//
// KhorosReader.java
//
/*
LOCI Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ Melissa Linkert, Curtis Rueden, Chris Allan,
Eric Kjellman and Brian Loranger.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU Library 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 Library General Public License for more details.
You should have received a copy of the GNU Library 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.*;
import loci.formats.*;
/**
* Reader for Khoros XV files.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/KhorosReader.java">Trac</a>,
* <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/KhorosReader.java">SVN</a></dd></dl>
*/
public class KhorosReader extends FormatReader {
// -- Fields --
/** Global lookup table. */
private byte[] lut;
/** Image offset. */
private long offset;
// -- Constructor --
/** Constructs a new Khoros reader. */
public KhorosReader() { super("Khoros XV", "xv"); }
// -- FormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(byte[]) */
public boolean isThisType(byte[] block) {
return block[0] == (byte) 0xab && block[1] == 1;
}
/* @see loci.formats.IFormatReader#get8BitLookupTable() */
public byte[][] get8BitLookupTable() throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
if (lut == null) return null;
byte[][] table = new byte[3][lut.length / 3];
int next = 0;
for (int i=0; i<table[0].length; i++) {
for (int j=0; j<table.length; j++) {
table[j][i] = lut[next++];
}
}
return table;
}
/* @see loci.formats.IFormatReader#openBytes(int, byte[]) */
public byte[] openBytes(int no, byte[] buf)
throws FormatException, IOException
{
FormatTools.assertId(currentId, true, 1);
FormatTools.checkPlaneNumber(this, no);
FormatTools.checkBufferSize(this, buf.length);
int bufSize = core.sizeX[0] * core.sizeY[0] *
FormatTools.getBytesPerPixel(core.pixelType[0]);
in.seek(offset + no * bufSize);
in.read(buf, 0, bufSize);
return buf;
}
/* @see loci.formats.IFormatReader#close() */
public void close() throws IOException {
super.close();
lut = null;
offset = 0;
}
/** Initialize the given file. */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessStream(id);
in.skipBytes(4);
in.order(true);
int dependency = in.readInt();
addMeta("Comment", in.readString(512));
in.order(dependency == 4 || dependency == 8);
core.sizeX[0] = in.readInt();
core.sizeY[0] = in.readInt();
in.skipBytes(28);
core.imageCount[0] = in.readInt();
if (core.imageCount[0] == 0) core.imageCount[0] = 1;
core.sizeC[0] = in.readInt();
int type = in.readInt();
switch (type) {
case 0:
case 1:
core.pixelType[0] = FormatTools.UINT8;
break;
case 2:
core.pixelType[0] = FormatTools.UINT16;
break;
case 4:
core.pixelType[0] = FormatTools.UINT32;
break;
case 5:
core.pixelType[0] = FormatTools.FLOAT;
break;
case 9:
core.pixelType[0] = FormatTools.DOUBLE;
break;
default: throw new FormatException("Unsupported pixel type : " + type);
}
in.skipBytes(12);
int c = in.readInt();
if (c > 1) {
core.sizeC[0] = c;
int n = in.readInt();
lut = new byte[n * c];
in.skipBytes(436);
for (int i=0; i<lut.length; i++) {
int value = in.read();
if (i < n) {
lut[i*3] = (byte) value;
lut[i*3 + 1] = (byte) value;
lut[i*3 + 2] = (byte) value;
}
else if (i < n*2) {
lut[(i % n)*3 + 1] = (byte) value;
}
else if (i < n*3) {
lut[(i % n)*3 + 2] = (byte) value;
}
}
}
else in.skipBytes(440);
offset = in.getFilePointer();
core.sizeZ[0] = core.imageCount[0];
core.sizeT[0] = 1;
core.rgb[0] = core.sizeC[0] > 1;
core.interleaved[0] = false;
core.littleEndian[0] = dependency == 4 || dependency == 8;
core.currentOrder[0] = "XYCZT";
core.indexed[0] = lut != null;
core.falseColor[0] = false;
core.metadataComplete[0] = true;
MetadataStore store = getMetadataStore();
store.setImage(currentId, null, null, null);
FormatTools.populatePixels(store, this);
for (int i=0; i<core.sizeC[0]; i++) {
store.setLogicalChannel(i, null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null, null);
}
}
}