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

Example 16 with Time

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

the class VectraReader 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++) {
        int coreIndex = seriesToCoreIndex(i);
        store.setImageName(getImageName(coreIndex), i);
        store.setImageDescription("", i);
        int ifdIndex = getIFDIndex(coreIndex, 0);
        IFD ifd = ifds.get(ifdIndex);
        double x = ifd.getXResolution();
        double y = ifd.getYResolution();
        store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(x), i);
        store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(y), i);
    }
    for (int c = 0; c < getSizeC(); c++) {
        String xml = getIFDComment(c);
        try {
            Element root = XMLTools.parseDOM(xml).getDocumentElement();
            NodeList children = root.getChildNodes();
            for (int i = 0; i < children.getLength(); i++) {
                if (!(children.item(i) instanceof Element)) {
                    continue;
                }
                Element e = (Element) children.item(i);
                String name = e.getNodeName();
                String value = e.getTextContent();
                if (name.equals("ScanProfile")) {
                    try {
                        Document profileRoot = XMLTools.createDocument();
                        Node tmp = profileRoot.importNode(e, true);
                        profileRoot.appendChild(tmp);
                        profileXML = XMLTools.getXML(profileRoot);
                        // scan profile XML is usually too long to be saved
                        // when original metadata filtering is enabled, but there
                        // is an API method below to retrieve it
                        addGlobalMeta(name, profileXML);
                    } catch (Exception ex) {
                        LOGGER.debug("Could not preserve scan profile metadata", ex);
                    }
                } else {
                    addGlobalMetaList(name, value);
                }
                if (name.equals("Name")) {
                    if (hasFlattenedResolutions()) {
                        for (int series = 0; series < pyramidDepth; series++) {
                            store.setChannelName(value, series, c);
                        }
                    } else {
                        store.setChannelName(value, 0, c);
                    }
                } else if (name.equals("Color")) {
                    String[] components = value.split(",");
                    Color color = new Color(Integer.parseInt(components[0]), Integer.parseInt(components[1]), Integer.parseInt(components[2]), 255);
                    if (hasFlattenedResolutions()) {
                        for (int series = 0; series < pyramidDepth; series++) {
                            store.setChannelColor(color, series, c);
                        }
                    } else {
                        store.setChannelColor(color, 0, c);
                    }
                } else if (name.equals("Objective") && c == 0) {
                    String instrument = MetadataTools.createLSID("Instrument", 0);
                    String objective = MetadataTools.createLSID("Objective", 0, 0);
                    store.setInstrumentID(instrument, 0);
                    store.setObjectiveID(objective, 0, 0);
                    store.setObjectiveModel(value, 0, 0);
                    try {
                        String mag = value.toLowerCase().replace("x", "");
                        Double magFactor = DataTools.parseDouble(mag);
                        store.setObjectiveNominalMagnification(magFactor, 0, 0);
                    } catch (NumberFormatException ex) {
                        LOGGER.info("Could not determine magnification: {}", value);
                    }
                    for (int series = 0; series < getSeriesCount(); series++) {
                        store.setImageInstrumentRef(instrument, series);
                        store.setObjectiveSettingsID(objective, series);
                    }
                } else if (name.equals("ExposureTime")) {
                    Time exposure = new Time(DataTools.parseDouble(value), UNITS.MICROSECOND);
                    store.setPlaneExposureTime(exposure, 0, c);
                    store.setPlaneTheZ(new NonNegativeInteger(0), 0, c);
                    store.setPlaneTheT(new NonNegativeInteger(0), 0, c);
                    store.setPlaneTheC(new NonNegativeInteger(c), 0, c);
                }
            }
        } catch (ParserConfigurationException | SAXException | IOException e) {
            LOGGER.warn("Could not parse XML for channel {}", c);
            LOGGER.debug("", e);
        }
    }
}

