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	Description
protected CodecOptions	FormatWriter.options	The options if required.

Methods in loci.formats that return CodecOptions

Modifier and Type	Method	Description
CodecOptions	FormatWriter.getCodecOptions()
default CodecOptions	ICompressedTileWriter.getCodecOptions()
CodecOptions	ImageWriter.getCodecOptions()
CodecOptions	WriterWrapper.getCodecOptions()
CodecOptions	ChannelFiller.getTileCodecOptions(int no, int x, int y)
CodecOptions	ChannelMerger.getTileCodecOptions(int no, int x, int y)
CodecOptions	ChannelSeparator.getTileCodecOptions(int no, int x, int y)
CodecOptions	DimensionSwapper.getTileCodecOptions(int no, int x, int y)
CodecOptions	FileStitcher.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.
CodecOptions	ImageReader.getTileCodecOptions(int no, int x, int y)
CodecOptions	ReaderWrapper.getTileCodecOptions(int no, int x, int y)
CodecOptions	TileStitcher.getTileCodecOptions(int no, int x, int y)

Methods in loci.formats with parameters of type CodecOptions

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

Uses of CodecOptions in loci.formats.codec

Subclasses of CodecOptions in loci.formats.codec

Modifier and Type	Class	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	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	Description
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[]	Codec.compress(byte[] data, CodecOptions options)	Compresses a block of data.
byte[]	JPEGXRCodec.compress(byte[] data, CodecOptions options)
byte[]	NikonCodec.compress(byte[] data, CodecOptions options)
byte[]	TargaRLECodec.compress(byte[] data, CodecOptions options)
byte[]	WrappedCodec.compress(byte[][] data, CodecOptions options)
byte[]	WrappedCodec.compress(byte[] data, CodecOptions options)
private static void	WrappedCodec.copyOptions(CodecOptions src, ome.codecs.CodecOptions dest)
byte[]	BaseCodec.decompress(byte[][] data, CodecOptions options)	2D data block decoding default implementation.
byte[]	BaseCodec.decompress(byte[] data, CodecOptions options)
abstract byte[]	BaseCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)
byte[]	Codec.decompress(byte[][] data, CodecOptions options)	Decompresses a block of data.
byte[]	Codec.decompress(byte[] data, CodecOptions options)	Decompresses a block of data.
byte[]	Codec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)	Decompresses data from the given RandomAccessInputStream.
byte[]	JPEGXRCodec.decompress(byte[] buf, CodecOptions options)	The CodecOptions parameter should have the following fields set: maxBytes interleaved bitsPerSample littleEndian width height
byte[]	JPEGXRCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)
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[]	TargaRLECodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)	The CodecOptions parameter should have the following fields set: maxBytes bitsPerSample
byte[]	WrappedCodec.decompress(byte[][] data, CodecOptions options)
byte[]	WrappedCodec.decompress(byte[] data, CodecOptions options)
byte[]	WrappedCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)
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(loci.common.RandomAccessInputStream bb, CodecOptions options)
int	HuffmanCodec.getSample(BitBuffer bb, CodecOptions options)	Deprecated.

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

Modifier	Constructor	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	Description
private CodecOptions	TissueFAXSReader.getCodecOptions(TissueFAXSReader.ScanRegion region)
CodecOptions	DicomReader.getTileCodecOptions(int no, int x, int y)
private CodecOptions	DicomReader.getTileCodecOptions(DicomTile tile)	Get a CodecOptions that can be used to decompress the given tile.
CodecOptions	NDPIReader.getTileCodecOptions(int no, int x, int y)
CodecOptions	SVSReader.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	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	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	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	TiffParser.setCodecOptions(CodecOptions codecOptions)	Sets the codec options to be used when decompressing pixel data.
void	TiffSaver.setCodecOptions(CodecOptions options)	Sets the codec options.