/*
* #%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 java.util.ArrayList;
import java.util.Hashtable;
import java.util.Map;
import loci.common.RandomAccessInputStream;
import loci.common.xml.XMLTools;
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.PositiveInteger;
import ome.xml.model.primitives.Timestamp;
import ome.units.quantity.ElectricPotential;
import ome.units.quantity.Frequency;
import ome.units.quantity.Length;
import ome.units.quantity.Temperature;
import ome.units.quantity.Time;
import ome.units.UNITS;
/**
* NikonElementsTiffReader is the file format reader for TIFF files produced
* by Nikon Elements.
*/
public class NikonElementsTiffReader extends BaseTiffReader {
// -- Constants --
private static final int NIKON_XML_TAG = 65332;
private static final int NIKON_XML_TAG_2 = 65333;
// -- Fields --
private ND2Handler handler;
// -- Constructor --
public NikonElementsTiffReader() {
super("Nikon Elements TIFF", new String[] {"tif", "tiff"});
suffixSufficient = false;
domains = new String[] {FormatTools.LM_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;
return ifd.containsKey(NIKON_XML_TAG);
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
handler = null;
}
}
// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
String xml = ifds.get(0).getIFDTextValue(NIKON_XML_TAG).trim();
if (xml.length() == 0) {
xml = ifds.get(0).getIFDTextValue(NIKON_XML_TAG_2).trim();
}
int open = xml.indexOf("<");
if (open >= 0) {
xml = xml.substring(open);
}
xml = "<NIKON>" + xml + "</NIKON>";
xml = XMLTools.sanitizeXML(xml);
handler = new ND2Handler(core, false, getImageCount());
try {
XMLTools.parseXML(xml, handler);
final Map<String, Object> globalMetadata = handler.getMetadata();
for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
addGlobalMeta(entry.getKey(), entry.getValue());
}
}
catch (IOException e) { }
}
/* @see BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
String date = handler.getDate();
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
return;
}
Length sizeX = FormatTools.getPhysicalSizeX(handler.getPixelSizeX());
Length sizeY = FormatTools.getPhysicalSizeY(handler.getPixelSizeY());
Length sizeZ = FormatTools.getPhysicalSizeZ(handler.getPixelSizeZ());
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
if (sizeZ != null) {
store.setPixelsPhysicalSizeZ(sizeZ, 0);
}
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
store.setImageInstrumentRef(instrument, 0);
ArrayList<Double> exposureTimes = handler.getExposureTimes();
ArrayList<Length> posX = handler.getXPositions();
ArrayList<Length> posY = handler.getYPositions();
ArrayList<Length> posZ = handler.getZPositions();
for (int i=0; i<getImageCount(); i++) {
int c = getZCTCoords(i)[1];
if (c < exposureTimes.size() && exposureTimes.get(c) != null) {
store.setPlaneExposureTime(new Time(exposureTimes.get(c), UNITS.S), 0, i);
}
if (i < posX.size()) {
store.setPlanePositionX(posX.get(i), 0, i);
}
if (i < posY.size()) {
store.setPlanePositionY(posY.get(i), 0, i);
}
if (i < posZ.size()) {
store.setPlanePositionZ(posZ.get(i), 0, i);
}
}
String detector = MetadataTools.createLSID("Detector", 0, 0);
store.setDetectorID(detector, 0, 0);
store.setDetectorModel(handler.getCameraModel(), 0, 0);
store.setDetectorType(getDetectorType("Other"), 0, 0);
ArrayList<String> channelNames = handler.getChannelNames();
ArrayList<String> modality = handler.getModalities();
ArrayList<String> binning = handler.getBinnings();
ArrayList<Double> speed = handler.getSpeeds();
ArrayList<Double> gain = handler.getGains();
ArrayList<Double> temperature = handler.getTemperatures();
ArrayList<Double> exWave = handler.getExcitationWavelengths();
ArrayList<Double> emWave = handler.getEmissionWavelengths();
ArrayList<Integer> power = handler.getPowers();
ArrayList<Hashtable<String, String>> rois = handler.getROIs();
Double pinholeSize = handler.getPinholeSize();
for (int c=0; c<getEffectiveSizeC(); c++) {
if (pinholeSize != null) {
store.setChannelPinholeSize(new Length(pinholeSize, UNITS.MICROM), 0, c);
}
if (c < channelNames.size()) {
store.setChannelName(channelNames.get(c), 0, c);
}
if (c < modality.size()) {
store.setChannelAcquisitionMode(
getAcquisitionMode(modality.get(c)), 0, c);
}
if (c < emWave.size()) {
Length em = FormatTools.getEmissionWavelength(emWave.get(c));
if (em != null) {
store.setChannelEmissionWavelength(em, 0, c);
}
}
if (c < exWave.size()) {
Length ex = FormatTools.getExcitationWavelength(exWave.get(c));
if (ex != null) {
store.setChannelExcitationWavelength(ex, 0, c);
}
}
if (c < binning.size()) {
store.setDetectorSettingsBinning(getBinning(binning.get(c)), 0, c);
}
if (c < gain.size()) {
store.setDetectorSettingsGain(gain.get(c), 0, c);
}
if (c < speed.size()) {
store.setDetectorSettingsReadOutRate(
new Frequency(speed.get(c), UNITS.HZ), 0, c);
}
store.setDetectorSettingsID(detector, 0, c);
}
if (temperature.size() > 0) {
store.setImagingEnvironmentTemperature(new Temperature(
temperature.get(0), UNITS.DEGREEC), 0);
}
Double voltage = handler.getVoltage();
if (voltage != null) {
store.setDetectorSettingsVoltage(
new ElectricPotential(voltage, UNITS.V), 0, 0);
}
Double na = handler.getNumericalAperture();
if (na != null) store.setObjectiveLensNA(na, 0, 0);
Double mag = handler.getMagnification();
if (mag != null) store.setObjectiveCalibratedMagnification(mag, 0, 0);
store.setObjectiveModel(handler.getObjectiveModel(), 0, 0);
String immersion = handler.getImmersion();
if (immersion == null) immersion = "Other";
store.setObjectiveImmersion(getImmersion(immersion), 0, 0);
String correction = handler.getCorrection();
if (correction == null || correction.length() == 0) correction = "Other";
store.setObjectiveCorrection(getCorrection(correction), 0, 0);
String objective = MetadataTools.createLSID("Objective", 0, 0);
store.setObjectiveID(objective, 0, 0);
store.setObjectiveSettingsID(objective, 0);
Double refractiveIndex = handler.getRefractiveIndex();
if (refractiveIndex != null) {
store.setObjectiveSettingsRefractiveIndex(refractiveIndex, 0);
}
if (getMetadataOptions().getMetadataLevel() == MetadataLevel.NO_OVERLAYS) {
return;
}
handler.populateROIs(store);
}
}