Examples with Time ome.units.quantity.Time used on opensource projects

Example 61 with Time

use of ome.units.quantity.Time in project bioformats by openmicroscopy.

the class NiftiReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    // the dataset has two files - we want the one ending in '.hdr'
    if (id.endsWith(".img")) {
        LOGGER.info("Looking for header file");
        String header = id.substring(0, id.lastIndexOf(".")) + ".hdr";
        if (new Location(header).exists()) {
            setId(header);
            return;
        } else
            throw new FormatException("Header file not found.");
    }
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    in.seek(40);
    short check = in.readShort();
    boolean little = check < 1 || check > 7;
    in.seek(40);
    if (id.endsWith(".hdr")) {
        pixelsFilename = id.substring(0, id.lastIndexOf(".")) + ".img";
        pixelFile = new RandomAccessInputStream(pixelsFilename);
    } else if (checkSuffix(id, "nii")) {
        pixelsFilename = id;
        pixelFile = in;
    } else {
        throw new FormatException("File does not have one of the required NIfTI extensions (.img, .hdr, .nii, .nii.gz)");
    }
    in.order(little);
    pixelFile.order(little);
    m.littleEndian = little;
    LOGGER.info("Reading header");
    nDimensions = in.readShort();
    m.sizeX = in.readShort();
    m.sizeY = in.readShort();
    m.sizeZ = in.readShort();
    m.sizeT = in.readShort();
    m.sizeC = 1;
    int[] extraDims = new int[3];
    extraDims[0] = in.readShort();
    extraDims[1] = in.readShort();
    extraDims[2] = in.readShort();
    if (nDimensions > 4) {
        LOGGER.debug("nDimensions = {}", nDimensions);
        for (int i = 0; i < nDimensions - 4; i++) {
            LOGGER.debug("  processing dimension = {}, Z = {}, T = {}, C = {}", extraDims[i], getSizeZ(), getSizeT(), getSizeC());
            m.sizeC *= extraDims[i];
        }
    }
    in.skipBytes(14);
    short dataType = in.readShort();
    in.skipBytes(36);
    pixelOffset = (int) in.readFloat();
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        populateExtendedMetadata();
    }
    LOGGER.info("Populating core metadata");
    if (getSizeZ() == 0)
        m.sizeZ = 1;
    if (getSizeT() == 0)
        m.sizeT = 1;
    m.imageCount = getSizeZ() * getSizeT() * getSizeC();
    m.indexed = false;
    m.dimensionOrder = "XYCZT";
    populatePixelType(dataType);
    m.rgb = getSizeC() > 1 && getImageCount() == getSizeZ() * getSizeT();
    m.interleaved = isRGB();
    LOGGER.info("Populating MetadataStore");
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        store.setImageDescription(description, 0);
        Length sizeX = FormatTools.getPhysicalSizeX(new Double(voxelWidth), spatialUnit);
        Length sizeY = FormatTools.getPhysicalSizeY(new Double(voxelHeight), spatialUnit);
        Length sizeZ = FormatTools.getPhysicalSizeZ(new Double(sliceThickness), spatialUnit);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
        store.setPixelsTimeIncrement(new Time(new Double(deltaT), timeUnit), 0);
    }
}

Example 62 with Time

use of ome.units.quantity.Time in project bioformats by openmicroscopy.

the class NikonElementsTiffReader method initMetadataStore.

/* @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.SECOND), 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.MICROMETER), 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.HERTZ), 0, c);
        }
        store.setDetectorSettingsID(detector, 0, c);
    }
    if (temperature.size() > 0) {
        store.setImagingEnvironmentTemperature(new Temperature(temperature.get(0), UNITS.CELSIUS), 0);
    }
    Double voltage = handler.getVoltage();
    if (voltage != null) {
        store.setDetectorSettingsVoltage(new ElectricPotential(voltage, UNITS.VOLT), 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);
}

Example 63 with Time

use of ome.units.quantity.Time in project bioformats by openmicroscopy.

