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

Example 11 with CommentAnnotation

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

the class InOutCurrentTest method testValidObjectiveAnnotation.

@Test(dependsOnMethods = { "testValidObjectiveNode" })
public void testValidObjectiveAnnotation() {
    Annotation n = ome.getInstrument(0).getObjective(0).getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(OBJECTIVE_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertTrue(n instanceof CommentAnnotation);
    CommentAnnotation string = (CommentAnnotation) n;
    assertEquals(OBJECTIVE_ANNOTATION_VALUE, string.getValue());
}

Example 12 with CommentAnnotation

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

the class InOutCurrentTest method testValidEmissionFilterAnnotation.

@Test(dependsOnMethods = { "testValidEmissionFilterNode" })
public void testValidEmissionFilterAnnotation() {
    Annotation n = ome.getInstrument(0).getFilter(0).getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(EM_FILTER_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertTrue(n instanceof CommentAnnotation);
    CommentAnnotation string = (CommentAnnotation) n;
    assertEquals(EM_FILTER_ANNOTATION_VALUE, string.getValue());
}

Example 13 with CommentAnnotation

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

the class InOutCurrentTest method testValidFilamentAnnotation.

@Test(dependsOnMethods = { "testValidFilamentNode" }, enabled = false)
public void testValidFilamentAnnotation() {
    Annotation n = ome.getInstrument(0).getLightSource(3).getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(LIGHTSOURCE_FILAMENT_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertTrue(n instanceof CommentAnnotation);
    CommentAnnotation string = (CommentAnnotation) n;
    assertEquals(LIGHTSOURCE_FILAMENT_ANNOTATION_VALUE, string.getValue());
}

Example 14 with CommentAnnotation

use of ome.xml.model.CommentAnnotation 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;
}