Examples with MetadataStore loci.formats.meta.MetadataStore used on opensource projects

Example 11 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class NikonReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    original = ifds.get(0);
    if (cfaPattern != null) {
        original.putIFDValue(IFD.COLOR_MAP, (int[]) cfaPattern);
    }
    ifds.set(0, original);
    CoreMetadata m = core.get(0);
    m.imageCount = 1;
    m.sizeT = 1;
    if (ifds.get(0).getSamplesPerPixel() == 1) {
        m.interleaved = true;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 12 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class OIRReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    Location current = new Location(id).getAbsoluteFile();
    Location parent = current.getParentFile();
    ArrayList<String> extraFiles = new ArrayList<String>();
    if (parent != null) {
        String[] fileList = parent.list();
        Arrays.sort(fileList);
        String prefix = current.getName();
        if (prefix.indexOf(".") > 0) {
            prefix = prefix.substring(0, prefix.lastIndexOf("."));
        } else if (!checkSuffix(id, "oir")) {
            prefix = prefix.substring(0, prefix.lastIndexOf("_"));
        }
        for (String file : fileList) {
            // look for files ending with an underscore plus a 5 digit number
            if (file.startsWith(prefix + "_") && file.length() == prefix.length() + 6) {
                try {
                    int index = Integer.parseInt(file.substring(file.lastIndexOf("_") + 1));
                    if (index != extraFiles.size() + 1) {
                        LOGGER.warn("Found file {} with index {}; expected index {}", file, index, extraFiles.size() + 1);
                    }
                    extraFiles.add(new Location(parent, file).getAbsolutePath());
                } catch (NumberFormatException e) {
                }
            } else if (file.startsWith(prefix) && checkSuffix(file, "oir")) {
                current = new Location(parent, file);
                currentId = current.getAbsolutePath();
            }
        }
    }
    CoreMetadata m = core.get(0);
    m.littleEndian = true;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.indexed = true;
    m.falseColor = true;
    try (RandomAccessInputStream s = new RandomAccessInputStream(currentId, BUFFER_SIZE)) {
        readPixelsFile(current.getAbsolutePath(), s);
    }
    for (String file : extraFiles) {
        try (RandomAccessInputStream s = new RandomAccessInputStream(file, BUFFER_SIZE)) {
            readPixelsFile(file, s);
        }
    }
    m.sizeC *= channels.size();
    m.imageCount = getSizeC() * getSizeZ() * getSizeT();
    LOGGER.debug("blocks per plane = {}", blocksPerPlane);
    LOGGER.debug("number of pixel blocks = {}", pixelBlocks.size());
    if (blocksPerPlane * getImageCount() != pixelBlocks.size()) {
        // if blocks are missing, set the Z and T dimensions to match the last
        // plane for which at least one block exists
        int maxZ = 0;
        int maxT = 0;
        for (String uid : pixelBlocks.keySet()) {
            LOGGER.debug("  checking uid = {}", uid);
            int thisZ = getZ(uid);
            int thisT = getT(uid);
            int block = getBlock(uid);
            // only count through last full plane
            if (block == blocksPerPlane - 1) {
                if (thisZ > maxZ) {
                    maxZ = thisZ;
                }
                if (thisT > maxT) {
                    maxT = thisT;
                }
                if (thisZ < minZ) {
                    minZ = thisZ;
                }
                if (thisT < minT) {
                    minT = thisT;
                }
            }
        }
        m.sizeZ = (maxZ - minZ) + 1;
        m.sizeT = (maxT - minT) + 1;
        m.imageCount = getSizeC() * getSizeZ() * getSizeT();
    } else {
        minZ = 0;
        minT = 0;
    }
    m.dimensionOrder = "XYC";
    if (getSizeZ() == 1 || getSizeT() == 1) {
        m.dimensionOrder += "ZT";
    } else {
        int zIndex = baseName.toLowerCase().indexOf("z");
        int tIndex = baseName.toLowerCase().indexOf("t");
        if (zIndex < tIndex) {
            m.dimensionOrder += "TZ";
        } else {
            m.dimensionOrder += "ZT";
        }
    }
    pixelUIDs = pixelBlocks.keySet().toArray(new String[pixelBlocks.size()]);
    Arrays.sort(pixelUIDs, new Comparator<String>() {

        @Override
        public int compare(String s1, String s2) {
