A B C D F G H I J L M N O P Q R S T U V W Y Z

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

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.

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(int) - Constructor for class ome.codecs.ByteVector

ByteVector(byte[]) - Constructor for class ome.codecs.ByteVector

C

channels - Variable in class ome.codecs.CodecOptions

Number of channels.

clear() - Method in class ome.codecs.ByteVector

close() - Method in class ome.codecs.JPEGTileDecoder

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).

compress(byte[], CodecOptions) - Method in class ome.codecs.Base64Codec

compress(byte[][], CodecOptions) - Method in class ome.codecs.BaseCodec

2D data block encoding default implementation.

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(byte[], CodecOptions) - Method in interface ome.codecs.Codec

Compresses a block of data.

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(ByteBuffer, 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

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.

createCompatibleWritableRaster(int, int) - Method in class ome.codecs.gui.UnsignedIntColorModel

CS_2C - Static variable in class ome.codecs.gui.TwoChannelColorSpace

D

decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.Base64Codec

decompress(byte[]) - Method in class ome.codecs.BaseCodec

decompress(byte[][]) - Method in class ome.codecs.BaseCodec

decompress(byte[], CodecOptions) - Method in class ome.codecs.BaseCodec

decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.BaseCodec

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[][], CodecOptions) - Method in interface ome.codecs.Codec

Decompresses a block of data.

decompress(byte[]) - Method in interface ome.codecs.Codec

Decompresses a block of data.

decompress(byte[][]) - Method in interface ome.codecs.Codec

Decompresses a block of data.

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(byte[], 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(byte[]) - Method in class ome.codecs.LZ4Codec

decompress(byte[], CodecOptions) - Method in class ome.codecs.LZ4Codec

decompress(byte[], int, int, int) - Method in class ome.codecs.LZ4Codec

Decompresses a block of data of specified length from an initial offset.

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(byte[], CodecOptions) - Method in class ome.codecs.PassthroughCodec

decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.PassthroughCodec

decompress(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.QTRLECodec

decompress(byte[], CodecOptions) - Method in class ome.codecs.QTRLECodec

The CodecOptions parameter should have the following fields set: width height bitsPerSample previousImage

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

decompress(byte[]) - Method in class ome.codecs.ZstdCodec

decompress(byte[], CodecOptions) - Method in class ome.codecs.ZstdCodec

decompress(byte[], int, int) - Method in class ome.codecs.ZstdCodec

Decompresses a block of data of specified length from an initial offset.

disableChromaSubsampling - Variable in class ome.codecs.CodecOptions

Whether or not use chroma subsampling.

F

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(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.

getBytes(BufferedImage, boolean) - Static method in class ome.codecs.gui.AWTImageTools

Get the bytes from an image, merging the channels as necessary.

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(int) - Method in class ome.codecs.gui.SignedByteBuffer

getData() - Method in class ome.codecs.gui.SignedShortBuffer

getData(int) - Method in class ome.codecs.gui.SignedShortBuffer

getData() - Method in class ome.codecs.gui.UnsignedIntBuffer

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, int) - Method in class ome.codecs.gui.SignedByteBuffer

getElem(int, int) - Method in class ome.codecs.gui.SignedShortBuffer

getElem(int) - Method in class ome.codecs.gui.UnsignedIntBuffer

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(int) - Method in class ome.codecs.gui.TwoChannelColorSpace

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.

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(WritableRaster, 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, 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(BitBuffer, CodecOptions) - Method in class ome.codecs.HuffmanCodec

Deprecated.

getSample(RandomAccessInputStream, CodecOptions) - Method in class ome.codecs.HuffmanCodec

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

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

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

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

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.

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

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

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 single-channel byte 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(int[], int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools

Creates an image from the given single-channel int data.

makeImage(float[], int, int) - Static method in class ome.codecs.gui.AWTImageTools

Creates an image from the given single-channel float data.

makeImage(double[], int, int) - Static method in class ome.codecs.gui.AWTImageTools

Creates an image from the given single-channel double 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(short[], int, int, int, boolean, boolean) - Static method in class ome.codecs.gui.AWTImageTools

Creates an image from the given short 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(float[], int, int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools

Creates an image from the given float data.

makeImage(double[], int, int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools

Creates an image from the given double data.

makeImage(byte[][], int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools

Creates an image from the given byte data.

makeImage(short[][], int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools

Creates an image from the given short data.

makeImage(int[][], int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools

Creates an image from the given int 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(double[][], int, int) - Static method in class ome.codecs.gui.AWTImageTools

Creates an image from the given double-precision floating point 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(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.

makeRGBImage(byte[], int, int, int, boolean) - Static method in class ome.codecs.gui.AWTImageTools

makeRGBImage(byte[][], int, int) - 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

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

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

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

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, JPEG2000CodecOptions) - Method in interface ome.codecs.services.JAIIIOService

Reads an image using JAI Image I/O using the JPEG 2000 codec.

readImage(InputStream) - 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

readImage(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) - 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

readRaster(InputStream) - Method in class ome.codecs.services.JAIIIOServiceImpl

resolution - Variable in class ome.codecs.JPEG2000CodecOptions

The resolution level as would be provided to: J2KImageReadParam.setResolution(int) (READ).

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, int) - Method in class ome.codecs.gui.SignedByteBuffer

setElem(int, int, int) - Method in class ome.codecs.gui.SignedShortBuffer

setElem(int, int) - Method in class ome.codecs.gui.UnsignedIntBuffer

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

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 byte array.

SignedByteBuffer(byte[][], int) - Constructor for class ome.codecs.gui.SignedByteBuffer

Construct a new buffer of signed bytes using the given 2D 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

size() - Method in class ome.codecs.ByteVector

skipBits(long) - Method in class ome.codecs.BitBuffer

Deprecated.

Skips a number of bits in the BitBuffer.

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).

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

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 int array.

UnsignedIntBuffer(int[][], int) - Constructor for class ome.codecs.gui.UnsignedIntBuffer

Construct a new buffer of unsigned ints using the given 2D 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

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

Y

ycbcr - Variable in class ome.codecs.CodecOptions

Whether or not the decompressed data will be stored as YCbCr.

Z

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

A B C D F G H I J L M N O P Q R S T U V W Y Z