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

Example 1 with OMEModel

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

the class OMEXMLServiceImpl method createRoot.

/**
 * Constructs an OME root node. <b>NOTE:</b> This method is mostly here to
 * ensure type safety of return values as instances of service dependency
 * classes should not leak out of the interface.
 * @param xml String of XML to create the root node from.
 * @return An ome.xml.model.OMEModelObject subclass root node.
 * @throws IOException If there is an error reading from the string.
 * @throws SAXException If there is an error parsing the XML.
 * @throws ParserConfigurationException If there is an error preparing the
 * parsing infrastructure.
 */
private OMEXMLMetadataRoot createRoot(String xml) throws ServiceException {
    try {
        OMEModel model = new OMEModelImpl();
        OMEXMLMetadataRoot ome = new OMEXMLMetadataRoot(XMLTools.parseDOM(xml).getDocumentElement(), model);
        model.resolveReferences();
        return ome;
    } catch (Exception e) {
        throw new ServiceException(e);
    }
}

Example 2 with OMEModel

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

the class XMLAnnotationTest method setUp.

@BeforeClass
public void setUp() throws Exception {
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    DocumentBuilder parser = factory.newDocumentBuilder();
    Document document = parser.parse(this.getClass().getResourceAsStream("XMLAnnotationTest.ome"));
    OMEModel model = new OMEModelImpl();
    // Read string XML in as a DOM tree and parse into the object hierarchy
    ome = new OME(document.getDocumentElement(), model);
    model.resolveReferences();
}

Example 3 with OMEModel

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

the class GenericExcitationMapTest method testGenericExcitationSourceMapContent.

@Test
public void testGenericExcitationSourceMapContent() throws Exception {
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    DocumentBuilder parser = factory.newDocumentBuilder();
    Document document = parser.newDocument();
    // Produce a valid OME DOM element hierarchy
    Element root = ome.asXMLElement(document);
    SPWModelMock.postProcess(root, document, false);
    OMEModel model = new OMEModelImpl();
    ome = new OME(document.getDocumentElement(), model);
    model.resolveReferences();
    assertNotNull(ome);
    assertEquals(ome.getImage(0).getPixels().getChannel(0).getLightSourceSettings().getID(), "LightSource:0");
    assertNotNull(ome.getInstrument(0).getLightSource(0));
    GenericExcitationSource geSource = (GenericExcitationSource) ome.getInstrument(0).getLightSource(0);
    List<MapPair> dataMap = geSource.getMap();
    assertEquals(6, dataMap.size());
    assertPair(dataMap, 0, "a", "1");
    assertPair(dataMap, 1, "d", "2");
    assertPair(dataMap, 2, "c", "3");
    assertPair(dataMap, 3, "b", "4");
    assertPair(dataMap, 4, "e", "5");
    assertPair(dataMap, 5, "c", "6");
}

Example 4 with OMEModel

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

the class GenericExcitationMapTest method testGenericExcitationSourceValid.

@Test
public void testGenericExcitationSourceValid() throws Exception {
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    DocumentBuilder parser = factory.newDocumentBuilder();
    Document document = parser.newDocument();
    // Produce a valid OME DOM element hierarchy
    Element root = ome.asXMLElement(document);
    SPWModelMock.postProcess(root, document, false);
    OMEModel model = new OMEModelImpl();
    ome = new OME(document.getDocumentElement(), model);
    model.resolveReferences();
}

Example 5 with OMEModel

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

the class ImagingEnvironmentMapTest method testGenericExcitationSourceMapContent.

@Test
public void testGenericExcitationSourceMapContent() throws Exception {
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    DocumentBuilder parser = factory.newDocumentBuilder();
    Document document = parser.newDocument();
    // Produce a valid OME DOM element hierarchy
    Element root = ome.asXMLElement(document);
    SPWModelMock.postProcess(root, document, false);
    OMEModel model = new OMEModelImpl();
    ome = new OME(document.getDocumentElement(), model);
    model.resolveReferences();
    assertNotNull(ome);
    assertEquals(ome.getImage(0).getPixels().getID(), "Pixels:0");
    assertNotNull(ome.getImage(0).getImagingEnvironment());
    ImagingEnvironment imagingEnvironment = ome.getImage(0).getImagingEnvironment();
    List<MapPair> dataMap = imagingEnvironment.getMap();
    assertEquals(6, dataMap.size());
    assertPair(dataMap, 0, "a", "1");
    assertPair(dataMap, 1, "d", "2");
    assertPair(dataMap, 2, "c", "3");
    assertPair(dataMap, 3, "b", "4");
    assertPair(dataMap, 4, "e", "5");
    assertPair(dataMap, 5, "c", "6");
}