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

Example 6 with CommentAnnotation

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

the class InOutCurrentTest method testValidDetectorAnnotation.

@Test(dependsOnMethods = { "testValidDetectorNode" })
public void testValidDetectorAnnotation() {
    Annotation n = ome.getInstrument(0).getDetector(0).getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(DETECTOR_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertTrue(n instanceof CommentAnnotation);
    CommentAnnotation string = (CommentAnnotation) n;
    assertEquals(DETECTOR_ANNOTATION_VALUE, string.getValue());
}

Example 7 with CommentAnnotation

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

the class ObjectBasedOMEModelMock method makeROI.

private ROI makeROI() {
    ROI roi = new ROI();
    roi.setID(InOutCurrentTest.ROI_ID);
    CommentAnnotation roiAnnotation = new CommentAnnotation();
    roiAnnotation.setID(InOutCurrentTest.ROI_ANNOTATION_ID);
    roiAnnotation.setValue(InOutCurrentTest.ROI_ANNOTATION_VALUE);
    roiAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    roi.linkAnnotation(roiAnnotation);
    annotations.addCommentAnnotation(roiAnnotation);
    Union shapeUnion = new Union();
    Rectangle rect = new Rectangle();
    rect.setID(InOutCurrentTest.SHAPE_ID);
    rect.setX(InOutCurrentTest.RECTANGLE_X);
    rect.setY(InOutCurrentTest.RECTANGLE_Y);
    rect.setWidth(InOutCurrentTest.RECTANGLE_WIDTH);
    rect.setHeight(InOutCurrentTest.RECTANGLE_HEIGHT);
    shapeUnion.addShape(rect);
    roi.setUnion(shapeUnion);
    return roi;
}

Example 8 with CommentAnnotation

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

the class Upgrade201004Test method validateUpgrade.

@Test
public void validateUpgrade() throws ServiceException {
    assertEquals(1, ome.sizeOfImageList());
    // StringAnnotation --> CommentAnnotation
    StructuredAnnotations structuredAnnotations = ome.getStructuredAnnotations();
    assertNotNull(structuredAnnotations);
    assertEquals(1, structuredAnnotations.sizeOfCommentAnnotationList());
    CommentAnnotation commentAnnotation = structuredAnnotations.getCommentAnnotation(0);
    assertEquals("StringAnnotation:0", commentAnnotation.getID());
    assertEquals("Transform", commentAnnotation.getNamespace());
    assertEquals("Foobar", commentAnnotation.getValue());
}

Example 9 with CommentAnnotation

use of ome.xml.model.CommentAnnotation 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 10 with CommentAnnotation

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

the class InOutCurrentTest method testValidLaserAnnotation.

@Test(dependsOnMethods = { "testValidLaserMetadata" }, enabled = false)
public void testValidLaserAnnotation() {
    Annotation n = ome.getInstrument(0).getLightSource(0).getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(LIGHTSOURCE_LASER_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertTrue(n instanceof CommentAnnotation);
    CommentAnnotation string = (CommentAnnotation) n;
    assertEquals(LIGHTSOURCE_LASER_ANNOTATION_VALUE, string.getValue());
}