
synthetize_hpf(int[], int, int, int, int[], int, int, int, int[], int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
An implementation of the synthetize_hpf() method that works on int data, for the inverse 5x3 wavelet transform using thelifting scheme.
synthetize_lpf(Object, int, int, int, Object, int, int, int, Object, int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilter
Reconstructs the output signal by the synthesis filter, recomposing the low-pass and high-pass input signals in one output signal.
synthetize_lpf(float[], int, int, int, float[], int, int, int, float[], int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloat
A specific version of the synthetize_lpf() method that works on float data.
synthetize_lpf(Object, int, int, int, Object, int, int, int, Object, int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloat
The general version of the synthetize_lpf() method, it just calls the specialized version.
synthetize_lpf(float[], int, int, int, float[], int, int, int, float[], int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
An implementation of the synthetize_lpf() method that works on int data, for the inverse 9x7 wavelet transform using the lifting scheme.
synthetize_lpf(int[], int, int, int, int[], int, int, int, int[], int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterInt
A specific version of the synthetize_lpf() method that works on int data.
synthetize_lpf(Object, int, int, int, Object, int, int, int, Object, int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterInt
The general version of the synthetize_lpf() method, it just calls the specialized version.
synthetize_lpf(int[], int, int, int, int[], int, int, int, int[], int, int) - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
An implementation of the synthetize_lpf() method that works on int data, for the inverse 5x3 wavelet transform using the lifting scheme.
SynWTFilter - Class in io.scif.jj2000.j2k.wavelet.synthesis
This abstract class defines the methods of all synthesis wavelet filters.
SynWTFilter() - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilter
 
SynWTFilterFloat - Class in io.scif.jj2000.j2k.wavelet.synthesis
This extends the synthesis wavelet filter general definitions of SynWTFilter by adding methods that work for float data specifically.
SynWTFilterFloat() - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloat
 
SynWTFilterFloatLift9x7 - Class in io.scif.jj2000.j2k.wavelet.synthesis
This class inherits from the synthesis wavelet filter definition for int data.
SynWTFilterFloatLift9x7() - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
 
SynWTFilterInt - Class in io.scif.jj2000.j2k.wavelet.synthesis
This extends the synthesis wavelet filter general definitions of SynWTFilter by adding methods that work for int data specifically.
SynWTFilterInt() - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterInt
 
SynWTFilterIntLift5x3 - Class in io.scif.jj2000.j2k.wavelet.synthesis
This class inherits from the synthesis wavelet filter definition for int data.
SynWTFilterIntLift5x3() - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
 
SynWTFilterSpec - Class in io.scif.jj2000.j2k.wavelet.synthesis
This class extends ModuleSpec class for synthesis filters specification holding purpose.
SynWTFilterSpec(int, int, byte) - Constructor for class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterSpec
Constructs a new 'SynWTFilterSpec' for the specified number of components and tiles.
synZC - Variable in class io.scif.lifesci.SDTInfo
 
SZ_INCR - Static variable in class io.scif.jj2000.j2k.codestream.writer.BitOutputBuffer
The increment size for the buffer, 16 bytes.
SZ_INIT - Static variable in class io.scif.jj2000.j2k.codestream.writer.BitOutputBuffer
The initial size for the buffer, 32 bytes.

T

T4_OPTIONS_2D_CODING - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A mask to be used with the "T4Options" tag.
T4_OPTIONS_EOL_BYTE_ALIGNED - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A mask to be used with the "T4Options" tag.
T4_OPTIONS_UNCOMPRESSED - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A mask to be used with the "T4Options" tag.
T6_OPTIONS_UNCOMPRESSED - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A mask to be used with the "T6Options" tag.
T_STRING - Static variable in class io.scif.lifesci.SDTInfo
 
tables - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
tacG - Variable in class io.scif.lifesci.SDTInfo
 
