//
// DNGReader.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.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.Arrays;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.ImageTools;
import loci.formats.MetadataTools;
import loci.formats.codec.BitBuffer;
import loci.formats.codec.NikonCodec;
import loci.formats.codec.NikonCodecOptions;
import loci.formats.meta.MetadataStore;
import loci.formats.tiff.IFD;
import loci.formats.tiff.IFDList;
import loci.formats.tiff.PhotoInterp;
import loci.formats.tiff.TiffCompression;
import loci.formats.tiff.TiffParser;
import loci.formats.tiff.TiffRational;
/**
* DNGReader is the file format reader for Canon DNG (TIFF) files.
*
* <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/DNGReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/DNGReader.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class DNGReader extends BaseTiffReader {
// -- Constants --
/** Logger for this class. */
private static final Logger LOGGER =
LoggerFactory.getLogger(DNGReader.class);
private static final int TIFF_EPS_STANDARD = 37398;
private static final int COLOR_MAP = 33422;
private static final int WHITE_BALANCE_RGB_COEFFS = 12;
// -- Fields --
/** The original IFD. */
protected IFD original;
private TiffRational[] whiteBalance;
private Object cfaPattern;
private byte[] lastPlane = null;
private int lastIndex = -1;
// -- Constructor --
/** Constructs a new DNG reader. */
public DNGReader() {
super("DNG",
new String[] {"cr2", "crw", "jpg", "thm", "wav", "tif", "tiff"});
suffixSufficient = false;
domains = new String[] {FormatTools.GRAPHICS_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
TiffParser tp = new TiffParser(stream);
IFD ifd = tp.getFirstIFD();
if (ifd == null) return false;
boolean hasEPSTag = ifd.containsKey(TIFF_EPS_STANDARD);
String make = ifd.getIFDTextValue(IFD.MAKE);
return make != null && make.indexOf("Canon") != -1 && hasEPSTag;
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
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);
IFD ifd = ifds.get(no);
int[] bps = ifd.getBitsPerSample();
int dataSize = bps[0];
long[] byteCounts = ifd.getStripByteCounts();
long totalBytes = 0;
for (long b : byteCounts) {
totalBytes += b;
}
if (totalBytes == FormatTools.getPlaneSize(this) || bps.length > 1) {
return super.openBytes(no, buf, x, y, w, h);
}
if (lastPlane == null || lastIndex != no) {
long[] offsets = ifd.getStripOffsets();
ByteArrayOutputStream src = new ByteArrayOutputStream();
for (int i=0; i<byteCounts.length; i++) {
byte[] t = new byte[(int) byteCounts[i]];
in.seek(offsets[i]);
in.read(t);
src.write(t);
}
int[] colorMap = {1, 0, 2, 1}; // default color map
short[] ifdColors = (short[]) ifd.get(COLOR_MAP);
if (ifdColors != null && ifdColors.length >= colorMap.length) {
boolean colorsValid = true;
for (int q=0; q<colorMap.length; q++) {
if (ifdColors[q] < 0 || ifdColors[q] > 2) {
// found invalid channel index, use default color map instead
colorsValid = false;
break;
}
}
if (colorsValid) {
for (int q=0; q<colorMap.length; q++) {
colorMap[q] = ifdColors[q];
}
}
}
lastPlane = new byte[FormatTools.getPlaneSize(this)];
BitBuffer bb = new BitBuffer(src.toByteArray());
src.close();
short[] pix = new short[getSizeX() * getSizeY() * 3];
for (int row=0; row<getSizeY(); row++) {
int realRow = row;
for (int col=0; col<getSizeX(); col++) {
short val = (short) (bb.getBits(dataSize) & 0xffff);
int mapIndex = (realRow % 2) * 2 + (col % 2);
int redOffset = realRow * getSizeX() + col;
int greenOffset = (getSizeY() + realRow) * getSizeX() + col;
