//
// HuffmanCodec.java
//
/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.formats.codec;
import java.io.IOException;
import java.util.HashMap;
import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.UnsupportedCompressionException;
/**
* This class implements Huffman decoding.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/codec/HuffmanCodec.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/codec/HuffmanCodec.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class HuffmanCodec extends BaseCodec {
// -- Constants --
private static final int LEAVES_OFFSET = 16;
// -- Fields --
private int leafCounter;
private HashMap<short[], Decoder> cachedDecoders =
new HashMap<short[], Decoder>();
// -- Codec API methods --
/* @see Codec#compress(byte[], CodecOptions) */
public byte[] compress(byte[] data, CodecOptions options)
throws FormatException
{
throw new UnsupportedCompressionException(
"Huffman encoding not currently supported");
}
/**
* The CodecOptions parameter must be an instance of
* {@link HuffmanCodecOptions}, and should have the following fields set:
* {@link HuffmanCodecOptions#table table}
* {@link CodecOptions#bitsPerSample bitsPerSample}
* {@link CodecOptions#maxBytes maxBytes}
*
* @see Codec#decompress(RandomAccessInputStream, CodecOptions)
*/
public byte[] decompress(RandomAccessInputStream in, CodecOptions options)
throws FormatException, IOException
{
if (in == null)
throw new IllegalArgumentException("No data to decompress.");
if (options == null || !(options instanceof HuffmanCodecOptions)) {
throw new FormatException("Options must be an instance of " +
"loci.formats.codec.HuffmanCodecOptions.");
}
HuffmanCodecOptions huffman = (HuffmanCodecOptions) options;
byte[] pix = new byte[huffman.maxBytes];
in.read(pix);
BitBuffer bb = new BitBuffer(pix);
int nSamples = (huffman.maxBytes * 8) / huffman.bitsPerSample;
int bytesPerSample = huffman.bitsPerSample / 8;
if ((huffman.bitsPerSample % 8) != 0) bytesPerSample++;
BitWriter out = new BitWriter();
for (int i=0; i<nSamples; i++) {
int sample = getSample(bb, options);
out.write(sample, bytesPerSample * 8);
}
return out.toByteArray();
}
// -- HuffmanCodec API methods --
public int getSample(BitBuffer bb, CodecOptions options)
throws FormatException
{
if (bb == null) {
throw new IllegalArgumentException("No data to handle.");
}
if (options == null || !(options instanceof HuffmanCodecOptions)) {
throw new FormatException("Options must be an instance of " +
"loci.formats.codec.HuffmanCodecOptions.");
}
HuffmanCodecOptions huffman = (HuffmanCodecOptions) options;
Decoder decoder = cachedDecoders.get(huffman.table);
if (decoder == null) {
decoder = new Decoder(huffman.table);
cachedDecoders.put(huffman.table, decoder);
}
int bitCount = decoder.decode(bb);
if (bitCount < 0) bitCount = 0;
int v = bb.getBits(bitCount) & ((int) Math.pow(2, bitCount) - 1);
if ((v & (1 << (bitCount - 1))) == 0) {
v -= (1 << bitCount) - 1;
}
return v;
}
// -- Helper class --
class Decoder {
public Decoder[] branch = new Decoder[2];
private int leafValue = -1;
public Decoder() { }
public Decoder(short[] source) {
leafCounter = 0;
createDecoder(this, source, 0, 0);
}
private Decoder createDecoder(short[] source, int start, int level) {
Decoder dest = new Decoder();
createDecoder(dest, source, start, level);
return dest;
}
private void createDecoder(Decoder dest, short[] source, int start,
int level)
{
int next = 0;
int i = 0;
while (i <= leafCounter && next < LEAVES_OFFSET) {
i += source[start + next++] & 0xff;
}
if (level < next && next < LEAVES_OFFSET) {
dest.branch[0] = createDecoder(source, start, level + 1);
dest.branch[1] = createDecoder(source, start, level + 1);
}
else {
i = start + LEAVES_OFFSET + leafCounter++;
if (i < source.length) {
dest.leafValue = source[i] & 0xff;
}
}
}
public int decode(BitBuffer bb) {
Decoder d = this;
while (d.branch[0] != null) {
int v = bb.getBits(1);
if (v < 0) break; // eof
d = d.branch[v];
}
return d.leafValue;
}
}
}