tacLH - Variable in class io.scif.lifesci.SDTInfo
 
tacLL - Variable in class io.scif.lifesci.SDTInfo
 
tacOF - Variable in class io.scif.lifesci.SDTInfo
 
tacR - Variable in class io.scif.lifesci.SDTInfo
 
TAG_APERTURE_VALUE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the lens aperture (type RATIONAL).
TAG_ARTIST - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Artist" tag.
TAG_BAD_FAX_LINES - Static variable in class io.scif.media.imageio.plugins.tiff.FaxTIFFTagSet
Tag indicating the number of bad fax lines (type SHORT or LONG).
TAG_BITS_PER_SAMPLE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "BitsPerSample" tag.
TAG_BRIGHTNESS_VALUE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the value of brightness (type SRATIONAL).
TAG_CELL_LENGTH - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "cell_length" tag.
TAG_CELL_WIDTH - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Cell_Width" tag.
TAG_CFA_PATTERN - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the color filter array geometric pattern of the image sensor when a one-chip color area sensor if used (type UNDEFINED).
TAG_CLEAN_FAX_DATA - Static variable in class io.scif.media.imageio.plugins.tiff.FaxTIFFTagSet
Tag indicating the number of lines of clean fax data (type SHORT).
TAG_COLOR_MAP - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "ColorMap" tag.
TAG_COLOR_SPACE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the color space information (type SHORT).
TAG_COMPONENTS_CONFIGURATION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag containing the components configuration information (type UNDEFINED, count = 4).
TAG_COMPRESSED_BITS_PER_PIXEL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the number of compressed bits per pixel (type RATIONAL).
TAG_COMPRESSION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Compression" tag.
TAG_CONSECUTIVE_BAD_LINES - Static variable in class io.scif.media.imageio.plugins.tiff.FaxTIFFTagSet
Tag indicating the number of consecutive bad lines (type SHORT or LONG).
TAG_CONTRAST - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the direction of contrast processing applied by the camera when the image was shot.
TAG_COPYRIGHT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Copyright" tag.
TAG_CUSTOM_RENDERED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the use of special processing on image data, such as rendering geared to output.
TAG_DATE_TIME - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "DateTime" tag.
TAG_DATE_TIME_DIGITIZED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the date and time when the image was stored as digital data (type ASCII).
TAG_DATE_TIME_ORIGINAL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the date and time when the original image was generated (type ASCII).
TAG_DEVICE_SETTING_DESCRIPTION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating information on the picture-taking conditions of a particular camera model.
TAG_DIGITAL_ZOOM_RATIO - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the digital zoom ratio when the image was shot.
TAG_DOCUMENT_NAME - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "document_name" tag.
TAG_DOT_RANGE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "DotRange" tag.
TAG_EXIF_IFD_POINTER - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFParentTIFFTagSet
Tag pointing to the EXIF IFD (type LONG).
TAG_EXIF_VERSION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag containing the EXIF version number (type UNDEFINED, count = 4).
TAG_EXPOSURE_BIAS_VALUE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the exposure bias (type SRATIONAL).
TAG_EXPOSURE_INDEX - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the exposure index selected on the camera or input device at the time the image was captured (type RATIONAL).
TAG_EXPOSURE_MODE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the exposure mode set when the image was shot.
TAG_EXPOSURE_PROGRAM - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the class of the programs used to set exposure when the picture was taken (type SHORT).
TAG_EXPOSURE_TIME - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the exposure time, in seconds (type RATIONAL).
TAG_EXTRA_SAMPLES - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "ExtraSamples" tag.
TAG_F_NUMBER - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the F number (type RATIONAL).
TAG_FILE_SOURCE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the image source (type UNDEFINED).
TAG_FILL_ORDER - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "fill_order" tag.
TAG_FLASH - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the flash firing status and flash return status (type SHORT).
TAG_FLASH_ENERGY - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the strobe energy at the time the image was captured, as measured in Beam Candle Power Seconds (BCPS) (type RATIONAL).
TAG_FLASHPIX_VERSION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the FlashPix version number (type UNDEFINED, count = 4).
TAG_FOCAL_LENGTH - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the actual focal length of the lens, in millimeters (type RATIONAL).
TAG_FOCAL_LENGTH_IN_35MM_FILM - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the equivalent focal length assuming a 35mm film camera, in millimeters.
TAG_FOCAL_PLANE_RESOLUTION_UNIT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
Indicates the unit for measuring FocalPlaneXResolution and FocalPlaneYResolution (type SHORT).
TAG_FOCAL_PLANE_X_RESOLUTION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
Indicates the number of pixels in the image width (X) direction per FocalPlaneResolutionUnit on the camera focal plane (type RATIONAL).
TAG_FOCAL_PLANE_Y_RESOLUTION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
Indicate the number of pixels in the image height (Y) direction per FocalPlaneResolutionUnit on the camera focal plane (type RATIONAL).
TAG_FREE_BYTE_COUNTS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "FreeByteCounts" tag.
TAG_FREE_OFFSETS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "FreeOffsets" tag.
TAG_GAIN_CONTROL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the degree of overall image gain adjustment.
TAG_GEO_ASCII_PARAMS - Static variable in class io.scif.media.imageio.plugins.tiff.GeoTIFFTagSet
A tag used to store all ASCII-values GeoKeys.
TAG_GEO_DOUBLE_PARAMS - Static variable in class io.scif.media.imageio.plugins.tiff.GeoTIFFTagSet
A tag used to store all double-values GeoKeys.
TAG_GEO_KEY_DIRECTORY - Static variable in class io.scif.media.imageio.plugins.tiff.GeoTIFFTagSet
A tag used to store the GeoKey directory.
TAG_GPS_ALTITUDE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Altitude (type RATIONAL, count = 1).
TAG_GPS_ALTITUDE_REF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Altitude reference (type BYTE, count = 1);
TAG_GPS_AREA_INFORMATION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Name of GPS area (type UNDEFINED).
TAG_GPS_DATE_STAMP - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the GPS date (type ASCII, count 11).
TAG_GPS_DEST_BEARING - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Bearing of destination (type RATIONAL, count = 1).
TAG_GPS_DEST_BEARING_REF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Reference for bearing of destination (type ASCII, count = 2).
TAG_GPS_DEST_DISTANCE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Distance to destination (type RATIONAL, count = 1).
TAG_GPS_DEST_DISTANCE_REF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Reference for distance to destination (type ASCII, count = 2).
TAG_GPS_DEST_LATITUDE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Latitude of destination (type RATIONAL, count = 3).
TAG_GPS_DEST_LATITUDE_REF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Reference for latitude of destination (type ASCII, count = 2).
TAG_GPS_DEST_LONGITUDE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Longitude of destination (type RATIONAL, count = 3).
TAG_GPS_DEST_LONGITUDE_REF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Reference for longitude of destination (type ASCII, count = 2).
TAG_GPS_DIFFERENTIAL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the GPS differential correction (type SHORT, count = 1).
TAG_GPS_DOP - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Measurement precision (type RATIONAL, count = 1).
TAG_GPS_IMG_DIRECTION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Direction of image (type RATIONAL, count = 1).
TAG_GPS_IMG_DIRECTION_REF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Reference for direction of image (type ASCII, count = 2).
TAG_GPS_INFO_IFD_POINTER - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFParentTIFFTagSet
Tag pointing to a GPS info IFD (type LONG).
TAG_GPS_INFO_IFD_POINTER - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
TAG_GPS_LATITUDE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Latitude (type RATIONAL, count = 3).
TAG_GPS_LATITUDE_REF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the North or South latitude (type ASCII, count = 2).
TAG_GPS_LONGITUDE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Longitude (type RATIONAL, count = 3).
TAG_GPS_LONGITUDE_REF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the East or West Longitude (type ASCII, count = 2).
TAG_GPS_MAP_DATUM - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Geodetic survey data used (type ASCII).
TAG_GPS_MEASURE_MODE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the GPS measurement mode (type ASCII, count = 2).
TAG_GPS_PROCESSING_METHOD - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Name of GPS processing method (type UNDEFINED).
TAG_GPS_SATELLITES - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the GPS satellites used for measurement (type ASCII).
TAG_GPS_SPEED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Speed of GPS receiver (type RATIONAL, count = 1).
TAG_GPS_SPEED_REF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Speed unit (type ASCII, count = 2).
TAG_GPS_STATUS - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the GPS receiver status (type ASCII, count = 2).
TAG_GPS_TIME_STAMP - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the GPS time (atomic clock) (type RATIONAL, count = 3).
TAG_GPS_TRACK - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Direction of movement (type RATIONAL, count = 1).
TAG_GPS_TRACK_REF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the Reference for direction of movement (type ASCII, count = 2).
TAG_GPS_VERSION_ID - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFGPSTagSet
A tag indicating the GPS tag version (type BYTE, count = 4).
TAG_GRAY_RESPONSE_CURVE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "GrayResponseCurve" tag.
TAG_GRAY_RESPONSE_UNIT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "GrayResponseUnit" tag.
TAG_HALFTONE_HINTS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "HalftoneHints" tag.
TAG_HOST_COMPUTER - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "HostComputer" tag.
TAG_ICC_PROFILE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "ICC Profile" tag.
TAG_IMAGE_DESCRIPTION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Image_description" tag.
TAG_IMAGE_LENGTH - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "ImageLength" tag.
TAG_IMAGE_UNIQUE_ID - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating an identifier assigned uniquely to each image.
TAG_IMAGE_WIDTH - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "ImageWidth" tag.
TAG_INK_NAMES - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "InkNames" tag.
TAG_INK_SET - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "InkSet" tag.
TAG_INTEROPERABILITY_IFD_POINTER - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag pointing to an interoperability IFD (type LONG).
TAG_INTEROPERABILITY_INDEX - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFInteroperabilityTagSet
A tag indicating the identification of the Interoperability rule (type ASCII).
TAG_ISO_SPEED_RATINGS - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the ISO speed and ISO latitude of the camera or input device, as specified in ISO 12232xiv (type SHORT).
TAG_JPEG_AC_TABLES - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "JPEGACTables" tag.
TAG_JPEG_DC_TABLES - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "JPEGDCTables" tag.
TAG_JPEG_INTERCHANGE_FORMAT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "JPEGInterchangeFormat" tag.
TAG_JPEG_INTERCHANGE_FORMAT_LENGTH - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "JPEGInterchangeFormatLength" tag.
TAG_JPEG_LOSSLESS_PREDICTORS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "JPEGLosslessPredictors" tag.
TAG_JPEG_POINT_TRANSFORMS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "JPEGPointTransforms" tag.
TAG_JPEG_PROC - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "JPEGProc" tag.
TAG_JPEG_Q_TABLES - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "JPEGQTables" tag.
TAG_JPEG_RESTART_INTERVAL - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "JPEGRestartInterval" tag.
TAG_JPEG_TABLES - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "JPEGTables" tag.
TAG_LIGHT_SOURCE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicatingthe kind of light source (type SHORT).
TAG_MAKE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Make" tag.
TAG_MAKER_NOTE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating a manufacturer-defined maker note (type UNDEFINED).
TAG_MARKER_NOTE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
Deprecated.
TAG_MAX_APERTURE_VALUE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the smallest F number of the lens (type RATIONAL).
TAG_MAX_SAMPLE_VALUE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Max_sample_value" tag.
TAG_METERING_MODE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the metering mode (type SHORT).
TAG_MIN_SAMPLE_VALUE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Min_sample_value" tag.
TAG_MODEL - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Model" tag.
TAG_MODEL_PIXEL_SCALE - Static variable in class io.scif.media.imageio.plugins.tiff.GeoTIFFTagSet
A tag used to specify the size of raster pixel spacing in model space units.
TAG_MODEL_TIE_POINT - Static variable in class io.scif.media.imageio.plugins.tiff.GeoTIFFTagSet
A tag used to store raster->model tiepoint pairs.
TAG_MODEL_TRANSFORMATION - Static variable in class io.scif.media.imageio.plugins.tiff.GeoTIFFTagSet
A tag used to specify the transformation matrix between the raster space and the model space.
TAG_NEW_SUBFILE_TYPE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "NewSubfileType" tag.
TAG_NUMBER_OF_INKS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "NumberOfInks" tag.
TAG_OECF - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the optoelectric conversion function, specified in ISO 14254xv (type UNDEFINED).
TAG_ORIENTATION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Orientation" tag.
TAG_PAGE_NAME - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "PageName" tag.
TAG_PAGE_NUMBER - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "PageNumber" tag.
TAG_PHOTOMETRIC_INTERPRETATION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "PhotometricInterpretation" tag.
TAG_PIXEL_X_DIMENSION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the pixel X dimension (type SHORT or LONG).
TAG_PIXEL_Y_DIMENSION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the pixel Y dimension (type SHORT or LONG).
TAG_PLANAR_CONFIGURATION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "PlanarConfiguration" tag.
TAG_PREDICTOR - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Predictor" tag.
TAG_PRIMARY_CHROMATICITES - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "PrimaryChromaticites" tag.
TAG_REFERENCE_BLACK_WHITE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "ReferenceBlackWhite" tag.
TAG_RELATED_SOUND_FILE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the name of a related sound file (type ASCII).
TAG_RESOLUTION_UNIT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "ResolutionUnit" tag.
TAG_ROWS_PER_STRIP - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Rows_per_strip" tag.
TAG_S_MAX_SAMPLE_VALUE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "SMaxSampleValue" tag.
TAG_S_MIN_SAMPLE_VALUE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "SMinSampleValue" tag.
TAG_SAMPLE_FORMAT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "SampleFormat" tag.
TAG_SAMPLES_PER_PIXEL - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Samples_per_pixel" tag.
TAG_SATURATION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the direction of saturation processing applied by the camera when the image was shot.
TAG_SCENE_CAPTURE_TYPE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the type of scene that was shot.
TAG_SCENE_TYPE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the type of scene (type UNDEFINED).
TAG_SENSING_METHOD - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the sensor type on the camera or input device (type SHORT).
TAG_SHARPNESS - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the direction of sharpness processing applied by the camera when the image was shot.
TAG_SHUTTER_SPEED_VALUE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the shutter speed (type SRATIONAL).
TAG_SOFTWARE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Software" tag.
TAG_SPATIAL_FREQUENCY_RESPONSE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the camera or input device spatial frequency table and SFR values in the direction of image width, image height, and diagonal direction, as specified in ISO 12233xvi (type UNDEFINED).
TAG_SPECTRAL_SENSITIVITY - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the spectral sensitivity of each channel of the camera used (type ASCII).
TAG_STRIP_BYTE_COUNTS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Strip_byte_counts" tag.
TAG_STRIP_OFFSETS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Strip_offsets" tag.
TAG_SUB_SEC_TIME - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag used to record fractions of seconds for the "DateTime" tag (type ASCII).
TAG_SUB_SEC_TIME_DIGITIZED - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag used to record fractions of seconds for the "DateTimeDigitized" tag (type ASCII).
TAG_SUB_SEC_TIME_ORIGINAL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag used to record fractions of seconds for the "DateTimeOriginal" tag (type ASCII).
TAG_SUBFILE_TYPE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "SubfileType" tag.
TAG_SUBJECT_AREA - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the location and area of the main subject in the overall scene.
TAG_SUBJECT_DISTANCE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the distance to the subject, in meters (type RATIONAL).
TAG_SUBJECT_DISTANCE_RANGE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the distance to the subject.
TAG_SUBJECT_LOCATION - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the column and row of the center pixel of the main subject in the scene (type SHORT, count = 2).
TAG_T4_OPTIONS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "T4Options" tag.
TAG_T6_OPTIONS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "T6Options" tag.
TAG_TARGET_PRINTER - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "TargetPrinter" tag.
TAG_THRESHHOLDING - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "Threshholding" tag.
TAG_TILE_BYTE_COUNTS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "TileByteCounts" tag.
TAG_TILE_LENGTH - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "TileLength" tag.
TAG_TILE_OFFSETS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "TileOffsets" tag.
TAG_TILE_WIDTH - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "TileWidth" tag.
TAG_TRANSFER_FUNCTION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "TransferFunction" tag.
TAG_TRANSFER_RANGE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "TransferRange" tag.
TAG_USER_COMMENT - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating a user comment (type UNDEFINED).
TAG_WHITE_BALANCE - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A tag indicating the white balance mode set when the image was shot.
TAG_WHITE_POINT - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "WhitePoint" tag.
TAG_X_POSITION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "XPosition" tag.
TAG_X_RESOLUTION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "XResolution" tag.
TAG_Y_CB_CR_COEFFICIENTS - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "YCbCrCoefficients" tag.
TAG_Y_CB_CR_POSITIONING - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "YCbCrPositioning" tag.
TAG_Y_CB_CR_SUBSAMPLING - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "YCbCrSubsampling" tag.
TAG_Y_POSITION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "YPosition" tag.
TAG_Y_RESOLUTION - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
Constant specifying the "YResolution" tag.
TagTreeDecoder - Class in io.scif.jj2000.j2k.codestream.reader
This class implements the tag tree decoder.
TagTreeDecoder(int, int) - Constructor for class io.scif.jj2000.j2k.codestream.reader.TagTreeDecoder
Creates a tag tree decoder with 'w' elements along the horizontal dimension and 'h' elements along the vertical direction.
TagTreeEncoder - Class in io.scif.jj2000.j2k.codestream.writer
This class implements the tag tree encoder.
TagTreeEncoder(int, int) - Constructor for class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Creates a tag tree encoder with 'w' elements along the horizontal dimension and 'h' elements along the vertical direction.
TagTreeEncoder(int, int, int[]) - Constructor for class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
Creates a tag tree encoder with 'w' elements along the horizontal dimension and 'h' elements along the vertical direction.
targetRes - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Image resolution level to generate
TERM_EASY - Static variable in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
The identifier for the easy termination that is simpler than the 'TERM_NEAR_OPT' one but slightly less efficient.
TERM_FULL - Static variable in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
The identifier fort the termination that uses a full flush.
TERM_NEAR_OPT - Static variable in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
The identifier for the termination that uses the near optimal length calculation to terminate the arithmetic codewrod
TERM_PRED_ER - Static variable in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
The identifier for the predictable termination policy for error resilience.
termCodes - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Black and white terminating code table.
termCodesBlack - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Terminating codes for black runs.
termCodesWhite - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Terminating codes for white runs.
terminate() - Method in class io.scif.jj2000.j2k.entropy.encoder.MQCoder
This function flushes the remaining encoded bits and makes sure that enough information is written to the bit stream to be able to finish decoding, and then it reinitializes the internal state of the MQ coder but without modifying the context states.
terminateProgressWatch() - Method in interface io.scif.jj2000.j2k.util.ProgressWatch
Terminate the progress watch process
text - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
textBackgroundColor - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
textForegroundColor - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
textGridHeight - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
textGridLeft - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
textGridTop - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
textGridWidth - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
ThreadPool - Class in io.scif.jj2000.j2k.util
This class implements a thread pool.
ThreadPool(int, int, String) - Constructor for class io.scif.jj2000.j2k.util.ThreadPool
Creates a new thread pool of the given size, thread priority and pool name.
THREADS_PRIORITY_INC - Static variable in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
The increase in priority for the compressor threads, currently 3.
THREADS_PROP_NAME - Static variable in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
The Java system property name for the number of threads to use: io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder.nthreads
THRESHHOLDING_NONE - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Thresholding" tag.
THRESHHOLDING_ORDERED_DITHER - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Thresholding" tag.
THRESHHOLDING_RANDOMIZED_DITHER - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "Thresholding" tag.
tIdx - Variable in class io.scif.jj2000.j2k.image.ImgDataAdapter
Index of the current tile
tIdx - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.MultiResImgDataAdapter
Index of the current tile
TIFF_ASCII - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for null-terminated ASCII strings.
TIFF_BYTE - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for 8 bit unsigned integers.
TIFF_DOUBLE - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for 64 bit IEEE doubles.
TIFF_FLOAT - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for 32 bit IEEE floats.
TIFF_IFD_POINTER - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for IFD pointer defined in TIFF Tech Note 1 in TIFF Specification Supplement 1.
TIFF_LONG - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for 32 bit unsigned integers.
TIFF_RATIONAL - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for pairs of 32 bit unsigned integers.
TIFF_SBYTE - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for 8 bit signed integers.
TIFF_SHORT - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for 16 bit unsigned integers.
TIFF_SLONG - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for 32 bit signed integers.
TIFF_SRATIONAL - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for pairs of 32 bit signed integers.
TIFF_SSHORT - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for 16 bit signed integers.
TIFF_UNDEFINED - Static variable in class io.scif.media.imageio.plugins.tiff.TIFFTag
Flag for 8 bit uninterpreted bytes.
TIFFAttrInfo - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFAttrInfo() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFAttrInfo
 
