/*
* #%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.BufferedReader;
import java.io.IOException;
import java.io.StringReader;
import loci.common.Constants;
import loci.common.DateTools;
import loci.common.IniList;
import loci.common.IniParser;
import loci.common.IniTable;
import loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
import loci.formats.tiff.IFD;
import loci.formats.tiff.TiffParser;
import ome.xml.model.primitives.PositiveFloat;
import ome.xml.model.primitives.Timestamp;
import ome.units.quantity.Length;
/**
* SISReader is the file format reader for Olympus Soft Imaging Solutions
* TIFF files.
*/
public class SISReader extends BaseTiffReader {
// -- Constants --
private static final int SIS_TAG = 33560;
private static final int SIS_INI_TAG = 33471;
private static final int SIS_TAG_2 = 34853;
// -- Fields --
private String imageName;
private double magnification;
private String channelName;
private String cameraName;
private double physicalSizeX, physicalSizeY;
private String acquisitionDate;
// -- Constructor --
public SISReader() {
super("Olympus SIS TIFF", new String[] {"tif", "tiff"});
suffixSufficient = false;
suffixNecessary = true;
domains = new String[] {FormatTools.UNKNOWN_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
TiffParser tp = new TiffParser(stream);
IFD ifd = tp.getFirstIFD();
if (ifd == null) return false;
String software = ifd.getIFDTextValue(IFD.SOFTWARE);
String make = ifd.getIFDTextValue(IFD.MAKE);
return (ifd.get(SIS_TAG) != null &&
(software == null || software.startsWith("analySIS"))) ||
(ifd.get(SIS_TAG_2) != null &&
(make != null && make.startsWith("Olympus")));
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
imageName = null;
channelName = null;
cameraName = null;
magnification = 0d;
physicalSizeX = physicalSizeY = 0d;
}
}
// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
IFD ifd = ifds.get(0);
CoreMetadata m = core.get(0);
String iniMetadata = ifd.getIFDTextValue(SIS_INI_TAG);
if (iniMetadata != null) {
IniParser parser = new IniParser();
IniList ini =
parser.parseINI(new BufferedReader(new StringReader(iniMetadata)));
IniTable dimensions = ini.getTable("Dimension");
int z = Integer.parseInt(dimensions.get("Z"));
int c = Integer.parseInt(dimensions.get("Band"));
int t = Integer.parseInt(dimensions.get("Time"));
if (z * c * t == ifds.size()) {
m.sizeZ = z;
m.sizeT = t;
m.sizeC *= c;
}
// TODO : parse more metadata from the INI tables
}
if (!ifd.containsKey(SIS_TAG)) {
// TODO: parse this metadata more thoroughly
in.seek(ifd.getIFDLongValue(SIS_TAG_2, 0));
while (!in.readString(2).equals("IS")) {
in.seek(in.getFilePointer() - 1);
}
in.skipBytes(28);
in.seek(in.readLong() - 84);
physicalSizeX = in.readDouble() * 1000;
physicalSizeY = in.readDouble() * 1000;
return;
}
long metadataPointer = ifd.getIFDLongValue(SIS_TAG, 0);
in.seek(metadataPointer);
in.skipBytes(4);
in.skipBytes(6);
int minute = in.readShort();
int hour = in.readShort();
int day = in.readShort();
int month = in.readShort() + 1;
int year = 1900 + in.readShort();
acquisitionDate =
year + "-" + month + "-" + day + " " + hour + ":" + minute;
acquisitionDate = DateTools.formatDate(acquisitionDate, "yyyy-M-d H:m");
in.skipBytes(6);
imageName = in.readCString();
if ((in.getFilePointer() % 2) == 1) {
in.skipBytes(1);
}
short check = in.readShort();
while (check != 7 && check != 8) {
check = in.readShort();
if (check == 0x700 || check == 0x800 || check == 0xa00) {
in.skipBytes(1);
break;
}
}
in.skipBytes(4);
long pos = in.readInt() & 0xffffffffL;
if (pos >= in.length()) {
return;
}
in.seek(pos);
in.skipBytes(12);
physicalSizeX = in.readDouble();
physicalSizeY = in.readDouble();
if (Math.abs(physicalSizeX - physicalSizeY) > Constants.EPSILON) { // ??
physicalSizeX = physicalSizeY;
physicalSizeY = in.readDouble();
}
in.skipBytes(8);
magnification = in.readDouble();
int cameraNameLength = in.readShort();
channelName = in.readCString();
if (channelName.length() > 128) {
channelName = "";
}
int length = (int) Math.min(cameraNameLength, channelName.length());
if (length > 0) {
cameraName = channelName.substring(0, length);
}
// these are no longer valid
getGlobalMetadata().remove("XResolution");
getGlobalMetadata().remove("YResolution");
addGlobalMeta("Nanometers per pixel (X)", physicalSizeX);
addGlobalMeta("Nanometers per pixel (Y)", physicalSizeY);
addGlobalMeta("Magnification", magnification);
addGlobalMeta("Channel name", channelName);
addGlobalMeta("Camera name", cameraName);
addGlobalMeta("Image name", imageName);
addGlobalMeta("Acquisition date", acquisitionDate);
}
/* @see BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
store.setImageName(imageName, 0);
if (acquisitionDate != null) {
store.setImageAcquisitionDate(new Timestamp(acquisitionDate), 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
store.setImageInstrumentRef(instrument, 0);
String objective = MetadataTools.createLSID("Objective", 0, 0);
store.setObjectiveID(objective, 0, 0);
store.setObjectiveNominalMagnification(magnification, 0, 0);
store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
store.setObjectiveSettingsID(objective, 0);
String detector = MetadataTools.createLSID("Detector", 0, 0);
store.setDetectorID(detector, 0, 0);
store.setDetectorModel(cameraName, 0, 0);
store.setDetectorType(getDetectorType("Other"), 0, 0);
store.setDetectorSettingsID(detector, 0, 0);
physicalSizeX /= 1000;
physicalSizeY /= 1000;
Length sizeX = FormatTools.getPhysicalSizeX(physicalSizeX);
Length sizeY = FormatTools.getPhysicalSizeY(physicalSizeY);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
store.setChannelName(channelName, 0, 0);
}
}
}