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

Example 21 with Timestamp

use of ome.xml.model.primitives.Timestamp 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 22 with Timestamp

use of ome.xml.model.primitives.Timestamp 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 23 with Timestamp

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

the class WATOPReader 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());
    String comment = null;
    MetadataLevel level = getMetadataOptions().getMetadataLevel();
    if (level != MetadataLevel.MINIMUM) {
        in.seek(49);
        comment = in.readString(33);
    }
    in.seek(211);
    int year = in.readInt();
    int month = in.readInt();
    int day = in.readInt();
    int hour = in.readInt();
    int min = in.readInt();
    String date = year + "-" + month + "-" + day + "T" + hour + ":" + min;
    date = DateTools.formatDate(date, "yyyy-MM-dd'T'HH:mm");
    in.skipBytes(8);
    double xSize = in.readInt() / 100d;
    double ySize = in.readInt() / 100d;
    double zSize = in.readInt() / 100d;
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    if (level != MetadataLevel.MINIMUM) {
        double tunnelCurrent = in.readInt() / 1000d;
        double sampleVolts = in.readInt() / 1000d;
        in.skipBytes(180);
        int originalZMax = in.readInt();
        int originalZMin = in.readInt();
        int zMax = in.readInt();
        int zMin = in.readInt();
        addGlobalMeta("Comment", comment);
        addGlobalMeta("X size (in um)", xSize);
        addGlobalMeta("Y size (in um)", ySize);
        addGlobalMeta("Z size (in um)", zSize);
        addGlobalMeta("Tunnel current (in amps)", tunnelCurrent);
        addGlobalMeta("Sample volts", sampleVolts);
        addGlobalMeta("Acquisition date", date);
    }
    m.pixelType = FormatTools.INT16;
    m.sizeC = 1;
    m.sizeZ = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYZCT";
    m.rgb = false;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    if (level != MetadataLevel.MINIMUM) {
        store.setImageDescription(comment, 0);
        Length sizeX = FormatTools.getPhysicalSizeX((double) xSize / getSizeX());
        Length sizeY = FormatTools.getPhysicalSizeY((double) ySize / getSizeY());
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
    }
}

Example 24 with Timestamp

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

the class ObjectBasedOMEModelMock method makePlate.

private Plate makePlate() {
    Plate plate = new Plate();
    plate.setID(InOutCurrentTest.PLATE_ID);
    plate.setRows(InOutCurrentTest.WELL_ROWS);
    plate.setColumns(InOutCurrentTest.WELL_COLS);
    plate.setRowNamingConvention(InOutCurrentTest.WELL_ROW);
    plate.setColumnNamingConvention(InOutCurrentTest.WELL_COL);
    TimestampAnnotation plateAnnotation = new TimestampAnnotation();
    plateAnnotation.setID(InOutCurrentTest.PLATE_ANNOTATION_ID);
    plateAnnotation.setValue(new Timestamp(InOutCurrentTest.PLATE_ANNOTATION_VALUE));
    plateAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    plate.linkAnnotation(plateAnnotation);
    annotations.addTimestampAnnotation(plateAnnotation);
    int wellSampleIndex = 0;
    for (int row = 0; row < InOutCurrentTest.WELL_ROWS.getValue(); row++) {
        for (int col = 0; col < InOutCurrentTest.WELL_COLS.getValue(); col++) {
            Well well = new Well();
            well.setID(String.format("Well:%d_%d", row, col));
            well.setRow(new NonNegativeInteger(row));
            well.setColumn(new NonNegativeInteger(col));
            if (row == 0 && col == 0) {
                LongAnnotation annotation = new LongAnnotation();
                annotation.setID(InOutCurrentTest.WELL_ANNOTATION_ID);
                annotation.setValue(InOutCurrentTest.WELL_ANNOTATION_VALUE);
                annotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
                well.linkAnnotation(annotation);
                annotations.addLongAnnotation(annotation);
            }
            WellSample sample = new WellSample();
            sample.setID(String.format("WellSample:%d_%d", row, col));
            sample.setIndex(new NonNegativeInteger(wellSampleIndex));
            sample.linkImage(ome.getImage(0));
            well.addWellSample(sample);
            plate.addWell(well);
            wellSampleIndex++;
        }
    }
    return plate;
}