TIFFBaseJPEGCompressor - Class in io.scif.media.imageioimpl.plugins.tiff
Base class for all possible forms of JPEG compression in TIFF.
TIFFBaseJPEGCompressor(String, int, boolean, ImageWriteParam) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
TIFFCIELabColorConverter - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFCIELabColorConverter() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFCIELabColorConverter
 
TIFFColorConverter - Class in io.scif.media.imageio.plugins.tiff
An abstract class that performs simple color conversion on 3-banded source images, for use with the TIFF Image I/O plug-in.
TIFFColorConverter() - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFColorConverter
Constructs an instance of a TIFFColorConverter.
TIFFCompressionTypes - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
Supported TIFF compression types.
TIFFCompressor - Class in io.scif.media.imageio.plugins.tiff
An abstract superclass for pluggable TIFF compressors.
TIFFCompressor(String, int, boolean) - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFCompressor
Creates a compressor object for use in compressing TIFF data.
TIFFDecompressor - Class in io.scif.media.imageio.plugins.tiff
A class defining a pluggable TIFF decompressor.
TIFFDecompressor() - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFDecompressor
 
TIFFDeflateCompressor - Class in io.scif.media.imageioimpl.plugins.tiff
Compressor for Deflate compression.
TIFFDeflateCompressor(ImageWriteParam, int) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFDeflateCompressor
 
TIFFDeflateDecompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFDeflateDecompressor(int) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFDeflateDecompressor
 
TIFFDeflater - Class in io.scif.media.imageioimpl.plugins.tiff
Compressor superclass for Deflate and ZLib compression.
TIFFDeflater(String, int, ImageWriteParam, int) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFDeflater
 
TIFFDirectory - Class in io.scif.media.imageio.plugins.tiff
A convenience class for simplifying interaction with TIFF native image metadata.
TIFFDirectory(TIFFTagSet[], TIFFTag) - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFDirectory
Constructs a TIFFDirectory which is aware of a given group of TIFFTagSets.
TIFFElementInfo - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFElementInfo(String[], String[], int) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
TIFFEXIFJPEGCompressor - Class in io.scif.media.imageioimpl.plugins.tiff
A TIFFCompressor for the JPEG variant of EXIF.
TIFFEXIFJPEGCompressor(ImageWriteParam) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFEXIFJPEGCompressor
 
TIFFFaxCompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFFaxCompressor(String, int, boolean) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Constructor.
TIFFFaxDecompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFFaxDecompressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
TIFFField - Class in io.scif.media.imageio.plugins.tiff
A class representing a field in a TIFF 6.0 Image File Directory.
TIFFField(TIFFTag, int, int, Object) - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFField
Constructs a TIFFField with arbitrary data.
TIFFField(TIFFTag, int, int) - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFField
Constructs a data array using createArrayForType() and invokes TIFFField(TIFFTag,int,int,Object) with the supplied parameters and the created array.
TIFFField(TIFFTag, int) - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFField
Constructs a TIFFField with a single integral value.
TIFFFieldNode - Class in io.scif.media.imageioimpl.plugins.tiff
The Node representation of a TIFFField wherein the child node is procedural rather than buffered.
TIFFFieldNode(TIFFField) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
TIFFIFD - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFIFD(List, TIFFTag) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
 