the class PCIReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    imageFiles = new HashMap<Integer, String>();
    timestamps = new HashMap<Integer, Double>();
    uniqueZ = new ArrayList<Double>();
    CoreMetadata m = core.get(0);
    initPOIService();
    double scaleFactor = 1;
    final List<String> allFiles = poi.getDocumentList();
    if (allFiles.isEmpty()) {
        throw new FormatException("No files were found - the .cxd may be corrupt.");
    }
    double firstZ = 0d, secondZ = 0d;
    int mode = 0;
    for (String name : allFiles) {
        int separator = name.lastIndexOf(File.separator);
        String parent = name.substring(0, separator);
        String relativePath = name.substring(separator + 1);
        RandomAccessInputStream stream = null;
        if (!(relativePath.startsWith("Bitmap") || (relativePath.equals("Data") && parent.indexOf("Image") != -1))) {
            stream = poi.getDocumentStream(name);
            stream.order(true);
        }
        if (stream != null && stream.length() == 8) {
            double value = stream.readDouble();
            stream.seek(0);
            String key = name.replace(File.separatorChar, ' ');
            key = key.replaceAll("Root Entry ", "");
            key = key.replaceAll("Field Data ", "");
            key = key.replaceAll("Details ", "");
            addGlobalMeta(key, value);
        }
        if (relativePath.equals("Field Count")) {
            m.imageCount = stream.readInt();
        } else if (relativePath.equals("File Has Image")) {
            if (stream.readShort() == 0) {
                throw new FormatException("This file does not contain image data.");
            }
        } else if (relativePath.startsWith("Bitmap") || (relativePath.equals("Data") && parent.indexOf("Image") != -1)) {
            imageFiles.put(imageFiles.size(), name);
            if (getSizeX() != 0 && getSizeY() != 0) {
                int bpp = FormatTools.getBytesPerPixel(getPixelType());
                int plane = getSizeX() * getSizeY() * bpp;
                if (getSizeC() == 0 || getSizeC() * plane > poi.getFileSize(name)) {
                    m.sizeC = poi.getFileSize(name) / plane;
                }
            }
        } else if (relativePath.indexOf("Image_Depth") != -1) {
            boolean firstBits = m.bitsPerPixel == 0;
            int bits = (int) stream.readDouble();
            m.bitsPerPixel = bits;
            while (bits % 8 != 0 || bits == 0) bits++;
            if (bits % 3 == 0) {
                m.sizeC = 3;
                bits /= 3;
                m.bitsPerPixel /= 3;
            }
            bits /= 8;
            m.pixelType = FormatTools.pixelTypeFromBytes(bits, false, false);
            if (getSizeC() > 1 && firstBits) {
                m.sizeC /= bits;
            }
        } else if (relativePath.indexOf("Image_Height") != -1 && getSizeY() == 0) {
            m.sizeY = (int) stream.readDouble();
        } else if (relativePath.indexOf("Image_Width") != -1 && getSizeX() == 0) {
            m.sizeX = (int) stream.readDouble();
        } else if (relativePath.indexOf("Time_From_Start") != -1) {
            timestamps.put(getTimestampIndex(parent), stream.readDouble());
        } else if (relativePath.indexOf("Position_Z") != -1) {
            double zPos = stream.readDouble();
            if (!uniqueZ.contains(zPos) && getSizeZ() <= 1) {
                uniqueZ.add(zPos);
            }
            if (name.indexOf("Field 1" + File.separator) != -1)
                firstZ = zPos;
            else if (name.indexOf("Field 2" + File.separator) != -1)
                secondZ = zPos;
        } else if (relativePath.equals("First Field Date & Time")) {
            long date = (long) stream.readDouble() * 1000;
            creationDate = DateTools.convertDate(date, DateTools.COBOL);
        } else if (relativePath.equals("GroupMode")) {
            mode = stream.readInt();
        } else if (relativePath.equals("GroupSelectedFields")) {
            m.sizeZ = (int) (stream.length() / 8);
        } else if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            if (relativePath.equals("Binning")) {
                binning = (int) stream.readDouble();
            } else if (relativePath.equals("Comments")) {
                String comments = stream.readString((int) stream.length());
                String[] lines = comments.split("\n");
                for (String line : lines) {
                    int eq = line.indexOf('=');
                    if (eq != -1) {
                        String key = line.substring(0, eq).trim();
                        String value = line.substring(eq + 1).trim();
                        addGlobalMeta(key, value);
                        if (key.equals("factor")) {
                            if (value.indexOf(';') != -1) {
                                value = value.substring(0, value.indexOf(';'));
                            }
                            scaleFactor = Double.parseDouble(value.trim());
                        }
                    }
                }
            }
        }
        if (stream != null) {
            stream.close();
        }
    }
    boolean zFirst = Math.abs(firstZ - secondZ) > Constants.EPSILON;
    if (getSizeC() == 0)
        m.sizeC = 1;
    if (mode == 0) {
        m.sizeZ = 0;
    }
    if (getSizeZ() <= 1 || (getImageCount() % getSizeZ()) != 0) {
        m.sizeZ = uniqueZ.isEmpty() ? 1 : uniqueZ.size();
    }
    m.sizeT = getImageCount() / getSizeZ();
    while (getSizeZ() * getSizeT() < getImageCount()) {
        m.sizeZ++;
        m.sizeT = getImageCount() / getSizeZ();
    }
    m.rgb = getSizeC() > 1;
    if (imageFiles.size() > getImageCount() && getSizeC() == 1) {
        m.sizeC = imageFiles.size() / getImageCount();
        m.imageCount *= getSizeC();
    } else {
        m.imageCount = getSizeZ() * getSizeT();
    }
    m.interleaved = false;
    m.dimensionOrder = zFirst ? "XYCZT" : "XYCTZ";
    m.littleEndian = true;
    m.indexed = false;
    m.falseColor = false;
    m.metadataComplete = true;
    // re-index image files
    String[] files = imageFiles.values().toArray(new String[imageFiles.size()]);
    for (String file : files) {
        int separator = file.lastIndexOf(File.separator);
        String parent = file.substring(0, separator);
        imageFiles.put(getImageIndex(parent), file);
    }
    int bpp = FormatTools.getBytesPerPixel(m.pixelType);
    int expectedPlaneSize = m.sizeX * m.sizeY * bpp * m.sizeC;
    String file = imageFiles.get(0);
    RandomAccessInputStream s = poi.getDocumentStream(file);
    TiffParser tp = new TiffParser(s);
    // don't correct the image width if it's stored as a TIFF
    if (!tp.isValidHeader() && s.length() > expectedPlaneSize) {
        m.sizeX += (s.length() - expectedPlaneSize) / (m.sizeY * bpp * m.sizeC);
    }
    s.close();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (creationDate != null) {
        store.setImageAcquisitionDate(new Timestamp(creationDate), 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(scaleFactor);
        Length sizeY = FormatTools.getPhysicalSizeY(scaleFactor);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        for (int i = 0; i < timestamps.size(); i++) {
            if (i >= getImageCount()) {
                break;
            }
            Double timestamp = timestamps.get(i);
            if (timestamp != null) {
                store.setPlaneDeltaT(new Time(timestamp, UNITS.SECOND), 0, i);
            }
            if (i == 2) {
                Double first = timestamps.get(1);
                Double increment = timestamp - first;
                if (increment != null) {
                    store.setPixelsTimeIncrement(new Time(increment, UNITS.SECOND), 0);
                }
            }
        }
        if (binning > 0) {
            String instrumentID = MetadataTools.createLSID("Instrument", 0);
            String detectorID = MetadataTools.createLSID("Detector", 0);
            store.setInstrumentID(instrumentID, 0);
            store.setDetectorID(detectorID, 0, 0);
            store.setDetectorType(getDetectorType("Other"), 0, 0);
            store.setImageInstrumentRef(instrumentID, 0);
            Binning binningEnum = getBinning(binning + "x" + binning);
            for (int c = 0; c < getEffectiveSizeC(); c++) {
                store.setDetectorSettingsID(detectorID, 0, c);
                store.setDetectorSettingsBinning(binningEnum, 0, c);
            }
        }
    }
}

