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All Classes All Packages

A

add(byte) - Method in class ome.codecs.ByteVector
 
add(byte[]) - Method in class ome.codecs.ByteVector
 
add(byte[], int, int) - Method in class ome.codecs.ByteVector
 
ANIMATION - ome.codecs.CompressionType
 
ASSOCIATION - ome.codecs.JPEG2000BoxType
 
AWTImageTools - Class in ome.codecs.gui
A utility class with convenience methods for manipulating images in BufferedImage form.

B

Base64Codec - Class in ome.codecs
Implements encoding (compress) and decoding (decompress) methods for Base64.
Base64Codec() - Constructor for class ome.codecs.Base64Codec
 
BaseCodec - Class in ome.codecs
BaseCodec contains default implementation and testing for classes implementing the Codec interface, and acts as a base class for any of the compression classes.
BaseCodec() - Constructor for class ome.codecs.BaseCodec
 
BitBuffer - Class in ome.codecs
Deprecated.
Use loci.common.RandomAccessInputStream instead
BitBuffer(byte[]) - Constructor for class ome.codecs.BitBuffer
Deprecated.
Default constructor.
BITS_PER_COMPONENT - ome.codecs.JPEG2000BoxType
 
bitsPerSample - Variable in class ome.codecs.CodecOptions
Number of bits per channel.
BitWriter - Class in ome.codecs
Deprecated.
Use loci.common.RandomAccessOutputStream instead
BitWriter() - Constructor for class ome.codecs.BitWriter
Deprecated.
Constructs a new bit writer.
BitWriter(int) - Constructor for class ome.codecs.BitWriter
Deprecated.
Constructs a new bit writer with the given initial buffer size.
ByteVector - Class in ome.codecs
A growable array of bytes.
ByteVector() - Constructor for class ome.codecs.ByteVector
 
ByteVector(byte[]) - Constructor for class ome.codecs.ByteVector
 
ByteVector(int) - Constructor for class ome.codecs.ByteVector
 

C

CAPTURE_RESOLUTION - ome.codecs.JPEG2000BoxType
 
CHANNEL_DEFINITION - ome.codecs.JPEG2000BoxType
 
channels - Variable in class ome.codecs.CodecOptions
Number of channels.
CINEPAK - ome.codecs.CompressionType
 
clear() - Method in class ome.codecs.ByteVector
 
close() - Method in class ome.codecs.JPEGTileDecoder
 
COC - ome.codecs.JPEG2000SegmentMarker
 
COD - ome.codecs.JPEG2000SegmentMarker
 
codeBlockSize - Variable in class ome.codecs.JPEG2000CodecOptions
The maximum code-block size to use per tile-component as it would be provided to: J2KImageWriteParam.setCodeBlockSize(int[]) (WRITE).
Codec - Interface in ome.codecs
This class is an interface for any kind of compression or decompression.
CodecException - Exception in ome.codecs
CodecException is the exception thrown when something goes wrong performing a file format operation.
CodecException() - Constructor for exception ome.codecs.CodecException
 
CodecException(String) - Constructor for exception ome.codecs.CodecException
 
CodecException(String, Throwable) - Constructor for exception ome.codecs.CodecException
 
CodecException(Throwable) - Constructor for exception ome.codecs.CodecException
 
CodecOptions - Class in ome.codecs
Options for compressing and decompressing data.
CodecOptions() - Constructor for class ome.codecs.CodecOptions
Construct a new CodecOptions.
CodecOptions(CodecOptions) - Constructor for class ome.codecs.CodecOptions
Construct a new CodecOptions using the given CodecOptions.
colorModel - Variable in class ome.codecs.CodecOptions
Color model to use when constructing an image (WRITE).
COLOUR_SPECIFICATION - ome.codecs.JPEG2000BoxType
 