TIFFIFD(List) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
 
TIFFImageMetadata - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFImageMetadata(List) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
TIFFImageMetadata(TIFFIFD) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
TIFFImageMetadataFormat - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFImageMetadataFormatResources - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFImageMetadataFormatResources() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFImageMetadataFormatResources
 
TIFFImageReader - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFImageReader(ImageReaderSpi) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReader
 
TIFFImageReaderSpi - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFImageReaderSpi() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
TIFFImageReadParam - Class in io.scif.media.imageio.plugins.tiff
A subclass of ImageReadParam allowing control over the TIFF reading process.
TIFFImageReadParam() - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFImageReadParam
Constructs a TIFFImageReadParam.
TIFFImageWriteParam - Class in io.scif.media.imageio.plugins.tiff
A subclass of ImageWriteParam allowing control over the TIFF writing process.
TIFFImageWriteParam(Locale) - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFImageWriteParam
Constructs a TIFFImageWriteParam instance for a given Locale.
TIFFImageWriter - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFImageWriter(ImageWriterSpi) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
TIFFImageWriterSpi - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFImageWriterSpi() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
TIFFJPEGCompressor - Class in io.scif.media.imageioimpl.plugins.tiff
Compressor for encoding compression type 7, TTN2/Adobe JPEG-in-TIFF.
TIFFJPEGCompressor(ImageWriteParam) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGCompressor
 
TIFFJPEGDecompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFJPEGDecompressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
TIFFLSBCompressor - Class in io.scif.media.imageioimpl.plugins.tiff
Uncompressed data with LSB-to-MSB fill order.
TIFFLSBCompressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFLSBCompressor
 
TIFFLSBDecompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFLSBDecompressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFLSBDecompressor
 
TIFFLZWCompressor - Class in io.scif.media.imageioimpl.plugins.tiff
LZW Compressor.
TIFFLZWCompressor(int) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWCompressor
 
TIFFLZWDecompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFLZWDecompressor(int) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
TIFFLZWUtil - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFLZWUtil() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
TIFFMetadataFormat - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFMetadataFormat() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
TIFFNullCompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFNullCompressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFNullCompressor
 
TIFFNullDecompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFNullDecompressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFNullDecompressor
 
TIFFOldJPEGDecompressor - Class in io.scif.media.imageioimpl.plugins.tiff
TIFFDecompressor for "Old JPEG" compression.
TIFFOldJPEGDecompressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFOldJPEGDecompressor
 
TIFFOMETranslator() - Constructor for class io.scif.ome.translators.TIFFTranslator.TIFFOMETranslator
 
TIFFPackBitsCompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFPackBitsCompressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFPackBitsCompressor
 
TIFFPackBitsDecompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFPackBitsDecompressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFPackBitsDecompressor
 
TIFFPackBitsUtil - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFPackBitsUtil() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFPackBitsUtil
 
TIFFRenderedImage - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFRenderedImage(TIFFImageReader, int, ImageReadParam, int, int) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFRenderedImage
 
TIFFRLECompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFRLECompressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFRLECompressor
 
TIFFStreamMetadata - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFStreamMetadata() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
TIFFStreamMetadataFormat - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFStreamMetadataFormatResources - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFStreamMetadataFormatResources() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFStreamMetadataFormatResources
 
TIFFT4Compressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFT4Compressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFT4Compressor
 
TIFFT6Compressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFT6Compressor() - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFT6Compressor
 
TIFFTag - Class in io.scif.media.imageio.plugins.tiff
A class defining the notion of a TIFF tag.
TIFFTag(String, int, int, TIFFTagSet) - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFTag
Constructs a TIFFTag with a given name, tag number, set of legal data types, and TIFFTagSet to which it refers.
TIFFTag(String, int, int) - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFTag
Constructs a TIFFTag with a given name, tag number, and set of legal data types.
TIFFTagSet - Class in io.scif.media.imageio.plugins.tiff
A class representing a set of TIFF tags.
TIFFTagSet(List) - Constructor for class io.scif.media.imageio.plugins.tiff.TIFFTagSet
Constructs a TIFFTagSet, given a List of TIFFTag objects.
TIFFTranslator - Class in io.scif.ome.translators
Container class for translators between OME and TIFF formats.
TIFFTranslator() - Constructor for class io.scif.ome.translators.TIFFTranslator
 
TIFFTranslator.OMETIFFTranslator - Class in io.scif.ome.translators
Translator class from TIFFFormat.Metadata to OMEMetadata.
TIFFTranslator.TIFFOMETranslator - Class in io.scif.ome.translators
Translator class from TIFFFormat.Metadata to OMEMetadata
TIFFYCbCrColorConverter - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFYCbCrColorConverter(TIFFImageMetadata) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
TIFFYCbCrDecompressor - Class in io.scif.media.imageioimpl.plugins.tiff
 
TIFFYCbCrDecompressor(TIFFDecompressor, boolean) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
TIFFZLibCompressor - Class in io.scif.media.imageioimpl.plugins.tiff
Compressor for ZLib compression.
TIFFZLibCompressor(ImageWriteParam, int) - Constructor for class io.scif.media.imageioimpl.plugins.tiff.TIFFZLibCompressor
 
tileChanged() - Method in class io.scif.jj2000.j2k.roi.encoder.ROIMaskGenerator
This function is called every time the tile is changed to indicate that there is need to make a new mask
tileCompVal - Variable in class io.scif.jj2000.j2k.ModuleSpec
The specific value for each tile-component.
tileDef - Variable in class io.scif.jj2000.j2k.ModuleSpec
The default value for each tile.
tileGridXOffset - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The X coordinate of the upper-left pixel of tile (0, 0).
tileGridYOffset - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The Y coordinate of the upper-left pixel of tile (0, 0).
tileHeight - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The height of a tile.
tileMaskMade - Variable in class io.scif.jj2000.j2k.roi.encoder.ROIMaskGenerator
Flag indicating whether a mask has been made for the current tile
tileOfTileParts - Variable in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Vector containing info as to which tile each tilepart belong
tiler - Variable in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Reference to the tiler module
Tiler - Class in io.scif.jj2000.j2k.image
This class places an image in the canvas coordinate system, tiles it, if so specified, and performs the coordinate conversions transparently.
Tiler(BlkImgDataSrc, int, int, int, int, int, int) - Constructor for class io.scif.jj2000.j2k.image.Tiler
Constructs a new tiler with the specified 'BlkImgDataSrc' source, image origin, tiling origin and nominal tile size.
tileWidth - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The width of a tile.
tileXToX(int, int, int) - Static method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Converts a horizontal tile index into the X coordinate of its upper left pixel relative to a given tile grid layout specified by its X offset and tile width.
tileXToX(int) - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Converts a horizontal tile index into the X coordinate of its upper left pixel.
tileYToY(int, int, int) - Static method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Converts a vertical tile index into the Y coordinate of its upper left pixel relative to a given tile grid layout specified by its Y offset and tile height.
tileYToY(int) - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Converts a vertical tile index into the Y coordinate of its upper left pixel.
time - Variable in class io.scif.lifesci.SDTInfo
Time of creation.
timeBins - Variable in class io.scif.lifesci.SDTInfo
 
TimePoint - Class in io.scif.formats.imaris
 
TimePoint(ResolutionLevel[], int[], int, int, int, boolean) - Constructor for class io.scif.formats.imaris.TimePoint
 
timepoints - Variable in class io.scif.lifesci.SDTInfo
 
TLM - Static variable in interface io.scif.jj2000.j2k.codestream.Markers
Tile-part lengths (TLM): 0xFF55
tnbytes - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Number of bytes targeted to be read
tnsot - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SOT
 
toByteArray(byte[]) - Method in class io.scif.jj2000.j2k.codestream.writer.BitOutputBuffer
Returns the byte buffer data in a new array.
toByteArray(int, int, byte[], int) - Method in class io.scif.jj2000.j2k.entropy.encoder.ByteOutputBuffer
Copies the specified part of the stream to the 'outbuf' byte array.
toCIEXYZ(float[]) - Method in class io.scif.media.imageioimpl.common.BogusColorSpace
 
toCIEXYZ(float[]) - Method in class io.scif.media.imageioimpl.common.InvertedCMYKColorSpace
 
toCIEXYZ(float[]) - Method in class io.scif.media.imageioimpl.common.SimpleCMYKColorSpace
 
