How to use loci.formats.codec

/** Creates a new instance. */
public JPEG2000Writer() {
 super("JPEG-2000", "jp2");
 compressionTypes = new String[] {CompressionType.J2K_LOSSY.getCompression(), 
   CompressionType.J2K.getCompression()};
 //The default codec options
 options = JPEG2000CodecOptions.getDefaultOptions();
}

/** Return JPEG2000CodecOptions with reasonable default values. */
public static JPEG2000CodecOptions getDefaultOptions() {
 CodecOptions options = CodecOptions.getDefaultOptions();
 return getDefaultOptions(options);
}

/** Return CodecOptions with reasonable default values. */
public static CodecOptions getDefaultOptions() {
 CodecOptions options = new CodecOptions();
 options.littleEndian = false;
 options.interleaved = false;
 options.lossless = true;
 options.ycbcr = false;
 return options;
}

private Codec createCodec(boolean isJPEG) {
 return isJPEG ? new JPEG2000Codec() : new ZlibCodec();
}

@Deprecated
public int getSample(BitBuffer bb, CodecOptions options)
 throws FormatException
{
 try {
  return ((ome.codecs.HuffmanCodec) this.codec).getSample(bb.getWrapped(), getOptions(options));
 }
 catch(ome.codecs.CodecException e) {
  throw WrappedCodec.unwrapCodecException(e);
 }
}

public OMEXMLWriter() {
 super("OME-XML", new String[] {"ome", "ome.xml"});
 compressionTypes =
  new String[] {CompressionType.UNCOMPRESSED.getCompression(),
   CompressionType.ZLIB.getCompression()};
 compression = compressionTypes[0];
}

 public int getSample(RandomAccessInputStream bb, CodecOptions options)
  throws FormatException
 {
  try {
   return ((ome.codecs.HuffmanCodec) this.codec).getSample(bb, getOptions(options));
  }
  catch(ome.codecs.CodecException e) {
   throw WrappedCodec.unwrapCodecException(e);
  }
 }
}

@Override
public byte[] decompress(byte[] data) throws FormatException {
 return decompress(data, null);
}

/**
 * Return JPEG2000CodecOptions using the given CodecOptions as the default.
 * @param options The specified options.
 */
public static JPEG2000CodecOptions getDefaultOptions(CodecOptions options) {
 JPEG2000CodecOptions j2kOptions = new JPEG2000CodecOptions(options);
 j2kOptions.quality = j2kOptions.lossless ? Double.MAX_VALUE : 10;
 j2kOptions.codeBlockSize = new int[] {64, 64};
 j2kOptions.writeBox = true;
 return j2kOptions;
}

/** Creates a new instance. */
public JPEG2000Writer() {
 super("JPEG-2000", "jp2");
 compressionTypes = new String[] {CompressionType.J2K_LOSSY.getCompression(), 
   CompressionType.J2K.getCompression()};
 //The default codec options
 options = JPEG2000CodecOptions.getDefaultOptions();
}

/** Return JPEG2000CodecOptions with reasonable default values. */
public static JPEG2000CodecOptions getDefaultOptions() {
 CodecOptions options = CodecOptions.getDefaultOptions();
 return getDefaultOptions(options);
}

private Codec createCodec(boolean isJPEG) {
 return isJPEG ? new JPEG2000Codec() : new ZlibCodec();
}

/** Return CodecOptions with reasonable default values. */
public static CodecOptions getDefaultOptions() {
 CodecOptions options = new CodecOptions();
 options.littleEndian = false;
 options.interleaved = false;
 options.lossless = true;
 options.ycbcr = false;
 return options;
}

@Deprecated
public int getSample(BitBuffer bb, CodecOptions options)
 throws FormatException
{
 try {
  return ((ome.codecs.HuffmanCodec) this.codec).getSample(bb.getWrapped(), getOptions(options));
 }
 catch(ome.codecs.CodecException e) {
  throw WrappedCodec.unwrapCodecException(e);
 }
}

public OMEXMLWriter() {
 super("OME-XML", new String[] {"ome", "ome.xml"});
 compressionTypes =
  new String[] {CompressionType.UNCOMPRESSED.getCompression(),
   CompressionType.ZLIB.getCompression()};
 compression = compressionTypes[0];
}

 public int getSample(RandomAccessInputStream bb, CodecOptions options)
  throws FormatException
 {
  try {
   return ((ome.codecs.HuffmanCodec) this.codec).getSample(bb, getOptions(options));
  }
  catch(ome.codecs.CodecException e) {
   throw WrappedCodec.unwrapCodecException(e);
  }
 }
}

@Override
public byte[] decompress(byte[][] data) throws FormatException {
 return decompress(data, null);
}

/**
 * Return JPEG2000CodecOptions using the given CodecOptions as the default.
 * @param options The specified options.
 */
public static JPEG2000CodecOptions getDefaultOptions(CodecOptions options) {
 JPEG2000CodecOptions j2kOptions = new JPEG2000CodecOptions(options);
 j2kOptions.quality = j2kOptions.lossless ? Double.MAX_VALUE : 10;
 j2kOptions.codeBlockSize = new int[] {64, 64};
 j2kOptions.writeBox = true;
 return j2kOptions;
}

@Override
public byte[] decompress(byte[][] data) throws FormatException {
 return decompress(data, null);
}

@Override
public byte[] decompress(byte[] data) throws FormatException {
 return decompress(data, null);
}