/*
* #%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
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* 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.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).
*/
public class MNGReader extends BIFormatReader {
// -- Constants --
public static final long MNG_MAGIC_BYTES = 0x8a4d4e470d0a1a0aL;
// -- Fields --
private Vector<SeriesInfo> seriesInfo;
private boolean isJNG = false;
// -- 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) */
@Override
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) */
@Override
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(getSeries());
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) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
seriesInfo = null;
isJNG = false;
}
}
// -- 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);
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("JDAT")) {
isJNG = true;
seriesInfo.get(0).offsets.add(fp);
}
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.");
}
int seriesCount = keys.length;
core.clear();
seriesInfo.clear();
for (int i=0; i<seriesCount; i++) {
CoreMetadata ms = new CoreMetadata();
core.add(ms);
String[] tokens = keys[i].split("-");
ms.sizeX = Integer.parseInt(tokens[0]);
ms.sizeY = Integer.parseInt(tokens[1]);
ms.sizeC = Integer.parseInt(tokens[2]);
ms.pixelType = Integer.parseInt(tokens[3]);
ms.rgb = ms.sizeC > 1;
ms.sizeZ = 1;
ms.dimensionOrder = "XYCZT";
ms.interleaved = false;
ms.metadataComplete = true;
ms.indexed = false;
ms.littleEndian = false;
ms.falseColor = false;
SeriesInfo inf = new SeriesInfo();
inf.offsets = seriesOffsets.get(keys[i]);
inf.lengths = seriesLengths.get(keys[i]);
seriesInfo.add(inf);
ms.imageCount = inf.offsets.size();
ms.sizeT = ms.imageCount;
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
for (int i=0; i<getSeriesCount(); i++) {
store.setImageName("Series " + (i + 1), i);
}
}
// -- Helper methods --
private BufferedImage readImage(long end) throws IOException {
int headerSize = isJNG ? 0 : 8;
byte[] b = new byte[(int) (end - in.getFilePointer() + headerSize)];
in.read(b, headerSize, b.length - headerSize);
if (!isJNG) {
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>();
}
}