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

Example 1 with Pixels

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

the class OMEXMLServiceImpl method addMetadataOnly.

/**
 * @see OMEXMLService#addMetadataOnly(OMEXMLMetadata, int, boolean)
 */
public void addMetadataOnly(OMEXMLMetadata omexmlMeta, int image, boolean resolve) {
    if (resolve) {
        omexmlMeta.resolveReferences();
    }
    MetadataOnly meta = new MetadataOnly();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    Pixels pix = root.getImage(image).getPixels();
    pix.setMetadataOnly(meta);
}

Example 2 with Pixels

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

the class OMEXMLServiceImpl method removeBinData.

/**
 * @see OMEXMLService#removeBinData(OMEXMLMetadata)
 */
@Override
public void removeBinData(OMEXMLMetadata omexmlMeta) {
    omexmlMeta.resolveReferences();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    List<Image> images = root.copyImageList();
    for (Image img : images) {
        Pixels pix = img.getPixels();
        List<BinData> binData = pix.copyBinDataList();
        for (BinData bin : binData) {
            pix.removeBinData(bin);
        }
        pix.setMetadataOnly(null);
    }
    omexmlMeta.setRoot(root);
}

Example 3 with Pixels

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

the class ObjectBasedOMEModelMock method makeImage.

private Image makeImage() {
    // Create <Image/>
    Image image = new Image();
    image.setID(InOutCurrentTest.IMAGE_ID);
    ListAnnotation listAnnotation = new ListAnnotation();
    listAnnotation.setID(InOutCurrentTest.IMAGE_LIST_ANNOTATION_ID);
    listAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    annotations.addListAnnotation(listAnnotation);
    BooleanAnnotation annotation = new BooleanAnnotation();
    annotation.setID(InOutCurrentTest.IMAGE_ANNOTATION_ID);
    annotation.setValue(InOutCurrentTest.IMAGE_ANNOTATION_VALUE);
    annotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    listAnnotation.linkAnnotation(annotation);
    image.linkAnnotation(listAnnotation);
    annotations.addBooleanAnnotation(annotation);
    // Create <Pixels/>
    Pixels pixels = new Pixels();
    pixels.setID(InOutCurrentTest.PIXELS_ID);
    pixels.setSizeX(new PositiveInteger(InOutCurrentTest.SIZE_X));
    pixels.setSizeY(new PositiveInteger(InOutCurrentTest.SIZE_Y));
    pixels.setSizeZ(new PositiveInteger(InOutCurrentTest.SIZE_Z));
    pixels.setSizeC(new PositiveInteger(InOutCurrentTest.SIZE_C));
    pixels.setSizeT(new PositiveInteger(InOutCurrentTest.SIZE_T));
    pixels.setDimensionOrder(InOutCurrentTest.DIMENSION_ORDER);
    pixels.setType(InOutCurrentTest.PIXEL_TYPE);
    // Create <TiffData/>
    TiffData tiffData = new TiffData();
    // Create <UUID/>
    UUID uuid = new UUID();
    uuid.setValue(InOutCurrentTest.TIFF_DATA_UUID);
    tiffData.setUUID(uuid);
    pixels.addTiffData(tiffData);
    // Create <Channel/> under <Pixels/>
    for (int i = 0; i < InOutCurrentTest.SIZE_C; i++) {
        Channel channel = new Channel();
        channel.setID("Channel:" + i);
        if (i == 0) {
            XMLAnnotation channelAnnotation = new XMLAnnotation();
            channelAnnotation.setID(InOutCurrentTest.CHANNEL_ANNOTATION_ID);
            channelAnnotation.setValue(InOutCurrentTest.CHANNEL_ANNOTATION_VALUE);
            channelAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
            channel.linkAnnotation(channelAnnotation);
            annotations.addXMLAnnotation(channelAnnotation);
        }
        pixels.addChannel(channel);
    }
    // Put <Pixels/> under <Image/>
    image.setPixels(pixels);
    return image;
}

Example 4 with Pixels

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

the class XMLAnnotationTest method testValidXMLAnnotation.

@Test
public void testValidXMLAnnotation() throws EnumerationException {
    assertNotNull(ome);
    assertEquals(1, ome.sizeOfImageList());
    Image image = ome.getImage(0);
    Pixels pixels = image.getPixels();
    assertNotNull(pixels);
    assertEquals(3, pixels.sizeOfChannelList());
    Channel channel = pixels.getChannel(0);
    assertEquals(1, channel.sizeOfLinkedAnnotationList());
    Annotation annotation = channel.getLinkedAnnotation(0);
    assertEquals(XMLAnnotation.class, annotation.getClass());
    String annotationValue = ((XMLAnnotation) annotation).getValue();
    // normalize line endings if the test is run on Windows
    annotationValue = annotationValue.replaceAll("\r\n", "\n");
    assertEquals("<TestData>\n                    <key>foo</key>\n\t\t\t\t\t<value>bar</value>\n                </TestData>", annotationValue);
}

Example 5 with Pixels

use of ome.xml.model.Pixels 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);
}