            int lastUnderscore1 = s1.lastIndexOf("_");
            int lastUnderscore2 = s2.lastIndexOf("_");
            Integer block1 = new Integer(s1.substring(lastUnderscore1 + 1));
            Integer block2 = new Integer(s2.substring(lastUnderscore2 + 1));
            int underscore1 = s1.lastIndexOf("_", lastUnderscore1 - 1);
            int underscore2 = s2.lastIndexOf("_", lastUnderscore2 - 1);
            String prefix1 = s1.substring(0, underscore1);
            String prefix2 = s2.substring(0, underscore2);
            String channel1 = s1.substring(underscore1 + 1, lastUnderscore1);
            String channel2 = s2.substring(underscore2 + 1, lastUnderscore2);
            if (!prefix1.equals(prefix2)) {
                return s1.compareTo(s2);
            }
            if (!channel1.equals(channel2)) {
                Integer index1 = -1;
                Integer index2 = -2;
                for (int i = 0; i < channels.size(); i++) {
                    if (channels.get(i).id.equals(channel1)) {
                        index1 = i;
                    }
                    if (channels.get(i).id.equals(channel2)) {
                        index2 = i;
                    }
                }
                return index1.compareTo(index2);
            }
            return block1.compareTo(block2);
        }
    });
    if (LOGGER.isTraceEnabled()) {
        for (int i = 0; i < pixelUIDs.length; i++) {
            LOGGER.trace("pixel UID #{} = {}", i, pixelUIDs[i]);
        }
    }
    // populate original metadata
    Hashtable<String, Object> tmpMeta = new Hashtable<String, Object>();
    addMeta("Creation date", acquisitionDate, tmpMeta);
    addMeta("Pixel Length X", physicalSizeX, tmpMeta);
    addMeta("Pixel Length Y", physicalSizeY, tmpMeta);
    addMeta("Z step", physicalSizeZ, tmpMeta);
    for (Channel channel : channels) {
        String prefix = "Channel " + channel.name + " ";
        addMetaList(prefix + "ID", channel.id, tmpMeta);
        addMetaList(prefix + "color", channel.color, tmpMeta);
        addMetaList(prefix + "pinhole", channel.pinhole, tmpMeta);
        addMetaList(prefix + "start wavelength", channel.excitation, tmpMeta);
        addMetaList(prefix + "end wavelength", channel.emission, tmpMeta);
        addMetaList(prefix + "linked laser index", channel.laserIndex, tmpMeta);
    }
    for (Objective objective : objectives) {
        addMetaList("Objective Lens name", objective.name, tmpMeta);
        addMetaList("Objective Lens magnification", objective.magnification, tmpMeta);
        addMetaList("Objective Lens na", objective.na, tmpMeta);
        addMetaList("Objective Lens wd", objective.wd, tmpMeta);
        addMetaList("Objective Lens refractive index", objective.ri, tmpMeta);
        addMetaList("Objective Lens immersion", objective.immersion, tmpMeta);
    }
    for (Laser laser : lasers) {
        String prefix = "Laser " + laser.name + " ";
        addMetaList(prefix + "ID", laser.id, tmpMeta);
        addMetaList(prefix + "data ID", laser.dataId, tmpMeta);
        addMetaList(prefix + "power", laser.power, tmpMeta);
        addMetaList(prefix + "transmissivity", laser.transmissivity, tmpMeta);
        addMetaList(prefix + "wavelength", laser.wavelength, tmpMeta);
    }
    for (Detector detector : detectors) {
        addMetaList("Detector ID", detector.id, tmpMeta);
        addMetaList("Detector linked channel ID", detector.channelId, tmpMeta);
        addMetaList("Detector voltage", detector.voltage, tmpMeta);
        addMetaList("Detector offset", detector.offset, tmpMeta);
        addMetaList("Detector gain", detector.gain, tmpMeta);
    }
    // this ensures that global metadata keys will be sorted before series keys
    MetadataTools.merge(tmpMeta, metadata, "- ");
    // populate MetadataStore
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String instrumentID = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrumentID, 0);
    store.setImageInstrumentRef(instrumentID, 0);
    for (int i = 0; i < lasers.size(); i++) {
        Laser l = lasers.get(i);
        String lsid = MetadataTools.createLSID("LightSource", 0, i);
        store.setLaserID(lsid, 0, i);
        store.setLaserModel(l.id, 0, i);
        if (l.wavelength != null) {
            store.setLaserWavelength(FormatTools.getWavelength(l.wavelength, null), 0, i);
        }
    }
    for (int i = 0; i < detectors.size(); i++) {
        Detector detector = detectors.get(i);
        String lsid = MetadataTools.createLSID("Detector", 0, i);
