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

Example 1 with BinData

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

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

the class SPWModelMock method makeImage.

private Image makeImage(int index) {
    // <Instrument/> for later linking, etc.
    Instrument instrument = ome.getInstrument(0);
    // Create <Image/>
    Image image = new Image();
    image.setID("Image:" + index);
    CommentAnnotation commentAnnotation = new CommentAnnotation();
    commentAnnotation.setID("Annotation:" + index);
    commentAnnotation.setNamespace(GENERAL_ANNOTATION_NAMESPACE);
    commentAnnotation.setValue("Image:" + index + " annotation.");
    annotations.addCommentAnnotation(commentAnnotation);
    image.linkAnnotation(commentAnnotation);
    // Create <Pixels/>
    Pixels pixels = new Pixels();
    pixels.setID("Pixels:" + index);
    pixels.setSizeX(new PositiveInteger(SIZE_X));
    pixels.setSizeY(new PositiveInteger(SIZE_Y));
    pixels.setSizeZ(new PositiveInteger(SIZE_Z));
    pixels.setSizeC(new PositiveInteger(SIZE_C));
    pixels.setSizeT(new PositiveInteger(SIZE_T));
    pixels.setDimensionOrder(DIMENSION_ORDER);
    pixels.setType(PIXEL_TYPE);
    // Create <BinData/>
    for (int i = 0; i < SIZE_Z * SIZE_C * SIZE_T; i++) {
        BinData binData = new BinData();
        binData.setBigEndian(false);
        binData.setCompression(Compression.NONE);
        binData.setLength(new NonNegativeLong((long) (SIZE_X * SIZE_Y * BYTES_PER_PIXEL)));
        pixels.addBinData(binData);
    }
    // Create <Channel/> under <Pixels/>
    for (int i = 0; i < SIZE_C; i++) {
        Channel channel = new Channel();
        channel.setID("Channel:" + i);
        // Create <LightSourceSettings/> and link to <Channel/>
        LightSourceSettings settings = new LightSourceSettings();
        settings.setID(LIGHTSOURCE_LASER_ID);
        channel.setLightSourceSettings(settings);
        // Create <LightPath/> and link to <Channel/>
        LightPath lightPath = new LightPath();
        lightPath.linkEmissionFilter(instrument.getFilter(0));
        lightPath.linkExcitationFilter(instrument.getFilter(1));
        channel.setLightPath(lightPath);
        pixels.addChannel(channel);
    }
    // Put <Pixels/> under <Image/>
    image.setPixels(pixels);
    // Link <Instrument/> to <Image/>
    image.linkInstrument(instrument);
    // Create <ObjectiveSettings/> and link to <Image/>
    ObjectiveSettings settings = new ObjectiveSettings();
    settings.setID(OBJECTIVE_ID);
    image.setObjectiveSettings(settings);
    return image;
}

Example 3 with BinData

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

the class BaseModelMock method makeImage.

private Image makeImage(int index) {
    // Create <Image/>
    Image image = new Image();
    image.setID("Image:" + index);
    // Create <Pixels/>
    Pixels pixels = new Pixels();
    pixels.setID("Pixels:" + index);
    pixels.setSizeX(new PositiveInteger(SIZE_X));
    pixels.setSizeY(new PositiveInteger(SIZE_Y));
    pixels.setSizeZ(new PositiveInteger(SIZE_Z));
    pixels.setSizeC(new PositiveInteger(SIZE_C));
    pixels.setSizeT(new PositiveInteger(SIZE_T));
    pixels.setDimensionOrder(DIMENSION_ORDER);
    pixels.setType(PIXEL_TYPE);
    // Create <BinData/>
    for (int i = 0; i < SIZE_Z * SIZE_C * SIZE_T; i++) {
        BinData binData = new BinData();
        binData.setBigEndian(false);
        binData.setCompression(Compression.NONE);
        binData.setLength(new NonNegativeLong((long) (SIZE_X * SIZE_Y * BYTES_PER_PIXEL)));
        pixels.addBinData(binData);
    }
    // Create <Channel/> under <Pixels/>
    for (int i = 0; i < SIZE_C; i++) {
        Channel channel = new Channel();
        channel.setID("Channel:" + i);
        pixels.addChannel(channel);
    }
    // Put <Pixels/> under <Image/>
    image.setPixels(pixels);
    return image;
}