Uses of Class
loci.formats.codec.CodecOptions

Packages that use CodecOptions

Package	Description
loci.formats	Bio-Formats: a library for reading and writing popular microscopy file formats.
loci.formats.codec
loci.formats.in	Package containing Bio-Formats file format readers.
loci.formats.tiff	Package containing Bio-Formats TIFF code of general utility.

Uses of CodecOptions in loci.formats

Fields in loci.formats declared as CodecOptions

Modifier and Type	Field and Description
protected CodecOptions	FormatWriter.options The options if required.

Methods in loci.formats that return CodecOptions

Modifier and Type	Method and Description
CodecOptions	WriterWrapper.getCodecOptions()
CodecOptions	ImageWriter.getCodecOptions()
default CodecOptions	ICompressedTileWriter.getCodecOptions()
CodecOptions	FormatWriter.getCodecOptions()
CodecOptions	TileStitcher.getTileCodecOptions(int no, int x, int y)
CodecOptions	FileStitcher.getTileCodecOptions(int no, int x, int y)
CodecOptions	DimensionSwapper.getTileCodecOptions(int no, int x, int y)
CodecOptions	ChannelSeparator.getTileCodecOptions(int no, int x, int y)
CodecOptions	ChannelMerger.getTileCodecOptions(int no, int x, int y)
CodecOptions	ChannelFiller.getTileCodecOptions(int no, int x, int y)
CodecOptions	ReaderWrapper.getTileCodecOptions(int no, int x, int y)
CodecOptions	ImageReader.getTileCodecOptions(int no, int x, int y)
default CodecOptions	ICompressedTileReader.getTileCodecOptions(int no, int x, int y) Retrieve codec options that can be used to decompressed the specified tile.

Methods in loci.formats with parameters of type CodecOptions

Modifier and Type	Method and Description
void	WriterWrapper.setCodecOptions(CodecOptions options)
void	ImageWriter.setCodecOptions(CodecOptions options)
void	IFormatWriter.setCodecOptions(CodecOptions options) Sets the codec options.
void	FormatWriter.setCodecOptions(CodecOptions options)

Uses of CodecOptions in loci.formats.codec

Subclasses of CodecOptions in loci.formats.codec

Modifier and Type	Class and Description
class	HuffmanCodecOptions Options for compressing and decompressing Huffman data.
class	JPEG2000CodecOptions Options for compressing and decompressing JPEG-2000 data.
class	MJPBCodecOptions Options for compressing and decompressing MJPB data.
class	NikonCodecOptions Options for compressing and decompressing Nikon NEF data.

Methods in loci.formats.codec that return CodecOptions

Modifier and Type	Method and Description
static CodecOptions	CodecOptions.getDefaultOptions() Return CodecOptions with reasonable default values.

Methods in loci.formats.codec with parameters of type CodecOptions

Modifier and Type	Method and Description
byte[]	WrappedCodec.compress(byte[][] data, CodecOptions options)
byte[]	BaseCodec.compress(byte[][] data, CodecOptions options) 2D data block encoding default implementation.
byte[]	Codec.compress(byte[][] data, CodecOptions options) Compresses a block of data.
byte[]	WrappedCodec.compress(byte[] data, CodecOptions options)
byte[]	TargaRLECodec.compress(byte[] data, CodecOptions options)
byte[]	NikonCodec.compress(byte[] data, CodecOptions options)
byte[]	JPEGXRCodec.compress(byte[] data, CodecOptions options)
byte[]	Codec.compress(byte[] data, CodecOptions options) Compresses a block of data.
private static void	WrappedCodec.copyOptions(CodecOptions src, ome.codecs.CodecOptions dest)
byte[]	WrappedCodec.decompress(byte[][] data, CodecOptions options)
byte[]	BaseCodec.decompress(byte[][] data, CodecOptions options) 2D data block decoding default implementation.
byte[]	Codec.decompress(byte[][] data, CodecOptions options) Decompresses a block of data.
byte[]	WrappedCodec.decompress(byte[] data, CodecOptions options)
byte[]	JPEGXRCodec.decompress(byte[] buf, CodecOptions options) The CodecOptions parameter should have the following fields set: maxBytes interleaved bitsPerSample littleEndian width height
byte[]	BaseCodec.decompress(byte[] data, CodecOptions options)
byte[]	Codec.decompress(byte[] data, CodecOptions options) Decompresses a block of data.
byte[]	WrappedCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)
byte[]	TargaRLECodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options) The CodecOptions parameter should have the following fields set: maxBytes bitsPerSample
byte[]	NikonCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options) The CodecOptions parameter must be an instance of NikonCodecOptions, and should have the following fields set: lossless vPredictor curve split bitsPerSample maxBytes width height
byte[]	JPEGXRCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)
abstract byte[]	BaseCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)
byte[]	Codec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options) Decompresses data from the given RandomAccessInputStream.
static JPEG2000CodecOptions	JPEG2000CodecOptions.getDefaultOptions(CodecOptions options) Return JPEG2000CodecOptions using the given CodecOptions as the default.
protected static ome.codecs.CodecOptions	WrappedCodec.getOptions(CodecOptions options)
int	HuffmanCodec.getSample(BitBuffer bb, CodecOptions options) Deprecated.
int	HuffmanCodec.getSample(loci.common.RandomAccessInputStream bb, CodecOptions options)

Constructors in loci.formats.codec with parameters of type CodecOptions

Constructor and Description
CodecOptions(CodecOptions options) Construct a new CodecOptions using the given CodecOptions.
JPEG2000CodecOptions(CodecOptions options) Creates a new instance with options.

Uses of CodecOptions in loci.formats.in

Methods in loci.formats.in that return CodecOptions

Modifier and Type	Method and Description
private CodecOptions	DicomReader.getTileCodecOptions(DicomTile tile) Get a CodecOptions that can be used to decompress the given tile.
CodecOptions	SVSReader.getTileCodecOptions(int no, int x, int y)
CodecOptions	NDPIReader.getTileCodecOptions(int no, int x, int y)
CodecOptions	DicomReader.getTileCodecOptions(int no, int x, int y)

Uses of CodecOptions in loci.formats.tiff

Fields in loci.formats.tiff declared as CodecOptions

Modifier and Type	Field and Description
private CodecOptions	TiffParser.codecOptions Codec options to be used when decoding compressed pixel data.
private CodecOptions	TiffSaver.options The codec options if set.

Methods in loci.formats.tiff that return CodecOptions

Modifier and Type	Method and Description
CodecOptions	TiffParser.getCodecOptions() Retrieves the current set of codec options being used to decompress pixel data.
CodecOptions	TiffCompression.getCompressionCodecOptions(IFD ifd) Creates a set of codec options for compression.
CodecOptions	TiffCompression.getCompressionCodecOptions(IFD ifd, CodecOptions opt) Creates a set of codec options for compression.

Methods in loci.formats.tiff with parameters of type CodecOptions

Modifier and Type	Method and Description
byte[]	TiffCompression.compress(byte[] input, CodecOptions options) Encodes a strip of data.
byte[]	TiffCompression.decompress(byte[] input, CodecOptions options) Decodes a strip of data.
CodecOptions	TiffCompression.getCompressionCodecOptions(IFD ifd, CodecOptions opt) Creates a set of codec options for compression.
void	TiffSaver.setCodecOptions(CodecOptions options) Sets the codec options.
void	TiffParser.setCodecOptions(CodecOptions codecOptions) Sets the codec options to be used when decompressing pixel data.