Example 25 with Timestamp

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

the class ColumbusReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
    Location xml = findXML(id);
    if (null == xml) {
        throw new FormatException("Could not find " + XML_FILE);
    }
    id = xml.getAbsolutePath();
    super.initFile(id);
    Location parent = new Location(currentId).getAbsoluteFile().getParentFile();
    // parse plate layout and image dimensions from the XML files
    String xmlData = DataTools.readFile(id);
    MeasurementHandler handler = new MeasurementHandler();
    XMLTools.parseXML(xmlData, handler);
    String[] parentDirectories = parent.list(true);
    Arrays.sort(parentDirectories);
    ArrayList<String> timepointDirs = new ArrayList<String>();
    for (String file : parentDirectories) {
        Location absFile = new Location(parent, file);
        if (absFile.isDirectory()) {
            timepointDirs.add(absFile.getAbsolutePath());
            for (String f : absFile.list(true)) {
                if (!checkSuffix(f, "tif")) {
                    if (!metadataFiles.contains(file + File.separator + f)) {
                        metadataFiles.add(file + File.separator + f);
                    }
                }
            }
        }
    }
    for (int i = 0; i < metadataFiles.size(); i++) {
        String metadataFile = metadataFiles.get(i);
        int end = metadataFile.indexOf(File.separator);
        String timepointPath = end < 0 ? "" : parent + File.separator + metadataFile.substring(0, end);
        Location f = new Location(parent + File.separator + metadataFile);
        if (!f.exists()) {
            metadataFile = metadataFile.substring(end + 1);
            f = new Location(parent, metadataFile);
        }
        String path = f.getAbsolutePath();
        metadataFiles.set(i, path);
        if (checkSuffix(path, "columbusidx.xml")) {
            int timepoint = timepointDirs.indexOf(timepointPath);
            if (timepointDirs.size() == 0) {
                timepoint = 0;
            }
            parseImageXML(path, timepoint);
        }
    }
    // process plane list to determine plate size
    Comparator<Plane> planeComp = new Comparator<Plane>() {

