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

Example 1 with LightSourceSettings

use of ome.xml.model.LightSourceSettings 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 LightSourceSettings

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

the class Schema2011_06_Instrument_Upgrade_Test method testChannel0ToLightsourceSettings.

@Test(groups = { "11-06-i-links" }, dependsOnGroups = { "11-06-i-image", "11-06-i-lightsource" })
public void testChannel0ToLightsourceSettings() {
    Assert.assertNotNull(channel0);
    LightSourceSettings lightsourceSettings = channel0.getLightSourceSettings();
    Assert.assertNotNull(lightsourceSettings);
    Assert.assertEquals(ref.Image0LightSourceSettings0Attenuation, lightsourceSettings.getAttenuation());
    Assert.assertEquals(ref.Image0LightSourceSettings0Wavelength, lightsourceSettings.getWavelength());
    Assert.assertNull(lightsourceSettings.getMicrobeamManipulation());
}

Example 3 with LightSourceSettings

use of ome.xml.model.LightSourceSettings 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 LightSourceSettings

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

the class Schema2011_06_Instrument_Upgrade_Test method testChannel0ToLightsourceLinkage.

@Test(enabled = false, groups = { "11-06-i-links" }, dependsOnGroups = { "11-06-i-image", "11-06-i-lightsource" })
public void testChannel0ToLightsourceLinkage() {
    Assert.assertNotNull(channel0);
    LightSourceSettings lightsourceSettings = channel0.getLightSourceSettings();
    Assert.assertNotNull(lightsourceSettings);
    Assert.assertNotNull(lightsourceSettings.getLightSource());
    Assert.assertEquals(lightsource0, lightsourceSettings.getLightSource());
}

Example 5 with LightSourceSettings

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