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

Example 6 with Annotation

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

the class InOutCurrentTest method testValidArcAnnotation.

@Test(dependsOnMethods = { "testValidArcNode" }, enabled = false)
public void testValidArcAnnotation() {
    Annotation n = ome.getInstrument(0).getLightSource(2).getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(LIGHTSOURCE_ARC_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertTrue(n instanceof CommentAnnotation);
    CommentAnnotation string = (CommentAnnotation) n;
    assertEquals(LIGHTSOURCE_ARC_ANNOTATION_VALUE, string.getValue());
}

Example 7 with Annotation

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

the class InOutCurrentTest method testValidLightEmittingDiodeAnnotation.

@Test(dependsOnMethods = { "testValidLightEmittingDiodeNode" }, enabled = false)
public void testValidLightEmittingDiodeAnnotation() {
    LightEmittingDiode led = (LightEmittingDiode) ome.getInstrument(0).getLightSource(4);
    Annotation n = led.getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(LIGHTSOURCE_LED_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertTrue(n instanceof CommentAnnotation);
    CommentAnnotation string = (CommentAnnotation) n;
    assertEquals(LIGHTSOURCE_LED_ANNOTATION_VALUE, string.getValue());
}

Example 8 with Annotation

use of ome.xml.model.Annotation 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 9 with Annotation

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

the class XMLAnnotationTest method testValidXMLAnnotation.

@Test
public void testValidXMLAnnotation() throws EnumerationException {
    assertNotNull(ome);
    assertEquals(1, ome.sizeOfImageList());
    Image image = ome.getImage(0);
    Pixels pixels = image.getPixels();
    assertNotNull(pixels);
    assertEquals(3, pixels.sizeOfChannelList());
    Channel channel = pixels.getChannel(0);
    assertEquals(1, channel.sizeOfLinkedAnnotationList());
    Annotation annotation = channel.getLinkedAnnotation(0);
    assertEquals(XMLAnnotation.class, annotation.getClass());
    String annotationValue = ((XMLAnnotation) annotation).getValue();
    // normalize line endings if the test is run on Windows
    annotationValue = annotationValue.replaceAll("\r\n", "\n");
    assertEquals("<TestData>\n                    <key>foo</key>\n\t\t\t\t\t<value>bar</value>\n                </TestData>", annotationValue);
}

Example 10 with Annotation

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

the class OMEXMLServiceImpl method getModuloAlong.

/**
 * Create a {@link loci.formats.Modulo} corresponding to the given ModuloAlong* tag.
 * @param omexml the OMEXMLMetadata from which to retrieve the ModuloAlong* tag
 * @param tag the tag name (e.g. "ModuloAlongC")
 * @param image the Image index within the OMEXMLMetadata
 * @return the corresponding Modulo object
 */
private Modulo getModuloAlong(OMEXMLMetadata omexml, String tag, int image) {
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot();
    Image img = root.getImage(image);
    if (img == null) {
        return null;
    }
    for (int i = 0; i < img.sizeOfLinkedAnnotationList(); i++) {
        Annotation annotation = img.getLinkedAnnotation(i);
        if (!(annotation instanceof XMLAnnotation)) {
            continue;
        }
        String xml = ((XMLAnnotation) annotation).getValue();
        try {
            Document annotationRoot = XMLTools.parseDOM(xml);
            NodeList nodes = annotationRoot.getElementsByTagName(tag);
            if (nodes.getLength() > 0) {
                Element modulo = (Element) nodes.item(0);
                NamedNodeMap attrs = modulo.getAttributes();
                Modulo m = new Modulo(tag.substring(tag.length() - 1));
                Node start = attrs.getNamedItem("Start");
                Node end = attrs.getNamedItem("End");
                Node step = attrs.getNamedItem("Step");
                Node type = attrs.getNamedItem("Type");
                Node typeDescription = attrs.getNamedItem("TypeDescription");
                Node unit = attrs.getNamedItem("Unit");
                if (start != null) {
                    m.start = Double.parseDouble(start.getNodeValue());
                }
                if (end != null) {
                    m.end = Double.parseDouble(end.getNodeValue());
                }
                if (step != null) {
                    m.step = Double.parseDouble(step.getNodeValue());
                }
                if (type != null) {
                    m.type = type.getNodeValue();
                }
                if (typeDescription != null) {
                    m.typeDescription = typeDescription.getNodeValue();
                }
                if (unit != null) {
                    m.unit = unit.getNodeValue();
                }
                NodeList labels = modulo.getElementsByTagName("Label");
                if (labels != null && labels.getLength() > 0) {
                    m.labels = new String[labels.getLength()];
                    for (int q = 0; q < labels.getLength(); q++) {
                        m.labels[q] = labels.item(q).getTextContent();
                    }
                }
                return m;
            }
        } catch (ParserConfigurationException e) {
            LOGGER.debug("Failed to parse ModuloAlong", e);
        } catch (SAXException e) {
            LOGGER.debug("Failed to parse ModuloAlong", e);
        } catch (IOException e) {
            LOGGER.debug("Failed to parse ModuloAlong", e);
        }
    }
    return null;
}