//
// MRWReader.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.IOException;
import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.ImageTools;
import loci.formats.MetadataTools;
import loci.formats.codec.BitBuffer;
import loci.formats.meta.MetadataStore;
import loci.formats.tiff.IFD;
import loci.formats.tiff.IFDList;
import loci.formats.tiff.TiffParser;
/**
* MRWReader is the file format reader for Minolta MRW 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/MRWReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/MRWReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class MRWReader extends FormatReader {
// -- Constants --
public static final String MRW_MAGIC_STRING = "MRM";
private static final int[] COLOR_MAP_1 = {0, 1, 1, 2};
private static final int[] COLOR_MAP_2 = {1, 2, 0, 1};
// -- Fields --
/** Offset to image data. */
private int offset;
private int sensorWidth, sensorHeight;
private int bayerPattern;
private int storageMethod;
private int dataSize;
private float[] wbg;
// -- Constructor --
/** Constructs a new MRW reader. */
public MRWReader() {
super("Minolta MRW", "mrw");
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 = 4;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readString(4).endsWith(MRW_MAGIC_STRING);
}
/**
* @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);
int nBytes = sensorWidth * sensorHeight;
if (dataSize == 12) nBytes *= 3;
else if (dataSize == 16) nBytes *= 4;
byte[] tmp = new byte[nBytes];
in.seek(offset);
in.read(tmp);
BitBuffer bb = new BitBuffer(tmp);
short[] s = new short[getSizeX() * getSizeY() * 3];
for (int row=0; row<getSizeY(); row++) {
boolean evenRow = (row % 2) == 0;
for (int col=0; col<getSizeX(); col++) {
boolean evenCol = (col % 2) == 0;
short val = (short) (bb.getBits(dataSize) & 0xffff);
int redOffset = row * getSizeX() + col;
int greenOffset = (getSizeY() + row) * getSizeX() + col;
int blueOffset = (2 * getSizeY() + row) * getSizeX() + col;
if (evenRow) {
if (evenCol) {
val = (short) (val * wbg[0]);
if (bayerPattern == 1) s[redOffset] = val;
else s[greenOffset] = val;
}
else {
val = (short) (val * wbg[1]);
if (bayerPattern == 1) s[greenOffset] = val;
else s[blueOffset] = val;
}
}
else {
if (evenCol) {
val = (short) (val * wbg[2]);
if (bayerPattern == 1) s[greenOffset] = val;
else s[redOffset] = val;
}
else {
val = (short) (val * wbg[3]);
if (bayerPattern == 1) s[blueOffset] = val;
else s[greenOffset] = val;
}
}
}
bb.skipBits(dataSize * (sensorWidth - getSizeX()));
}
int[] colorMap = bayerPattern == 1 ? COLOR_MAP_1 : COLOR_MAP_2;
return ImageTools.interpolate(s, buf, colorMap, w, h, isLittleEndian());
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
offset = 0;
sensorWidth = sensorHeight = 0;
bayerPattern = 0;
storageMethod = 0;
dataSize = 0;
wbg = 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.skipBytes(4); // magic number
offset = in.readInt() + 8;
while (in.getFilePointer() < offset) {
String blockName = in.readString(4);
int len = in.readInt();
long fp = in.getFilePointer();
if (blockName.endsWith("PRD")) {
in.skipBytes(8);
sensorHeight = in.readShort();
sensorWidth = in.readShort();
core[0].sizeY = in.readShort();
core[0].sizeX = in.readShort();
dataSize = in.read();
in.skipBytes(1);
storageMethod = in.read();
in.skipBytes(4);
bayerPattern = in.read();
}
else if (blockName.endsWith("WBG")) {
wbg = new float[4];
byte[] wbScale = new byte[4];
in.read(wbScale);
for (int i=0; i<wbg.length; i++) {
float coeff = in.readShort();
wbg[i] = coeff / (64 << wbScale[i]);
}
}
else if (blockName.endsWith("TTW") &&
getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM)
{
byte[] b = new byte[len];
in.read(b);
RandomAccessInputStream ras = new RandomAccessInputStream(b);
TiffParser tp = new TiffParser(ras);
IFDList ifds = tp.getIFDs();
for (IFD ifd : ifds) {
Integer[] keys = (Integer[]) ifd.keySet().toArray(new Integer[0]);
// CTR FIXME - getIFDTagName is for debugging only!
for (int q=0; q<keys.length; q++) {
addGlobalMeta(IFD.getIFDTagName(keys[q].intValue()),
ifd.get(keys[q]));
}
}
IFDList exifIFDs = tp.getExifIFDs();
for (IFD exif : exifIFDs) {
for (Integer key : exif.keySet()) {
addGlobalMeta(IFD.getIFDTagName(key.intValue()), exif.get(key));
}
}
ras.close();
}
in.seek(fp + len);
}
core[0].pixelType = FormatTools.UINT16;
core[0].rgb = true;
core[0].littleEndian = false;
core[0].dimensionOrder = "XYCZT";
core[0].imageCount = 1;
core[0].sizeC = 3;
core[0].sizeZ = 1;
core[0].sizeT = 1;
core[0].interleaved = true;
core[0].bitsPerPixel = dataSize;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
MetadataTools.setDefaultCreationDate(store, id, 0);
}
}