//
// QTRLECodec.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 loci.common.ByteArrayHandle;
import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.UnsupportedCompressionException;
/**
* Methods for compressing and decompressing data using QuickTime RLE.
*
* <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/QTRLECodec.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/codec/QTRLECodec.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class QTRLECodec extends BaseCodec {
/* @see Codec#compress(byte[], CodecOptions) */
public byte[] compress(byte[] data, CodecOptions options)
throws FormatException
{
throw new UnsupportedCompressionException(
"QTRLE compression not supported.");
}
/* @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.");
byte[] b = new byte[(int) (in.length() - in.getFilePointer())];
in.read(b);
return decompress(b, options);
}
/**
* The CodecOptions parameter should have the following fields set:
* {@link CodecOptions#width width}
* {@link CodecOptions#height height}
* {@link CodecOptions#bitsPerSample bitsPerSample}
* {@link CodecOptions#previousImage previousImage}
*
* @see Codec#decompress(byte[], CodecOptions)
*/
public byte[] decompress(byte[] data, CodecOptions options)
throws FormatException
{
if (options == null) options = CodecOptions.getDefaultOptions();
if (data == null || data.length == 0)
throw new IllegalArgumentException("No data to decompress.");
int numLines = options.height;
if (data.length < 8) return options.previousImage;
int bpp = options.bitsPerSample / 8;
int line = options.width * bpp;
try {
ByteArrayHandle s = new ByteArrayHandle(data);
s.skipBytes(4);
int header = s.readShort();
int off = 0;
int start = 0;
byte[] output = new byte[options.height * line];
if ((header & 8) == 8) {
start = s.readShort();
s.skipBytes(2);
numLines = s.readShort();
s.skipBytes(2);
if (options.previousImage != null) {
for (int i=0; i<start; i++) {
System.arraycopy(options.previousImage, off, output, off, line);
off += line;
}
}
if (options.previousImage != null) {
off = line * (start + numLines);
for (int i=start+numLines; i<options.height; i++) {
System.arraycopy(options.previousImage, off, output, off, line);
off += line;
}
}
}
else throw new FormatException("Unsupported header : " + header);
// uncompress remaining lines
int skip = 0; // number of bytes to skip
byte rle = 0; // RLE code
int rowPointer = start * line;
for (int i=0; i<numLines; i++) {
skip = s.readUnsignedByte();
if (skip < 0) skip += 256;
if (options.previousImage != null) {
try {
System.arraycopy(options.previousImage, rowPointer, output,
rowPointer, (skip - 1) * bpp);
}
catch (ArrayIndexOutOfBoundsException e) { }
}
off = rowPointer + ((skip - 1) * bpp);
while (true) {
rle = (byte) (s.readUnsignedByte() & 0xff);
if (rle == 0) {
skip = s.readUnsignedByte();
if (options.previousImage != null) {
try {
System.arraycopy(options.previousImage, off, output, off,
(skip - 1) * bpp);
}
catch (ArrayIndexOutOfBoundsException e) { }
}
off += (skip - 1) * bpp;
}
else if (rle == -1) {
if (off < (rowPointer + line) && options.previousImage != null) {
System.arraycopy(options.previousImage, off, output, off,
rowPointer + line - off);
}
break;
}
else if (rle < -1) {
// unpack next pixel and copy it to output -(rle) times
for (int j=0; j<(-1*rle); j++) {
if (off < output.length) {
System.arraycopy(data, (int) s.getFilePointer(), output,
off, bpp);
off += bpp;
}
else break;
}
s.skipBytes(bpp);
}
else {
// copy (rle) pixels to output
int len = rle * bpp;
if (output.length - off < len) len = output.length - off;
if (s.length() - s.getFilePointer() < len) {
len = (int) (s.length() - s.getFilePointer());
}
if (len < 0) len = 0;
if (off > output.length) off = output.length;
s.read(output, off, len);
off += len;
}
if (s.getFilePointer() >= s.length()) return output;
}
rowPointer += line;
}
return output;
}
catch (IOException e) {
throw new FormatException(e);
}
}
}