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

Example 11 with Pixels

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

the class OMEXMLServiceImpl method removeChannels.

/**
 * @see OMEXMLService#removeChannels(OMEXMLMetadata, int, int)
 */
@Override
public void removeChannels(OMEXMLMetadata omexmlMeta, int image, int sizeC) {
    omexmlMeta.resolveReferences();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    Pixels img = root.getImage(image).getPixels();
    List<Channel> channels = img.copyChannelList();
    for (int c = 0; c < channels.size(); c++) {
        Channel channel = channels.get(c);
        if (channel.getID() == null || c >= sizeC) {
            img.removeChannel(channel);
        }
    }
    omexmlMeta.setRoot(root);
}

Example 12 with Pixels

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

the class PumpWithLightSourceSettingsTest method setUp.

@BeforeClass
public void setUp() throws Exception {
    Instrument instrument = new Instrument();
    instrument.setID("Instrument:0");
    // Add a Laser with an Arc pump
    Laser laser = new Laser();
    laser.setID("Laser:0");
    Arc pump = new Arc();
    pump.setID("Arc:0");
    laser.linkPump(pump);
    instrument.addLightSource(laser);
    instrument.addLightSource(pump);
    ome.addInstrument(instrument);
    // Add an Image/Pixels with a LightSourceSettings reference to the Pump
    // 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("Arc:0");
    channel.setLightSourceSettings(settings);
    pixels.addChannel(channel);
    image.setPixels(pixels);
    ome.addImage(image);
}

Example 13 with Pixels

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

Example 14 with Pixels

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

the class InOutCurrentTest method testValidPixelsNode.

@Test(dependsOnMethods = { "testValidImageNode" })
public void testValidPixelsNode() {
    Pixels pixels = ome.getImage(0).getPixels();
    assertEquals(SIZE_X, pixels.getSizeX().getValue());
    assertEquals(SIZE_Y, pixels.getSizeY().getValue());
    assertEquals(SIZE_Z, pixels.getSizeZ().getValue());
    assertEquals(SIZE_C, pixels.getSizeC().getValue());
    assertEquals(SIZE_T, pixels.getSizeT().getValue());
    assertEquals(DIMENSION_ORDER, pixels.getDimensionOrder());
    assertEquals(PIXEL_TYPE, pixels.getType());
    assertEquals(1, pixels.sizeOfTiffDataList());
}

Example 15 with Pixels

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

the class InOutCurrentTest method testValidChannelNode.

@Test(dependsOnMethods = { "testValidPixelsNode" })
public void testValidChannelNode() {
    Pixels pixels = ome.getImage(0).getPixels();
    assertEquals(3, pixels.sizeOfChannelList());
    for (Channel channel : pixels.copyChannelList()) {
        assertNotNull(channel.getID());
    }
}