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

Example 6 with XMLAnnotation

use of ome.xml.model.XMLAnnotation 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;
}

Example 7 with XMLAnnotation

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

the class OMEXMLServiceTest method testOriginalMetadata.

@Test
public void testOriginalMetadata() throws ServiceException {
    OMEXMLMetadata metadata = service.createOMEXMLMetadata();
    service.populateOriginalMetadata(metadata, "testKey", "testValue");
    Hashtable metadataTable = service.getOriginalMetadata(metadata);
    assertEquals(metadataTable.size(), 1);
    assertTrue("testValue".equals(metadataTable.get("testKey")));
    OME root = (OME) metadata.getRoot();
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    assertEquals(annotations.sizeOfXMLAnnotationList(), 1);
    XMLAnnotation xmlAnn = annotations.getXMLAnnotation(0);
    String txt = "<OriginalMetadata><Key>testKey</Key><Value>testValue</Value></OriginalMetadata>";
    assertEquals(txt, xmlAnn.getValue());
    OriginalMetadataAnnotation omAnn = (OriginalMetadataAnnotation) xmlAnn;
    assertEquals("testValue", omAnn.getValueForKey());
}

Example 8 with XMLAnnotation

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

the class InOutCurrentTest method testValidChannelAnnotation.

@Test(dependsOnMethods = { "testValidChannelNode" })
public void testValidChannelAnnotation() {
    Channel c = ome.getImage(0).getPixels().getChannel(0);
    Annotation n = c.getLinkedAnnotation(0);
    assertNotNull(n);
    assertTrue(n instanceof XMLAnnotation);
    assertEquals(CHANNEL_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertEquals(CHANNEL_ANNOTATION_VALUE, ((XMLAnnotation) n).getValue());
}