        store.setDetectorID(lsid, 0, i);
        store.setDetectorOffset(detector.offset, 0, i);
        store.setDetectorVoltage(FormatTools.createElectricPotential(detector.voltage, UNITS.VOLT), 0, i);
        store.setDetectorGain(detector.gain, 0, i);
    }
    for (int i = 0; i < objectives.size(); i++) {
        Objective objective = objectives.get(i);
        String lsid = MetadataTools.createLSID("Objective", 0, i);
        store.setObjectiveID(lsid, 0, i);
        store.setObjectiveModel(objective.name, 0, i);
        store.setObjectiveNominalMagnification(objective.magnification, 0, i);
        store.setObjectiveLensNA(objective.na, 0, i);
        store.setObjectiveWorkingDistance(FormatTools.createLength(objective.wd, UNITS.MILLIMETRE), 0, i);
        store.setObjectiveImmersion(objective.immersion, 0, i);
        if (i == 0) {
            store.setObjectiveSettingsID(lsid, 0);
            store.setObjectiveSettingsRefractiveIndex(objective.ri, 0);
        }
    }
    if (acquisitionDate != null) {
        store.setImageAcquisitionDate(acquisitionDate, 0);
    }
    if (physicalSizeX != null) {
        store.setPixelsPhysicalSizeX(physicalSizeX, 0);
    }
    if (physicalSizeY != null) {
        store.setPixelsPhysicalSizeY(physicalSizeY, 0);
    }
    if (physicalSizeZ != null) {
        store.setPixelsPhysicalSizeZ(physicalSizeZ, 0);
    }
    for (int c = 0; c < channels.size(); c++) {
        Channel ch = channels.get(c);
        store.setChannelName(ch.name, 0, c);
        if (ch.color != null) {
            store.setChannelColor(ch.color, 0, c);
        }
        if (ch.pinhole != null) {
            store.setChannelPinholeSize(ch.pinhole, 0, c);
        }
        if (ch.emission != null) {
            store.setChannelEmissionWavelength(ch.emission, 0, c);
        }
        if (ch.excitation != null) {
            store.setChannelExcitationWavelength(ch.excitation, 0, c);
        }
        for (int d = 0; d < detectors.size(); d++) {
            if (detectors.get(d).channelId.equals(ch.id)) {
                store.setDetectorSettingsID(MetadataTools.createLSID("Detector", 0, d), 0, c);
            }
        }
        if (ch.laserIndex >= 0 && ch.laserIndex < lasers.size()) {
            String laserId = MetadataTools.createLSID("LightSource", 0, ch.laserIndex);
            store.setChannelLightSourceSettingsID(laserId, 0, c);
        }
    }
}

Example 13 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class OpenlabRawReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    // read the 12 byte file header
    LOGGER.info("Verifying Openlab RAW format");
    if (!in.readString(4).equals("OLRW")) {
        throw new FormatException("Openlab RAW magic string not found.");
    }
    LOGGER.info("Populating metadata");
    CoreMetadata m = core.get(0);
    int version = in.readInt();
    m.imageCount = in.readInt();
    offsets = new int[getImageCount()];
    offsets[0] = 12;
    in.skipBytes(8);
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(1);
    m.sizeC = in.read();
    bytesPerPixel = in.read();
    in.skipBytes(1);
    long stampMs = in.readLong();
    if (stampMs > 0) {
        stampMs /= 1000000;
        stampMs -= (67 * 365.25 * 24 * 60 * 60);
    } else
        stampMs = System.currentTimeMillis();
    String stamp = DateTools.convertDate(stampMs, DateTools.UNIX);
    in.skipBytes(4);
    int len = in.read() & 0xff;
    String imageName = in.readString(len - 1).trim();
    if (getSizeC() <= 1)
        m.sizeC = 1;
    else
        m.sizeC = 3;
    int plane = getSizeX() * getSizeY() * bytesPerPixel;
    for (int i = 1; i < getImageCount(); i++) {
        offsets[i] = offsets[i - 1] + HEADER_SIZE + plane;
    }
    m.sizeZ = getImageCount();
    m.sizeT = 1;
    m.rgb = getSizeC() > 1;
    m.dimensionOrder = isRGB() ? "XYCZT" : "XYZTC";
    m.interleaved = false;
    m.littleEndian = false;
    m.metadataComplete = true;
    m.indexed = false;
    m.falseColor = false;
    switch(bytesPerPixel) {
        case 1:
        case 3:
            m.pixelType = FormatTools.UINT8;
            break;
        case 2:
            m.pixelType = FormatTools.UINT16;
            break;
        default:
            m.pixelType = FormatTools.FLOAT;
    }
    addGlobalMeta("Width", getSizeX());
    addGlobalMeta("Height", getSizeY());
    addGlobalMeta("Bytes per pixel", bytesPerPixel);
    addGlobalMeta("Image name", imageName);
    addGlobalMeta("Timestamp", stamp);
    addGlobalMeta("Version", version);
    // The metadata store we're working with.
