//
// MNGReader.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.in;
import java.awt.image.BufferedImage;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.util.Hashtable;
import java.util.Vector;
import javax.imageio.ImageIO;
import loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.gui.AWTImageTools;
import loci.formats.meta.MetadataStore;
/**
* MNGReader is the file format reader for Multiple Network Graphics (MNG)
* files. Does not support JNG (JPEG Network Graphics).
*
* <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/in/MNGReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/MNGReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class MNGReader extends BIFormatReader {
// -- Constants --
public static final long MNG_MAGIC_BYTES = 0x8a4d4e470d0a1a0aL;
// -- Fields --
private Vector<SeriesInfo> seriesInfo;
// -- Constructor --
/** Constructs a new MNG reader. */
public MNGReader() {
super("Multiple Network Graphics", "mng");
domains = new String[] {FormatTools.GRAPHICS_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 8;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readLong() == MNG_MAGIC_BYTES;
}
/* @see loci.formats.IFormatReader#openPlane(int, int, int, int, int int) */
public Object openPlane(int no, int x, int y, int w, int h)
throws FormatException, IOException
{
FormatTools.checkPlaneParameters(this, no, -1, x, y, w, h);
SeriesInfo info = seriesInfo.get(series);
long offset = info.offsets.get(no);
in.seek(offset);
long end = info.lengths.get(no);
BufferedImage img = readImage(end);
// reconstruct the image to use an appropriate raster
// ImageIO often returns images that cannot be scaled because a
// BytePackedRaster is used
return AWTImageTools.getSubimage(img, isLittleEndian(), x, y, w, h);
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) seriesInfo = null;
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
in.order(false);
LOGGER.info("Verifying MNG format");
seriesInfo = new Vector<SeriesInfo>();
seriesInfo.add(new SeriesInfo());
in.skipBytes(12);
if (!"MHDR".equals(in.readString(4))) {
throw new FormatException("Invalid MNG file.");
}
LOGGER.info("Reading dimensions");
in.skipBytes(32);
Vector<Long> stack = new Vector<Long>();
int maxIterations = 0;
int currentIteration = 0;
LOGGER.info("Finding image offsets");
// read sequence of [len, code, value] tags
while (in.getFilePointer() < in.length()) {
int len = in.readInt();
String code = in.readString(4);
long fp = in.getFilePointer();
if (code.equals("IHDR")) {
seriesInfo.get(0).offsets.add(fp - 8);
}
else if (code.equals("IEND")) {
seriesInfo.get(0).lengths.add(fp + len + 4);
}
else if (code.equals("LOOP")) {
stack.add(fp + len + 4);
in.skipBytes(1);
maxIterations = in.readInt();
}
else if (code.equals("ENDL")) {
long seek = stack.get(stack.size() - 1).longValue();
if (currentIteration < maxIterations) {
in.seek(seek);
currentIteration++;
}
else {
stack.remove(stack.size() - 1);
maxIterations = 0;
currentIteration = 0;
}
}
in.seek(fp + len + 4);
}
LOGGER.info("Populating metadata");
// easiest way to get image dimensions is by opening the first plane
Hashtable<String, Vector> seriesOffsets = new Hashtable<String, Vector>();
Hashtable<String, Vector> seriesLengths = new Hashtable<String, Vector>();
SeriesInfo info = seriesInfo.get(0);
addGlobalMeta("Number of frames", info.offsets.size());
for (int i=0; i<info.offsets.size(); i++) {
long offset = info.offsets.get(i);
in.seek(offset);
long end = info.lengths.get(i);
if (end < offset) continue;
BufferedImage img = readImage(end);
String data = img.getWidth() + "-" + img.getHeight() + "-" +
img.getRaster().getNumBands() + "-" + AWTImageTools.getPixelType(img);
Vector<Long> v = new Vector<Long>();
if (seriesOffsets.containsKey(data)) {
v = seriesOffsets.get(data);
}
v.add(new Long(offset));
seriesOffsets.put(data, v);
v = new Vector();
if (seriesLengths.containsKey(data)) {
v = seriesLengths.get(data);
}
v.add(new Long(end));
seriesLengths.put(data, v);
}
String[] keys = seriesOffsets.keySet().toArray(new String[0]);
if (keys.length == 0) {
throw new FormatException("Pixel data not found.");
}
core = new CoreMetadata[keys.length];
seriesInfo.clear();
for (int i=0; i<keys.length; i++) {
core[i] = new CoreMetadata();
String[] tokens = keys[i].split("-");
core[i].sizeX = Integer.parseInt(tokens[0]);
core[i].sizeY = Integer.parseInt(tokens[1]);
core[i].sizeC = Integer.parseInt(tokens[2]);
core[i].pixelType = Integer.parseInt(tokens[3]);
core[i].rgb = core[i].sizeC > 1;
core[i].sizeZ = 1;
core[i].dimensionOrder = "XYCZT";
core[i].interleaved = false;
core[i].metadataComplete = true;
core[i].indexed = false;
core[i].littleEndian = false;
core[i].falseColor = false;
SeriesInfo inf = new SeriesInfo();
inf.offsets = seriesOffsets.get(keys[i]);
inf.lengths = seriesLengths.get(keys[i]);
seriesInfo.add(inf);
core[i].imageCount = inf.offsets.size();
core[i].sizeT = core[i].imageCount;
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
for (int i=0; i<getSeriesCount(); i++) {
store.setImageName("Series " + (i + 1), i);
MetadataTools.setDefaultCreationDate(store, id, i);
}
}
// -- Helper methods --
private BufferedImage readImage(long end) throws IOException {
byte[] b = new byte[(int) (end - in.getFilePointer() + 8)];
in.read(b, 8, b.length - 8);
b[0] = (byte) 0x89;
b[1] = 0x50;
b[2] = 0x4e;
b[3] = 0x47;
b[4] = 0x0d;
b[5] = 0x0a;
b[6] = 0x1a;
b[7] = 0x0a;
return ImageIO.read(new ByteArrayInputStream(b));
}
// -- Helper class --
private class SeriesInfo {
public Vector<Long> offsets = new Vector<Long>();
public Vector<Long> lengths = new Vector<Long>();
}
}