List of sizeOfPlaneList() Examples

Examples of sizeOfPlaneList()

ome.xml.model.Pixels.sizeOfPlaneList()

Examples of ome.xml.model.Pixels.sizeOfPlaneList()

    final OME imageFileMetadata = imageFile.getMetadata();
    for (int series=0; series < imageFileMetadata.sizeOfImageList(); series++) {
      final ImageSeries imageSeries = new ImageSeries(imageFile, series);
      final ImageSeriesDetails imageSeriesDetails = new ImageSeriesDetails(imageSeries, imageFileDetails);
      final Pixels pixels = imageSeries.getOMEImage().getPixels();
      for (int index=0; index<pixels.sizeOfPlaneList(); index++) {
        final ImagePlane imagePlane = new ImagePlane(imageSeries, index, ImagePlane.ALWAYS_MONOCHROME);
        result.add(new ImagePlaneDetails(imagePlane, imageSeriesDetails));
      }
    }
    return result;

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Examples of ome.xml.model.Pixels.sizeOfPlaneList()

        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) {
            // The planes aren't populated - need to infer from size{C / Z / T}
            int nChannels = pixels.sizeOfChannelList();
            if (nChannels == 0) nChannels = pixels.getSizeC().getValue();
            nPlanes = nChannels * pixels.getSizeT().getValue() * pixels.getSizeZ().getValue();

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Examples of ome.xml.model.Pixels.sizeOfPlaneList()

   */
  public Plane getOMEPlane() {
    final Image image = imageSeries.getOMEImage();
    if (image == null) return null;
    final Pixels pixels = image.getPixels();
    if (pixels.sizeOfPlaneList() <= index) return null;
    return pixels.getPlane(index);
  }
  @Override
  public String toString() {
    return String.format("ImagePlane: %s, series=%d, index=%d, channel=%s",

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Examples of ome.xml.model.Pixels.sizeOfPlaneList()

  private void loadFromOMEImage(Image omeImage) throws URISyntaxException {
    Map<URI, ImageFileDetails> imageFiles = new HashMap<URI, ImageFileDetails>();
    Map<URI, Map<Integer, ImageSeriesDetails>> imageSeries = new HashMap<URI, Map<Integer,ImageSeriesDetails>>();
    final Pixels pixels = omeImage.getPixels();
    int [] coords = new int[numDimensions()];
    for (int planeIdx=0; planeIdx<pixels.sizeOfPlaneList() && planeIdx<pixels.sizeOfTiffDataList(); planeIdx++) {
      final Plane plane = pixels.getPlane(planeIdx);
      final TiffData location = pixels.getTiffData(planeIdx);
      final URI uri = new URI(location.getUUID().getFileName());
      if (! imageFiles.containsKey(uri)) {
        imageFiles.put(uri, new ImageFileDetails(new ImageFile(uri)));

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