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

Example 21 with Image

use of ome.xml.model.Image 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);
}

Example 22 with Image

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

the class InOutCurrentTest method testValidImageNode.

@Test(dependsOnMethods = { "testValidOMENode" })
public void testValidImageNode() {
    Image image = ome.getImage(0);
    assertNotNull(image);
    assertEquals(IMAGE_ID, image.getID());
}

Example 23 with Image

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

the class InOutCurrentTest method testImageInstrumentLinkage.

@Test(dependsOnMethods = { "testValidInstrumentNode", "testValidImageNode" })
public void testImageInstrumentLinkage() {
    Instrument instrument = ome.getInstrument(0);
    Image image = ome.getImage(0);
    Instrument linkedInstrument = image.getLinkedInstrument();
    assertNotNull(linkedInstrument);
    assertEquals(instrument.getID(), linkedInstrument.getID());
    assertEquals(1, instrument.sizeOfLinkedImageList());
    Image linkedImage = instrument.getLinkedImage(0);
    assertNotNull(linkedImage);
    assertEquals(image.getID(), linkedImage.getID());
}

Example 24 with Image

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

the class FileWriteSPW method export.

/**
 * Save a single byte plane of data.
 * @param plane  data
 * @param series  image no in plate
 * @param index t plane within image
 */
private void export(byte[] plane, int series, int index, String imageDescription) {
    Exception exception = null;
    if (initializationSuccess) {
        if (series != writer.getSeries()) {
            try {
                writer.setSeries(series);
            } catch (FormatException e) {
                exception = e;
            }
        }
        try {
            writer.saveBytes(index, plane);
            if (index == 0) {
                OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot();
                Plate plate = root.getPlate(0);
                Image im = root.getImage(series);
                im.setDescription(imageDescription);
            }
            expectedImages[series]++;
        } catch (FormatException | IOException e) {
            exception = e;
        }
    }
    if (exception != null) {
        System.err.println("Failed to write data!");
    }
}

Example 25 with Image

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

the class ObjectBasedOMEModelMock method makeInstrument.

