//
// JPEG2000Codec.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.awt.image.BufferedImage;
import java.awt.image.DataBuffer;
import java.awt.image.DataBufferByte;
import java.awt.image.DataBufferUShort;
import java.awt.image.WritableRaster;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import loci.common.DataTools;
import loci.common.RandomAccessInputStream;
import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.FormatException;
import loci.formats.MissingLibraryException;
import loci.formats.gui.AWTImageTools;
import loci.formats.services.JAIIIOService;
import loci.formats.services.JAIIIOServiceImpl;
/**
* This class implements JPEG 2000 compression and decompression.
*
* <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/JPEG2000Codec.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/codec/JPEG2000Codec.java;hb=HEAD">Gitweb</a></dd></dl>
* </dl>
*/
public class JPEG2000Codec extends BaseCodec {
// -- Fields --
private JAIIIOService service;
// -- Codec API methods --
/**
* The CodecOptions parameter should have the following fields set:
* {@link CodecOptions#width width}
* {@link CodecOptions#height height}
* {@link CodecOptions#bitsPerSample bitsPerSample}
* {@link CodecOptions#channels channels}
* {@link CodecOptions#interleaved interleaved}
* {@link CodecOptions#littleEndian littleEndian}
* {@link CodecOptions#lossless lossless}
*
* @see Codec#compress(byte[], CodecOptions)
*/
public byte[] compress(byte[] data, CodecOptions options)
throws FormatException
{
if (data == null || data.length == 0) return data;
initialize();
JPEG2000CodecOptions j2kOptions;
if (options instanceof JPEG2000CodecOptions) {
j2kOptions = (JPEG2000CodecOptions) options;
}
else {
j2kOptions = (JPEG2000CodecOptions)
JPEG2000CodecOptions.getDefaultOptions(options);
}
ByteArrayOutputStream out = new ByteArrayOutputStream();
BufferedImage img = null;
int next = 0;
// NB: Construct BufferedImages manually, rather than using
// AWTImageTools.makeImage. The AWTImageTools.makeImage methods construct
// images that are not properly handled by the JPEG2000 writer.
// Specifically, 8-bit multi-channel images are constructed with type
// DataBuffer.TYPE_INT (so a single int is used to store all of the
// channels for a specific pixel).
int plane = j2kOptions.width * j2kOptions.height;
if (j2kOptions.bitsPerSample == 8) {
byte[][] b = new byte[j2kOptions.channels][plane];
if (j2kOptions.interleaved) {
for (int q=0; q<plane; q++) {
for (int c=0; c<j2kOptions.channels; c++) {
b[c][q] = data[next++];
}
}
}
else {
for (int c=0; c<j2kOptions.channels; c++) {
System.arraycopy(data, c * plane, b[c], 0, plane);
}
}
DataBuffer buffer = new DataBufferByte(b, plane);
img = AWTImageTools.constructImage(b.length, DataBuffer.TYPE_BYTE,
j2kOptions.width, j2kOptions.height, false, true, buffer,
j2kOptions.colorModel);
}
else if (j2kOptions.bitsPerSample == 16) {
short[][] s = new short[j2kOptions.channels][plane];
if (j2kOptions.interleaved) {
for (int q=0; q<plane; q++) {
for (int c=0; c<j2kOptions.channels; c++) {
s[c][q] = DataTools.bytesToShort(data, next, 2,
j2kOptions.littleEndian);
next += 2;
}
}
}
else {
for (int c=0; c<j2kOptions.channels; c++) {
for (int q=0; q<plane; q++) {
s[c][q] = DataTools.bytesToShort(data, next, 2,
j2kOptions.littleEndian);
next += 2;
}
}
}
DataBuffer buffer = new DataBufferUShort(s, plane);
img = AWTImageTools.constructImage(s.length, DataBuffer.TYPE_USHORT,
j2kOptions.width, j2kOptions.height, false, true, buffer,
j2kOptions.colorModel);
}
try {
service.writeImage(out, img, j2kOptions);
}
catch (IOException e) {
throw new FormatException("Could not compress JPEG-2000 data.", e);
}
catch (ServiceException e) {
throw new FormatException("Could not compress JPEG-2000 data.", e);
}
return out.toByteArray();
}
/**
* The CodecOptions parameter should have the following fields set:
* {@link CodecOptions#interleaved interleaved}
* {@link CodecOptions#littleEndian littleEndian}
*
* @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 JPEG2000CodecOptions)) {
options = JPEG2000CodecOptions.getDefaultOptions(options);
}
byte[] buf = null;
long fp = in.getFilePointer();
if (options.maxBytes == 0) {
buf = new byte[(int) (in.length() - fp)];
}
else {
buf = new byte[(int) (options.maxBytes - fp)];
}
in.read(buf);
return decompress(buf, options);
}
/**
* The CodecOptions parameter should have the following fields set:
* {@link CodecOptions#interleaved interleaved}
* {@link CodecOptions#littleEndian littleEndian}
*
* @see Codec#decompress(byte[], CodecOptions)
*/
public byte[] decompress(byte[] buf, CodecOptions options)
throws FormatException
{
initialize();
if (options == null || !(options instanceof JPEG2000CodecOptions)) {
options = JPEG2000CodecOptions.getDefaultOptions(options);
}
else {
options = new JPEG2000CodecOptions(options);
}
byte[][] single = null;
WritableRaster b = null;
try {
ByteArrayInputStream bis = new ByteArrayInputStream(buf);
b = (WritableRaster) service.readRaster(
bis, (JPEG2000CodecOptions) options);
single = AWTImageTools.getPixelBytes(b, options.littleEndian);
bis.close();
b = null;
}
catch (IOException e) {
throw new FormatException("Could not decompress JPEG2000 image. Please " +
"make sure that jai_imageio.jar is installed.", e);
}
catch (ServiceException e) {
throw new FormatException("Could not decompress JPEG2000 image. Please " +
"make sure that jai_imageio.jar is installed.", e);
}
if (single.length == 1) return single[0];
byte[] rtn = new byte[single.length * single[0].length];
if (options.interleaved) {
int next = 0;
for (int i=0; i<single[0].length; i++) {
for (int j=0; j<single.length; j++) {
rtn[next++] = single[j][i];
}
}
}
else {
for (int i=0; i<single.length; i++) {
System.arraycopy(single[i], 0, rtn, i * single[0].length,
single[i].length);
}
}
single = null;
return rtn;
}
// -- Helper methods --
/**
* Initializes the JAI ImageIO dependency service. This is called at the
* beginning of the {@link #compress} and {@link #decompress} methods to
* avoid having the constructor's method definition contain a checked
* exception.
*
* @throws FormatException If there is an error initializing JAI ImageIO
* services.
*/
private void initialize() throws FormatException {
if (service != null) return;
try {
ServiceFactory factory = new ServiceFactory();
service = factory.getInstance(JAIIIOService.class);
}
catch (DependencyException de) {
throw new MissingLibraryException(JAIIIOServiceImpl.NO_J2K_MSG, de);
}
}
}