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

Example 6 with MapPair

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

the class FakeReader method fillAnnotations.

private void fillAnnotations(MetadataStore store, int imageIndex) {
    int annotationRefCount = 0;
    String annotationID;
    for (int i = 0; i < annBool; i++) {
        annotationID = ANNOTATION_PREFIX + annotationCount;
        store.setBooleanAnnotationID(annotationID, annotationBoolCount);
        store.setBooleanAnnotationNamespace(ANNOTATION_NAMESPACE, annotationBoolCount);
        store.setBooleanAnnotationValue(ANN_BOOLEAN_VALUE, annotationBoolCount);
        store.setImageAnnotationRef(annotationID, imageIndex, annotationRefCount);
        annotationBoolCount++;
        annotationCount++;
        annotationRefCount++;
    }
    for (int i = 0; i < annComment; i++) {
        annotationID = ANNOTATION_PREFIX + annotationCount;
        store.setCommentAnnotationID(annotationID, annotationCommentCount);
        store.setCommentAnnotationNamespace(ANNOTATION_NAMESPACE, annotationCommentCount);
        store.setCommentAnnotationValue(ANN_COMMENT_VALUE + (annotationCount + 1), annotationCommentCount);
        store.setImageAnnotationRef(annotationID, imageIndex, annotationRefCount);
        annotationCommentCount++;
        annotationCount++;
        annotationRefCount++;
    }
    for (int i = 0; i < annDouble; i++) {
        annotationID = ANNOTATION_PREFIX + annotationCount;
        store.setDoubleAnnotationID(annotationID, annotationDoubleCount);
        store.setDoubleAnnotationNamespace(ANNOTATION_NAMESPACE, annotationDoubleCount);
        store.setDoubleAnnotationValue(ANN_DOUBLE_VALUE * (annotationCount + 1), annotationDoubleCount);
        store.setImageAnnotationRef(annotationID, imageIndex, annotationRefCount);
        annotationDoubleCount++;
        annotationCount++;
        annotationRefCount++;
    }
    for (int i = 0; i < annLong; i++) {
        annotationID = ANNOTATION_PREFIX + annotationCount;
        store.setLongAnnotationID(annotationID, annotationLongCount);
        store.setLongAnnotationNamespace(ANNOTATION_NAMESPACE, annotationLongCount);
        store.setLongAnnotationValue(ANN_LONG_VALUE + annotationCount, annotationLongCount);
        store.setImageAnnotationRef(annotationID, imageIndex, annotationRefCount);
        annotationLongCount++;
        annotationCount++;
        annotationRefCount++;
    }
    for (int i = 0; i < annMap; i++) {
        annotationID = ANNOTATION_PREFIX + annotationCount;
        store.setMapAnnotationID(annotationID, annotationMapCount);
        store.setMapAnnotationNamespace(ANNOTATION_NAMESPACE, annotationMapCount);
        List<MapPair> mapValue = new ArrayList<MapPair>();
        for (int keyNum = 0; keyNum < 10; keyNum++) {
            mapValue.add(new MapPair("keyS" + imageIndex + "N" + keyNum, "val" + (keyNum + 1) * (annotationCount + 1)));
        }
        store.setMapAnnotationValue(mapValue, annotationMapCount);
        store.setImageAnnotationRef(annotationID, imageIndex, annotationRefCount);
        annotationMapCount++;
        annotationCount++;
        annotationRefCount++;
    }
    for (int i = 0; i < annTag; i++) {
        annotationID = ANNOTATION_PREFIX + annotationCount;
        store.setTagAnnotationID(annotationID, annotationTagCount);
        store.setTagAnnotationNamespace(ANNOTATION_NAMESPACE, annotationTagCount);
        store.setTagAnnotationValue(ANN_TAG_VALUE + (annotationCount + 1), annotationTagCount);
        store.setImageAnnotationRef(annotationID, imageIndex, annotationRefCount);
        annotationTagCount++;
        annotationCount++;
        annotationRefCount++;
    }
    for (int i = 0; i < annTerm; i++) {
        annotationID = ANNOTATION_PREFIX + annotationCount;
        store.setTermAnnotationID(annotationID, annotationTermCount);
        store.setTermAnnotationNamespace(ANNOTATION_NAMESPACE, annotationTermCount);
        store.setTermAnnotationValue(ANN_TERM_VALUE + (annotationCount + 1), annotationTermCount);
        store.setImageAnnotationRef(annotationID, imageIndex, annotationRefCount);
        annotationTermCount++;
        annotationCount++;
        annotationRefCount++;
    }
    for (int i = 0; i < annTime; i++) {
        annotationID = ANNOTATION_PREFIX + annotationCount;
        store.setTimestampAnnotationID(annotationID, annotationTimeCount);
        store.setTimestampAnnotationNamespace(ANNOTATION_NAMESPACE, annotationTimeCount);
        store.setTimestampAnnotationValue(ANN_TIME_VALUE, annotationTimeCount);
        store.setImageAnnotationRef(annotationID, imageIndex, annotationRefCount);
        annotationTimeCount++;
        annotationCount++;
        annotationRefCount++;
    }
    for (int i = 0; i < annXml; i++) {
        annotationID = ANNOTATION_PREFIX + annotationCount;
        store.setXMLAnnotationID(annotationID, annotationXmlCount);
        store.setXMLAnnotationNamespace(ANNOTATION_NAMESPACE, annotationXmlCount);
        store.setXMLAnnotationValue(ANN_XML_VALUE_START + (annotationCount + 1) + ANN_XML_VALUE_END, annotationXmlCount);
        store.setImageAnnotationRef(annotationID, imageIndex, annotationRefCount);
        annotationXmlCount++;
        annotationCount++;
        annotationRefCount++;
    }
}