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (stamp != null) {
        store.setImageAcquisitionDate(new Timestamp(stamp), 0);
    }
    store.setImageName(imageName, 0);
}

Example 14 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class OxfordInstrumentsReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    m.littleEndian = true;
    in.order(isLittleEndian());
    in.seek(48);
    String comment = in.readString(32);
    String dateTime = readDate();
    in.skipBytes(8);
    double xSize = -in.readFloat() + in.readFloat();
    in.skipBytes(20);
    double ySize = -in.readFloat() + in.readFloat();
    in.skipBytes(24);
    double zMin = in.readFloat();
    double zMax = in.readFloat();
    in.skipBytes(864);
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(28);
    if (getSizeX() == 0 && getSizeY() == 0) {
        m.sizeX = in.readInt();
        m.sizeY = in.readInt();
        in.skipBytes(196);
    } else
        in.skipBytes(204);
    m.pixelType = FormatTools.UINT16;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.rgb = false;
    m.indexed = false;
    m.dimensionOrder = "XYZCT";
    m.interleaved = false;
    if (FormatTools.getPlaneSize(this) + in.getFilePointer() > in.length()) {
        m.sizeY = 1;
    }
    int lutSize = in.readInt();
    in.skipBytes(lutSize);
    headerSize = in.getFilePointer();
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        in.skipBytes(FormatTools.getPlaneSize(this));
        int nMetadataStrings = in.readInt();
        for (int i = 0; i < nMetadataStrings; i++) {
            int length = in.readInt();
            String s = in.readString(length);
            if (s.indexOf(':') != -1) {
                String key = s.substring(0, s.indexOf(':')).trim();
                String value = s.substring(s.indexOf(':') + 1).trim();
                if (!value.equals("-")) {
                    addGlobalMeta(key, value);
                }
            }
        }
        addGlobalMeta("Description", comment);
        addGlobalMeta("Acquisition date", dateTime);
        addGlobalMeta("X size (um)", xSize);
        addGlobalMeta("Y size (um)", ySize);
        addGlobalMeta("Z minimum (um)", zMin);
        addGlobalMeta("Z maximum (um)", zMax);
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setImageDescription(comment, 0);
    if (dateTime != null) {
        store.setImageAcquisitionDate(new Timestamp(dateTime), 0);
    }
    double physicalSizeX = xSize / getSizeX();
    double physicalSizeY = ySize / getSizeY();
    Length sizeX = FormatTools.getPhysicalSizeX(physicalSizeX);
    Length sizeY = FormatTools.getPhysicalSizeY(physicalSizeY);
    if (sizeX != null) {
        store.setPixelsPhysicalSizeX(sizeX, 0);
    }
    if (sizeY != null) {
        store.setPixelsPhysicalSizeY(sizeY, 0);
    }
}

Example 15 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class LEOReader method initMetadataStore.

/* @see BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
    super.initMetadataStore();
    MetadataStore store = makeFilterMetadata();
    date = DateTools.formatDate(date, "HH:mm dd-MMM-yyyy");
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(xSize);
        Length sizeY = FormatTools.getPhysicalSizeY(xSize);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        String instrument = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrument, 0);
        store.setImageInstrumentRef(instrument, 0);
        store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0);
        store.setObjectiveWorkingDistance(new Length(workingDistance, UNITS.MICROMETER), 0, 0);
        store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
        store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
    }
}