COM - ome.codecs.JPEG2000SegmentMarker
 
COMPONENT_MAPPING - ome.codecs.JPEG2000BoxType
 
compress(byte[][], CodecOptions) - Method in class ome.codecs.BaseCodec
2D data block encoding default implementation.
compress(byte[][], CodecOptions) - Method in interface ome.codecs.Codec
Compresses a block of data.
compress(byte[], CodecOptions) - Method in class ome.codecs.Base64Codec
 
compress(byte[], CodecOptions) - Method in interface ome.codecs.Codec
Compresses a block of data.
compress(byte[], CodecOptions) - Method in class ome.codecs.HuffmanCodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.JPEG2000Codec
The CodecOptions parameter should have the following fields set: width height bitsPerSample channels interleaved littleEndian lossless
compress(byte[], CodecOptions) - Method in class ome.codecs.JPEGCodec
The CodecOptions parameter should have the following fields set: width height channels bitsPerSample interleaved littleEndian signed
compress(byte[], CodecOptions) - Method in class ome.codecs.LosslessJPEGCodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.LZ4Codec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.LZOCodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.LZWCodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.MJPBCodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.MSRLECodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.MSVideoCodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.PackbitsCodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.PassthroughCodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.QTRLECodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.RPZACodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.ZlibCodec
 
compress(byte[], CodecOptions) - Method in class ome.codecs.ZstdCodec
 
compress(ByteBuffer, byte[], CodecOptions) - Method in class ome.codecs.BaseCodec
Compress using ByteBuffers.
compress(ByteBuffer, byte[], CodecOptions) - Method in interface ome.codecs.Codec
Compresses data from an array into a ByteBuffer.
compress(ByteBuffer, byte[], CodecOptions) - Method in class ome.codecs.LZWCodec
 
CompressionType - Enum in ome.codecs
An enumeration of compression types.
constructImage(int, int, int, int, boolean, boolean, DataBuffer) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image with the given DataBuffer.
constructImage(int, int, int, int, boolean, boolean, DataBuffer, ColorModel) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image with the given DataBuffer.
CONTIGUOUS_CODESTREAM - ome.codecs.JPEG2000BoxType
 
createCompatibleWritableRaster(int, int) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
CRG - ome.codecs.JPEG2000SegmentMarker
 
CS_2C - Static variable in class ome.codecs.gui.TwoChannelColorSpace
 

D

decompress(byte[]) - Method in class ome.codecs.BaseCodec
 
decompress(byte[]) - Method in interface ome.codecs.Codec
Decompresses a block of data.
decompress(byte[]) - Method in class ome.codecs.LZ4Codec
 
decompress(byte[]) - Method in class ome.codecs.ZstdCodec
 
decompress(byte[][]) - Method in class ome.codecs.BaseCodec
 
decompress(byte[][]) - Method in interface ome.codecs.Codec
Decompresses a block of data.
decompress(byte[][], CodecOptions) - Method in class ome.codecs.BaseCodec
2D data block decoding default implementation.
decompress(byte[][], CodecOptions) - Method in interface ome.codecs.Codec
Decompresses a block of data.
decompress(byte[], int, int) - Method in class ome.codecs.ZstdCodec
Decompresses a block of data of specified length from an initial offset.
decompress(byte[], int, int, int) - Method in class ome.codecs.LZ4Codec
Decompresses a block of data of specified length from an initial offset.
decompress(byte[], CodecOptions) - Method in class ome.codecs.BaseCodec
 
decompress(byte[], CodecOptions) - Method in interface ome.codecs.Codec
Decompresses a block of data.
decompress(byte[], CodecOptions) - Method in class ome.codecs.JPEG2000Codec
The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(byte[], CodecOptions) - Method in class ome.codecs.LZ4Codec
 
decompress(byte[], CodecOptions) - Method in class ome.codecs.PassthroughCodec
 
decompress(byte[], CodecOptions) - Method in class ome.codecs.QTRLECodec
The CodecOptions parameter should have the following fields set: width height bitsPerSample previousImage
decompress(byte[], CodecOptions) - Method in class ome.codecs.ZstdCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.Base64Codec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.BaseCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in interface ome.codecs.Codec
Decompresses data from the given RandomAccessInputStream.
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.HuffmanCodec
The CodecOptions parameter must be an instance of HuffmanCodecOptions, and should have the following fields set: table bitsPerSample maxBytes
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.JPEG2000Codec
The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.JPEGCodec
The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.LosslessJPEGCodec
The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.LZ4Codec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.LZOCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.LZWCodec
The CodecOptions parameter should have the following fields set: maxBytes
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.MJPBCodec
The CodecOptions parameter must be an instance of MJPBCodecOptions, and should have the following fields set: interlaced width height bitsPerSample littleEndian interleaved
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.MSRLECodec
The CodecOptions parameter should have the following fields set: width height previousImage
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.MSVideoCodec
The CodecOptions parameter should have the following fields set: width height bitsPerSample previousImage
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.PackbitsCodec
The CodecOptions parameter should have the following fields set: maxBytes
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.PassthroughCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.QTRLECodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.RPZACodec
The CodecOptions parameter should have the following fields set: width height
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.ZlibCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.ZstdCodec
 
