//
// SeikoReader.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.MetadataTools;
import loci.formats.meta.MetadataStore;
import ome.xml.model.primitives.PositiveFloat;
/**
* SeikoReader is the file format reader for Seiko .xqd/.xqf 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/SeikoReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/SeikoReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class SeikoReader extends FormatReader {
// -- Constants --
private static final int HEADER_SIZE = 2944;
// -- Fields --
// -- Constructor --
/** Constructs a new Seiko reader. */
public SeikoReader() {
super("Seiko", new String[] {"xqd", "xqf"});
domains = new String[] {FormatTools.SEM_DOMAIN};
}
// -- IFormatReader API methods --
/**
* @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);
in.seek(HEADER_SIZE);
readPlane(in, x, y, w, h, buf);
return buf;
}
// -- 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);
core[0].littleEndian = true;
in.order(isLittleEndian());
String comment = null;
double xSize = 0d, ySize = 0d;
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
in.seek(40);
comment = in.readCString();
in.seek(156);
xSize = in.readFloat();
in.skipBytes(4);
ySize = in.readFloat();
addGlobalMeta("Comment", comment);
}
in.seek(1402);
core[0].sizeX = in.readShort();
core[0].sizeY = in.readShort();
core[0].sizeZ = 1;
core[0].sizeC = 1;
core[0].sizeT = 1;
core[0].imageCount = 1;
core[0].dimensionOrder = "XYZCT";
core[0].pixelType = FormatTools.UINT16;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
MetadataTools.setDefaultCreationDate(store, currentId, 0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(comment, 0);
store.setPixelsPhysicalSizeX(new PositiveFloat(xSize), 0);
store.setPixelsPhysicalSizeY(new PositiveFloat(ySize), 0);
}
}
}