## 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` | TissueFAXSReader.`getCodecOptions(TissueFAXSReader.ScanRegion region)`
    `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.

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