DEFAULT_DISPLAY_RESOLUTION - ome.codecs.JPEG2000BoxType
 
disableChromaSubsampling - Variable in class ome.codecs.CodecOptions
Whether or not use chroma subsampling.

E

EOC - ome.codecs.JPEG2000SegmentMarker
 
EPH - ome.codecs.JPEG2000SegmentMarker
 

F

FILE - ome.codecs.JPEG2000BoxType
 
fromCIEXYZ(float[]) - Method in class ome.codecs.gui.TwoChannelColorSpace
 
fromRGB(float[]) - Method in class ome.codecs.gui.TwoChannelColorSpace
 

G

get(int) - Method in class ome.codecs.ByteVector
 
get(int) - Static method in enum ome.codecs.CompressionType
Retrieves the compression by reverse lookup of its "code".
get(int) - Static method in enum ome.codecs.JPEG2000BoxType
Retrieves the box type by reverse lookup of its "code".
get(int) - Static method in enum ome.codecs.JPEG2000SegmentMarker
Retrieves the segment marker by reverse lookup of its "code".
getAlpha(int) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
getAlpha(Object) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
getBits(int) - Method in class ome.codecs.BitBuffer
Deprecated.
Returns an int value representing the value of the bits read from the byte array, from the current position.
getBlue(int) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
getBlue(Object) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
getByteBuffer() - Method in class ome.codecs.BitBuffer
Deprecated.
Return the backing byte array.
getBytes(BufferedImage) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(BufferedImage, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Get the bytes from an image, merging the channels as necessary.
getBytes(WritableRaster) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(WritableRaster, int, int, int, int) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getCode() - Method in enum ome.codecs.CompressionType
Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum ome.codecs.JPEG2000BoxType
Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum ome.codecs.JPEG2000SegmentMarker
Implemented as specified by the CodedEnum I/F.
getCompression() - Method in enum ome.codecs.CompressionType
Returns the compression.
getData() - Method in class ome.codecs.gui.SignedByteBuffer
 
getData() - Method in class ome.codecs.gui.SignedShortBuffer
 
getData() - Method in class ome.codecs.gui.UnsignedIntBuffer
 
getData(int) - Method in class ome.codecs.gui.SignedByteBuffer
 
getData(int) - Method in class ome.codecs.gui.SignedShortBuffer
 
getData(int) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
getDataElements(int, Object) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
getDefaultOptions() - Static method in class ome.codecs.CodecOptions
Return CodecOptions with reasonable default values.
getDefaultOptions() - Static method in class ome.codecs.JPEG2000CodecOptions
Return JPEG2000CodecOptions with reasonable default values.
getDefaultOptions(CodecOptions) - Static method in class ome.codecs.JPEG2000CodecOptions
Return JPEG2000CodecOptions using the given CodecOptions as the default.
getDoubles(BufferedImage) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster, int, int, int, int) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of doubles, one per channel.
getElem(int) - Method in class ome.codecs.gui.SignedByteBuffer
 
getElem(int) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
getElem(int, int) - Method in class ome.codecs.gui.SignedByteBuffer
 
getElem(int, int) - Method in class ome.codecs.gui.SignedShortBuffer
 
getElem(int, int) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
getElemDouble(int) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
getElemDouble(int, int) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
getElemFloat(int) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
getElemFloat(int, int) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
getFloats(BufferedImage) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster, int, int, int, int) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of floats, one per channel.
getGreen(int) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
getGreen(Object) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
getHeight() - Method in class ome.codecs.JPEGTileDecoder
 
