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

Example 1 with MapPair

use of ome.xml.model.MapPair 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 2 with MapPair

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

the class ImagingEnvironmentMapTest 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 an ImagingEnvironment with an Map
    ImagingEnvironment imagingEnvironment = new ImagingEnvironment();
    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"));
    assertEquals(6, map.size());
    imagingEnvironment.setMap(map);
    image.setImagingEnvironment(imagingEnvironment);
    ome.addImage(image);
}

Example 3 with MapPair

use of ome.xml.model.MapPair 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");
}

Example 4 with MapPair

use of ome.xml.model.MapPair 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 5 with MapPair

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

the class writeMapAnnotationsExample method main.

public static void main(String[] args) throws Exception {
    if (args.length < 1) {
        System.out.println("Please specify an output file name.");
        System.exit(1);
    }
    String id = args[0];
    // create blank 512x512 image
    System.out.println("Creating random image...");
    int w = 512, h = 512, c = 1;
    int pixelType = FormatTools.UINT16;
    byte[] img = new byte[w * h * c * FormatTools.getBytesPerPixel(pixelType)];
    // fill with random data
    for (int i = 0; i < img.length; i++) img[i] = (byte) (256 * Math.random());
    // Create MapPair Object and add to List
    List<MapPair> mapList = new ArrayList<MapPair>();
    mapList.add(new MapPair("Example Key", "Example Value"));
    mapList.add(new MapPair("Bio-Formats Version", FormatTools.VERSION));
    // create metadata object with minimum required metadata fields
    System.out.println("Populating metadata...");
    // add (minimum+Map)Annotations to the metadata object
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata metadata = service.createOMEXMLMetadata();
    metadata.createRoot();
    MetadataTools.populateMetadata(metadata, 0, null, false, "XYZCT", FormatTools.getPixelTypeString(pixelType), w, h, 1, c, 1, c);
    int mapAnnotationIndex = 0;
    int annotationRefIndex = 0;
    String mapAnnotationID = MetadataTools.createLSID("MapAnnotation", 0, mapAnnotationIndex);
    metadata.setMapAnnotationID(mapAnnotationID, mapAnnotationIndex);
    metadata.setMapAnnotationValue(mapList, mapAnnotationIndex);
    metadata.setMapAnnotationAnnotator("Example Map Annotation", mapAnnotationIndex);
    metadata.setMapAnnotationDescription("Example Description", mapAnnotationIndex);
    metadata.setMapAnnotationNamespace("Example NameSpace", mapAnnotationIndex);
    metadata.setImageAnnotationRef(mapAnnotationID, 0, annotationRefIndex);
    mapAnnotationIndex = 1;
    annotationRefIndex = 1;
    mapAnnotationID = MetadataTools.createLSID("MapAnnotation", 0, mapAnnotationIndex);
    metadata.setMapAnnotationID(mapAnnotationID, mapAnnotationIndex);
    metadata.setMapAnnotationValue(mapList, mapAnnotationIndex);
    metadata.setMapAnnotationAnnotator("Example Map Annotation 1", mapAnnotationIndex);
    metadata.setMapAnnotationDescription("Example Description 1", mapAnnotationIndex);
    metadata.setMapAnnotationNamespace("Example NameSpace 1", mapAnnotationIndex);
    metadata.setImageAnnotationRef(mapAnnotationID, 0, annotationRefIndex);
    // Initialize writer and save file
    ImageWriter writer = new ImageWriter();
    writer.setMetadataRetrieve(metadata);
    writer.setId(id);
    writer.saveBytes(0, img);
    writer.close();
    System.out.println("Done.");
}