Examples with Instrument ome.xml.model.Instrument used on opensource projects

Example 1 with Instrument

use of ome.xml.model.Instrument in project bioformats by openmicroscopy.

the class SPWModelMock method makeImage.

private Image makeImage(int index) {
    // <Instrument/> for later linking, etc.
    Instrument instrument = ome.getInstrument(0);
    // Create <Image/>
    Image image = new Image();
    image.setID("Image:" + index);
    CommentAnnotation commentAnnotation = new CommentAnnotation();
    commentAnnotation.setID("Annotation:" + index);
    commentAnnotation.setNamespace(GENERAL_ANNOTATION_NAMESPACE);
    commentAnnotation.setValue("Image:" + index + " annotation.");
    annotations.addCommentAnnotation(commentAnnotation);
    image.linkAnnotation(commentAnnotation);
    // Create <Pixels/>
    Pixels pixels = new Pixels();
    pixels.setID("Pixels:" + index);
    pixels.setSizeX(new PositiveInteger(SIZE_X));
    pixels.setSizeY(new PositiveInteger(SIZE_Y));
    pixels.setSizeZ(new PositiveInteger(SIZE_Z));
    pixels.setSizeC(new PositiveInteger(SIZE_C));
    pixels.setSizeT(new PositiveInteger(SIZE_T));
    pixels.setDimensionOrder(DIMENSION_ORDER);
    pixels.setType(PIXEL_TYPE);
    // Create <BinData/>
    for (int i = 0; i < SIZE_Z * SIZE_C * SIZE_T; i++) {
        BinData binData = new BinData();
        binData.setBigEndian(false);
        binData.setCompression(Compression.NONE);
        binData.setLength(new NonNegativeLong((long) (SIZE_X * SIZE_Y * BYTES_PER_PIXEL)));
        pixels.addBinData(binData);
    }
    // Create <Channel/> under <Pixels/>
    for (int i = 0; i < SIZE_C; i++) {
        Channel channel = new Channel();
        channel.setID("Channel:" + i);
        // Create <LightSourceSettings/> and link to <Channel/>
        LightSourceSettings settings = new LightSourceSettings();
        settings.setID(LIGHTSOURCE_LASER_ID);
        channel.setLightSourceSettings(settings);
        // Create <LightPath/> and link to <Channel/>
        LightPath lightPath = new LightPath();
        lightPath.linkEmissionFilter(instrument.getFilter(0));
        lightPath.linkExcitationFilter(instrument.getFilter(1));
        channel.setLightPath(lightPath);
        pixels.addChannel(channel);
    }
    // Put <Pixels/> under <Image/>
    image.setPixels(pixels);
    // Link <Instrument/> to <Image/>
    image.linkInstrument(instrument);
    // Create <ObjectiveSettings/> and link to <Image/>
    ObjectiveSettings settings = new ObjectiveSettings();
    settings.setID(OBJECTIVE_ID);
    image.setObjectiveSettings(settings);
    return image;
}

Example 2 with Instrument

use of ome.xml.model.Instrument in project bioformats by openmicroscopy.