getInstance(int) - Static method in class ome.codecs.gui.TwoChannelColorSpace
 
getInts(BufferedImage) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of signed integers, one per channel.
getInts(WritableRaster) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of signed integers, one per channel.
getInts(WritableRaster, int, int, int, int) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of signed integers, one per channel.
getName() - Method in enum ome.codecs.JPEG2000BoxType
Returns the name of the box type.
getName() - Method in enum ome.codecs.JPEG2000SegmentMarker
Returns the name of the segment marker.
getName(int) - Method in class ome.codecs.gui.TwoChannelColorSpace
 
getNumComponents() - Method in class ome.codecs.gui.TwoChannelColorSpace
 
getPixelBytes(BufferedImage, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Return a 2D array of bytes representing the image.
getPixelBytes(BufferedImage, boolean, int, int, int, int) - Static method in class ome.codecs.gui.AWTImageTools
Return a 2D array of bytes representing the image.
getPixelBytes(WritableRaster, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Return a 2D array of bytes representing the image.
getPixelBytes(WritableRaster, boolean, int, int, int, int) - Static method in class ome.codecs.gui.AWTImageTools
Return a 2D array of bytes representing the image.
getPixels(BufferedImage) - Static method in class ome.codecs.gui.AWTImageTools
Gets the image's pixel data as arrays of primitives, one per channel.
getPixels(BufferedImage, int, int, int, int) - Static method in class ome.codecs.gui.AWTImageTools
Gets the image's pixel data as arrays of primitives, one per channel.
getPixels(WritableRaster) - Static method in class ome.codecs.gui.AWTImageTools
Gets the raster's pixel data as arrays of primitives, one per channel.
getPixels(WritableRaster, int, int, int, int) - Static method in class ome.codecs.gui.AWTImageTools
Gets the raster's pixel data as arrays of primitives, one per channel.
getRed(int) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
getRed(Object) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
getSample(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.HuffmanCodec
 
getSample(BitBuffer, CodecOptions) - Method in class ome.codecs.HuffmanCodec
Deprecated.
getScanline(int) - Method in class ome.codecs.JPEGTileDecoder
 
getShorts(BufferedImage) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of unsigned shorts, one per channel.
getShorts(WritableRaster) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of unsigned shorts, one per channel.
getShorts(WritableRaster, int, int, int, int) - Static method in class ome.codecs.gui.AWTImageTools
Extracts pixel data as arrays of unsigned shorts, one per channel.
getType() - Method in class ome.codecs.gui.TwoChannelColorSpace
 
getWidth() - Method in class ome.codecs.JPEGTileDecoder
 

H

H_263 - ome.codecs.CompressionType
 
HEADER - ome.codecs.JPEG2000BoxType
 
height - Variable in class ome.codecs.CodecOptions
Height, in pixels, of the image.
HuffmanCodec - Class in ome.codecs
This class implements Huffman decoding.
HuffmanCodec() - Constructor for class ome.codecs.HuffmanCodec
 
HuffmanCodecOptions - Class in ome.codecs
Options for compressing and decompressing Huffman data.
HuffmanCodecOptions() - Constructor for class ome.codecs.HuffmanCodecOptions
 

I

IMAGE_HEADER - ome.codecs.JPEG2000BoxType
 
initialize(String, int) - Method in class ome.codecs.JPEGTileDecoder
 
initialize(RandomAccessInputStream, int) - Method in class ome.codecs.JPEGTileDecoder
 
initialize(RandomAccessInputStream, int, int, int) - Method in class ome.codecs.JPEGTileDecoder
 
INTELLECTUAL_PROPERTY - ome.codecs.JPEG2000BoxType
 
interlaced - Variable in class ome.codecs.MJPBCodecOptions
Indicates whether or not channels are interlaced.
interleaved - Variable in class ome.codecs.CodecOptions
Indicates whether or not channels are interleaved.
isBitOnByteBoundary() - Method in class ome.codecs.BitBuffer
Deprecated.
Checks if the current position is on a byte boundary, that is the next bit in the byte array is the first bit in a byte.
isCompatibleRaster(Raster) - Method in class ome.codecs.gui.UnsignedIntColorModel
 
isCS_sRGB() - Method in class ome.codecs.gui.TwoChannelColorSpace
 

J

J2K - ome.codecs.CompressionType
 
J2K_LOSSY - ome.codecs.CompressionType
 
JAIIIOService - Interface in ome.codecs.services
Interface defining methods for reading data using JAI Image I/O.
JAIIIOServiceImpl - Class in ome.codecs.services
Implementation of JAIIIOService for reading and writing JPEG-2000 data.
JAIIIOServiceImpl() - Constructor for class ome.codecs.services.JAIIIOServiceImpl
Default constructor.
JPEG - ome.codecs.CompressionType
 
