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

Example 6 with StructuredAnnotations

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

the class MapAnnotationTest method setUp.

@BeforeClass
public void setUp() throws Exception {
    // Add an Image/Pixels
    Image image = new Image();
    image.setID("Image:0");
    Pixels pixels = new Pixels();
    pixels.setID("Pixels:0");
    image.setPixels(pixels);
    // Add a Map Annotation
    List<MapPair> map = new ArrayList<MapPair>();
    map.add(new MapPair("a", "1"));
    map.add(new MapPair("d", "2"));
    map.add(new MapPair("c", "3"));
    map.add(new MapPair("b", "4"));
    map.add(new MapPair("e", "5"));
    map.add(new MapPair("c", "6"));
    MapAnnotation mapAnnotation = new MapAnnotation();
    mapAnnotation.setID("Annotation:0");
    mapAnnotation.setValue(map);
    StructuredAnnotations structuredAnnotations = new StructuredAnnotations();
    structuredAnnotations.addMapAnnotation(mapAnnotation);
    ome.setStructuredAnnotations(structuredAnnotations);
    image.linkAnnotation(mapAnnotation);
    ome.addImage(image);
}

Example 7 with StructuredAnnotations

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

the class OMEXMLServiceImpl method getOriginalMetadata.

/**
 * @see OMEXMLService#getOriginalMetadata(loci.formats.ome.OMEXMLMetadata)
 */
@Override
public Hashtable getOriginalMetadata(OMEXMLMetadata omexmlMeta) {
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    if (annotations == null) {
        return null;
    }
    Hashtable metadata = new Hashtable();
    for (int i = 0; i < annotations.sizeOfXMLAnnotationList(); i++) {
        XMLAnnotation annotation = annotations.getXMLAnnotation(i);
        if (annotation instanceof OriginalMetadataAnnotation) {
            OriginalMetadataAnnotation original = (OriginalMetadataAnnotation) annotation;
            metadata.put(original.getKey(), original.getValueForKey());
            continue;
        }
        String xml = annotation.getValue();
        try {
            Document annotationRoot = XMLTools.parseDOM(xml);
            NodeList metadataNodes = annotationRoot.getElementsByTagName("OriginalMetadata");
            for (int meta = 0; meta < metadataNodes.getLength(); meta++) {
                Element metadataNode = (Element) metadataNodes.item(meta);
                NodeList keys = metadataNode.getElementsByTagName("Key");
                NodeList values = metadataNode.getElementsByTagName("Value");
                for (int q = 0; q < keys.getLength(); q++) {
                    Node key = keys.item(q);
                    Node value = values.item(q);
                    metadata.put(key.getTextContent(), value.getTextContent());
                }
            }
            if (metadataNodes.getLength() == 0) {
                metadataNodes = annotationRoot.getDocumentElement().getChildNodes();
                for (int meta = 0; meta < metadataNodes.getLength(); meta++) {
                    // com.sun.org.apache.xerces.internal.dom.DeferredCommentImpl.
                    if (metadataNodes.item(meta) instanceof Element) {
                        Element node = (Element) metadataNodes.item(meta);
                        String name = node.getNodeName();
                        NamedNodeMap attrs = node.getAttributes();
                        Node value = attrs.getNamedItem("Value");
                        if (value != null) {
                            metadata.put(name, value.getNodeValue());
                        }
                    }
                }
            }
        } catch (ParserConfigurationException e) {
            LOGGER.debug("Failed to parse OriginalMetadata", e);
        } catch (SAXException e) {
            LOGGER.debug("Failed to parse OriginalMetadata", e);
        } catch (IOException e) {
            LOGGER.debug("Failed to parse OriginalMetadata", e);
        }
    }
    return metadata;
}

Example 8 with StructuredAnnotations

use of ome.xml.model.StructuredAnnotations 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());
}