the class CellWorxReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "htd")) {
        LOGGER.info("Searching for .htd file");
        String base = new Location(id).getAbsolutePath();
        base = base.substring(0, base.lastIndexOf("_"));
        id = base + ".HTD";
        if (!new Location(id).exists()) {
            Location parent = new Location(id).getAbsoluteFile().getParentFile();
            directoryList = parent.list(true);
            for (String f : directoryList) {
                if (checkSuffix(f, "htd")) {
                    id = new Location(parent, f).getAbsolutePath();
                    LOGGER.info("Found .htd file {}", f);
                    break;
                }
            }
        }
    }
    super.initFile(id);
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
    } catch (DependencyException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    String plateData = DataTools.readFile(id);
    String[] lines = plateData.split("\n");
    int xWells = 0, yWells = 0;
    int xFields = 0, yFields = 0;
    String[] wavelengths = null;
    int nTimepoints = 1;
    // determine dataset dimensions
    for (String line : lines) {
        int split = line.indexOf("\",");
        if (split < 1)
            continue;
        String key = line.substring(1, split).trim();
        String value = line.substring(split + 2).trim();
        if (key.equals("XWells")) {
            xWells = Integer.parseInt(value);
        } else if (key.equals("YWells")) {
            yWells = Integer.parseInt(value);
            wellFiles = new String[yWells][xWells][];
            logFiles = new String[yWells][xWells];
        } else if (key.startsWith("WellsSelection")) {
            int row = Integer.parseInt(key.substring(14)) - 1;
            String[] mapping = value.split(",");
            for (int col = 0; col < xWells; col++) {
                if (new Boolean(mapping[col].trim()).booleanValue()) {
                    wellFiles[row][col] = new String[1];
                }
            }
        } else if (key.equals("XSites")) {
            xFields = Integer.parseInt(value);
        } else if (key.equals("YSites")) {
            yFields = Integer.parseInt(value);
            fieldMap = new boolean[yFields][xFields];
        } else if (key.equals("TimePoints")) {
            nTimepoints = Integer.parseInt(value);
        } else if (key.startsWith("SiteSelection")) {
            int row = Integer.parseInt(key.substring(13)) - 1;
            String[] mapping = value.split(",");
            for (int col = 0; col < xFields; col++) {
                fieldMap[row][col] = new Boolean(mapping[col].trim()).booleanValue();
            }
        } else if (key.equals("Waves")) {
            doChannels = new Boolean(value.toLowerCase());
        } else if (key.equals("NWavelengths")) {
            wavelengths = new String[Integer.parseInt(value)];
        } else if (key.startsWith("WaveName")) {
            int index = Integer.parseInt(key.substring(8)) - 1;
            wavelengths[index] = value.replaceAll("\"", "");
        }
    }
    for (int row = 0; row < fieldMap.length; row++) {
        for (int col = 0; col < fieldMap[row].length; col++) {
            if (fieldMap[row][col])
                fieldCount++;
        }
    }
    // find pixels files
    String plateName = new Location(id).getAbsolutePath();
    plateName = plateName.substring(0, plateName.lastIndexOf(".")) + "_";
    int wellCount = 0;
    for (int row = 0; row < wellFiles.length; row++) {
        for (int col = 0; col < wellFiles[row].length; col++) {
            if (wellFiles[row][col] != null) {
                wellCount++;
                char rowLetter = (char) (row + 'A');
                String base = plateName + rowLetter + String.format("%02d", col + 1);
                wellFiles[row][col][0] = base + ".pnl";
                logFiles[row][col] = base + "_scan.log";
                if (!new Location(wellFiles[row][col][0]).exists()) {
                    // using TIFF files instead
                    wellFiles[row][col] = getTiffFiles(plateName, rowLetter, col, wavelengths.length, nTimepoints);
                }
            }
        }
    }
    plateLogFile = plateName + "scan.log";
    String serialNumber = null;
    if (new Location(plateLogFile).exists()) {
        String[] f = DataTools.readFile(plateLogFile).split("\n");
        for (String line : f) {
            if (line.trim().startsWith("Z Map File")) {
                String file = line.substring(line.indexOf(':') + 1);
                file = file.substring(file.lastIndexOf("/") + 1).trim();
                String parent = new Location(id).getAbsoluteFile().getParent();
                zMapFile = new Location(parent, file).getAbsolutePath();
            } else if (line.trim().startsWith("Scanner SN")) {
                serialNumber = line.substring(line.indexOf(':') + 1).trim();
            }
        }
    }
    int seriesCount = fieldCount * wellCount;
    int planeIndex = 0;
    int seriesIndex = 0;
    String file = getFile(seriesIndex, planeIndex);
