ome.codecs

Class LZWCodec

java.lang.Object

ome.codecs.BaseCodec

ome.codecs.LZWCodec

All Implemented Interfaces:

Codec

public class LZWCodec
extends BaseCodec

This is an optimized LZW codec for use with TIFF files. Most of the code is inlined, and specifics of TIFF usage of LZW (known size of decompressor output; possible lengths of LZW codes; specified values for CLEAR and END_OF_INFORMATION codes) are taken in account.

Estimating the worst-case size of compressor output:

• The worst case means that there is no compression at all, and every input byte generates code to output.
• This means that the LZW table will be full (and reset) after reading each portion of 4096-256-2-1=3837 bytes of input (first 256 codes are preallocated, 2 codes are used for CLEAR and END_OF_IFORMATION, 1 code is lost due to original bug in TIFF library that now is a feature).
• Each full portion of 3837 byte will produce in output:
  • 9 bits for CLEAR code;
  • 9*253 + 10*512 + 11*1024 + 12*2048 = 43237 bits for character codes.
• Let n=3837, m=(number of bytes in the last incomplete portion), N=(number of bytes in compressed complete portion with CLEAR code), M=(number of bytes in compressed last incomplete portion). We have inequalities:
  • N <= 1.41 * n
  • M <= 1.41 * m
  • The last incomplete portion should also include CLEAR and END_OF_INFORMATION codes; they occupy less than 3 bytes.
  Thus, we can claim than the number of bytes in compressed output never exceeds 1.41*(number of input bytes)+3.

Author:

Mikhail Kovtun mikhail.kovtun at duke.edu

Field Summary

Fields inherited from class ome.codecs.BaseCodec

LOGGER

Constructor Summary

Constructors

Constructor and Description
LZWCodec()

Method Summary

Modifier and Type	Method and Description
byte[]	compress(byte[] input, CodecOptions options) Compresses a block of data.
ByteBuffer	compress(ByteBuffer output, byte[] input, CodecOptions options) Compress using ByteBuffers.
byte[]	decompress(loci.common.RandomAccessInputStream in, CodecOptions options) The CodecOptions parameter should have the following fields set: maxBytes

Methods inherited from class ome.codecs.BaseCodec

compress, decompress, decompress, decompress, decompress, test

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

LZWCodec

public LZWCodec()

Method Detail

compress

public byte[] compress(byte[] input,
                       CodecOptions options)
                throws CodecException

Description copied from interface: Codec

Compresses a block of data.

Parameters:

input - The data to be compressed.

options - Options to be used during compression, if appropriate.

Returns:

The compressed data.

Throws:

CodecException - If input is not a compressed data block of the appropriate type.

compress

public ByteBuffer compress(ByteBuffer output,
                           byte[] input,
                           CodecOptions options)
                    throws CodecException

Description copied from class: BaseCodec

Compress using ByteBuffers. This implementation just calls the byte array based compression method and wraps the result properly.

Specified by:

compress in interface Codec

Overrides:

compress in class BaseCodec

Parameters:

output - A preallocated ByteBuffer that may be used for the compressed data. This may be null to force the compressor to allocate a fresh buffer.

input - The data to be compressed.

options - Options to be used during compression, if appropriate.

Returns:

The ByteBuffer holding the compressed data.

Throws:

CodecException - If input cannot be processed.

See Also:

Codec.compress(ByteBuffer, byte[], CodecOptions)

decompress

public byte[] decompress(loci.common.RandomAccessInputStream in,
                         CodecOptions options)
                  throws CodecException,
                         IOException

The CodecOptions parameter should have the following fields set: maxBytes

Specified by:

decompress in interface Codec

Specified by:

decompress in class BaseCodec

Parameters:

in - The stream from which to read compressed data.

options - Options to be used during decompression.

Returns:

The decompressed data.

Throws:

CodecException - If data is not valid compressed data for this decompressor.

IOException

See Also:

Codec.decompress(RandomAccessInputStream, CodecOptions)