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

Example 6 with Image

use of ome.xml.model.Image 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 7 with Image

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

the class FileWriteSPW method cleanup.

/**
 * Close the file writer.
 */
public void cleanup() {
    // No of planes expected for each image = 1 if not FLIM
    int validPlanes = 1;
    if (delays != null) {
        validPlanes = sizet;
    }
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot();
    Plate plate = root.getPlate(0);
    StructuredAnnotations anns = root.getStructuredAnnotations();
    ArrayList<Image> invalidImages = new ArrayList<>();
    // if not record those images as being invalid
    for (int i = 0; i < expectedImages.length; i++) {
        if (expectedImages[i] < validPlanes) {
            Image im = root.getImage(i);
            invalidImages.add(im);
            // remove modulo Annotation if FLIM
            if (delays != null) {
                XMLAnnotation ann = (XMLAnnotation) im.getLinkedAnnotation(0);
                anns.removeXMLAnnotation(ann);
            }
        }
    }
    // Now remove all limked wellSnmples and then invalid images
    for (int i = 0; i < invalidImages.size(); i++) {
        Image im = invalidImages.get(i);
        List<WellSample> list = im.copyLinkedWellSampleList();
        if (!list.isEmpty()) {
            WellSample wellSample = im.getLinkedWellSample(0);
            Well well = wellSample.getWell();
            well.removeWellSample(wellSample);
        }
        root.removeImage(im);
    }
    if (writer != null) {
        try {
            writer.close();
        } catch (IOException e) {
            System.err.println("Failed to close file writer.");
        }
    }
}

Example 8 with Image

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

the class Upgrade201106Test method validateUpgrade.

@Test
public void validateUpgrade() throws ServiceException {
    assertEquals(1, ome.sizeOfImageList());
    Image image = ome.getImage(0);
    assertNotNull(image.getAcquisitionDate());
    assertEquals(1, ome.sizeOfROIList());
    ROI roi = ome.getROI(0);
    Union union = roi.getUnion();
    assertEquals(1, union.sizeOfShapeList());
    Shape shape = union.getShape(0);
    assertTrue(shape instanceof Label);
    assertNotNull(shape.getText());
}

Example 9 with Image

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

the class Schema2011_06_TO_2012_06_Test method testDate.

@Test
public void testDate() {
    Assert.assertNotNull(ome);
    Assert.assertEquals(1, ome.sizeOfImageList());
    Image image = ome.getImage(0);
    Assert.assertNotNull(image);
    Assert.assertEquals(IMAGE_DATE, image.getAcquisitionDate());
}

Example 10 with Image

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