Example 64 with Time

use of ome.units.quantity.Time 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);
}

Example 65 with Time

use of ome.units.quantity.Time in project bioformats by openmicroscopy.

the class KodakReader method readExtraMetadata.

private void readExtraMetadata(MetadataStore store) throws IOException {
    if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
        return;
    }
    in.seek(0);
    findString("Image Capture Source");
    String metadata = in.readCString();
    if (metadata == null) {
        return;
    }
    String[] lines = metadata.split("\n");
    for (String line : lines) {
        int index = line.indexOf(':');
        if (index < 0 || line.startsWith("#") || line.startsWith("-")) {
            continue;
        }
        String key = line.substring(0, index).trim();
        String value = line.substring(index + 1).trim();
        addGlobalMeta(key, value);
        if (key.equals("Image Capture Source")) {
            String instrument = MetadataTools.createLSID("Instrument", 0);
            store.setInstrumentID(instrument, 0);
            store.setImageInstrumentRef(instrument, 0);
            store.setMicroscopeModel(value, 0);
        } else if (key.equals("Capture Time/Date")) {
            String date = DateTools.formatDate(value, DATE_FORMAT);
            if (date != null) {
                store.setImageAcquisitionDate(new Timestamp(date), 0);
            }
        } else if (key.equals("Exposure Time")) {
            Double exposureTime = new Double(value.substring(0, value.indexOf(' ')));
            if (exposureTime != null) {
                store.setPlaneExposureTime(new Time(exposureTime, UNITS.SECOND), 0, 0);
            }
        } else if (key.equals("Vertical Resolution")) {
            // resolution stored in pixels per inch
            if (value.indexOf(' ') > 0) {
                value = value.substring(0, value.indexOf(' '));
            }
            Double size = new Double(value);
            size = 1.0 / (size * (1.0 / 25400));
            Length sizeY = FormatTools.getPhysicalSizeY(size);
            if (sizeY != null) {
                store.setPixelsPhysicalSizeY(sizeY, 0);
            }
        } else if (key.equals("Horizontal Resolution")) {
            // resolution stored in pixels per inch
            if (value.indexOf(' ') > 0) {
                value = value.substring(0, value.indexOf(' '));
            }
            Double size = new Double(value);
            size = 1.0 / (size * (1.0 / 25400));
            Length sizeX = FormatTools.getPhysicalSizeX(size);
            if (sizeX != null) {
                store.setPixelsPhysicalSizeX(sizeX, 0);
            }
        } else if (key.equals("CCD Temperature")) {
            Double temp;
            Matcher hexMatcher = Pattern.compile("0x([0-9A-F]+)").matcher(value);
            if (hexMatcher.matches()) {
                // CCD temperature stored as a hexadecimal string such as "0xEB".
                temp = new Double(Integer.parseInt(hexMatcher.group(1), 16));
                LOGGER.debug("CCD temperature detected as {}; assumed to be invalid", temp);
            } else {
                temp = new Double(value.substring(0, value.indexOf(' ')));
                store.setImagingEnvironmentTemperature(new Temperature(temp, UNITS.CELSIUS), 0);
            }
        }
    }
}