Examples with PositiveFloat ome.xml.model.primitives.PositiveFloat used on opensource projects

Example 6 with PositiveFloat

use of ome.xml.model.primitives.PositiveFloat in project bioformats by openmicroscopy.

the class PrairieReader method populateOMEMetadata.

/**
 * This step populates the OME {@link MetadataStore} by extracting relevant
 * values from the parsed {@link #meta} structure.
 */
private void populateOMEMetadata() throws FormatException {
    LOGGER.info("Populating OME metadata");
    // populate required Pixels metadata
    final boolean minimumMetadata = isMinimumMetadata();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, !minimumMetadata);
    // populate required AcquisitionDate
    final String date = DateTools.formatDate(meta.getDate(), DATE_FORMAT);
    final Timestamp acquisitionDate = Timestamp.valueOf(date);
    final int seriesCount = getSeriesCount();
    for (int s = 0; s < seriesCount; s++) {
        setSeries(s);
        if (date != null)
            store.setImageAcquisitionDate(acquisitionDate, s);
    }
    if (minimumMetadata)
        return;
    // create an Instrument
    final String instrumentID = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrumentID, 0);
    // populate Laser Power, if available
    final Double laserPower = meta.getLaserPower();
    if (laserPower != null) {
        // create a Laser
        final String laserID = MetadataTools.createLSID("LightSource", 0, 0);
        store.setLaserID(laserID, 0, 0);
        store.setLaserPower(new Power(laserPower, UNITS.MILLIWATT), 0, 0);
    }
    String objectiveID = null;
    for (int s = 0; s < seriesCount; s++) {
        setSeries(s);
        final Sequence sequence = sequence(s);
        final Frame firstFrame = sequence.getFirstFrame();
        // link Instrument and Image
        store.setImageInstrumentRef(instrumentID, s);
        // populate PhysicalSizeX
        final PositiveFloat physicalSizeX = pf(firstFrame.getMicronsPerPixelX(), "PhysicalSizeX");
        if (physicalSizeX != null) {
            store.setPixelsPhysicalSizeX(FormatTools.createLength(physicalSizeX, UNITS.MICROMETER), s);
        }
        // populate PhysicalSizeY
        final PositiveFloat physicalSizeY = pf(firstFrame.getMicronsPerPixelY(), "PhysicalSizeY");
        if (physicalSizeY != null) {
            store.setPixelsPhysicalSizeY(FormatTools.createLength(physicalSizeY, UNITS.MICROMETER), s);
        }
        // populate TimeIncrement
        final Double waitTime = meta.getWaitTime();
        if (waitTime != null)
            store.setPixelsTimeIncrement(new Time(waitTime, UNITS.SECOND), s);
        final String[] detectorIDs = new String[channels.length];
        for (int c = 0; c < channels.length; c++) {
            final int channel = channels[c];
            final PFile file = firstFrame.getFile(channel);
            // populate channel name
            final String channelName = file == null ? null : file.getChannelName();
            if (channelName != null)
                store.setChannelName(channelName, s, c);
            // populate emission wavelength
            if (file != null) {
                final Double waveMin = file.getWavelengthMin();
                final Double waveMax = file.getWavelengthMax();
                if (waveMin != null && waveMax != null) {
                    final double waveAvg = (waveMin + waveMax) / 2;
                    final Length wavelength = FormatTools.getEmissionWavelength(waveAvg);
                    store.setChannelEmissionWavelength(wavelength, s, c);
                }
            }
            if (detectorIDs[c] == null) {
                // create a Detector for this channel
                detectorIDs[c] = MetadataTools.createLSID("Detector", 0, c);
                store.setDetectorID(detectorIDs[c], 0, c);
                store.setDetectorType(getDetectorType("Other"), 0, c);
                // NB: Ideally we would populate the detector zoom differently for
                // each Image, rather than globally for the Detector, but
                // unfortunately it is a property of Detector, not DetectorSettings.
                final Double zoom = firstFrame.getOpticalZoom();
                if (zoom != null)
                    store.setDetectorZoom(zoom, 0, c);
            }
            // link DetectorSettings and Detector
            store.setDetectorSettingsID(detectorIDs[c], s, c);
            // populate Offset
            final Double offset = firstFrame.getOffset(c);
            if (offset != null)
                store.setDetectorSettingsOffset(offset, s, c);
            // populate Gain
            final Double gain = firstFrame.getGain(c);
            if (gain != null)
                store.setDetectorSettingsGain(gain, s, c);
        }
        if (objectiveID == null) {
            // create an Objective
            objectiveID = MetadataTools.createLSID("Objective", 0, 0);
            store.setObjectiveID(objectiveID, 0, 0);
            store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
            // populate Objective NominalMagnification
            final Double magnification = firstFrame.getMagnification();
            if (magnification != null) {
                store.setObjectiveNominalMagnification(magnification, 0, 0);
            }
            // populate Objective Manufacturer
            final String objectiveManufacturer = firstFrame.getObjectiveManufacturer();
            store.setObjectiveManufacturer(objectiveManufacturer, 0, 0);
            // populate Objective Immersion
            final String immersion = firstFrame.getImmersion();
            store.setObjectiveImmersion(getImmersion(immersion), 0, 0);
            // populate Objective LensNA
            final Double lensNA = firstFrame.getObjectiveLensNA();
            if (lensNA != null)
                store.setObjectiveLensNA(lensNA, 0, 0);
            // populate Microscope Model
            final String microscopeModel = firstFrame.getImagingDevice();
            store.setMicroscopeModel(microscopeModel, 0);
        }
        // link ObjectiveSettings and Objective
        store.setObjectiveSettingsID(objectiveID, s);
        // populate stage position coordinates
        for (int t = 0; t < getSizeT(); t++) {
            final Sequence tSequence = sequence(t, s);
            for (int z = 0; z < getSizeZ(); z++) {
                final int index = frameIndex(tSequence, z, t, s);
                final Frame zFrame = tSequence.getFrame(index);
                if (zFrame == null) {
                    warnFrame(sequence, index);
                    continue;
                }
                final Length posX = zFrame.getPositionX();
                final Length posY = zFrame.getPositionY();
                final Length posZ = zFrame.getPositionZ();
                final Double deltaT = zFrame.getRelativeTime();
                for (int c = 0; c < getSizeC(); c++) {
                    final int i = getIndex(z, c, t);
                    if (posX != null)
                        store.setPlanePositionX(posX, s, i);
                    if (posY != null)
                        store.setPlanePositionY(posY, s, i);
                    if (posZ != null)
                        store.setPlanePositionZ(posZ, s, i);
                    if (deltaT != null)
                        store.setPlaneDeltaT(new Time(deltaT, UNITS.SECOND), s, i);
                }
            }
        }
    }
    setSeries(0);
}