Example 17 with Time

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

the class ScanrReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    if (metadataFiles.size() > 0) {
        // this dataset has already been initialized
        return;
    }
    // make sure we have the .xml file
    if (!checkSuffix(id, "xml") && isGroupFiles()) {
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        if (checkSuffix(id, "tif") && parent.getName().equalsIgnoreCase("Data")) {
            parent = parent.getParentFile();
        }
        String[] list = parent.list();
        for (String file : list) {
            if (file.equals(XML_FILE)) {
                id = new Location(parent, file).getAbsolutePath();
                super.initFile(id);
                break;
            }
        }
        if (!checkSuffix(id, "xml")) {
            throw new FormatException("Could not find " + XML_FILE + " in " + parent.getAbsolutePath());
        }
    } else if (!isGroupFiles() && checkSuffix(id, "tif")) {
        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();
        tiffs = new String[] { id };
        reader = new MinimalTiffReader();
        return;
    }
    Location dir = new Location(id).getAbsoluteFile().getParentFile();
    String[] list = dir.list(true);
    for (String file : list) {
        Location f = new Location(dir, file);
        if (checkSuffix(file, METADATA_SUFFIXES) && !f.isDirectory()) {
            metadataFiles.add(f.getAbsolutePath());
        }
    }
    // parse XML metadata
    String xml = DataTools.readFile(id).trim();
    if (xml.startsWith("<?")) {
        xml = xml.substring(xml.indexOf("?>") + 2);
    }
    xml = "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>" + xml;
    XMLTools.parseXML(xml, new ScanrHandler());
    final List<String> uniqueRows = new ArrayList<String>();
    final List<String> uniqueColumns = new ArrayList<String>();
    if (wellRows == 0 || wellColumns == 0) {
        for (String well : wellLabels.keySet()) {
            if (!Character.isLetter(well.charAt(0)))
                continue;
            String row = well.substring(0, 1).trim();
            String column = well.substring(1).trim();
            if (!uniqueRows.contains(row) && row.length() > 0)
                uniqueRows.add(row);
            if (!uniqueColumns.contains(column) && column.length() > 0) {
                uniqueColumns.add(column);
            }
        }
        wellRows = uniqueRows.size();
        wellColumns = uniqueColumns.size();
        if (wellRows * wellColumns != wellCount) {
            adjustWellDimensions();
        }
    }
    int nChannels = getSizeC() == 0 ? channelNames.size() : (int) Math.min(channelNames.size(), getSizeC());
    if (nChannels == 0)
        nChannels = 1;
    int nSlices = getSizeZ() == 0 ? 1 : getSizeZ();
    int nTimepoints = getSizeT();
    int nWells = wellCount;
    int nPos = 0;
    if (foundPositions)
        nPos = fieldPositionX.length;
    else
        nPos = fieldRows * fieldColumns;
    if (nPos == 0)
        nPos = 1;
    // get list of TIFF files
    Location dataDir = new Location(dir, "data");
    list = dataDir.list(true);
    if (list == null) {
        // try to find the TIFFs in the current directory
        list = dir.list(true);
    } else
        dir = dataDir;
    if (nTimepoints == 0 || list.length < nTimepoints * nChannels * nSlices * nWells * nPos) {
        nTimepoints = list.length / (nChannels * nWells * nPos * nSlices);
        if (nTimepoints == 0)
            nTimepoints = 1;
    }
    tiffs = new String[nChannels * nWells * nPos * nTimepoints * nSlices];
    Arrays.sort(list, new Comparator<String>() {

        @Override
        public int compare(String s1, String s2) {
            int lastSeparator1 = s1.lastIndexOf(File.separator) + 1;
            int lastSeparator2 = s2.lastIndexOf(File.separator) + 1;
            String dir1 = s1.substring(0, lastSeparator1);
            String dir2 = s2.substring(0, lastSeparator2);
            if (!dir1.equals(dir2)) {
                return dir1.compareTo(dir2);
            }
            int dash1 = s1.indexOf("-", lastSeparator1);
            int dash2 = s2.indexOf("-", lastSeparator2);
            String label1 = dash1 < 0 ? "" : s1.substring(lastSeparator1, dash1);
            String label2 = dash2 < 0 ? "" : s2.substring(lastSeparator2, dash2);
            if (label1.equals(label2)) {
                String remainder1 = dash1 < 0 ? s1 : s1.substring(dash1);
                String remainder2 = dash2 < 0 ? s2 : s2.substring(dash2);
                return remainder1.compareTo(remainder2);
            }
            Integer index1 = wellLabels.get(label1);
            Integer index2 = wellLabels.get(label2);
            if (index1 == null && index2 != null) {
                return 1;
            } else if (index1 != null && index2 == null) {
                return -1;
            }
            return index1.compareTo(index2);
        }
    });
    int lastListIndex = 0;
    int next = 0;
    String[] keys = wellLabels.keySet().toArray(new String[wellLabels.size()]);
    Arrays.sort(keys, new Comparator<String>() {

