/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2015 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* 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, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
* #L%
*/
package loci.formats.in;
import java.io.IOException;
import loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
/**
* Reader for Khoros XV files.
*/
public class KhorosReader extends FormatReader {
// -- Constants --
public static final int KHOROS_MAGIC_BYTES = 0xab01;
// -- Fields --
/** Global lookup table. */
private byte[][] lut;
/** Image offset. */
private long offset;
// -- Constructor --
/** Constructs a new Khoros reader. */
public KhorosReader() {
super("Khoros XV", "xv");
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 = 2;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readShort() == KHOROS_MAGIC_BYTES;
}
/* @see loci.formats.IFormatReader#get8BitLookupTable() */
@Override
public byte[][] get8BitLookupTable() throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
return lut;
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
@Override
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 bufSize = FormatTools.getPlaneSize(this);
in.seek(offset + no * bufSize);
readPlane(in, x, y, w, h, buf);
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
lut = null;
offset = 0;
}
}
// -- 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.skipBytes(4);
in.order(true);
int dependency = in.readInt();
addGlobalMeta("Comment", in.readString(512));
in.order(dependency == 4 || dependency == 8);
CoreMetadata m = core.get(0);
m.sizeX = in.readInt();
m.sizeY = in.readInt();
in.skipBytes(28);
m.imageCount = in.readInt();
if (getImageCount() == 0) m.imageCount = 1;
m.sizeC = in.readInt();
int type = in.readInt();
switch (type) {
case 0:
m.pixelType = FormatTools.INT8;
break;
case 1:
m.pixelType = FormatTools.UINT8;
break;
case 2:
m.pixelType = FormatTools.UINT16;
break;
case 4:
m.pixelType = FormatTools.INT32;
break;
case 5:
m.pixelType = FormatTools.FLOAT;
break;
case 9:
m.pixelType = FormatTools.DOUBLE;
break;
default: throw new FormatException("Unsupported pixel type : " + type);
}
// read lookup table
in.skipBytes(12);
int c = in.readInt();
if (c > 1) {
m.sizeC = c;
int n = in.readInt();
lut = new byte[c][n];
in.skipBytes(436);
for (int i=0; i<lut.length; i++) {
for (int j=0; j<lut[0].length; j++) {
lut[i][j] = in.readByte();
}
}
}
else in.skipBytes(440);
offset = in.getFilePointer();
m.sizeZ = getImageCount();
m.sizeT = 1;
m.rgb = getSizeC() > 1;
m.interleaved = false;
m.littleEndian = dependency == 4 || dependency == 8;
m.dimensionOrder = "XYCZT";
m.indexed = lut != null;
m.falseColor = false;
m.metadataComplete = true;
if (isIndexed()) {
m.sizeC = 1;
m.rgb = false;
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
}