ToOMETranslator<M extends Metadata> - Class in io.scif.ome.translators
Abstract base class for all io.scif.Translators that translate to an OMEMetadata object.
ToOMETranslator() - Constructor for class io.scif.ome.translators.ToOMETranslator
 
toRGB(float, float, float, float[]) - Method in class io.scif.media.imageio.plugins.tiff.TIFFColorConverter
Converts a triple in the native color space of this TIFFColorConverter into an RGB triple, and stores the result in the first three entries of the rgb array.
toRGB(float[]) - Method in class io.scif.media.imageioimpl.common.BogusColorSpace
 
toRGB(float[]) - Method in class io.scif.media.imageioimpl.common.InvertedCMYKColorSpace
 
toRGB(float[]) - Method in class io.scif.media.imageioimpl.common.SimpleCMYKColorSpace
 
toRGB(float, float, float, float[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFCIELabColorConverter
 
toRGB(float, float, float, float[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
toString() - Method in class io.scif.cli.show.AsciiImage
 
toString() - Method in class io.scif.jj2000.j2k.codestream.CBlkCoordInfo
Returns code-block's information in a String
toString() - Method in class io.scif.jj2000.j2k.codestream.CoordInfo
Returns object's information in a String
toString() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.COC
Display information found in this COC marker segment
toString() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.COD
Display information found in this COD marker segment
toString() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.COM
Display information found in the COM marker segment
toString() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.CRG
Display information found in the CRG marker segment
toString() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.POC
Display information found in this POC marker segment
toString() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCC
Display information found in this QCC marker segment
toString() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.QCD
Display information found in this QCD marker segment
toString() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.RGN
Display information found in this RGN marker segment
toString() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
Display information found in SIZ marker segment
toString() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo.SOT
Display information found in this SOT marker segment
toString() - Method in class io.scif.jj2000.j2k.codestream.PrecCoordInfo
Returns precinct's information in a String
toString() - Method in class io.scif.jj2000.j2k.codestream.PrecInfo
Returns PrecInfo object information in a String
toString() - Method in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
Object information in a string.
toString() - Method in class io.scif.jj2000.j2k.codestream.reader.HeaderDecoder
Print information about the current header.
toString() - Method in class io.scif.jj2000.j2k.codestream.reader.PktInfo
Object information in a string.
toString() - Method in class io.scif.jj2000.j2k.codestream.writer.BitOutputBuffer
Prints information about this object for debugging purposes
toString() - Method in class io.scif.jj2000.j2k.entropy.CodedCBlk
Returns the contents of the object in a string.
toString() - Method in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
Object information in a string
toString() - Method in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
Returns the contents of the object in a string.
toString() - Method in class io.scif.jj2000.j2k.entropy.Progression
 
toString() - Method in class io.scif.jj2000.j2k.image.DataBlk
Returns a string of informations about the DataBlk
toString() - Method in class io.scif.jj2000.j2k.image.DataBlkFloat
Returns a string of informations about the DataBlkInt.
toString() - Method in class io.scif.jj2000.j2k.image.DataBlkInt
Returns a string of informations about the DataBlkInt.
toString() - Method in class io.scif.jj2000.j2k.image.forwcomptransf.ForwCompTransf
Returns a string with a descriptive text of which forward component transformation is used.
toString() - Method in class io.scif.jj2000.j2k.image.ImgDataJoiner
Returns a string of information about the object, more than 1 line long.
toString() - Method in class io.scif.jj2000.j2k.image.input.ImgReaderPGM
Returns a string of information about the object, more than 1 line long.
toString() - Method in class io.scif.jj2000.j2k.image.invcomptransf.InvCompTransf
Returns a string with a descriptive text of which inverse component transformation is used.
toString() - Method in class io.scif.jj2000.j2k.image.Tiler
Returns a String object representing Tiler's informations
toString() - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Returns a string of information about the file and the endianess
toString() - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Returns a string of information about the file
toString() - Method in class io.scif.jj2000.j2k.roi.encoder.ArbROIMaskGenerator
This function returns the relevant data of the mask generator
toString() - Method in class io.scif.jj2000.j2k.roi.encoder.RectROIMaskGenerator
This function returns the relevant data of the mask generator
toString() - Method in class io.scif.jj2000.j2k.roi.encoder.ROI
This function prints all relevant data for the ROI
toString() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
Debugging method
toString() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
Debugging method
toString() - Method in class io.scif.jj2000.j2k.wavelet.analysis.AnWTFilterSpec
Debugging method
toString() - Method in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
Returns a string of informations about the DataBlk
toString() - Method in class io.scif.jj2000.j2k.wavelet.Subband
Returns subband informations in a string.
toString() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
Returns a string of information about the synthesis wavelet filter
toString() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterIntLift5x3
Returns a string of information about the synthesis wavelet filter
toString() - Method in class io.scif.jj2000.j2k.wavelet.synthesis.SynWTFilterSpec
Debugging method
toStringMainHeader() - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Display information found in the different marker segments of the main header
toStringThNoSOT(int, int) - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns information found in the tile-part headers of a given tile exception the SOT marker segment.
toStringTileHeader(int, int) - Method in class io.scif.jj2000.j2k.codestream.HeaderInfo
Returns information found in the tile-part headers of a given tile.
tpsot - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SOT
 
transColor - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
transformToLatestVersion(String) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
transformToLatestVersion(String) - Method in interface io.scif.ome.services.OMEXMLService
 
translateFormatMetadata(BioFormatsFormat.Metadata, OMEMetadata) - Method in class io.scif.bf.ome.BioFormatsTranslator.BioFormatsOMETranslator
 
translateFormatMetadata(APNGFormat.Metadata, OMEMetadata) - Method in class io.scif.ome.translators.APNGTranslator.APNGOMETranslator
 
translateFormatMetadata(OMEMetadata, APNGFormat.Metadata) - Method in class io.scif.ome.translators.APNGTranslator.OMEAPNGTranslator
 
translateFormatMetadata(BMPFormat.Metadata, OMEMetadata) - Method in class io.scif.ome.translators.BMPTranslator.BMPOMETranslator
 
translateFormatMetadata(DICOMFormat.Metadata, OMEMetadata) - Method in class io.scif.ome.translators.DICOMTranslator.DICOMOMETranslator
 
translateFormatMetadata(OMEMetadata, EPSFormat.Metadata) - Method in class io.scif.ome.translators.EPSTranslator.OMEEPSTranslator
 
translateFormatMetadata(ICSFormat.Metadata, OMEMetadata) - Method in class io.scif.ome.translators.ICSTranslator.ICSOMETranslator
 
translateFormatMetadata(OMEMetadata, ICSFormat.Metadata) - Method in class io.scif.ome.translators.ICSTranslator.OMEICSTranslator
 
translateFormatMetadata(MicromanagerFormat.Metadata, OMEMetadata) - Method in class io.scif.ome.translators.MicromanagerTranslator.MicromanagerOMETranslator
 
translateFormatMetadata(NRRDFormat.Metadata, OMEMetadata) - Method in class io.scif.ome.translators.NRRDTranslator.NRRDOMETranslator
 
translateFormatMetadata(OBFFormat.Metadata, OMEMetadata) - Method in class io.scif.ome.translators.OBFTranslator.OBFOMETranslator
 
translateFormatMetadata(OMEMetadata, TIFFFormat.Metadata) - Method in class io.scif.ome.translators.TIFFTranslator.OMETIFFTranslator
 
translateFormatMetadata(TIFFFormat.Metadata, OMEMetadata) - Method in class io.scif.ome.translators.TIFFTranslator.TIFFOMETranslator
 
translateImageMetadata(List<ImageMetadata>, M) - Method in class io.scif.ome.translators.FromOMETranslator
 
translateImageMetadata(List<ImageMetadata>, OMEMetadata) - Method in class io.scif.ome.translators.ToOMETranslator
 
transparency - Variable in class io.scif.media.imageioimpl.common.PaletteBuilder
 
transparentColorFlag - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
transparentColorIndex - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
trate - Variable in class io.scif.jj2000.j2k.codestream.reader.BitstreamReaderAgent
Target decoding rate in bpp
treeS - Variable in class io.scif.jj2000.j2k.codestream.reader.TagTreeDecoder
The tag tree state.
treeS - Variable in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
The tag tree state.
treeSbak - Variable in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
The saved tag tree state.
treeV - Variable in class io.scif.jj2000.j2k.codestream.reader.TagTreeDecoder
The tag tree values.
treeV - Variable in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
The tag tree values.
treeVbak - Variable in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
The saved tag tree values.
trigger - Variable in class io.scif.lifesci.SDTInfo
 
truncDists - Variable in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
The distortion for each truncation point (valid and non-valid ones)
truncIdxs - Variable in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
The indices of the valid truncation points, in increasing order.
truncRates - Variable in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
The rate (in bytes) for each truncation point (valid and non-valid ones)
truncSlopes - Variable in class io.scif.jj2000.j2k.entropy.encoder.CBlkRateDistStats
The negative of the rate-distortion slope for each valid truncation point
tsLengths - Variable in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
The length of each terminated segment.
tts - Variable in class io.scif.jj2000.j2k.entropy.encoder.StdEntropyCoder
The termination type specifications
type - Variable in class io.scif.jj2000.j2k.entropy.Progression
Progression type as defined in ProgressionType interface
type - Variable in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
 
