/*
* #%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.DataTools;
import loci.common.DateTools;
import loci.common.Location;
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;
import ome.xml.model.primitives.PositiveFloat;
import ome.xml.model.primitives.Timestamp;
import ome.units.quantity.Length;
/**
* FujiReader is the file format reader for Fuji LAS 3000 datasets.
*
* @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) */
@Override
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) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
return false;
}
/* @see loci.formats.IFormatReader#isSingleFile(String) */
@Override
public boolean isSingleFile(String id) throws FormatException, IOException {
return false;
}
/**
* @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);
RandomAccessInputStream s = new RandomAccessInputStream(pixelsFile);
readPlane(s, x, y, w, h, buf);
s.close();
return buf;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
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) */
@Override
public int fileGroupOption(String id) throws FormatException, IOException {
return FormatTools.MUST_GROUP;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
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) */
@Override
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{0,1}\n");
int bits = Integer.parseInt(lines[5]);
CoreMetadata m = core.get(0);
m.pixelType = FormatTools.pixelTypeFromBytes(bits / 8, false, false);
m.sizeX = Integer.parseInt(lines[6]);
m.sizeY = Integer.parseInt(lines[7]);
m.sizeC = 1;
m.sizeT = 1;
m.sizeZ = 1;
m.imageCount = getSizeZ() * getSizeC() * getSizeT();
m.dimensionOrder = "XYCZT";
for (String line : lines) {
addGlobalMetaList("Line", line);
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
String imageName = lines[1];
String timestamp = lines[10];
timestamp = DateTools.formatDate(timestamp, DATE_FORMAT);
store.setImageName(imageName, 0);
if (timestamp != null) {
store.setImageAcquisitionDate(new Timestamp(timestamp), 0);
}
double physicalWidth = Double.parseDouble(lines[3]);
double physicalHeight = Double.parseDouble(lines[4]);
Length sizeX = FormatTools.getPhysicalSizeX(physicalWidth);
Length sizeY = FormatTools.getPhysicalSizeY(physicalHeight);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
String instrument = lines[13];
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
store.setMicroscopeModel(instrument, 0);
}
}
}