        @Override
        public int compare(String s1, String s2) {
            char row1 = s1.charAt(0);
            char row2 = s2.charAt(0);
            final Integer col1 = new Integer(s1.substring(1));
            final Integer col2 = new Integer(s2.substring(1));
            if (row1 < row2) {
                return -1;
            } else if (row1 > row2) {
                return 1;
            }
            return col1.compareTo(col2);
        }
    });
    int realPosCount = 0;
    for (int well = 0; well < nWells; well++) {
        int missingWellFiles = 0;
        int wellIndex = wellNumbers.get(well);
        String wellPos = getBlock(wellIndex, "W");
        int originalIndex = next;
        for (int pos = 0; pos < nPos; pos++) {
            String posPos = getBlock(pos + 1, "P");
            int posIndex = next;
            for (int z = 0; z < nSlices; z++) {
                String zPos = getBlock(z, "Z");
                for (int t = 0; t < nTimepoints; t++) {
                    String tPos = getBlock(t, "T");
                    for (int c = 0; c < nChannels; c++) {
                        for (int i = lastListIndex; i < list.length; i++) {
                            String file = list[i];
                            if (file.indexOf(wellPos) != -1 && file.indexOf(zPos) != -1 && file.indexOf(posPos) != -1 && file.indexOf(tPos) != -1 && file.indexOf(channelNames.get(c)) != -1) {
                                tiffs[next++] = new Location(dir, file).getAbsolutePath();
                                if (c == nChannels - 1) {
                                    lastListIndex = i;
                                }
                                break;
                            }
                        }
                        if (next == originalIndex) {
                            missingWellFiles++;
                        }
                    }
                }
            }
            if (posIndex != next)
                realPosCount++;
        }
        if (next == originalIndex && well < keys.length) {
            wellLabels.remove(keys[well]);
        }
        if (next == originalIndex && missingWellFiles == nSlices * nTimepoints * nChannels * nPos) {
            wellNumbers.remove(well);
        }
    }
    nWells = wellNumbers.size();
    if (wellLabels.size() > 0 && wellLabels.size() != nWells) {
        uniqueRows.clear();
        uniqueColumns.clear();
        for (String well : wellLabels.keySet()) {
            if (!Character.isLetter(well.charAt(0)))
                continue;
            String row = well.substring(0, 1).trim();
            String column = well.substring(1).trim();
            if (!uniqueRows.contains(row) && row.length() > 0)
                uniqueRows.add(row);
            if (!uniqueColumns.contains(column) && column.length() > 0) {
                uniqueColumns.add(column);
            }
        }
        nWells = uniqueRows.size() * uniqueColumns.size();
        adjustWellDimensions();
    }
    if (realPosCount < nPos) {
        nPos = realPosCount;
    }
    reader = new MinimalTiffReader();
    reader.setId(tiffs[0]);
    int sizeX = reader.getSizeX();
    int sizeY = reader.getSizeY();
    int pixelType = reader.getPixelType();
    tileWidth = reader.getOptimalTileWidth();
    tileHeight = reader.getOptimalTileHeight();
    switch(pixelType) {
        case FormatTools.INT8:
            pixelType = FormatTools.UINT8;
            break;
        case FormatTools.INT16:
            pixelType = FormatTools.UINT16;
            break;
    }
    boolean rgb = reader.isRGB();
    boolean interleaved = reader.isInterleaved();
    boolean indexed = reader.isIndexed();
    boolean littleEndian = reader.isLittleEndian();
    reader.close();
    int seriesCount = nWells * nPos;
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.sizeC = nChannels;
        ms.sizeZ = nSlices;
        ms.sizeT = nTimepoints;
        ms.sizeX = sizeX;
        ms.sizeY = sizeY;
        ms.pixelType = pixelType;
        ms.rgb = rgb;
        ms.interleaved = interleaved;
        ms.indexed = indexed;
        ms.littleEndian = littleEndian;
        ms.dimensionOrder = "XYCTZ";
