Examples of OME

ome.xml.model.OME

Examples of ome.xml.model.OME

   * @throws TransformerException 
   * @throws IOException 
   */
  public byte [] compress(List<String> ids, Deflater deflater) 
  throws TransformerFactoryConfigurationError, TransformerException, IOException {
    OME ome = new OME();
    addToOME(ome, ids);
    Document document = documentBuilder.get().newDocument();
    Element omeElement = ome.asXMLElement(document);
    document.appendChild(omeElement);
    DOMSource domSource = new DOMSource(document);
    
    ByteArrayOutputStream baOS = new ByteArrayOutputStream();
    final Transformer transformer = TransformerFactory.newInstance().newTransformer();

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Examples of ome.xml.model.OME

    InputStream iis = new ByteArrayInputStream(bos.toByteArray());
    
    transformer.get().transform(new StreamSource(new InputStreamReader(iis)), domResult);
    Node documentOut = domResult.getNode();
    OMEModel model = new OMEModelImpl();
    OME ome = new OME((Element)(documentOut.getFirstChild()), model);
    model.resolveReferences();
    List<ImagePlaneDetailsStack> stacks = new ArrayList<ImagePlaneDetailsStack>();
    for (int i=0; i<ids.size(); i++) {
      final String id = ids.get(i);
      final TypedAxis [] axes = axesList.get(i);

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Examples of ome.xml.model.OME

    final List<ImagePlaneDetails> result = new ArrayList<ImagePlaneDetails> ();
    for (int i=0; i<urls.length; i++) {
      ImageFile imageFile = new ImageFile(new URI(urls[i]));
      if (metadata[i] != null) {
        imageFile.setXMLDocument(metadata[i]);
        final OME fileMetadata = imageFile.getMetadata();
        for (int series=0; series < fileMetadata.sizeOfImageList(); series++) {
          final ImageSeries imageSeries = new ImageSeries(imageFile, series);
          Image seriesMetadata = imageSeries.getOMEImage();
          final Pixels pixels = seriesMetadata.getPixels();
          int nPlanes = pixels.sizeOfPlaneList();
          if (nPlanes == 0) {

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Examples of ome.xml.model.OME

  
  /**
   * @return the OME XML image data or null if no OMEXML data
   */
  public Image getOMEImage() {
    final OME metadata = imageFile.getMetadata(); 
    if (metadata == null) return null;
    return metadata.getImage(series);
  }

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