JPEG2000BoxType - Enum in ome.codecs
An enumeration of JPEG 2000 box types.
JPEG2000Codec - Class in ome.codecs
This class implements JPEG 2000 compression and decompression.
JPEG2000Codec() - Constructor for class ome.codecs.JPEG2000Codec
 
JPEG2000CodecOptions - Class in ome.codecs
Options for compressing and decompressing JPEG-2000 data.
JPEG2000CodecOptions() - Constructor for class ome.codecs.JPEG2000CodecOptions
Creates a new instance.
JPEG2000CodecOptions(CodecOptions) - Constructor for class ome.codecs.JPEG2000CodecOptions
Creates a new instance with options.
JPEG2000SegmentMarker - Enum in ome.codecs
An enumeration of JPEG 2000 segment markers.
JPEGCodec - Class in ome.codecs
This class implements JPEG compression and decompression.
JPEGCodec() - Constructor for class ome.codecs.JPEGCodec
 
JPEGTileDecoder - Class in ome.codecs
 
JPEGTileDecoder() - Constructor for class ome.codecs.JPEGTileDecoder
 

L

LABEL - ome.codecs.JPEG2000BoxType
 
littleEndian - Variable in class ome.codecs.CodecOptions
Indicates endianness of pixel data.
LOGGER - Static variable in class ome.codecs.BaseCodec
 
LOGGER - Static variable in class ome.codecs.JPEGTileDecoder
 
lossless - Variable in class ome.codecs.CodecOptions
Used with codecs allowing lossy and lossless compression.
LosslessJPEGCodec - Class in ome.codecs
Decompresses lossless JPEG images.
LosslessJPEGCodec() - Constructor for class ome.codecs.LosslessJPEGCodec
 
LZ4Codec - Class in ome.codecs
This class implements LZ4 decompression.
LZ4Codec() - Constructor for class ome.codecs.LZ4Codec
 
LZOCodec - Class in ome.codecs
This class implements LZO decompression.
LZOCodec() - Constructor for class ome.codecs.LZOCodec
 
LZW - ome.codecs.CompressionType
 
LZWCodec - Class in ome.codecs
This is an optimized LZW codec for use with TIFF files.
LZWCodec() - Constructor for class ome.codecs.LZWCodec
 

M

main(String[]) - Static method in class ome.codecs.BitBuffer
Deprecated.
Testing method.
main(String[]) - Static method in class ome.codecs.BitWriter
Deprecated.
Tests the BitWriter class.
makeColorModel(int, int) - Static method in class ome.codecs.gui.AWTImageTools
Gets a color model for the given number of color components.
makeColorSpace(int) - Static method in class ome.codecs.gui.AWTImageTools
Gets a color space for the given number of color components.
makeImage(byte[][], int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given byte data.
makeImage(byte[][], int, int, int, boolean, boolean, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given raw byte array, performing any necessary type conversions.
makeImage(byte[], int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given single-channel byte data.
makeImage(byte[], int, int, int, boolean, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given byte data.
makeImage(byte[], int, int, int, boolean, int, boolean, boolean, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given raw byte array, performing any necessary type conversions.
makeImage(double[][], int, int) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given double-precision floating point data.
makeImage(double[], int, int) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given single-channel double data.
makeImage(double[], int, int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given double data.
makeImage(float[][], int, int) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given single-precision floating point data.
makeImage(float[], int, int) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given single-channel float data.
makeImage(float[], int, int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given float data.
makeImage(int[][], int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given int data.
makeImage(int[], int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given single-channel int data.
makeImage(int[], int, int, int, boolean, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given int data.
makeImage(short[][], int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given short data.
makeImage(short[], int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given single-channel short data.
makeImage(short[], int, int, int, boolean, boolean) - Static method in class ome.codecs.gui.AWTImageTools
Creates an image from the given short data.
makeRGBImage(byte[][], int, int) - Static method in class ome.codecs.gui.AWTImageTools
 
makeRGBImage(byte[], int, int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools
 
maxBytes - Variable in class ome.codecs.CodecOptions
If compressing, this is the maximum number of raw bytes to compress.
MissingLibraryException - Exception in ome.codecs
MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
MissingLibraryException() - Constructor for exception ome.codecs.MissingLibraryException
 