        ms.imageCount = nSlices * nTimepoints * nChannels;
        ms.bitsPerPixel = 12;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    store.setPlateColumns(new PositiveInteger(wellColumns), 0);
    store.setPlateRows(new PositiveInteger(wellRows), 0);
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    int nFields = 0;
    if (foundPositions) {
        nFields = fieldPositionX.length;
    } else {
        nFields = fieldRows * fieldColumns;
    }
    PositiveInteger fieldCount = FormatTools.getMaxFieldCount(nFields);
    if (fieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        int field = i % nFields;
        int well = i / nFields;
        int index = well;
        while (wellNumbers.get(index) == null && index < wellNumbers.size()) {
            index++;
        }
        int wellIndex = wellNumbers.get(index) == null ? index : wellNumbers.get(index) - 1;
        int wellRow = wellIndex / wellColumns;
        int wellCol = wellIndex % wellColumns;
        if (field == 0) {
            store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
            store.setWellColumn(new NonNegativeInteger(wellCol), 0, well);
            store.setWellRow(new NonNegativeInteger(wellRow), 0, well);
        }
        String wellSample = MetadataTools.createLSID("WellSample", 0, well, field);
        store.setWellSampleID(wellSample, 0, well, field);
        store.setWellSampleIndex(new NonNegativeInteger(i), 0, well, field);
        String imageID = MetadataTools.createLSID("Image", i);
        store.setWellSampleImageRef(imageID, 0, well, field);
        store.setImageID(imageID, i);
        String name = "Well " + (well + 1) + ", Field " + (field + 1) + " (Spot " + (i + 1) + ")";
        store.setImageName(name, i);
        store.setPlateAcquisitionWellSampleRef(wellSample, 0, 0, i);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        for (int i = 0; i < getSeriesCount(); i++) {
            for (int c = 0; c < getSizeC(); c++) {
                store.setChannelName(channelNames.get(c), i, c);
            }
            Length x = FormatTools.getPhysicalSizeX(pixelSize);
            Length y = FormatTools.getPhysicalSizeY(pixelSize);
            if (x != null) {
                store.setPixelsPhysicalSizeX(x, i);
            }
            if (y != null) {
                store.setPixelsPhysicalSizeY(y, i);
            }
            if (fieldPositionX != null && fieldPositionY != null) {
                int field = i % nFields;
                int well = i / nFields;
                final Length posX = fieldPositionX[field];
                final Length posY = fieldPositionY[field];
                store.setWellSamplePositionX(posX, 0, well, field);
                store.setWellSamplePositionY(posY, 0, well, field);
                for (int c = 0; c < getSizeC(); c++) {
                    int image = getIndex(0, c, 0);
                    store.setPlaneTheZ(new NonNegativeInteger(0), i, image);
                    store.setPlaneTheC(new NonNegativeInteger(c), i, image);
                    store.setPlaneTheT(new NonNegativeInteger(0), i, image);
                    store.setPlanePositionX(fieldPositionX[field], i, image);
                    store.setPlanePositionY(fieldPositionY[field], i, image);
                    // exposure time is stored in milliseconds
                    // convert to seconds before populating MetadataStore
                    Double time = exposures.get(c);
                    if (time != null) {
                        time /= 1000;
                        store.setPlaneExposureTime(new Time(time, UNITS.SECOND), i, image);
                    }
                    if (deltaT != null) {
                        store.setPlaneDeltaT(new Time(deltaT, UNITS.SECOND), i, image);
                    }
                }
            }
        }
        String row = wellRows > 26 ? "Number" : "Letter";
        String col = wellRows > 26 ? "Letter" : "Number";
        store.setPlateRowNamingConvention(getNamingConvention(row), 0);
        store.setPlateColumnNamingConvention(getNamingConvention(col), 0);
        store.setPlateName(plateName, 0);
    }
}

