/*
* #%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.FormatTools;
import loci.formats.tiff.IFD;
import loci.formats.tiff.TiffParser;
/**
* SEQReader is the file format reader for Image-Pro Sequence files.
*
* @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;
private static final int IMAGE_PRO_TAG_3 = 40100;
// -- Constructor --
/** Constructs a new Image-Pro SEQ reader. */
public SEQReader() {
super("Image-Pro Sequence", "seq");
domains = new String[] {FormatTools.UNKNOWN_DOMAIN};
suffixSufficient = false;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
TiffParser parser = new TiffParser(stream);
parser.setDoCaching(false);
IFD ifd = parser.getFirstIFD();
if (ifd == null) return false;
parser.fillInIFD(ifd);
Object tag1 = ifd.get(IMAGE_PRO_TAG_1);
Object tag3 = ifd.get(IMAGE_PRO_TAG_3);
return (tag1 != null && (tag1 instanceof short[])) || (tag3 != null &&
(tag3 instanceof int[]));
}
// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
CoreMetadata m = core.get(0);
m.sizeZ = 0;
m.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
m.sizeZ++;
addGlobalMeta("Frame Rate", tag2);
}
addGlobalMeta("Number of images", getSizeZ());
}
if (getSizeZ() == 0) m.sizeZ = 1;
if (getSizeT() == 0) m.sizeT = 1;
if (getSizeZ() == 1 && getSizeT() == 1) {
m.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")) m.sizeC = Integer.parseInt(data);
else if (label.equals("frames")) {
m.sizeT = Integer.parseInt(data);
}
else if (label.equals("slices")) {
m.sizeZ = Integer.parseInt(data);
}
}
}
}
if (isRGB() && getSizeC() != 3) m.sizeC *= 3;
m.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;
}
}
m.dimensionOrder += axes[maxNdx];
if (maxNdx != 1) {
if (getSizeC() > 1) {
m.dimensionOrder += "C";
m.dimensionOrder += (maxNdx == 0 ? axes[2] : axes[0]);
}
else m.dimensionOrder += (maxNdx == 0 ? axes[2] : axes[0]) + "C";
}
else {
if (getSizeZ() > getSizeT()) m.dimensionOrder += "ZT";
else m.dimensionOrder += "TZ";
}
}
}