MissingLibraryException(String) - Constructor for exception ome.codecs.MissingLibraryException
 
MissingLibraryException(String, Throwable) - Constructor for exception ome.codecs.MissingLibraryException
 
MissingLibraryException(Throwable) - Constructor for exception ome.codecs.MissingLibraryException
 
MJPBCodec - Class in ome.codecs
Methods for compressing and decompressing QuickTime Motion JPEG-B data.
MJPBCodec() - Constructor for class ome.codecs.MJPBCodec
 
MJPBCodecOptions - Class in ome.codecs
Options for compressing and decompressing MJPB data.
MJPBCodecOptions() - Constructor for class ome.codecs.MJPBCodecOptions
 
MPEG_4 - ome.codecs.CompressionType
 
MSRLECodec - Class in ome.codecs
Methods for compressing and decompressing data using Microsoft RLE.
MSRLECodec() - Constructor for class ome.codecs.MSRLECodec
 
MSVideoCodec - Class in ome.codecs
Methods for compressing and decompressing data using Microsoft Video 1.
MSVideoCodec() - Constructor for class ome.codecs.MSVideoCodec
 

N

NO_J2K_MSG - Static variable in class ome.codecs.services.JAIIIOServiceImpl
 
numDecompositionLevels - Variable in class ome.codecs.JPEG2000CodecOptions
The number of decomposition levels as would be provided to: J2KImageWriteParam.setNumDecompositionLevels(int) (WRITE).

O

OBS - Static variable in class ome.codecs.gui.AWTImageTools
ImageObserver for working with AWT images.
ome.codecs - package ome.codecs
Package containing Bio-Formats compression and decompression logic.
ome.codecs.gui - package ome.codecs.gui
 
ome.codecs.services - package ome.codecs.services
 

P

PackbitsCodec - Class in ome.codecs
This class implements packbits decompression.
PackbitsCodec() - Constructor for class ome.codecs.PackbitsCodec
 
PALETTE - ome.codecs.JPEG2000BoxType
 
PassthroughCodec - Class in ome.codecs
A codec which just returns the exact data it was given, performing no compression or decompression.
PassthroughCodec() - Constructor for class ome.codecs.PassthroughCodec
 
PLACEHOLDER - ome.codecs.JPEG2000BoxType
 
PLM - ome.codecs.JPEG2000SegmentMarker
 
PLT - ome.codecs.JPEG2000SegmentMarker
 
POC - ome.codecs.JPEG2000SegmentMarker
 
PPM - ome.codecs.JPEG2000SegmentMarker
 
PPT - ome.codecs.JPEG2000SegmentMarker
 
preprocess(RandomAccessInputStream) - Method in class ome.codecs.JPEGTileDecoder
Pre-process the stream to make sure that the image width and height are non-zero.
previousImage - Variable in class ome.codecs.CodecOptions
Pixels for preceding image (READ/WRITE).

Q

QCC - ome.codecs.JPEG2000SegmentMarker
 
QCD - ome.codecs.JPEG2000SegmentMarker
 
QTRLECodec - Class in ome.codecs
Methods for compressing and decompressing data using QuickTime RLE.
QTRLECodec() - Constructor for class ome.codecs.QTRLECodec
 
quality - Variable in class ome.codecs.CodecOptions
Compression quality level as it would be provided to: ImageWriteParam.compressionQuality (WRITE).

