/*
* #%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.FormatException;
import loci.formats.CoreMetadata;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.UnsupportedCompressionException;
import loci.formats.meta.MetadataStore;
/**
* LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.
*/
public class LIMReader extends FormatReader {
// -- Constants --
private static final int PIXELS_OFFSET = 0x94b;
// -- Fields --
private boolean isCompressed;
// -- Constructor --
/** Constructs a new LIM reader. */
public LIMReader() {
super("Laboratory Imaging", "lim");
domains = new String[] {FormatTools.LM_DOMAIN};
}
// -- IFormatReader API methods --
/**
* @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);
in.seek(PIXELS_OFFSET);
readPlane(in, x, y, w, h, buf);
// swap red and blue channels
if (isRGB()) {
for (int i=0; i<buf.length/3; i++) {
byte tmp = buf[i*3];
buf[i*3] = buf[i*3 + 2];
buf[i*3 + 2] = tmp;
}
}
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) isCompressed = 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);
CoreMetadata m = core.get(0);
m.littleEndian = true;
in.order(isLittleEndian());
m.sizeX = in.readShort() & 0x7fff;
m.sizeY = in.readShort();
int bits = in.readShort();
while (bits % 8 != 0) bits++;
if ((bits % 3) == 0) {
m.sizeC = 3;
bits /= 3;
}
m.pixelType = FormatTools.pixelTypeFromBytes(bits / 8, false, false);
isCompressed = in.readShort() != 0;
addGlobalMeta("Is compressed", isCompressed);
if (isCompressed) {
throw new UnsupportedCompressionException(
"Compressed LIM files not supported.");
}
m.imageCount = 1;
m.sizeZ = 1;
m.sizeT = 1;
if (getSizeC() == 0) m.sizeC = 1;
m.rgb = getSizeC() > 1;
m.dimensionOrder = "XYZCT";
m.indexed = false;
m.falseColor = false;
m.interleaved = true;
m.metadataComplete = true;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
}