loci.formats.codec

Class LZWCodec

java.lang.Object

loci.formats.codec.BaseCodec

loci.formats.codec.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

Modifier and Type	Field and Description
private static int	CLEAR_CODE
private static int[]	COMPR_MASKS Masks for writing bits in compressor.
private static int[]	DECOMPR_MASKS Masks for reading bits in decompressor.
private static int	EOI_CODE
private static int	FIRST_CODE
private static int	HASH_SIZE Size of hash table.
private static int	HASH_STEP Rehashing step.

Fields inherited from class loci.formats.codec.BaseCodec

LOGGER

Constructor Summary

Constructors

Constructor and Description
LZWCodec()

Method Summary

Methods

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

Methods inherited from class loci.formats.codec.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

Field Detail

HASH_SIZE

private static final int HASH_SIZE

Size of hash table. Must be greater 3837 (the number of possible codes). Bigger size reduces number of rehashing steps -- at expence of initialization time.

See Also:

Constant Field Values

HASH_STEP

private static final int HASH_STEP

Rehashing step. HASH_SIZE and HASH_STEP shoulg be coprime.

See Also:

Constant Field Values

CLEAR_CODE

private static final int CLEAR_CODE

See Also:

Constant Field Values

EOI_CODE

private static final int EOI_CODE

See Also:

Constant Field Values

FIRST_CODE

private static final int FIRST_CODE

See Also:

Constant Field Values

COMPR_MASKS

private static final int[] COMPR_MASKS

Masks for writing bits in compressor.

DECOMPR_MASKS

private static final int[] DECOMPR_MASKS

Masks for reading bits in decompressor.

Constructor Detail

LZWCodec

public LZWCodec()

Method Detail

compress

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

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:

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

decompress

public byte[] decompress(RandomAccessInputStream in,
                CodecOptions options)
                  throws FormatException,
                         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:

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

IOException

See Also:

Codec.decompress(RandomAccessInputStream, CodecOptions)