R

readImage(InputStream) - Method in interface ome.codecs.services.JAIIIOService
Reads an image using JAI Image I/O using the JPEG 2000 codec.
readImage(InputStream) - Method in class ome.codecs.services.JAIIIOServiceImpl
 
readImage(InputStream, JPEG2000CodecOptions) - Method in interface ome.codecs.services.JAIIIOService
Reads an image using JAI Image I/O using the JPEG 2000 codec.
readImage(InputStream, JPEG2000CodecOptions) - Method in class ome.codecs.services.JAIIIOServiceImpl
 
readRaster(InputStream) - Method in interface ome.codecs.services.JAIIIOService
Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.
readRaster(InputStream) - Method in class ome.codecs.services.JAIIIOServiceImpl
 
readRaster(InputStream, JPEG2000CodecOptions) - Method in interface ome.codecs.services.JAIIIOService
Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.
readRaster(InputStream, JPEG2000CodecOptions) - Method in class ome.codecs.services.JAIIIOServiceImpl
 
RESERVED_DELIMITER_MARKER_MAX - ome.codecs.JPEG2000SegmentMarker
 
RESERVED_DELIMITER_MARKER_MIN - ome.codecs.JPEG2000SegmentMarker
 
resolution - Variable in class ome.codecs.JPEG2000CodecOptions
The resolution level as would be provided to: J2KImageReadParam.setResolution(int) (READ).
RESOLUTION - ome.codecs.JPEG2000BoxType
 
RGN - ome.codecs.JPEG2000SegmentMarker
 
RPZACodec - Class in ome.codecs
Implements encoding and decoding methods for Apple RPZA.
RPZACodec() - Constructor for class ome.codecs.RPZACodec
 

S

setElem(int, int) - Method in class ome.codecs.gui.SignedByteBuffer
 
setElem(int, int) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
setElem(int, int, int) - Method in class ome.codecs.gui.SignedByteBuffer
 
setElem(int, int, int) - Method in class ome.codecs.gui.SignedShortBuffer
 
setElem(int, int, int) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
setElemDouble(int, double) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
setElemDouble(int, int, double) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
setElemFloat(int, float) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
setElemFloat(int, int, float) - Method in class ome.codecs.gui.UnsignedIntBuffer
 
SIGNATURE - ome.codecs.JPEG2000BoxType
 
SIGNATURE_WRONG_ENDIANNESS - ome.codecs.JPEG2000BoxType
 
signed - Variable in class ome.codecs.CodecOptions
Indicates whether or not the pixel data is signed.
SignedByteBuffer - Class in ome.codecs.gui
DataBuffer that stores signed bytes.
SignedByteBuffer(byte[][], int) - Constructor for class ome.codecs.gui.SignedByteBuffer
Construct a new buffer of signed bytes using the given 2D byte array.
SignedByteBuffer(byte[], int) - Constructor for class ome.codecs.gui.SignedByteBuffer
Construct a new buffer of signed bytes using the given byte array.
SignedShortBuffer - Class in ome.codecs.gui
DataBuffer that stores signed shorts.
SignedShortBuffer(int) - Constructor for class ome.codecs.gui.SignedShortBuffer
 
SignedShortBuffer(int, int) - Constructor for class ome.codecs.gui.SignedShortBuffer
 
SignedShortBuffer(short[][], int) - Constructor for class ome.codecs.gui.SignedShortBuffer
 
SignedShortBuffer(short[][], int, int[]) - Constructor for class ome.codecs.gui.SignedShortBuffer
 
SignedShortBuffer(short[], int) - Constructor for class ome.codecs.gui.SignedShortBuffer
 
SignedShortBuffer(short[], int, int) - Constructor for class ome.codecs.gui.SignedShortBuffer
 
SIZ - ome.codecs.JPEG2000SegmentMarker
 
size() - Method in class ome.codecs.ByteVector
 
skipBits(long) - Method in class ome.codecs.BitBuffer
Deprecated.
Skips a number of bits in the BitBuffer.
SOC - ome.codecs.JPEG2000SegmentMarker
 
