/*
* #%L
* BSD implementations of Bio-Formats readers and writers
* %%
* Copyright (C) 2005 - 2015 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package loci.formats.codec;
import java.io.IOException;
import java.util.HashMap;
import loci.common.ByteArrayHandle;
import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.UnsupportedCompressionException;
/**
* This class implements Huffman decoding.
*
* @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) */
@Override
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)
*/
@Override
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;
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(in, options);
out.write(sample, bytesPerSample * 8);
}
return out.toByteArray();
}
// -- HuffmanCodec API methods --
@Deprecated
public int getSample(BitBuffer bb, CodecOptions options)
throws FormatException
{
RandomAccessInputStream s = null;
try {
try {
s = new RandomAccessInputStream(new ByteArrayHandle(bb.getByteBuffer()));
return getSample(s, options);
}
finally {
s.close();
}
}
catch (IOException e) {
throw new FormatException(e);
}
}
public int getSample(RandomAccessInputStream 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);
}
try {
int bitCount = decoder.decode(bb);
if (bitCount == 16) {
return 0x8000;
}
if (bitCount < 0) bitCount = 0;
int v = bb.readBits(bitCount) & ((int) Math.pow(2, bitCount) - 1);
if ((v & (1 << (bitCount - 1))) == 0) {
v -= (1 << bitCount) - 1;
}
return v;
}
catch (IOException e) {
throw new FormatException(e);
}
}
// -- 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(RandomAccessInputStream bb) throws IOException {
Decoder d = this;
while (d.branch[0] != null) {
int v = bb.readBits(1);
if (v < 0) break; // eof
d = d.branch[v];
}
return d.leafValue;
}
}
}