    while (!new Location(file).exists()) {
        if (planeIndex < nTimepoints * wavelengths.length) {
            planeIndex++;
        } else if (seriesIndex < seriesCount - 1) {
            planeIndex = 0;
            seriesIndex++;
        } else {
            break;
        }
        file = getFile(seriesIndex, planeIndex);
    }
    IFormatReader pnl = getReader(file, true);
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        setSeries(i);
        ms.littleEndian = pnl.isLittleEndian();
        ms.sizeX = pnl.getSizeX();
        ms.sizeY = pnl.getSizeY();
        ms.pixelType = pnl.getPixelType();
        ms.sizeZ = 1;
        ms.sizeT = nTimepoints;
        ms.sizeC = wavelengths.length;
        ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
        ms.dimensionOrder = "XYCZT";
        ms.rgb = false;
        ms.interleaved = pnl.isInterleaved();
    }
    OMEXMLMetadata readerMetadata = (OMEXMLMetadata) pnl.getMetadataStore();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) readerMetadata.getRoot();
    Instrument instrument = root.getInstrument(0);
    List<Image> images = root.copyImageList();
    OMEXMLMetadataRoot convertRoot = new OMEXMLMetadataRoot();
    convertRoot.addInstrument(instrument);
    for (int i = 0; i < core.size() / images.size(); i++) {
        for (Image img : images) {
            convertRoot.addImage(img);
        }
    }
    OMEXMLMetadata convertMetadata;
    try {
        convertMetadata = service.createOMEXMLMetadata();
    } catch (ServiceException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    convertMetadata.setRoot(convertRoot);
    pnl.close();
    MetadataStore store = makeFilterMetadata();
    MetadataConverter.convertMetadata(convertMetadata, store);
    MetadataTools.populatePixels(store, this);
    String plateID = MetadataTools.createLSID("Plate", 0);
    Location plate = new Location(id).getAbsoluteFile();
    store.setPlateID(plateID, 0);
    plateName = plate.getName();
    if (plateName.indexOf('.') > 0) {
        plateName = plateName.substring(0, plateName.lastIndexOf('.'));
    }
    store.setPlateName(plateName, 0);
    store.setPlateRows(new PositiveInteger(wellFiles.length), 0);
    store.setPlateColumns(new PositiveInteger(wellFiles[0].length), 0);
    for (int i = 0; i < core.size(); i++) {
        store.setImageID(MetadataTools.createLSID("Image", i), i);
    }
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    PositiveInteger fieldCount = FormatTools.getMaxFieldCount(fieldMap.length * fieldMap[0].length);
    if (fieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
    }
    int nextImage = 0;
    for (int row = 0; row < wellFiles.length; row++) {
        for (int col = 0; col < wellFiles[row].length; col++) {
            int wellIndex = row * wellFiles[row].length + col;
            String wellID = MetadataTools.createLSID("Well", 0, wellIndex);
            store.setWellID(wellID, 0, wellIndex);
            store.setWellColumn(new NonNegativeInteger(col), 0, wellIndex);
            store.setWellRow(new NonNegativeInteger(row), 0, wellIndex);
            int fieldIndex = 0;
            for (int fieldRow = 0; fieldRow < fieldMap.length; fieldRow++) {
                for (int fieldCol = 0; fieldCol < fieldMap[fieldRow].length; fieldCol++) {
                    if (fieldMap[fieldRow][fieldCol] && wellFiles[row][col] != null) {
                        String wellSampleID = MetadataTools.createLSID("WellSample", 0, wellIndex, fieldIndex);
                        store.setWellSampleID(wellSampleID, 0, wellIndex, fieldIndex);
                        String imageID = MetadataTools.createLSID("Image", nextImage);
                        store.setWellSampleImageRef(imageID, 0, wellIndex, fieldIndex);
                        store.setWellSampleIndex(new NonNegativeInteger(nextImage), 0, wellIndex, fieldIndex);
                        store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, nextImage);
                        String well = (char) (row + 'A') + String.format("%02d", col + 1);
                        store.setImageName("Well " + well + " Field #" + (fieldIndex + 1), nextImage);
                        nextImage++;
                        fieldIndex++;
                    }
                }
            }
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (serialNumber != null) {
            store.setMicroscopeSerialNumber(serialNumber, 0);
        }
        for (int well = 0; well < wellCount; well++) {
            parseWellLogFile(well, store);
        }
        if (timestamps.size() > 0) {
            store.setPlateAcquisitionStartTime(timestamps.get(0), 0, 0);
            store.setPlateAcquisitionEndTime(timestamps.get(timestamps.size() - 1), 0, 0);
        }
        for (int i = 0; i < core.size(); i++) {
            for (int c = 0; c < getSizeC(); c++) {
                if (c < wavelengths.length && wavelengths[c] != null) {
                    store.setChannelName(wavelengths[c], i, c);
                }
            }
        }
    }
}