SOC_WRONG_ENDIANNESS - ome.codecs.JPEG2000SegmentMarker
 
SOD - ome.codecs.JPEG2000SegmentMarker
 
SOP - ome.codecs.JPEG2000SegmentMarker
 
SORENSON - ome.codecs.CompressionType
 
SORENSON_3 - ome.codecs.CompressionType
 
SOT - ome.codecs.JPEG2000SegmentMarker
 

T

table - Variable in class ome.codecs.HuffmanCodecOptions
 
test() - Method in class ome.codecs.BaseCodec
Main testing method default implementation.
tileGridXOffset - Variable in class ome.codecs.CodecOptions
Horizontal offset of the tile grid as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileGridYOffset - Variable in class ome.codecs.CodecOptions
Vertical offset of the tile grid as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileHeight - Variable in class ome.codecs.CodecOptions
Tile height as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileWidth - Variable in class ome.codecs.CodecOptions
Tile width as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
TLM - ome.codecs.JPEG2000SegmentMarker
 
toByteArray() - Method in class ome.codecs.BitWriter
Deprecated.
Gets an array containing all bits written thus far.
toByteArray() - Method in class ome.codecs.ByteVector
 
toCIEXYZ(float[]) - Method in class ome.codecs.gui.TwoChannelColorSpace
 
toRGB(float[]) - Method in class ome.codecs.gui.TwoChannelColorSpace
 
TwoChannelColorSpace - Class in ome.codecs.gui
ColorSpace for 2-channel images.
TwoChannelColorSpace(int, int) - Constructor for class ome.codecs.gui.TwoChannelColorSpace
 

U

UNCOMPRESSED - ome.codecs.CompressionType
 
UnsignedIntBuffer - Class in ome.codecs.gui
DataBuffer that stores unsigned ints.
UnsignedIntBuffer(int[][], int) - Constructor for class ome.codecs.gui.UnsignedIntBuffer
Construct a new buffer of unsigned ints using the given 2D int array.
UnsignedIntBuffer(int[], int) - Constructor for class ome.codecs.gui.UnsignedIntBuffer
Construct a new buffer of unsigned ints using the given int array.
UnsignedIntColorModel - Class in ome.codecs.gui
ColorModel that handles unsigned 32 bit data.
UnsignedIntColorModel(int, int, int) - Constructor for class ome.codecs.gui.UnsignedIntColorModel
 
UnsupportedCompressionException - Exception in ome.codecs
UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.
UnsupportedCompressionException() - Constructor for exception ome.codecs.UnsupportedCompressionException
 
UnsupportedCompressionException(String) - Constructor for exception ome.codecs.UnsupportedCompressionException
 
UnsupportedCompressionException(String, Throwable) - Constructor for exception ome.codecs.UnsupportedCompressionException
 
UnsupportedCompressionException(Throwable) - Constructor for exception ome.codecs.UnsupportedCompressionException
 
URL - ome.codecs.JPEG2000BoxType
 
UUID - ome.codecs.JPEG2000BoxType
 
UUID_INFO - ome.codecs.JPEG2000BoxType
 
UUID_LIST - ome.codecs.JPEG2000BoxType
 

V

valueOf(String) - Static method in enum ome.codecs.CompressionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.codecs.JPEG2000BoxType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.codecs.JPEG2000SegmentMarker
Returns the enum constant of this type with the specified name.
values() - Static method in enum ome.codecs.CompressionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.codecs.JPEG2000BoxType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.codecs.JPEG2000SegmentMarker
Returns an array containing the constants of this enum type, in the order they are declared.

W

width - Variable in class ome.codecs.CodecOptions
Width, in pixels, of the image.
write(int, int) - Method in class ome.codecs.BitWriter
Deprecated.
Writes the given value using the given number of bits.
write(String) - Method in class ome.codecs.BitWriter
Deprecated.
Writes the bits represented by a bit string to the buffer.
writeBox - Variable in class ome.codecs.JPEG2000CodecOptions
Whether or not to write a boxed stream, i.e.
writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) - Method in interface ome.codecs.services.JAIIIOService
Writes an image using JAI Image I/O using the JPEG 2000 codec.
writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) - Method in class ome.codecs.services.JAIIIOServiceImpl
 

X

XML - ome.codecs.JPEG2000BoxType
 

Y

ycbcr - Variable in class ome.codecs.CodecOptions
Whether or not the decompressed data will be stored as YCbCr.

Z

ZLIB - ome.codecs.CompressionType
 
ZlibCodec - Class in ome.codecs
This class implements ZLIB decompression.
ZlibCodec() - Constructor for class ome.codecs.ZlibCodec
 
ZstdCodec - Class in ome.codecs
This class implements Zstandard decompression.
ZstdCodec() - Constructor for class ome.codecs.ZstdCodec
 
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