//
// SEQReader.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.FormatTools;
import loci.formats.tiff.IFD;
import loci.formats.tiff.TiffParser;
/**
* SEQReader is the file format reader for Image-Pro Sequence 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/SEQReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/SEQReader.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class SEQReader extends BaseTiffReader {
// -- Constants --
/**
* An array of shorts (length 12) with identical values in all of our
* samples; assuming this is some sort of format identifier.
*/
private static final int IMAGE_PRO_TAG_1 = 50288;
/** Frame rate. */
private static final int IMAGE_PRO_TAG_2 = 40105;
// -- Constructor --
/** Constructs a new Image-Pro SEQ reader. */
public SEQReader() {
super("Image-Pro Sequence", "seq");
domains = new String[] {FormatTools.UNKNOWN_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
TiffParser parser = new TiffParser(stream);
parser.setDoCaching(false);
IFD ifd = parser.getFirstIFD();
if (ifd == null) return false;
Object tag = ifd.get(IMAGE_PRO_TAG_1);
return tag != null && (tag instanceof short[]);
}
// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
core[0].sizeZ = 0;
core[0].sizeT = 0;
MetadataLevel level = getMetadataOptions().getMetadataLevel();
for (IFD ifd : ifds) {
if (level != MetadataLevel.MINIMUM) {
short[] tag1 = (short[]) ifd.getIFDValue(IMAGE_PRO_TAG_1);
if (tag1 != null) {
String seqId = "";
for (int i=0; i<tag1.length; i++) seqId = seqId + tag1[i];
addGlobalMeta("Image-Pro SEQ ID", seqId);
}
}
int tag2 = ifds.get(0).getIFDIntValue(IMAGE_PRO_TAG_2);
if (tag2 != -1) {
// should be one of these for every image plane
core[0].sizeZ++;
addGlobalMeta("Frame Rate", tag2);
}
addGlobalMeta("Number of images", getSizeZ());
}
if (getSizeZ() == 0) core[0].sizeZ = 1;
if (getSizeT() == 0) core[0].sizeT = 1;
if (getSizeZ() == 1 && getSizeT() == 1) {
core[0].sizeZ = ifds.size();
}
// default values
addGlobalMeta("frames", getSizeZ());
addGlobalMeta("channels", super.getSizeC());
addGlobalMeta("slices", getSizeT());
// parse the description to get channels, slices and times where applicable
String descr = ifds.get(0).getComment();
metadata.remove("Comment");
if (descr != null) {
String[] lines = descr.split("\n");
for (String token : lines) {
token = token.trim();
int eq = token.indexOf("=");
if (eq == -1) eq = token.indexOf(":");
if (eq != -1) {
String label = token.substring(0, eq);
String data = token.substring(eq + 1);
addGlobalMeta(label, data);
if (label.equals("channels")) core[0].sizeC = Integer.parseInt(data);
else if (label.equals("frames")) {
core[0].sizeT = Integer.parseInt(data);
}
else if (label.equals("slices")) {
core[0].sizeZ = Integer.parseInt(data);
}
}
}
}
if (isRGB() && getSizeC() != 3) core[0].sizeC *= 3;
core[0].dimensionOrder = "XY";
int maxNdx = 0, max = 0;
int[] dims = {getSizeZ(), getSizeC(), getSizeT()};
String[] axes = {"Z", "C", "T"};
for (int i=0; i<dims.length; i++) {
if (dims[i] > max) {
max = dims[i];
maxNdx = i;
}
}
core[0].dimensionOrder += axes[maxNdx];
if (maxNdx != 1) {
if (getSizeC() > 1) {
core[0].dimensionOrder += "C";
core[0].dimensionOrder += (maxNdx == 0 ? axes[2] : axes[0]);
}
else core[0].dimensionOrder += (maxNdx == 0 ? axes[2] : axes[0]) + "C";
}
else {
if (getSizeZ() > getSizeT()) core[0].dimensionOrder += "ZT";
else core[0].dimensionOrder += "TZ";
}
}
}