Example 3 with Instrument

use of ome.xml.model.Instrument in project bioformats by openmicroscopy.

the class PumpWithLightSourceSettingsTest method setUp.

@BeforeClass
public void setUp() throws Exception {
    Instrument instrument = new Instrument();
    instrument.setID("Instrument:0");
    // Add a Laser with an Arc pump
    Laser laser = new Laser();
    laser.setID("Laser:0");
    Arc pump = new Arc();
    pump.setID("Arc:0");
    laser.linkPump(pump);
    instrument.addLightSource(laser);
    instrument.addLightSource(pump);
    ome.addInstrument(instrument);
    // Add an Image/Pixels with a LightSourceSettings reference to the Pump
    // on one of its channels.
    Image image = new Image();
    image.setID("Image:0");
    Pixels pixels = new Pixels();
    pixels.setID("Pixels:0");
    Channel channel = new Channel();
    channel.setID("Channel:0");
    LightSourceSettings settings = new LightSourceSettings();
    settings.setID("Arc:0");
    channel.setLightSourceSettings(settings);
    pixels.addChannel(channel);
    image.setPixels(pixels);
    ome.addImage(image);
}

Example 4 with Instrument

use of ome.xml.model.Instrument in project bioformats by openmicroscopy.

the class SPWModelMock method makeInstrument.

