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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
- 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
- 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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