Package ome.xml.model

Examples of ome.xml.model.OME

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   * @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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    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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    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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  /**
   * @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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Related Classes of ome.xml.model.OME

  • org.cellprofiler.imageset.ImagePlaneMetadataExtractor
  • org.cellprofiler.imageset.ImageSeries
  • org.cellprofiler.imageset.ImageSet
  • org.cellprofiler.imageset.Mocks
  • org.cellprofiler.imageset.TestImagePlaneDetailsStack
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