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

Example 36 with MetadataStore

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

the class JPKReader method initMetadataStore.

/* @see loci.formats.BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
    super.initMetadataStore();
    MetadataStore store = makeFilterMetadata();
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName("Series " + (i + 1), i);
    }
}

Example 37 with MetadataStore

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

the class KhorosReader 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);
    in.skipBytes(4);
    in.order(true);
    int dependency = in.readInt();
    addGlobalMeta("Comment", in.readString(512));
    in.order(dependency == 4 || dependency == 8);
    CoreMetadata m = core.get(0);
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(28);
    m.imageCount = in.readInt();
    if (getImageCount() == 0)
        m.imageCount = 1;
    m.sizeC = in.readInt();
    int type = in.readInt();
    switch(type) {
        case 0:
            m.pixelType = FormatTools.INT8;
            break;
        case 1:
            m.pixelType = FormatTools.UINT8;
            break;
        case 2:
            m.pixelType = FormatTools.UINT16;
            break;
        case 4:
            m.pixelType = FormatTools.INT32;
            break;
        case 5:
            m.pixelType = FormatTools.FLOAT;
            break;
        case 9:
            m.pixelType = FormatTools.DOUBLE;
            break;
        default:
            throw new FormatException("Unsupported pixel type : " + type);
    }
    // read lookup table
    in.skipBytes(12);
    int c = in.readInt();
    if (c > 1) {
        m.sizeC = c;
        int n = in.readInt();
        lut = new byte[c][n];
        in.skipBytes(436);
        for (int i = 0; i < lut.length; i++) {
            for (int j = 0; j < lut[0].length; j++) {
                lut[i][j] = in.readByte();
            }
        }
    } else
        in.skipBytes(440);
    offset = in.getFilePointer();
    m.sizeZ = getImageCount();
    m.sizeT = 1;
    m.rgb = getSizeC() > 1;
    m.interleaved = false;
    m.littleEndian = dependency == 4 || dependency == 8;
    m.dimensionOrder = "XYCZT";
    m.indexed = lut != null;
    m.falseColor = false;
    m.metadataComplete = true;
    if (isIndexed()) {
        m.sizeC = 1;
        m.rgb = false;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 38 with MetadataStore