Example 18 with Time

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

the class PrintTimestamps method printTimingPerPlane.

/**
 * Outputs timing details per plane.
 *
 * This information may seem redundant or unnecessary, but it is possible
 * that two image planes recorded at the same timepoint actually have
 * slightly different timestamps. Thus, OME allows for recording a separate
 * timestamp for every individual image plane.
 */
public static void printTimingPerPlane(IMetadata meta, int series) {
    System.out.println();
    System.out.println("Timing information per plane (from beginning of experiment):");
    int planeCount = meta.getPlaneCount(series);
    for (int i = 0; i < planeCount; i++) {
        Time deltaT = meta.getPlaneDeltaT(series, i);
        if (deltaT == null)
            continue;
        // convert plane ZCT coordinates into image plane index
        int z = meta.getPlaneTheZ(series, i).getValue().intValue();
        int c = meta.getPlaneTheC(series, i).getValue().intValue();
        int t = meta.getPlaneTheT(series, i).getValue().intValue();
        System.out.println("\tZ " + z + ", C " + c + ", T " + t + " = " + deltaT.value(UNITS.SECOND).doubleValue() + " s");
    }
}

Example 19 with Time

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

Example 20 with Time

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

the class FV1000Reader method populateMetadataStore.

private void populateMetadataStore(MetadataStore store, String path) throws FormatException, IOException {
    String instrumentID = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrumentID, 0);
    for (int i = 0; i < getSeriesCount(); i++) {
        // link Instrument and Image
        store.setImageInstrumentRef(instrumentID, i);
        if (pixelSizeX != null) {
            Double sizeX = new Double(pixelSizeX);
            Length size = FormatTools.getPhysicalSizeX(sizeX);
            if (size != null) {
                store.setPixelsPhysicalSizeX(size, i);
            }
        }
        if (pixelSizeY != null) {
            Double sizeY = new Double(pixelSizeY);
            Length size = FormatTools.getPhysicalSizeY(sizeY);
            if (size != null) {
                store.setPixelsPhysicalSizeY(size, i);
            }
        }
        if (pixelSizeZ == Double.NEGATIVE_INFINITY || pixelSizeZ == Double.POSITIVE_INFINITY || getSizeZ() == 1) {
            pixelSizeZ = 1d;
        }
        if (pixelSizeT == Double.NEGATIVE_INFINITY || pixelSizeT == Double.POSITIVE_INFINITY || getSizeT() == 1) {
            pixelSizeT = 1d;
        }
        Length sizeZ = FormatTools.getPhysicalSizeZ(pixelSizeZ);
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, i);
        }
        store.setPixelsTimeIncrement(new Time(pixelSizeT, UNITS.SECOND), i);
        for (int p = 0; p < core.get(i).imageCount; p++) {
            store.setPlaneDeltaT(new Time(pixelSizeT * p, UNITS.SECOND), i, p);
        }
        for (int c = 0; c < core.get(i).sizeC; c++) {
            if (c < illuminations.size()) {
                store.setChannelIlluminationType(getIlluminationType(illuminations.get(c)), i, c);
            }
        }
    }
    int channelIndex = 0;
    for (ChannelData channel : channels) {
        if (!channel.active)
            continue;
        if (channelIndex >= getEffectiveSizeC())
            break;
        // populate Detector data
        String detectorID = MetadataTools.createLSID("Detector", 0, channelIndex);
        store.setDetectorID(detectorID, 0, channelIndex);
        store.setDetectorSettingsID(detectorID, 0, channelIndex);
        store.setDetectorGain(channel.gain, 0, channelIndex);
        ElectricPotential theVoltage = FormatTools.createElectricPotential(channel.voltage, UNITS.VOLT);
        if (theVoltage != null) {
            store.setDetectorVoltage(theVoltage, 0, channelIndex);
        }
        store.setDetectorType(getDetectorType("PMT"), 0, channelIndex);
        // populate LogicalChannel data
        store.setChannelName(channel.name, 0, channelIndex);
        String lightSourceID = MetadataTools.createLSID("LightSource", 0, channelIndex);
        store.setChannelLightSourceSettingsID(lightSourceID, 0, channelIndex);
        Length wavelength = FormatTools.getWavelength(channel.exWave);
        Length emission = FormatTools.getEmissionWavelength(channel.emWave);
        Length excitation = FormatTools.getExcitationWavelength(channel.exWave);