Example 7 with MapPair

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

the class MapAnnotationTest method testMapAnnotationValueContent.

@Test
public void testMapAnnotationValueContent() 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).getLinkedAnnotation(0));
    MapAnnotation mapAnnotation = (MapAnnotation) ome.getImage(0).getLinkedAnnotation(0);
    List<MapPair> dataMap = mapAnnotation.getValue();
    assertEquals(6, dataMap.size());
    assertEquals("a", dataMap.get(0).getName());
    assertEquals("1", dataMap.get(0).getValue());
    assertEquals("d", dataMap.get(1).getName());
    assertEquals("2", dataMap.get(1).getValue());
    assertEquals("c", dataMap.get(2).getName());
    assertEquals("3", dataMap.get(2).getValue());
    assertEquals("b", dataMap.get(3).getName());
    assertEquals("4", dataMap.get(3).getValue());
    assertEquals("e", dataMap.get(4).getName());
    assertEquals("5", dataMap.get(4).getValue());
    assertEquals("c", dataMap.get(5).getName());
    assertEquals("6", dataMap.get(5).getValue());
}

Example 8 with MapPair

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

the class GenericExcitationMapTest method setUp.

@BeforeClass
public void setUp() throws Exception {
    Instrument instrument = new Instrument();
    instrument.setID("Instrument:0");
    // Add a GenericExcitationSource with an Map
    GenericExcitationSource geSource = new GenericExcitationSource();
    geSource.setID("LightSource:0");
    List<MapPair> dataMap = new ArrayList<MapPair>();
    dataMap.add(new MapPair("a", "1"));
    dataMap.add(new MapPair("d", "2"));
    dataMap.add(new MapPair("c", "3"));
    dataMap.add(new MapPair("b", "4"));
    dataMap.add(new MapPair("e", "5"));
    dataMap.add(new MapPair("c", "6"));
    assertEquals(6, dataMap.size());
    geSource.setMap(dataMap);
    instrument.addLightSource(geSource);
    ome.addInstrument(instrument);
    // Add an Image/Pixels with a LightSourceSettings reference to the
    // GenericExcitationSource on one of its channels.
    Image image = new Image();
    image.setID("Image:0");
    Pixels pixels = new Pixels();
    pixels.setID("Pixels:0");
    Channel channel = new Channel();
    channel.setID("Channel:0");
    LightSourceSettings settings = new LightSourceSettings();
    settings.setID("LightSource:0");
    channel.setLightSourceSettings(settings);
    pixels.addChannel(channel);
    image.setPixels(pixels);
    ome.addImage(image);
}