TYPE_BYTE - Static variable in class io.scif.jj2000.j2k.image.DataBlk
The identifier for the byte data type, as signed 8 bits.
TYPE_FLOAT - Static variable in class io.scif.jj2000.j2k.image.DataBlk
The identifier for the float data type
TYPE_INT - Static variable in class io.scif.jj2000.j2k.image.DataBlk
The identifier for the int data type, as signed 32 bits.
TYPE_SHORT - Static variable in class io.scif.jj2000.j2k.image.DataBlk
The identifier for the short data type, as signed 16 bits.
typedParse(DataHandle<Location>, BioFormatsFormat.Metadata, SCIFIOConfig) - Method in class io.scif.bf.BioFormatsFormat.Parser
 
typedParse(DataHandle<Location>, SDTFormat.Metadata, SCIFIOConfig) - Method in class io.scif.lifesci.SDTFormat.Parser
 

U

ulcx - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The horizontal coordinate of the upper-left corner of the subband, with respect to the canvas origin, in the component's grid and subband's decomposition level.
ulcy - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The vertical coordinate of the upper-left corner of the subband, with respect to the canvas origin, in the component's grid and subband's decomposition level.
ulx - Variable in class io.scif.jj2000.j2k.codestream.CoordInfo
Horizontal upper left coordinate in the subband
ulx - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Precinct horizontal upper-left coordinate in the corresponding resolution level
ulx - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
Upper-left x-coordinate of the code-block (relative to the tile)
ulx - Variable in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
The horizontal coordinate of the upper-left corner of the code-block
ulx - Variable in class io.scif.jj2000.j2k.image.DataBlk
The horizontal coordinate (in pixels) of the upper-left corner of the block of data.
ulx - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
x coordinate of upper left corner of rectangular ROI
ulx - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
Horizontal uper-left coordinate of the subband mask
ulx - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The horizontal coordinate of the upper-left corner of the code-block
ulx - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The horizontal coordinate of the upper-left corner of the subband
ulxs - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandRectROIMask
The upper left x coordinates of the applicable ROIs
uly - Variable in class io.scif.jj2000.j2k.codestream.CoordInfo
Vertical upper left coordinate in the subband
uly - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Precinct vertical upper-left coordinate in the corresponding resolution level
uly - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
Upper-left y-coordinate of the code-block (relative to the tile)
uly - Variable in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
The vertical coordinate of the upper left corner of the code-block
uly - Variable in class io.scif.jj2000.j2k.image.DataBlk
The vertical coordinate of the upper-left corner of the block of data.
uly - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
y coordinate of upper left corner of rectangular ROI
uly - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
Vertical uper-left coordinate of the subband mask
uly - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The vertical coordinate of the upper left corner of the code-block
uly - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The vertical coordinate of the upper-left corner of the subband
ulys - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandRectROIMask
The upper left y coordinates of the applicable ROIs
uncompressedMode - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
Uncompressed mode flag: 1 if uncompressed, 0 if not.
unsetColorConverter() - Method in class io.scif.media.imageio.plugins.tiff.TIFFImageWriteParam
Removes any currently set ColorConverter object and PhotometricInterpretation tag value.
unwrap() - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
update(int, int, int, PktHeaderBitReader) - Method in class io.scif.jj2000.j2k.codestream.reader.TagTreeDecoder
Decodes information for the specified element of the tree, given the threshold, and updates its value.
updateProgressWatch(int, String) - Method in interface io.scif.jj2000.j2k.util.ProgressWatch
Update the progress watching process to the specified value
URL_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
useMotor - Variable in class io.scif.lifesci.SDTInfo
 
userInputFlag - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFImageMetadata
 
useRoi() - Method in class io.scif.jj2000.j2k.roi.encoder.ROIScaler
This function returns the flag indicating if any ROI functionality used
utrb - Variable in class io.scif.jj2000.j2k.quantization.dequantizer.Dequantizer
The "range bits" for each un-transformed component
UUID_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
UUID_INFO_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
UUID_LIST_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
UUID Info Boxes
UUIDBox - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is defined to represent a UUID Box of JPEG JP2 file format.
UUIDBox(byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDBox
Constructs a UUIDBox from its content data array.
UUIDBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDBox
Constructs a UUIDBox based on the provided org.w3c.dom.Node.
UUIDListBox - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is defined to represent a UUID list Box of JPEG JP2 file format.
UUIDListBox(short, byte[][]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDListBox
Constructs a UUIDListBox from the provided uuid number and uuids.
UUIDListBox(byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDListBox
Constructs a UUIDListBox from the provided content data array.
UUIDListBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.UUIDListBox
Constructs a UUIDListBox based on the provided org.w3c.dom.Node.

V

validateOMEXML(String) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
validateOMEXML(String, boolean) - Method in class io.scif.ome.services.DefaultOMEXMLService
 
validateOMEXML(String) - Method in interface io.scif.ome.services.OMEXMLService
 
validateOMEXML(String, boolean) - Method in interface io.scif.ome.services.OMEXMLService
 
validateParams() - Method in class io.scif.cli.AbstractSCIFIOToolCommand
Very that all parameters were set correctly, in case any need checking that the Parameter or Argument can't provide.
validateParams() - Method in class io.scif.cli.convert.Convert
 
validateParams() - Method in class io.scif.cli.help.Help
 
validateParams() - Method in class io.scif.cli.info.Info
 
validateParams() - Method in class io.scif.cli.show.Show
 
validateParams() - Method in class io.scif.ome.commands.OMEXMLToolCommand
 
verifyMinimumPopulated(MetadataRetrieve) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
verifyMinimumPopulated(MetadataRetrieve, int) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
verifyMinimumPopulated(MetadataRetrieve) - Method in interface io.scif.ome.services.OMEMetadataService
 
verifyMinimumPopulated(MetadataRetrieve, int) - Method in interface io.scif.ome.services.OMEMetadataService
 
version - Static variable in class io.scif.jj2000.j2k.JJ2KInfo
The version number (such as 2.0, 2.1.1, etc.)
version - Variable in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
VERSION_2 - Static variable in class io.scif.media.imageio.plugins.bmp.BMPImageWriteParam
Deprecated. 
VERSION_2 - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
VERSION_2_5 - Static variable in interface io.scif.media.imageioimpl.plugins.pcx.PCXConstants
 
VERSION_2_8_W_PALETTE - Static variable in interface io.scif.media.imageioimpl.plugins.pcx.PCXConstants
 
VERSION_2_8_WO_PALETTE - Static variable in interface io.scif.media.imageioimpl.plugins.pcx.PCXConstants
 
VERSION_3 - Static variable in class io.scif.media.imageio.plugins.bmp.BMPImageWriteParam
Deprecated. 
VERSION_3 - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
VERSION_3_0 - Static variable in interface io.scif.media.imageioimpl.plugins.pcx.PCXConstants
 
VERSION_3_NT - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
VERSION_4 - Static variable in class io.scif.media.imageio.plugins.bmp.BMPImageWriteParam
Deprecated. 
VERSION_4 - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
VERSION_5 - Static variable in class io.scif.media.imageio.plugins.bmp.BMPImageWriteParam
Deprecated. 
VERSION_5 - Static variable in interface io.scif.media.imageioimpl.plugins.bmp.BMPConstants
 
VERSION_PC_WINDOWS - Static variable in interface io.scif.media.imageioimpl.plugins.pcx.PCXConstants
 
versionStrings - Static variable in class io.scif.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
vert - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Black and white vertical mode table.
vertMode - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Vertical mode table.
vFilter - Variable in class io.scif.jj2000.j2k.wavelet.analysis.SubbandAn
The vertical analysis filter used to decompose this subband.
vFilter - Variable in class io.scif.jj2000.j2k.wavelet.synthesis.SubbandSyn
The vertical analysis filter used to decompose this subband, from its childs.

W

w - Variable in class io.scif.jj2000.j2k.codestream.CoordInfo
Object's width
w - Variable in class io.scif.jj2000.j2k.codestream.PrecInfo
Precinct width in the corresponding resolution level
w - Variable in class io.scif.jj2000.j2k.codestream.reader.CBlkInfo
Width of the code-block
w - Variable in class io.scif.jj2000.j2k.codestream.reader.TagTreeDecoder
The horizontal dimension of the base level
w - Variable in class io.scif.jj2000.j2k.codestream.writer.TagTreeEncoder
The horizontal dimension of the base level
w - Variable in class io.scif.jj2000.j2k.entropy.decoder.DecLyrdCBlk
The width of the code-block
w - Variable in class io.scif.jj2000.j2k.image.DataBlk
The width of the block, in pixels.
w - Variable in class io.scif.jj2000.j2k.image.input.ImgReader
The width of the image
w - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
width of rectangular ROI
w - Variable in class io.scif.jj2000.j2k.roi.encoder.SubbandROIMask
Width of the subband mask
w - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The width of the code-block
w - Variable in class io.scif.jj2000.j2k.wavelet.Subband
The width of the subband
W5X3 - Static variable in interface io.scif.jj2000.j2k.wavelet.FilterTypes
W5x3 filter: 0x01
W9X7 - Static variable in interface io.scif.jj2000.j2k.wavelet.FilterTypes
W7x9 filter: 0x00
warn(String) - Method in class io.scif.cli.AbstractSCIFIOToolCommand
 
