/*
* #%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
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*/
package loci.formats.in;
import java.io.IOException;
import java.util.ArrayList;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.codec.JPEG2000BoxType;
import loci.formats.codec.JPEG2000Codec;
import loci.formats.codec.JPEG2000CodecOptions;
import loci.formats.meta.MetadataStore;
/**
* JPEG2000Reader is the file format reader for JPEG-2000 images.
*/
public class JPEG2000Reader extends FormatReader {
// -- Constants --
/** Logger for this class. */
private static final Logger LOGGER =
LoggerFactory.getLogger(JPEG2000Reader.class);
// -- Fields --
/** The number of JPEG 2000 resolution levels the file has. */
private Integer resolutionLevels;
/** The color lookup table associated with this file. */
private int[][] lut;
private long pixelsOffset;
private int lastSeries = -1;
private byte[] lastSeriesPlane;
// -- Constructor --
/** Constructs a new JPEG2000Reader. */
public JPEG2000Reader() {
super("JPEG-2000", new String[] {"jp2", "j2k", "jpf"});
suffixSufficient = false;
suffixNecessary = false;
domains = new String[] {FormatTools.GRAPHICS_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 40;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
boolean validStart = (stream.readShort() & 0xffff) == 0xff4f;
if (!validStart) {
stream.skipBytes(2);
validStart = stream.readInt() == JPEG2000BoxType.SIGNATURE.getCode();
if (validStart) {
stream.skipBytes(12);
validStart = !stream.readString(4).equals("jpx ");
}
}
stream.seek(stream.length() - 2);
boolean validEnd = (stream.readShort() & 0xffff) == 0xffd9;
return validStart && validEnd;
}
/* @see loci.formats.IFormatReader#get8BitLookupTable() */
@Override
public byte[][] get8BitLookupTable() {
FormatTools.assertId(currentId, true, 1);
if (lut == null || FormatTools.getBytesPerPixel(getPixelType()) != 1) {
return null;
}
byte[][] byteLut = new byte[lut.length][lut[0].length];
for (int i=0; i<lut.length; i++) {
for (int j=0; j<lut[i].length; j++) {
byteLut[i][j] = (byte) (lut[i][j] & 0xff);
}
}
return byteLut;
}
/* @see loci.formats.IFormatReader#get16BitLookupTable() */
@Override
public short[][] get16BitLookupTable() {
FormatTools.assertId(currentId, true, 1);
if (lut == null || FormatTools.getBytesPerPixel(getPixelType()) != 2) {
return null;
}
short[][] shortLut = new short[lut.length][lut[0].length];
for (int i=0; i<lut.length; i++) {
for (int j=0; j<lut[i].length; j++) {
shortLut[i][j] = (short) (lut[i][j] & 0xffff);
}
}
return shortLut;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
resolutionLevels = null;
lut = null;
pixelsOffset = 0;
lastSeries = -1;
lastSeriesPlane = null;
}
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
if (lastSeries == getCoreIndex() && lastSeriesPlane != null) {
RandomAccessInputStream s = new RandomAccessInputStream(lastSeriesPlane);
readPlane(s, x, y, w, h, buf);
s.close();
return buf;
}
JPEG2000CodecOptions options = JPEG2000CodecOptions.getDefaultOptions();
options.interleaved = isInterleaved();
options.littleEndian = isLittleEndian();
if (resolutionLevels != null) {
options.resolution = Math.abs(getCoreIndex() - resolutionLevels);
}
else if (core.size() > 1) {
options.resolution = getCoreIndex();
}
in.seek(pixelsOffset);
lastSeriesPlane = new JPEG2000Codec().decompress(in, options);
RandomAccessInputStream s = new RandomAccessInputStream(lastSeriesPlane);
readPlane(s, x, y, w, h, buf);
s.close();
lastSeries = getCoreIndex();
return buf;
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
CoreMetadata ms0 = core.get(0);
JPEG2000MetadataParser metadataParser = new JPEG2000MetadataParser(in);
if (metadataParser.isRawCodestream()) {
LOGGER.info("Codestream is raw, using codestream dimensions.");
ms0.sizeX = metadataParser.getCodestreamSizeX();
ms0.sizeY = metadataParser.getCodestreamSizeY();
ms0.sizeC = metadataParser.getCodestreamSizeC();
ms0.pixelType = metadataParser.getCodestreamPixelType();
}
else {
LOGGER.info("Codestream is JP2 boxed, using header dimensions.");
ms0.sizeX = metadataParser.getHeaderSizeX();
ms0.sizeY = metadataParser.getHeaderSizeY();
ms0.sizeC = metadataParser.getHeaderSizeC();
ms0.pixelType = metadataParser.getHeaderPixelType();
}
lut = metadataParser.getLookupTable();
pixelsOffset = metadataParser.getCodestreamOffset();
ms0.sizeZ = 1;
ms0.sizeT = 1;
ms0.imageCount = 1;
ms0.dimensionOrder = "XYCZT";
ms0.rgb = getSizeC() > 1;
ms0.interleaved = true;
ms0.littleEndian = false;
ms0.indexed = !isRGB() && lut != null;
// New core metadata now that we know how many sub-resolutions we have.
if (resolutionLevels != null) {
int seriesCount = resolutionLevels + 1;
core.get(0).resolutionCount = seriesCount;
for (int i = 1; i < seriesCount; i++) {
CoreMetadata ms = new CoreMetadata(this, 0);
core.add(ms);
ms.sizeX = core.get(i - 1).sizeX / 2;
ms.sizeY = core.get(i - 1).sizeY / 2;
ms.thumbnail = true;
}
}
ArrayList<String> comments = metadataParser.getComments();
LOGGER.debug("Found {} comments", comments.size());
for (int i=0; i<comments.size(); i++) {
String comment = comments.get(i);
int equal = comment.indexOf("=");
if (equal >= 0) {
String key = comment.substring(0, equal);
String value = comment.substring(equal + 1);
addGlobalMeta(key, value);
}
else {
addGlobalMetaList("Comment", comment);
}
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
}
// -- Helper methods --
}