        public int compare(Plane p1, Plane p2) {
            if (p1.row != p2.row) {
                return p1.row - p2.row;
            }
            if (p1.col != p2.col) {
                return p1.col - p2.col;
            }
            if (p1.field != p2.field) {
                return p1.field - p2.field;
            }
            if (p1.timepoint != p2.timepoint) {
                return p1.timepoint - p2.timepoint;
            }
            if (p1.channel != p2.channel) {
                return p1.channel - p2.channel;
            }
            return 0;
        }
    };
    Plane[] tmpPlanes = planes.toArray(new Plane[planes.size()]);
    Arrays.sort(tmpPlanes, planeComp);
    planes.clear();
    reader = new MinimalTiffReader();
    reader.setId(tmpPlanes[0].file);
    core = reader.getCoreMetadataList();
    CoreMetadata m = core.get(0);
    m.sizeC = 0;
    m.sizeT = 0;
    ArrayList<Integer> uniqueSamples = new ArrayList<Integer>();
    ArrayList<Integer> uniqueRows = new ArrayList<Integer>();
    ArrayList<Integer> uniqueCols = new ArrayList<Integer>();
    for (Plane p : tmpPlanes) {
        planes.add(p);
        int sampleIndex = p.row * handler.getPlateColumns() + p.col;
        if (!uniqueSamples.contains(sampleIndex)) {
            uniqueSamples.add(sampleIndex);
        }
        if (!uniqueRows.contains(p.row)) {
            uniqueRows.add(p.row);
        }
        if (!uniqueCols.contains(p.col)) {
            uniqueCols.add(p.col);
        }
        // counts are assumed to be non-sparse
        if (p.field >= nFields) {
            nFields = p.field + 1;
        }
        if (p.channel >= getSizeC()) {
            m.sizeC = p.channel + 1;
        }
        if (p.timepoint >= getSizeT()) {
            m.sizeT = p.timepoint + 1;
        }
    }
    m.sizeZ = 1;
    m.imageCount = getSizeZ() * getSizeC() * getSizeT();
    m.dimensionOrder = "XYCTZ";
    m.rgb = false;
    int seriesCount = uniqueSamples.size() * nFields;
    for (int i = 1; i < seriesCount; i++) {
        core.add(m);
    }
    // populate the MetadataStore
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    store.setScreenID(MetadataTools.createLSID("Screen", 0), 0);
    store.setScreenName(handler.getScreenName(), 0);
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    store.setPlateName(handler.getPlateName(), 0);
    store.setPlateRows(new PositiveInteger(handler.getPlateRows()), 0);
    store.setPlateColumns(new PositiveInteger(handler.getPlateColumns()), 0);
    String imagePrefix = handler.getPlateName() + " Well ";
    int wellSample = 0;
    int nextWell = -1;
    Timestamp date = new Timestamp(acquisitionDate);
    long timestampSeconds = date.asInstant().getMillis() / 1000;
    for (Integer row : uniqueRows) {
        for (Integer col : uniqueCols) {
            if (!uniqueSamples.contains(row * handler.getPlateColumns() + col)) {
                continue;
            }
            nextWell++;
            store.setWellID(MetadataTools.createLSID("Well", 0, nextWell), 0, nextWell);
            store.setWellRow(new NonNegativeInteger(row), 0, nextWell);
            store.setWellColumn(new NonNegativeInteger(col), 0, nextWell);
            for (int field = 0; field < nFields; field++) {
                Plane p = lookupPlane(row, col, field, 0, 0);
                String wellSampleID = MetadataTools.createLSID("WellSample", 0, nextWell, field);
                store.setWellSampleID(wellSampleID, 0, nextWell, field);
                store.setWellSampleIndex(new NonNegativeInteger(wellSample), 0, nextWell, field);
                if (p != null) {
                    store.setWellSamplePositionX(new Length(p.positionX, UNITS.REFERENCEFRAME), 0, nextWell, field);
                    store.setWellSamplePositionY(new Length(p.positionY, UNITS.REFERENCEFRAME), 0, nextWell, field);
                }
                String imageID = MetadataTools.createLSID("Image", wellSample);
                store.setImageID(imageID, wellSample);
                store.setWellSampleImageRef(imageID, 0, nextWell, field);
                store.setImageName(imagePrefix + (char) (row + 'A') + (col + 1) + " Field #" + (field + 1), wellSample);
                store.setImageAcquisitionDate(date, wellSample);
                if (p != null) {
                    p.series = wellSample;
                    store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(p.sizeX), p.series);
                    store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(p.sizeY), p.series);
                    for (int c = 0; c < getSizeC(); c++) {
                        p = lookupPlane(row, col, field, 0, c);
                        if (p != null) {
                            p.series = wellSample;
                            store.setChannelName(p.channelName, p.series, p.channel);
                            if ((int) p.emWavelength > 0) {
                                store.setChannelEmissionWavelength(FormatTools.getEmissionWavelength(p.emWavelength), p.series, p.channel);
                            }
                            if ((int) p.exWavelength > 0) {
                                store.setChannelExcitationWavelength(FormatTools.getExcitationWavelength(p.exWavelength), p.series, p.channel);
                            }
                            store.setChannelColor(p.channelColor, p.series, p.channel);
                        }
                        for (int t = 0; t < getSizeT(); t++) {
                            p = lookupPlane(row, col, field, t, c);
                            if (p != null) {
                                p.series = wellSample;
                                store.setPlaneDeltaT(new Time(p.deltaT - timestampSeconds, UNITS.SECOND), p.series, getIndex(0, c, t));
                            }
                        }
                    }
                }
                wellSample++;
            }
        }
    }
}