WARNING - Static variable in interface io.scif.jj2000.j2k.util.MsgLogger
Severity of message.
WaveletFilter - Interface in io.scif.jj2000.j2k.wavelet
This interface defines how a wavelet filter implementation should present itself.
WaveletTransform - Interface in io.scif.jj2000.j2k.wavelet
This interface defines how a forward or inverse wavelet transform should present itself.
WBMPImageReader - Class in io.scif.media.imageioimpl.plugins.wbmp
This class is the Java Image IO plugin reader for WBMP images.
WBMPImageReader(ImageReaderSpi) - Constructor for class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReader
Constructs WBMPImageReader from the provided ImageReaderSpi.
WBMPImageReaderSpi - Class in io.scif.media.imageioimpl.plugins.wbmp
 
WBMPImageReaderSpi() - Constructor for class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
WBMPImageWriter - Class in io.scif.media.imageioimpl.plugins.wbmp
The Java Image IO plugin writer for encoding a binary RenderedImage into a WBMP format.
WBMPImageWriter(ImageWriterSpi) - Constructor for class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriter
Constructs WBMPImageWriter based on the provided ImageWriterSpi.
WBMPImageWriterSpi - Class in io.scif.media.imageioimpl.plugins.wbmp
 
WBMPImageWriterSpi() - Constructor for class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
WBMPMetadata - Class in io.scif.media.imageioimpl.plugins.wbmp
 
WBMPMetadata() - Constructor for class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
wbmpType - Variable in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
wfs - Variable in class io.scif.jj2000.j2k.decoder.DecoderSpecs
Analysis wavelet filters specifications
WHITE - Static variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
The CCITT numerical definition of white.
WHITE_BALANCE_AUTO - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "WhiteBalance" tag.
WHITE_BALANCE_MANUAL - Static variable in class io.scif.media.imageio.plugins.tiff.EXIFTIFFTagSet
A value to be used with the "WhiteBalance" tag.
width - Variable in class io.scif.lifesci.SDTInfo
 
width - Variable in class io.scif.media.imageioimpl.common.SimpleRenderedImage
The image's width in pixels.
width - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
width - Variable in class io.scif.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
wmseScaling - Variable in class io.scif.jj2000.j2k.wavelet.analysis.CBlkWTData
The WMSE scaling factor (multiplicative) to apply to the distortion measures of the data of this code-block.
wp - Variable in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
The encoder specifications
wp - Variable in class io.scif.jj2000.j2k.entropy.encoder.PostCompRateAllocator
The source of entropy coded data
write(int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
write(byte[]) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
write(byte[], int, int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
write(ByteBuffer) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
write(ByteBuffer, int, int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
write(int) - Method in class io.scif.jj2000.j2k.entropy.encoder.ByteOutputBuffer
Writes the specified byte to this byte array output stream.
write(int) - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Writes a byte to the stream.
write(byte) - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Writes a byte to the stream.
write(byte[], int, int) - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Writes aan array of bytes to the stream.
write(int) - Method in interface io.scif.jj2000.j2k.io.RandomAccessIO
Writes a byte to the stream.
write(int) - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Throws an IOException since this class does not implement data output.
write(int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
write(byte[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
write(IIOMetadata, IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
write(byte[]) - Method in class io.scif.media.imageioimpl.plugins.clib.OutputStreamAdapter
 
write(byte[], int, int) - Method in class io.scif.media.imageioimpl.plugins.clib.OutputStreamAdapter
 
write(int) - Method in class io.scif.media.imageioimpl.plugins.clib.OutputStreamAdapter
 
write(IIOMetadata, IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
write(ImageOutputStream) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.Box
Writes this box instance into a ImageOutputStream.
write(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
Throws an IOException as writing is not supported.
write(IIOMetadata, IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
write(IIOMetadata, IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.pcx.PCXImageWriter
 
write(IIOMetadata, IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.pnm.PNMImageWriter
 
write(IIOMetadata, IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.raw.RawImageWriter
 
write(IIOMetadata, IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
write(IIOMetadata, IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
WRITE_ABORTED - Static variable in class io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
When the writing is aborted, RenderedImageSrc throws a RuntimeException.
writeAbbreviatedStream - Variable in class io.scif.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
Whether to write abbreviated JPEG streams (default == false).
writeBit(int) - Method in class io.scif.jj2000.j2k.codestream.writer.BitOutputBuffer
Writes a bit to the buffer at the current position.
writeBits(int, int) - Method in class io.scif.jj2000.j2k.codestream.writer.BitOutputBuffer
Writes the n least significant bits of 'bits' to the buffer at the current position.
writeBits(int, int) - Method in class io.scif.media.imageioimpl.common.BitFile
 
writeBoolean(boolean) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
writeByte(int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
writeByte(int) - Method in interface io.scif.jj2000.j2k.io.BinaryDataOutput
Should write the byte value of v (i.e., 8 least significant bits) to the output.
writeByte(int) - Method in class io.scif.jj2000.j2k.io.BufferedRandomAccessFile
Writes the byte value of v (i.e., 8 least significant bits) to the output.
writeByte(int) - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Throws an IOException since this class does not implement data output.
writeByte(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
Throws an IOException as writing is not supported.
writeBytes(String) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
writeChar(int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
writeChars(String) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
writeChars(char[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
writeCOC(boolean, int, int) - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Writes COC marker segment .
writeCOD(boolean, int) - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Writes COD marker segment.
writeCompPosResLy(int, int, int, int, int, int[][], int) - Method in class io.scif.jj2000.j2k.entropy.encoder.EBCOTRateAllocator
Write a piece of bit stream according to the COMP_POS_RES_LY_PROG progression mode and between given bounds
writeContiguousCodeStreamBox() - Method in class io.scif.jj2000.j2k.fileformat.writer.FileFormatWriter
This method writes the Contiguous codestream box
writeDouble(double) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
writeDouble(double) - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Writes the IEEE double value v (i.e., 64 bits) to the output.
writeDouble(double) - Method in interface io.scif.jj2000.j2k.io.BinaryDataOutput
Should write the IEEE double value v (i.e., 64 bits) to the output.
writeDouble(double) - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Throws an IOException since this class does not implement data output.
writeDouble(double) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
Throws an IOException as writing is not supported.
writeDoubles(double[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
writeFileFormat() - Method in class io.scif.jj2000.j2k.fileformat.writer.FileFormatWriter
This method reads the codestream and writes the file format wrapper and the codestream to the same file
writeFloat(float) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
writeFloat(float) - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Writes the IEEE float value v (i.e., 32 bits) to the output.
writeFloat(float) - Method in interface io.scif.jj2000.j2k.io.BinaryDataOutput
Should write the IEEE float value v (i.e., 32 bits) to the output.
writeFloat(float) - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Throws an IOException since this class does not implement data output.
writeFloat(float) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
Throws an IOException as writing is not supported.
writeFloats(float[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
writeImage(PipelineImage) - Method in class io.scif.formats.imaris.HDFWriter
 
writeInsert(int, IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
writeInt(int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
writeInt(int) - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Writes the int value of v (i.e., the 32 bits) to the output.
writeInt(int) - Method in interface io.scif.jj2000.j2k.io.BinaryDataOutput
Should write the int value of v (i.e., the 32 bits) to the output.
writeInt(int) - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Throws an IOException since this class does not implement data output.
writeInt(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
Throws an IOException as writing is not supported.
writeInts(int[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
writeLong(long) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
writeLong(long) - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Writes the long value of v (i.e., the 64 bits) to the output.
writeLong(long) - Method in interface io.scif.jj2000.j2k.io.BinaryDataOutput
Should write the long value of v (i.e., the 64 bits) to the output.
writeLong(long) - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Throws an IOException since this class does not implement data output.
writeLong(long) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
Throws an IOException as writing is not supported.
writeLongs(long[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
writeLyResCompPos(int, int, int, int, int, int[][], int) - Method in class io.scif.jj2000.j2k.entropy.encoder.EBCOTRateAllocator
Write a piece of bit stream according to the LY_RES_COMP_POS_PROG progression mode and between given bounds
writeMainQCC(int) - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Writes QCC marker segment in main header.
writeMainQCD() - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Writes QCD marker segment in main header.
writeMaskToPalette(int, int, byte[], byte[], byte[], byte[]) - Method in class io.scif.media.imageioimpl.plugins.bmp.BMPImageWriter
 
writePacketBody(byte[], int, boolean, boolean, int) - Method in class io.scif.jj2000.j2k.codestream.writer.CodestreamWriter
Writes a packet body to the bit stream and returns the number of bytes used by this body .If in simulation mode then no data is written to the bit stream but the number of bytes is calculated.
writePacketBody(byte[], int, boolean, boolean, int) - Method in class io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
Writes a packet body to the bit stream and returns the number of bytes used by this body .If in simulation mode then no data is written to the bit stream but the number of bytes is calculated.
writePacketHead(byte[], int, boolean, boolean, boolean) - Method in class io.scif.jj2000.j2k.codestream.writer.CodestreamWriter
Writes a packet head to the bit stream and returns the number of bytes used by this header.
writePacketHead(byte[], int, boolean, boolean, boolean) - Method in class io.scif.jj2000.j2k.codestream.writer.FileCodestreamWriter
Writes a packet head to the bit stream and returns the number of bytes used by this header.
writePixels(PipelineImage) - Method in class io.scif.formats.imaris.TimePoint
 
