//
// FujiReader.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.DataTools;
import loci.common.DateTools;
import loci.common.Location;
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;
/**
* FujiReader is the file format reader for Fuji LAS 3000 datasets.
*
* <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/FujiReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/FujiReader.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class FujiReader extends FormatReader {
// -- Constants --
private static final String DATE_FORMAT = "ddd MMM dd HH:mm:ss yyyy";
// -- Fields --
private String infFile;
private String pixelsFile;
// -- Constructor --
/** Constructs a new Fuji reader. */
public FujiReader() {
super("Fuji LAS 3000", new String[] {"img", "inf"});
domains = new String[] {FormatTools.GEL_DOMAIN};
hasCompanionFiles = true;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
public boolean isThisType(String name, boolean open) {
if (!super.isThisType(name, open)) return false;
if (!open) return false;
String baseName = name.substring(0, name.lastIndexOf("."));
if (checkSuffix(name, "inf")) {
return new Location(baseName + ".img").exists();
}
else if (checkSuffix(name, "img")) {
return new Location(baseName + ".inf").exists();
}
return false;
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
return false;
}
/* @see loci.formats.IFormatReader#isSingleFile(String) */
public boolean isSingleFile(String id) throws FormatException, IOException {
return false;
}
/**
* @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);
RandomAccessInputStream s = new RandomAccessInputStream(pixelsFile);
readPlane(s, x, y, w, h, buf);
s.close();
return buf;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
if (noPixels) {
return new String[] {infFile};
}
return new String[] {infFile, pixelsFile};
}
/* @see loci.formats.IFormatReader#fileGroupOption(String) */
public int fileGroupOption(String id) throws FormatException, IOException {
return FormatTools.MUST_GROUP;
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
infFile = null;
pixelsFile = null;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
if (checkSuffix(id, "inf")) {
infFile = new Location(id).getAbsolutePath();
pixelsFile = infFile.substring(0, infFile.lastIndexOf(".")) + ".img";
}
else {
pixelsFile = new Location(id).getAbsolutePath();
infFile = pixelsFile.substring(0, pixelsFile.lastIndexOf(".")) + ".inf";
}
String[] lines = DataTools.readFile(infFile).split("\r\n");
int bits = Integer.parseInt(lines[5]);
core[0].pixelType = FormatTools.pixelTypeFromBytes(bits / 8, false, false);
core[0].sizeX = Integer.parseInt(lines[6]);
core[0].sizeY = Integer.parseInt(lines[7]);
core[0].sizeC = 1;
core[0].sizeT = 1;
core[0].sizeZ = 1;
core[0].imageCount = getSizeZ() * getSizeC() * getSizeT();
core[0].dimensionOrder = "XYCZT";
for (int i=0; i<lines.length; i++) {
addGlobalMeta("Line #" + (i + 1), lines[i]);
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
String imageName = lines[1];
String timestamp = lines[10];
store.setImageName(imageName, 0);
store.setImageAcquiredDate(DateTools.formatDate(timestamp, DATE_FORMAT), 0);
double physicalWidth = Double.parseDouble(lines[3]);
double physicalHeight = Double.parseDouble(lines[4]);
if (physicalWidth > 0) {
store.setPixelsPhysicalSizeX(new PositiveFloat(physicalWidth), 0);
}
if (physicalHeight > 0) {
store.setPixelsPhysicalSizeY(new PositiveFloat(physicalHeight), 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
String instrument = lines[13];
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
store.setMicroscopeModel(instrument, 0);
}
}
}