private Instrument makeInstrument() {
    // Create <Instrument/>
    Instrument instrument = new Instrument();
    instrument.setID(InOutCurrentTest.INSTRUMENT_ID);
    // Create <Detector/> under <Instrument/>
    Detector detector = new Detector();
    detector.setID(InOutCurrentTest.DETECTOR_ID);
    detector.setModel(InOutCurrentTest.DETECTOR_MODEL);
    CommentAnnotation detectorAnnotation = new CommentAnnotation();
    detectorAnnotation.setID(InOutCurrentTest.DETECTOR_ANNOTATION_ID);
    detectorAnnotation.setValue(InOutCurrentTest.DETECTOR_ANNOTATION_VALUE);
    detectorAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    detector.linkAnnotation(detectorAnnotation);
    annotations.addCommentAnnotation(detectorAnnotation);
    instrument.addDetector(detector);
    // Create <Laser/> under <Instrument/>
    Laser laser = new Laser();
    laser.setID(InOutCurrentTest.LIGHTSOURCE_LASER_ID);
    laser.setModel(InOutCurrentTest.LIGHTSOURCE_LASER_MODEL);
    laser.setType(InOutCurrentTest.LASER_TYPE);
    laser.setPower(new Power(InOutCurrentTest.LIGHTSOURCE_LASER_POWER, UNITS.MILLIWATT));
    CommentAnnotation laserAnnotation = new CommentAnnotation();
    laserAnnotation.setID(InOutCurrentTest.LIGHTSOURCE_LASER_ANNOTATION_ID);
    laserAnnotation.setValue(InOutCurrentTest.LIGHTSOURCE_LASER_ANNOTATION_VALUE);
    laserAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    laser.linkAnnotation(laserAnnotation);
    annotations.addCommentAnnotation(laserAnnotation);
    // with a <Pump/>
    Laser laserPump = new Laser();
    laserPump.setID(InOutCurrentTest.LIGHTSOURCE_PUMP_ID);
    laserPump.setModel(InOutCurrentTest.LIGHTSOURCE_PUMP_MODEL);
    laserPump.setType(InOutCurrentTest.LASER_TYPE);
    laserPump.setPower(new Power(InOutCurrentTest.LIGHTSOURCE_PUMP_POWER, UNITS.MILLIWATT));
    laser.linkPump(laserPump);
    instrument.addLightSource(laser);
    instrument.addLightSource(laserPump);
    // Create <Arc/> under <Instrument/>
    Arc arc = new Arc();
    arc.setID(InOutCurrentTest.LIGHTSOURCE_ARC_ID);
    arc.setModel(InOutCurrentTest.LIGHTSOURCE_ARC_MODEL);
    arc.setType(InOutCurrentTest.ARC_TYPE);
    arc.setPower(new Power(InOutCurrentTest.LIGHTSOURCE_ARC_POWER, UNITS.MILLIWATT));
    CommentAnnotation arcAnnotation = new CommentAnnotation();
    arcAnnotation.setID(InOutCurrentTest.LIGHTSOURCE_ARC_ANNOTATION_ID);
    arcAnnotation.setValue(InOutCurrentTest.LIGHTSOURCE_ARC_ANNOTATION_VALUE);
    arcAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    arc.linkAnnotation(arcAnnotation);
    annotations.addCommentAnnotation(arcAnnotation);
    instrument.addLightSource(arc);
    // Create <Filament/> under <Instrument/>
    Filament filament = new Filament();
    filament.setID(InOutCurrentTest.LIGHTSOURCE_FILAMENT_ID);
    filament.setModel(InOutCurrentTest.LIGHTSOURCE_FILAMENT_MODEL);
    filament.setType(InOutCurrentTest.FILAMENT_TYPE);
    filament.setPower(new Power(InOutCurrentTest.LIGHTSOURCE_FILAMENT_POWER, UNITS.MILLIWATT));
    CommentAnnotation filamentAnnotation = new CommentAnnotation();
    filamentAnnotation.setID(InOutCurrentTest.LIGHTSOURCE_FILAMENT_ANNOTATION_ID);
    filamentAnnotation.setValue(InOutCurrentTest.LIGHTSOURCE_FILAMENT_ANNOTATION_VALUE);
    filamentAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    filament.linkAnnotation(filamentAnnotation);
    annotations.addCommentAnnotation(filamentAnnotation);
    instrument.addLightSource(filament);
    // Create <LightEmittingDiode/> under <Instrument/>
    LightEmittingDiode led = new LightEmittingDiode();
    led.setID(InOutCurrentTest.LIGHTSOURCE_LED_ID);
    led.setModel(InOutCurrentTest.LIGHTSOURCE_LED_MODEL);
    led.setPower(new Power(InOutCurrentTest.LIGHTSOURCE_LED_POWER, UNITS.MILLIWATT));
    CommentAnnotation ledAnnotation = new CommentAnnotation();
    ledAnnotation.setID(InOutCurrentTest.LIGHTSOURCE_LED_ANNOTATION_ID);
    ledAnnotation.setValue(InOutCurrentTest.LIGHTSOURCE_LED_ANNOTATION_VALUE);
    ledAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    led.linkAnnotation(ledAnnotation);
    annotations.addCommentAnnotation(ledAnnotation);
    instrument.addLightSource(led);
    // Create <Dichroic/> under <Instrument/>
    Dichroic dichroic = new Dichroic();
    dichroic.setID(InOutCurrentTest.DICHROIC_ID);
    dichroic.setSerialNumber(InOutCurrentTest.DICHROIC_SN);
    CommentAnnotation dichroicAnnotation = new CommentAnnotation();
    dichroicAnnotation.setID(InOutCurrentTest.DICHROIC_ANNOTATION_ID);
    dichroicAnnotation.setValue(InOutCurrentTest.DICHROIC_ANNOTATION_VALUE);
    dichroicAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    dichroic.linkAnnotation(dichroicAnnotation);
    annotations.addCommentAnnotation(dichroicAnnotation);
    // Create <FilterSet/> under <Dichroic/>
    FilterSet filterSet = new FilterSet();
    filterSet.setID(InOutCurrentTest.FILTERSET_ID);
    filterSet.setLotNumber(InOutCurrentTest.FILTERSET_LOT);
    filterSet.linkDichroic(dichroic);
    Filter emFilter = new Filter();
    Filter exFilter = new Filter();
    // Create <Objective/> under <Instrument/>
    Objective objective = new Objective();
    objective.setID(InOutCurrentTest.OBJECTIVE_ID);
    objective.setModel(InOutCurrentTest.OBJECTIVE_MODEL);
    CommentAnnotation objectiveAnnotation = new CommentAnnotation();
    objectiveAnnotation.setID(InOutCurrentTest.OBJECTIVE_ANNOTATION_ID);
    objectiveAnnotation.setValue(InOutCurrentTest.OBJECTIVE_ANNOTATION_VALUE);
    objectiveAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    objective.linkAnnotation(objectiveAnnotation);
    annotations.addCommentAnnotation(objectiveAnnotation);
    emFilter.setID(InOutCurrentTest.EM_FILTER_ID);
    emFilter.setType(InOutCurrentTest.EM_FILTER_TYPE);
    exFilter.setID(InOutCurrentTest.EX_FILTER_ID);
    exFilter.setType(InOutCurrentTest.EX_FILTER_TYPE);
    CommentAnnotation emFilterAnnotation = new CommentAnnotation();
    emFilterAnnotation.setID(InOutCurrentTest.EM_FILTER_ANNOTATION_ID);
    emFilterAnnotation.setValue(InOutCurrentTest.EM_FILTER_ANNOTATION_VALUE);
    emFilterAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    emFilter.linkAnnotation(emFilterAnnotation);
    annotations.addCommentAnnotation(emFilterAnnotation);
    instrument.addFilter(emFilter);
    instrument.addFilter(exFilter);
    instrument.addObjective(objective);
    filterSet.linkEmissionFilter(emFilter);
    filterSet.linkExcitationFilter(exFilter);
    filterSet.linkDichroic(dichroic);
    instrument.addFilterSet(filterSet);
    instrument.addDichroic(dichroic);
    CommentAnnotation instrumentAnnotation = new CommentAnnotation();
    instrumentAnnotation.setID(InOutCurrentTest.INSTRUMENT_ANNOTATION_ID);
    instrumentAnnotation.setValue(InOutCurrentTest.INSTRUMENT_ANNOTATION_VALUE);
    instrumentAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    instrument.linkAnnotation(instrumentAnnotation);
    annotations.addCommentAnnotation(instrumentAnnotation);
    // link Instrument to the first Image
    Image image = ome.getImage(0);
    image.linkInstrument(instrument);
    return instrument;
}