writePlane(int, long, Plane, Interval) - Method in class io.scif.formats.ImarisFormat.Writer
 
writePOC(boolean, int) - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Writes POC marker segment.
writePosCompResLy(int, int, int, int, int, int[][], int) - Method in class io.scif.jj2000.j2k.entropy.encoder.EBCOTRateAllocator
Write a piece of bit stream according to the COMP_POS_RES_LY_PROG progression mode and between given bounds
Writer() - Constructor for class io.scif.formats.ImarisFormat.Writer
 
writer - Variable in class io.scif.media.imageio.plugins.tiff.TIFFCompressor
The ImageWriter calling this TIFFCompressor.
writeResLyCompPos(int, int, int, int, int, int[][], int) - Method in class io.scif.jj2000.j2k.entropy.encoder.EBCOTRateAllocator
Write a piece of bit stream according to the RES_LY_COMP_POS_PROG progression mode and between given bounds
writeResPosCompLy(int, int, int, int, int, int[][], int) - Method in class io.scif.jj2000.j2k.entropy.encoder.EBCOTRateAllocator
Write a piece of bit stream according to the RES_POS_COMP_LY_PROG progression mode and between given bounds
writeShort(int) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
writeShort(int) - Method in class io.scif.jj2000.j2k.io.BEBufferedRandomAccessFile
Writes the short value of v (i.e., 16 least significant bits) to the output.
writeShort(int) - Method in interface io.scif.jj2000.j2k.io.BinaryDataOutput
Should write the short value of v (i.e., 16 least significant bits) to the output.
writeShort(int) - Method in class io.scif.jj2000.j2k.util.ISRandomAccessIO
Throws an IOException since this class does not implement data output.
writeShort(int) - Method in class io.scif.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
Throws an IOException as writing is not supported.
writeShorts(short[], int, int) - Method in class io.scif.media.imageio.stream.FileChannelImageOutputStream
 
writeString(byte[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
Write out the string just uncompressed.
writeString(byte[]) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFLZWUtil
Write out the string just uncompressed.
writeStringAttribute(int, String, String) - Static method in class io.scif.formats.imaris.HDFUtils
 
writeTileQCC(int, int) - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Writes QCC marker segment in tile header.
writeTileQCD(int) - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Writes QCD marker segment in tile header.
writeTo(BinaryDataOutput) - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Writes the header to the specified BinaryDataOutput.
writeTo(OutputStream) - Method in class io.scif.jj2000.j2k.codestream.writer.HeaderEncoder
Writes the header to the specified OutputStream.
writeToSequence(IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.gif.GIFImageWriter
 
writeToSequence(IIOImage, ImageWriteParam) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
writeToStream(ImageOutputStream) - Method in class io.scif.media.imageioimpl.plugins.tiff.TIFFIFD
 
writeUTF(String) - Method in class io.scif.bf.wrapper.DataHandleAdapter
 
WT_DECOMP_DYADIC - Static variable in class io.scif.jj2000.j2k.wavelet.analysis.ForwardWT
ID for the dyadic wavelet tree decomposition (also called "Mallat" in JPEG 2000): 0x00.
WT_DECOMP_DYADIC - Static variable in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
ID for the dyadic wavelet tree decomposition (also called "Mallat" in JPEG 2000): 0x00.
WT_DECOMP_PACKET - Static variable in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
ID for the PACKET (as defined in JPEG 2000) wavelet tree decomposition (2 levels of decomposition in the high bands and some specified number for the lowest LL band): 0x01.
WT_DECOMP_SPACL - Static variable in class io.scif.jj2000.j2k.wavelet.WTDecompSpec
ID for the SPACL (as defined in JPEG 2000) wavelet tree decomposition (1 level of decomposition in the high bands and some specified number for the lowest LL band): 0x02.
WT_FILTER_FLOAT_CONVOL - Static variable in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
The ID for floatring-poitn convolution implementations
WT_FILTER_FLOAT_LIFT - Static variable in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
The ID for floating-point lifting spteps implementations
WT_FILTER_INT_LIFT - Static variable in interface io.scif.jj2000.j2k.wavelet.WaveletFilter
The ID for integer lifting spteps implementations
WT_IMPL_FULL - Static variable in interface io.scif.jj2000.j2k.wavelet.WaveletTransform
ID for full-page based implementations of wavelet transforms.
WT_IMPL_LINE - Static variable in interface io.scif.jj2000.j2k.wavelet.WaveletTransform
ID for line based implementations of wavelet transforms.
WT_ORIENT_HH - Static variable in class io.scif.jj2000.j2k.wavelet.Subband
The ID for the HH orientation
WT_ORIENT_HL - Static variable in class io.scif.jj2000.j2k.wavelet.Subband
The ID for the HL (horizontal high-pass) orientation
WT_ORIENT_LH - Static variable in class io.scif.jj2000.j2k.wavelet.Subband
The ID for the LH (vertical high-pass) orientation
WT_ORIENT_LL - Static variable in class io.scif.jj2000.j2k.wavelet.Subband
The ID for the LL orientation
WTDecompSpec - Class in io.scif.jj2000.j2k.wavelet
This class holds the decomposition type to be used in each part of the image; the default one, the component specific ones, the tile default ones and the component-tile specific ones.
WTDecompSpec(int, int, int) - Constructor for class io.scif.jj2000.j2k.wavelet.WTDecompSpec
Constructs a new 'WTDecompSpec' for the specified number of components and tiles, with the given main default decomposition type and number of levels.
WTFilterSpec - Class in io.scif.jj2000.j2k.wavelet
This is the generic class from which the ones that hold the analysis or synthesis filters to be used in each part of the image derive.
WTFilterSpec(int) - Constructor for class io.scif.jj2000.j2k.wavelet.WTFilterSpec
Constructs a 'WTFilterSpec' object, initializing all the components and tiles to the 'FILTER_SPEC_MAIN_DEF' spec type, for the specified number of components and tiles.

X

x - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
x coordinate of center of circular ROI
x0siz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
X_STRING - Static variable in class io.scif.lifesci.SDTInfo
 
xAxis - Variable in class io.scif.lifesci.SDTInfo
X axis representation (SPC-930).
xcrg - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.CRG
 
XML_BOX - Static variable in interface io.scif.jj2000.j2k.fileformat.FileFormatBoxes
 
XMLBox - Class in io.scif.media.imageioimpl.plugins.jpeg2000
This class is defined to represent a XML box of JPEG JP2 file format.
XMLBox(byte[]) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.XMLBox
Create a Box from its content.
XMLBox(Node) - Constructor for class io.scif.media.imageioimpl.plugins.jpeg2000.XMLBox
Constructs a UUIDListBox based on the provided org.w3c.dom.Node.
xPixelsPerMeter - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
xref - Variable in class io.scif.jj2000.j2k.codestream.PrecCoordInfo
Horizontal upper left coordinate in the reference grid
xrsiz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
xsiz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
xt0siz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
XToTileX(int, int, int) - Static method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Converts a pixel's X coordinate into a horizontal tile index relative to a given tile grid layout specified by its X offset and tile width.
XToTileX(int) - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Converts a pixel's X coordinate into a horizontal tile index.
XToTileX(int, int, int) - Static method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
Converts a pixel's X coordinate into a horizontal tile index relative to a given tile grid layout specified by its X offset and tile width.
xtsiz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
xyGain - Variable in class io.scif.lifesci.SDTInfo
Gain for XY ADCs (SPC930).

Y

y - Variable in class io.scif.jj2000.j2k.roi.encoder.ROI
y coordinate of center of circular ROI
y0siz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
Y_CB_CR_POSITIONING_CENTERED - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "YCbCrPositioning" tag.
Y_CB_CR_POSITIONING_COSITED - Static variable in class io.scif.media.imageio.plugins.tiff.BaselineTIFFTagSet
A value to be used with the "YCbCrPositioning" tag.
Y_STRING - Static variable in class io.scif.lifesci.SDTInfo
 
ycrg - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.CRG
 
yPixelsPerMeter - Variable in class io.scif.media.imageioimpl.plugins.bmp.BMPMetadata
 
yref - Variable in class io.scif.jj2000.j2k.codestream.PrecCoordInfo
Vertical upper left coordinate on the reference grid
yrsiz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
ysiz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
yt0siz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 
YToTileY(int, int, int) - Static method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Converts a pixel's Y coordinate into a vertical tile index relative to a given tile grid layout specified by its Y offset and tile height.
YToTileY(int) - Method in class io.scif.media.imageioimpl.common.SimpleRenderedImage
Converts a pixel's Y coordinate into a vertical tile index.
YToTileY(int, int, int) - Static method in class io.scif.media.imageioimpl.plugins.tiff.TIFFImageWriter
Converts a pixel's Y coordinate into a vertical tile index relative to a given tile grid layout specified by its Y offset and tile height.
ytsiz - Variable in class io.scif.jj2000.j2k.codestream.HeaderInfo.SIZ
 

Z

zctToArray(String, int, int, int) - Method in class io.scif.ome.services.DefaultOMEMetadataService
 
zctToArray(String, int, int, int) - Method in interface io.scif.ome.services.OMEMetadataService
Given a String dimension order, places the given z, c and t indices in the correct relative positions in a long array, which is returned.
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