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

the class L2DReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "l2d") && isGroupFiles()) {
        // find the corresponding .l2d file
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        parent = parent.getParentFile();
        String[] list = parent.list();
        for (String file : list) {
            if (checkSuffix(file, "l2d")) {
                initFile(new Location(parent, file).getAbsolutePath());
                return;
            }
        }
        throw new FormatException("Could not find .l2d file");
    } else if (!isGroupFiles()) {
        super.initFile(id);
        tiffs = new String[][] { { id } };
        TiffReader r = new TiffReader();
        r.setMetadataStore(getMetadataStore());
        r.setId(id);
        core = new ArrayList<CoreMetadata>(r.getCoreMetadataList());
        metadataStore = r.getMetadataStore();
        final Map<String, Object> globalMetadata = r.getGlobalMetadata();
        for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
            addGlobalMeta(entry.getKey(), entry.getValue());
        }
        r.close();
        reader = new MinimalTiffReader();
        return;
    }
    super.initFile(id);
    String[] scans = getScanNames();
    Location parent = new Location(id).getAbsoluteFile().getParentFile();
    // remove scan names that do not correspond to existing directories
    final List<String> validScans = new ArrayList<String>();
    for (String s : scans) {
        Location scanDir = new Location(parent, s);
        if (scanDir.exists() && scanDir.isDirectory())
            validScans.add(s);
    }
    scans = validScans.toArray(new String[validScans.size()]);
    // read metadata from each scan
    tiffs = new String[scans.length][];
    metadataFiles = new List[scans.length];
    core = new ArrayList<CoreMetadata>(scans.length);
    String[] comments = new String[scans.length];
    String[] wavelengths = new String[scans.length];
    String[] dates = new String[scans.length];
    String model = null;
    tileWidth = new int[scans.length];
    tileHeight = new int[scans.length];
    core.clear();
    for (int i = 0; i < scans.length; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        setSeries(i);
        metadataFiles[i] = new ArrayList<String>();
        String scanName = scans[i] + ".scn";
        Location scanDir = new Location(parent, scans[i]);
        // read .scn file from each scan
        String scanPath = new Location(scanDir, scanName).getAbsolutePath();
        addDirectory(scanDir.getAbsolutePath(), i);
        String scanData = DataTools.readFile(scanPath);
        String[] lines = scanData.split("\n");
        for (String line : lines) {
            if (!line.startsWith("#")) {
                String key = line.substring(0, line.indexOf('='));
                String value = line.substring(line.indexOf('=') + 1);
                addSeriesMeta(key, value);
                if (key.equals("ExperimentNames")) {
                // TODO : parse experiment metadata - this is typically a list of
                // overlay shapes, or analysis data
                } else if (key.equals("ImageNames")) {
                    tiffs[i] = value.split(",");
                    for (int t = 0; t < tiffs[i].length; t++) {
                        tiffs[i][t] = new Location(scanDir, tiffs[i][t].trim()).getAbsolutePath();
                    }
                } else if (key.equals("Comments")) {
                    comments[i] = value;
                } else if (key.equals("ScanDate")) {
                    dates[i] = value;
                } else if (key.equals("ScannerName")) {
                    model = value;
                } else if (key.equals("ScanChannels")) {
                    wavelengths[i] = value;
                }
            }
        }
    }
    setSeries(0);
    reader = new MinimalTiffReader();
    MetadataStore store = makeFilterMetadata();
    for (int i = 0; i < getSeriesCount(); i++) {
        CoreMetadata ms = core.get(i);
        ms.imageCount = tiffs[i].length;
        ms.sizeC = tiffs[i].length;
        ms.sizeT = 1;
        ms.sizeZ = 1;
        ms.dimensionOrder = "XYCZT";
        reader.setId(tiffs[i][0]);
        ms.sizeX = reader.getSizeX();
        ms.sizeY = reader.getSizeY();
        ms.sizeC *= reader.getSizeC();
        ms.rgb = reader.isRGB();
        ms.indexed = reader.isIndexed();
        ms.littleEndian = reader.isLittleEndian();
        ms.pixelType = reader.getPixelType();
        tileWidth[i] = reader.getOptimalTileWidth();
        tileHeight[i] = reader.getOptimalTileHeight();
    }
    MetadataTools.populatePixels(store, this);
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName(scans[i], i);
        if (dates[i] != null) {
            dates[i] = DateTools.formatDate(dates[i], DATE_FORMAT);
            if (dates[i] != null) {
                store.setImageAcquisitionDate(new Timestamp(dates[i]), i);
            }
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        for (int i = 0; i < getSeriesCount(); i++) {
            store.setImageInstrumentRef(instrumentID, i);
            store.setImageDescription(comments[i], i);
            if (wavelengths[i] != null) {
                String[] waves = wavelengths[i].split("[, ]");
                if (waves.length < getEffectiveSizeC()) {
                    LOGGER.debug("Expected {} wavelengths; got {} wavelengths.", getEffectiveSizeC(), waves.length);
                }
                for (int q = 0; q < waves.length; q++) {
                    String laser = MetadataTools.createLSID("LightSource", 0, q);
                    store.setLaserID(laser, 0, q);
                    Double wave = new Double(waves[q].trim());
                    Length wavelength = FormatTools.getWavelength(wave);
                    if (wavelength != null) {
                        store.setLaserWavelength(wavelength, 0, q);
                    }
                    store.setLaserType(getLaserType("Other"), 0, q);
                    store.setLaserLaserMedium(getLaserMedium("Other"), 0, q);
                    store.setChannelLightSourceSettingsID(laser, i, q);
                }
            }
        }
        store.setMicroscopeModel(model, 0);
        store.setMicroscopeType(getMicroscopeType("Other"), 0);
    }
}

