/*
* #%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.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
import ome.units.quantity.Time;
import ome.units.UNITS;
/**
* SIFReader is the file format reader for Andor SIF files.
*/
public class SIFReader extends FormatReader {
// -- Constants --
private static final String MAGIC_STRING = "Andor Technology";
private static final int FOOTER_SIZE = 8;
// -- Fields --
private long pixelOffset;
// -- Constructor --
/** Constructs a new SIF reader. */
public SIFReader() {
super("Andor SIF", "sif");
domains = new String[] {FormatTools.LM_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 16;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readString(blockLen).equals(MAGIC_STRING);
}
/**
* @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(pixelOffset + no * FormatTools.getPlaneSize(this));
readPlane(in, x, y, w, h, buf);
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
pixelOffset = 0;
}
}
// -- 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);
double[] timestamp = null;
int lineNumber = 1;
String line = in.readLine();
int endLine = -1;
while (endLine < 0 || lineNumber < endLine) {
lineNumber++;
if (line.startsWith("Pixel number")) {
String[] tokens = line.split(" ");
if (tokens.length > 2) {
m.sizeC = Integer.parseInt(tokens[2]);
m.sizeX = Integer.parseInt(tokens[3]);
m.sizeY = Integer.parseInt(tokens[4]);
m.sizeZ = Integer.parseInt(tokens[5]);
m.sizeT = Integer.parseInt(tokens[6]);
m.imageCount = getSizeZ() * getSizeT() * getSizeC();
timestamp = new double[getImageCount()];
endLine = lineNumber;
pixelOffset = in.length() - FOOTER_SIZE -
(getImageCount() * getSizeX() * getSizeY() * 4);
}
}
else if (lineNumber < endLine) {
int index = lineNumber - (endLine - getImageCount()) - 1;
if (index >= 0) {
try {
timestamp[index] = Double.parseDouble(line.trim());
}
catch (NumberFormatException e) {
LOGGER.debug("Could not parse timestamp #" + index, e);
}
}
}
else {
addGlobalMetaList("Line", line.trim());
}
line = in.readLine();
}
m.pixelType = FormatTools.FLOAT;
m.dimensionOrder = "XYCZT";
m.littleEndian = true;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this,
getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
for (int i=0; i<getImageCount(); i++) {
store.setPlaneDeltaT(new Time(timestamp[i], UNITS.S), 0, i);
}
}
}
}