int blueOffset = (2 * getSizeY() + realRow) * getSizeX() + col;
if (colorMap[mapIndex] == 0) {
pix[redOffset] = adjustForWhiteBalance(val, 0);
}
else if (colorMap[mapIndex] == 1) {
pix[greenOffset] = adjustForWhiteBalance(val, 1);
}
else if (colorMap[mapIndex] == 2) {
pix[blueOffset] = adjustForWhiteBalance(val, 2);
}
}
}
ImageTools.interpolate(pix, buf, colorMap, getSizeX(), getSizeY(),
isLittleEndian());
lastIndex = no;
}
int bpp = FormatTools.getBytesPerPixel(getPixelType()) * 3;
int rowLen = w * bpp;
int width = getSizeX() * bpp;
for (int row=0; row<h; row++) {
System.arraycopy(
lastPlane, (row + y) * width + x * bpp, buf, row * rowLen, rowLen);
}
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
original = null;
whiteBalance = null;
cfaPattern = null;
lastPlane = null;
lastIndex = -1;
}
}
// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
// reset image dimensions
// the actual image data is stored in IFDs referenced by the SubIFD tag
// in the 'real' IFD
core[0].imageCount = ifds.size();
IFD firstIFD = ifds.get(0);
PhotoInterp photo = firstIFD.getPhotometricInterpretation();
int samples = firstIFD.getSamplesPerPixel();
core[0].rgb = samples > 1 || photo == PhotoInterp.RGB ||
photo == PhotoInterp.CFA_ARRAY;
if (photo == PhotoInterp.CFA_ARRAY) samples = 3;
core[0].sizeX = (int) firstIFD.getImageWidth();
core[0].sizeY = (int) firstIFD.getImageLength();
core[0].sizeZ = 1;
core[0].sizeC = isRGB() ? samples : 1;
core[0].sizeT = ifds.size();
core[0].pixelType = firstIFD.getPixelType();
core[0].indexed = false;
// now look for the EXIF IFD pointer
IFDList exifIFDs = tiffParser.getExifIFDs();
if (exifIFDs.size() > 0) {
IFD exifIFD = exifIFDs.get(0);
tiffParser.fillInIFD(exifIFD);
// put all the EXIF data in the metadata hashtable
for (Integer key : exifIFD.keySet()) {
int tag = key.intValue();
String name = IFD.getIFDTagName(tag);
/* debug */ System.out.println("tag = " + tag);
/* debug */ System.out.println(exifIFD.get(key));
/* debug */ System.out.println();
if (tag == IFD.CFA_PATTERN) {
byte[] cfa = (byte[]) exifIFD.get(key);
int[] colorMap = new int[cfa.length];
for (int i=0; i<cfa.length; i++) colorMap[i] = (int) cfa[i];
addGlobalMeta(name, colorMap);
cfaPattern = colorMap;
}
else {
addGlobalMeta(name, exifIFD.get(key));
if (name.equals("MAKER_NOTE")) {
byte[] b = (byte[]) exifIFD.get(key);
int extra = new String(b, 0, 10).startsWith("Canon") ? 10 : 0;
byte[] buf = new byte[b.length];
System.arraycopy(b, extra, buf, 0, buf.length - extra);
RandomAccessInputStream makerNote =
new RandomAccessInputStream(buf);
TiffParser tp = new TiffParser(makerNote);
IFD note = null;
try {
note = tp.getFirstIFD();
}
catch (Exception e) {
LOGGER.debug("Failed to parse first IFD", e);
}
if (note != null) {
for (Integer nextKey : note.keySet()) {
int nextTag = nextKey.intValue();
addGlobalMeta(name, note.get(nextKey));
if (nextTag == WHITE_BALANCE_RGB_COEFFS) {
/* debug */ System.out.println("setting whiteBalance");
whiteBalance = (TiffRational[]) note.get(nextKey);
}
}
}
makerNote.close();
}
}
}
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
original = ifds.get(0);
if (cfaPattern != null) {
original.putIFDValue(IFD.COLOR_MAP, (int[]) cfaPattern);
}
ifds.set(0, original);
core[0].imageCount = 1;
core[0].sizeT = 1;
if (ifds.get(0).getSamplesPerPixel() == 1) {
core[0].interleaved = true;
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
// -- Helper methods --
private short adjustForWhiteBalance(short val, int index) {
if (whiteBalance != null && whiteBalance.length == 3) {
return (short) (val * whiteBalance[index].doubleValue());
}
return val;
}
}