Example 39 with MetadataStore

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

the class SBIGReader 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);
    Double sizeX = null, sizeY = null;
    String date = null, description = null;
    String[] lines = DataTools.readFile(currentId).split("\n");
    for (String line : lines) {
        line = line.trim();
        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("Width")) {
                m.sizeX = Integer.parseInt(value);
            } else if (key.equals("Height")) {
                m.sizeY = Integer.parseInt(value);
            } else if (key.equals("Note")) {
                description = value;
            } else if (key.equals("X_pixel_size")) {
                sizeX = new Double(value) * 1000;
            } else if (key.equals("Y_pixel_size")) {
                sizeY = new Double(value) * 1000;
            } else if (key.equals("Date")) {
                date = value;
            } else if (key.equals("Time")) {
                date += " " + value;
            }
        } else if (line.indexOf("Compressed") != -1) {
            compressed = true;
        } else if (line.equals("End"))
            break;
    }
    m.pixelType = FormatTools.UINT16;
    m.littleEndian = true;
    m.rgb = false;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYZCT";
    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 (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length x = FormatTools.getPhysicalSizeX(sizeX);
        Length y = FormatTools.getPhysicalSizeY(sizeY);
        if (x != null) {
            store.setPixelsPhysicalSizeX(x, 0);
        }
        if (y != null) {
            store.setPixelsPhysicalSizeY(y, 0);
        }
        store.setImageDescription(description, 0);
    }
}

Example 40 with MetadataStore

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

the class SDTReader 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);
    in.order(true);
    LOGGER.info("Reading header");
    // read file header information
    info = new SDTInfo(in, metadata);
    timeBins = info.timeBins;
    channels = info.channels;
    addGlobalMeta("time bins", timeBins);
    addGlobalMeta("channels", channels);
    double timeBase = 1e9 * info.tacR / info.tacG;
    addGlobalMeta("time base", timeBase);
    LOGGER.info("Populating metadata");
    CoreMetadata m = core.get(0);
    int timepoints = info.timepoints;
    if (timepoints == 0) {
        timepoints = 1;
    }
    m.sizeX = info.width;
    m.sizeY = info.height;
    m.sizeZ = 1;
    m.sizeT = intensity ? timepoints : timeBins * timepoints;
    m.sizeC = channels;
    m.dimensionOrder = "XYZTC";
    m.pixelType = FormatTools.UINT16;
    m.rgb = false;
    m.littleEndian = true;
    m.imageCount = m.sizeZ * m.sizeC * m.sizeT;
    m.indexed = false;
    m.falseColor = false;
    m.metadataComplete = true;
    if (intensity) {
        m.moduloT.parentType = FormatTools.SPECTRA;
    } else {
        m.moduloT.type = FormatTools.LIFETIME;
        m.moduloT.parentType = FormatTools.SPECTRA;
        m.moduloT.typeDescription = "TCSPC";
        m.moduloT.start = 0;
        timeBase *= 1000;
        m.moduloT.step = timeBase / timeBins;
        m.moduloT.end = m.moduloT.step * (m.sizeT - 1);
        m.moduloT.unit = "ps";
    }
    for (int i = 1; i < info.allBlockOffsets.length; i++) {
        CoreMetadata p = new CoreMetadata(m);
        core.add(p);
        int planeSize = m.sizeX * m.sizeY * FormatTools.getBytesPerPixel(m.pixelType);
        if (info.allBlockLengths[i] != planeSize * m.imageCount) {
            if (info.mcstaPoints * planeSize == info.allBlockLengths[i]) {
                p.sizeT = info.mcstaPoints;
                p.moduloT.end = p.moduloT.step * (p.sizeT - 1);
                p.imageCount = p.sizeZ * p.sizeC * p.sizeT;
            }
        }
    }
    // Arbitrarily chosen size limit for buffer
    int sizeThreshold = 512 * 512 * 512;
    // default No of bins in buffer
    blockLength = 2048;
    while (blockLength * m.sizeX * m.sizeY > sizeThreshold) {
        blockLength = blockLength / 2;
    }
    if (blockLength > timeBins) {
        blockLength = timeBins;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}