private Instrument makeInstrument(boolean makeLightSources) {
    // Create <Instrument/>
    Instrument instrument = new Instrument();
    instrument.setID(INSTRUMENT_ID);
    // Create <Detector/> under <Instrument/>
    Detector detector = new Detector();
    detector.setID(DETECTOR_ID);
    detector.setModel(DETECTOR_MODEL);
    instrument.addDetector(detector);
    if (makeLightSources) {
        // Create <Laser/> under <Instrument/>
        Laser laser = new Laser();
        laser.setID(LIGHTSOURCE_LASER_ID);
        laser.setModel(LIGHTSOURCE_LASER_MODEL);
        laser.setType(LASER_TYPE);
        laser.setPower(new Power(LIGHTSOURCE_LASER_POWER, UNITS.MILLIWATT));
        // with a <Pump/>
        Laser laserPump = new Laser();
        laserPump.setID(LIGHTSOURCE_PUMP_ID);
        laserPump.setModel(LIGHTSOURCE_PUMP_MODEL);
        laserPump.setType(LASER_TYPE);
        laserPump.setPower(new Power(LIGHTSOURCE_PUMP_POWER, UNITS.MILLIWATT));
        laser.linkPump(laserPump);
        instrument.addLightSource(laser);
        instrument.addLightSource(laserPump);
        // Create <Arc/> under <Instrument/>
        Arc arc = new Arc();
        arc.setID(LIGHTSOURCE_ARC_ID);
        arc.setModel(LIGHTSOURCE_ARC_MODEL);
        arc.setType(ARC_TYPE);
        arc.setPower(new Power(LIGHTSOURCE_ARC_POWER, UNITS.MILLIWATT));
        instrument.addLightSource(arc);
        // Create <Filament/> under <Instrument/>
        Filament filament = new Filament();
        filament.setID(LIGHTSOURCE_FILAMENT_ID);
        filament.setModel(LIGHTSOURCE_FILAMENT_MODEL);
        filament.setType(FILAMENT_TYPE);
        filament.setPower(new Power(LIGHTSOURCE_FILAMENT_POWER, UNITS.MILLIWATT));
        instrument.addLightSource(filament);
        // Create <LightEmittingDiode/> under <Instrument/>
        LightEmittingDiode led = new LightEmittingDiode();
        led.setID(LIGHTSOURCE_LED_ID);
        led.setModel(LIGHTSOURCE_LED_MODEL);
        led.setPower(new Power(LIGHTSOURCE_LED_POWER, UNITS.MILLIWATT));
        instrument.addLightSource(led);
    }
    // Create <Dichroic/> under <Instrument/>
    Dichroic dichroic = new Dichroic();
    dichroic.setID(DICHROIC_ID);
    dichroic.setSerialNumber(DICHROIC_SN);
    // Create <FilterSet/> under <Dichroic/>
    FilterSet filterSet = new FilterSet();
    filterSet.setID(FILTERSET_ID);
    filterSet.setLotNumber(FILTERSET_LOT);
    filterSet.linkDichroic(dichroic);
    Filter emFilter = new Filter();
    Filter exFilter = new Filter();
    // Create <Objective/> under <Instrument/>
    Objective objective = new Objective();
    objective.setID(OBJECTIVE_ID);
    objective.setModel(OBJECTIVE_MODEL);
    emFilter.setID(EM_FILTER_ID);
    emFilter.setType(EM_FILTER_TYPE);
    exFilter.setID(EX_FILTER_ID);
    exFilter.setType(EX_FILTER_TYPE);
    instrument.addFilter(emFilter);
    instrument.addFilter(exFilter);
    instrument.addObjective(objective);
    filterSet.linkEmissionFilter(emFilter);
    filterSet.linkExcitationFilter(exFilter);
    filterSet.linkDichroic(dichroic);
    instrument.addFilterSet(filterSet);
    instrument.addDichroic(dichroic);
    return instrument;
}

Example 5 with Instrument

use of ome.xml.model.Instrument in project bioformats by openmicroscopy.

the class GenericExcitationMapTest method setUp.

@BeforeClass
public void setUp() throws Exception {
    Instrument instrument = new Instrument();
    instrument.setID("Instrument:0");
    // Add a GenericExcitationSource with an Map
    GenericExcitationSource geSource = new GenericExcitationSource();
    geSource.setID("LightSource:0");
    List<MapPair> dataMap = new ArrayList<MapPair>();
    dataMap.add(new MapPair("a", "1"));
    dataMap.add(new MapPair("d", "2"));
    dataMap.add(new MapPair("c", "3"));
    dataMap.add(new MapPair("b", "4"));
    dataMap.add(new MapPair("e", "5"));
    dataMap.add(new MapPair("c", "6"));
    assertEquals(6, dataMap.size());
    geSource.setMap(dataMap);
    instrument.addLightSource(geSource);
    ome.addInstrument(instrument);
    // Add an Image/Pixels with a LightSourceSettings reference to the
    // GenericExcitationSource on one of its channels.
    Image image = new Image();
    image.setID("Image:0");
    Pixels pixels = new Pixels();
    pixels.setID("Pixels:0");
    Channel channel = new Channel();
    channel.setID("Channel:0");
    LightSourceSettings settings = new LightSourceSettings();
    settings.setID("LightSource:0");
    channel.setLightSourceSettings(settings);
    pixels.addChannel(channel);
    image.setPixels(pixels);
    ome.addImage(image);
}