//
// JPKReader.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.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.meta.MetadataStore;
import loci.formats.tiff.IFD;
import loci.formats.tiff.PhotoInterp;
/**
* JPKReader is the file format reader for JPK Instruments 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/JPKReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/JPKReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class JPKReader extends BaseTiffReader {
// -- Constructor --
/** Constructs a new JPK reader. */
public JPKReader() {
super("JPK Instruments", "jpk");
domains = new String[] {FormatTools.SEM_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
public boolean isThisType(String name, boolean open) {
return checkSuffix(name, "jpk");
}
/**
* @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
{
if (getSeriesCount() == 1) {
return super.openBytes(no, buf, x, y, w, h);
}
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
int ifd = series == 0 ? 0 : no + 1;
tiffParser.fillInIFD(ifds.get(ifd));
tiffParser.getSamples(ifds.get(ifd), buf, x, y, w, h);
return buf;
}
// -- Internal BaseTiffReader API methods --
/* @see loci.formats.BaseTiffReader#initStandardMetadata() */
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
ifds = tiffParser.getIFDs();
core = new CoreMetadata[ifds.size() > 1 ? 2 : 1];
// repopulate core metadata
for (int s=0; s<core.length; s++) {
core[s] = new CoreMetadata();
IFD ifd = ifds.get(s);
tiffParser.fillInIFD(ifd);
PhotoInterp p = ifd.getPhotometricInterpretation();
int samples = ifd.getSamplesPerPixel();
core[s].rgb = samples > 1 || p == PhotoInterp.RGB;
core[s].sizeX = (int) ifd.getImageWidth();
core[s].sizeY = (int) ifd.getImageLength();
core[s].sizeZ = 1;
core[s].sizeT = s == 0 ? 1 : ifds.size() - 1;
core[s].sizeC = core[s].rgb ? samples : 1;
core[s].littleEndian = ifd.isLittleEndian();
core[s].indexed = p == PhotoInterp.RGB_PALETTE &&
(get8BitLookupTable() != null || get16BitLookupTable() != null);
core[s].imageCount = s == 0 ? 1 : ifds.size() - 1;
core[s].pixelType = ifd.getPixelType();
core[s].metadataComplete = true;
core[s].interleaved = false;
core[s].falseColor = false;
core[s].dimensionOrder = "XYCZT";
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
setSeries(s);
for (Integer key : ifds.get(s).keySet()) {
if (key >= 32848) {
addSeriesMeta("Tag " + key, ifds.get(s).get(key));
}
}
}
}
setSeries(0);
}
/* @see loci.formats.BaseTiffReader#initMetadataStore() */
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
for (int i=0; i<getSeriesCount(); i++) {
store.setImageName("Series " + (i + 1), i);
}
}
}