/* @see BaseTiffReader#initMetadataStore() */
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
if (date != null) {
date = DateTools.formatDate(date, DATE_FORMAT);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(MAGIC_STRING, 0);
if (scaling > 0) {
store.setPixelsPhysicalSizeX(new PositiveFloat(scaling), 0);
store.setPixelsPhysicalSizeY(new PositiveFloat(scaling), 0);
} else {
LOGGER.warn("Expected positive value for PhysicalSize; got {}", scaling);
}
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
store.setImageInstrumentRef(instrument, 0);
store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0);
if (magnification > 0) {
store.setObjectiveNominalMagnification(new PositiveInteger(magnification), 0, 0);
} else {
LOGGER.warn("Expected positive value for NominalMagnification; got {}", magnification);
}
store.setObjectiveImmersion(getImmersion(immersion), 0, 0);
String detector = MetadataTools.createLSID("Detector", 0, 0);
store.setDetectorID(detector, 0, 0);
store.setDetectorModel(cameraType + " " + cameraName, 0, 0);
store.setDetectorType(getDetectorType("CCD"), 0, 0);
for (int i = 0; i < getSizeC(); i++) {
store.setDetectorSettingsID(detector, 0, i);
store.setDetectorSettingsBinning(getBinning(binning), 0, i);
}
for (int i = 0; i < getImageCount(); i++) {
int[] zct = getZCTCoords(i);
store.setPlaneExposureTime(exposureTimes.get(zct[1]) / 1000000, 0, i);
}
}
}
private void populateMetadata() throws FormatException, IOException {
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
for (int i = 0; i < positions.size(); i++) {
Position p = positions.get(i);
if (p.time != null) {
String date = DateTools.formatDate(p.time, DATE_FORMAT);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), i);
}
}
if (positions.size() > 1) {
Location parent = new Location(p.metadataFile).getParentFile();
store.setImageName(parent.getName(), i);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(p.comment, i);
// link Instrument and Image
store.setImageInstrumentRef(instrumentID, i);
for (int c = 0; c < p.channels.length; c++) {
store.setChannelName(p.channels[c], i, c);
}
if (p.pixelSize != null && p.pixelSize > 0) {
store.setPixelsPhysicalSizeX(new PositiveFloat(p.pixelSize), i);
store.setPixelsPhysicalSizeY(new PositiveFloat(p.pixelSize), i);
} else {
LOGGER.warn("Expected positive value for PhysicalSizeX; got {}", p.pixelSize);
}
if (p.sliceThickness != null && p.sliceThickness > 0) {
store.setPixelsPhysicalSizeZ(new PositiveFloat(p.sliceThickness), i);
} else {
LOGGER.warn("Expected positive value for PhysicalSizeZ; got {}", p.sliceThickness);
}
int nextStamp = 0;
for (int q = 0; q < getImageCount(); q++) {
store.setPlaneExposureTime(p.exposureTime, i, q);
String tiff = positions.get(getSeries()).getFile(q);
if (tiff != null && new Location(tiff).exists() && nextStamp < p.timestamps.length) {
store.setPlaneDeltaT(p.timestamps[nextStamp++], i, q);
}
}
String serialNumber = p.detectorID;
p.detectorID = MetadataTools.createLSID("Detector", 0, i);
for (int c = 0; c < p.channels.length; c++) {
store.setDetectorSettingsBinning(getBinning(p.binning), i, c);
store.setDetectorSettingsGain(new Double(p.gain), i, c);
if (c < p.voltage.size()) {
store.setDetectorSettingsVoltage(p.voltage.get(c), i, c);
}
store.setDetectorSettingsID(p.detectorID, i, c);
}
store.setDetectorID(p.detectorID, 0, i);
if (p.detectorModel != null) {
store.setDetectorModel(p.detectorModel, 0, i);
}
if (serialNumber != null) {
store.setDetectorSerialNumber(serialNumber, 0, i);
}
if (p.detectorManufacturer != null) {
store.setDetectorManufacturer(p.detectorManufacturer, 0, i);
}
if (p.cameraMode == null) p.cameraMode = "Other";
store.setDetectorType(getDetectorType(p.cameraMode), 0, i);
store.setImagingEnvironmentTemperature(p.temperature, i);
}
}
}
/* @see BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
if (date != null) {
date = DateTools.formatDate(date, DATE_FORMAT);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
}
if (imageName != null) {
store.setImageName(imageName, 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (imageDescription != null) {
store.setImageDescription(imageDescription, 0);
}
if (userName != null) {
store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0);
store.setExperimenterLastName(userName, 0);
}
if (microscopeModel != null) {
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
store.setImageInstrumentRef(instrument, 0);
store.setMicroscopeModel(microscopeModel, 0);
}
if (detectors != null && detectors.size() > 0) {
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
store.setImageInstrumentRef(instrument, 0);
for (int i = 0; i < detectors.size(); i++) {
String detectorID = MetadataTools.createLSID("Detector", 0, i);
store.setDetectorID(detectorID, 0, i);
store.setDetectorModel(detectors.get(i), 0, i);
store.setDetectorType(getDetectorType("Other"), 0, i);
}
}
if (magnification != null) {
store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0);
store.setObjectiveNominalMagnification(magnification, 0, 0);
store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
}
store.setStageLabelX(stageX, 0);
store.setStageLabelY(stageY, 0);
store.setStageLabelZ(stageZ, 0);
store.setStageLabelName("", 0);
Length physicalSizeX = FormatTools.getPhysicalSizeX(sizeX);
Length physicalSizeY = FormatTools.getPhysicalSizeY(sizeY);
if (physicalSizeX != null) {
store.setPixelsPhysicalSizeX(physicalSizeX, 0);
}
if (physicalSizeY != null) {
store.setPixelsPhysicalSizeY(physicalSizeY, 0);
}
if (timeIncrement != null) {
store.setPixelsTimeIncrement(new Time(timeIncrement, UNITS.S), 0);
}
}
}