        if (emission != null) {
            store.setChannelEmissionWavelength(emission, 0, channelIndex);
        }
        if (excitation != null) {
            store.setChannelExcitationWavelength(excitation, 0, channelIndex);
        }
        if (wavelength != null) {
            store.setChannelLightSourceSettingsWavelength(wavelength, 0, channelIndex);
        }
        // populate Filter data
        if (channel.barrierFilter != null) {
            String filterID = MetadataTools.createLSID("Filter", 0, channelIndex);
            store.setFilterID(filterID, 0, channelIndex);
            store.setFilterModel(channel.barrierFilter, 0, channelIndex);
            if (channel.barrierFilter.indexOf('-') != -1) {
                String[] emValues = channel.barrierFilter.split("-");
                for (int i = 0; i < emValues.length; i++) {
                    emValues[i] = emValues[i].replaceAll("\\D", "");
                }
                try {
                    Double cutIn = new Double(emValues[0]);
                    Double cutOut = new Double(emValues[1]);
                    Length in = FormatTools.getCutIn(cutIn);
                    Length out = FormatTools.getCutOut(cutOut);
                    if (in != null) {
                        store.setTransmittanceRangeCutIn(in, 0, channelIndex);
                    }
                    if (out != null) {
                        store.setTransmittanceRangeCutOut(out, 0, channelIndex);
                    }
                } catch (NumberFormatException e) {
                }
            }
            store.setLightPathEmissionFilterRef(filterID, 0, channelIndex, 0);
        }
        // populate FilterSet data
        int emIndex = channelIndex * 2;
        int exIndex = channelIndex * 2 + 1;
        String emFilter = MetadataTools.createLSID("Dichroic", 0, emIndex);
        String exFilter = MetadataTools.createLSID("Dichroic", 0, exIndex);
        // populate Dichroic data
        store.setDichroicID(emFilter, 0, emIndex);
        store.setDichroicModel(channel.emissionFilter, 0, emIndex);
        store.setDichroicID(exFilter, 0, exIndex);
        store.setDichroicModel(channel.excitationFilter, 0, exIndex);
        store.setLightPathDichroicRef(exFilter, 0, channelIndex);
        // populate Laser data
        store.setLaserID(lightSourceID, 0, channelIndex);
        store.setLaserLaserMedium(getLaserMedium(channel.dyeName), 0, channelIndex);
        if (channelIndex < wavelengths.size()) {
            Length wave = FormatTools.getWavelength(wavelengths.get(channelIndex));
            if (wave != null) {
                store.setLaserWavelength(wave, 0, channelIndex);
            }
        }
        store.setLaserType(getLaserType("Other"), 0, channelIndex);
        channelIndex++;
    }
    if (lensNA != null)
        store.setObjectiveLensNA(new Double(lensNA), 0, 0);
    store.setObjectiveModel(objectiveName, 0, 0);
    if (magnification != null) {
        Double mag = Double.parseDouble(magnification);
        store.setObjectiveNominalMagnification(mag, 0, 0);
    }
    if (workingDistance != null) {
        store.setObjectiveWorkingDistance(new Length(new Double(workingDistance), UNITS.MICROMETER), 0, 0);
    }
    store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
    store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
    // link Objective to Image using ObjectiveSettings
    String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
    store.setObjectiveID(objectiveID, 0, 0);
    store.setObjectiveSettingsID(objectiveID, 0);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.NO_OVERLAYS) {
        int nextROI = -1;
        // populate ROI data - there is one ROI file per plane
        for (int i = 0; i < roiFilenames.size(); i++) {
            if (i >= getImageCount())
                break;
            String filename = roiFilenames.get(i);
            filename = sanitizeFile(filename, path);
            nextROI = parseROIFile(filename, store, nextROI, i);
        }
    }
    // Populate metadata for the planes
    for (int i = 0; i < planes.size(); i++) {
        PlaneData plane = planes.get(i);
        if (plane.deltaT != null) {
            store.setPlaneDeltaT(new Time(plane.deltaT, UNITS.SECOND), 0, i);
        }
        store.setPlanePositionX(plane.positionX, 0, i);
        store.setPlanePositionY(plane.positionY, 0, i);
        store.setPlanePositionZ(plane.positionZ, 0, i);
    }
}