Package ome.xml.model

Examples of ome.xml.model.Image

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        final WellSample qSample = new WellSample();
        qSample.setIndex(new NonNegativeInteger(well.sizeOfWellSampleList()));
        well.addWellSample(qSample);
      }
      final WellSample sample = well.getWellSample(d.site);
      Image image = new Image();
      Pixels pixels = new Pixels();
      Channel [] channels = new Channel[d.sizeC];
      for (int i=0; i<d.sizeC; i++) {
        Channel c = new Channel();
        c.setName(MockImageDescription.DEFAULT_CHANNEL_NAMES[i]);
        pixels.addChannel(c);
        channels[i] = c;
      }
      pixels.setSizeX(new PositiveInteger(d.sizeX));
      pixels.setSizeY(new PositiveInteger(d.sizeY));
      pixels.setSizeC(new PositiveInteger(d.sizeC));
      pixels.setSizeZ(new PositiveInteger(d.sizeZ));
      pixels.setSizeT(new PositiveInteger(d.sizeT));
      pixels.setDimensionOrder(d.order);
      for (int i=0; i<d.sizeC*d.sizeZ*d.sizeT; i++) {
        int c=0, z=0, t=0;
        switch(d.order) {
        case XYCTZ:
          c = i % d.sizeC;
          t = (i / d.sizeC) % d.sizeT;
          z = i / d.sizeC / d.sizeT;
          break;
        case XYCZT:
          c = i % d.sizeC;
          z = (i / d.sizeC) % d.sizeZ;
          t = i / d.sizeC / d.sizeZ;
          break;
        case XYTCZ:
          t = i % d.sizeT;
          c = (i / d.sizeT) % d.sizeC;
          z = i / d.sizeC / d.sizeT;
          break;
        case XYTZC:
          t = i % d.sizeT;
          z = (i / d.sizeT) % d.sizeZ;
          c = i / d.sizeZ / d.sizeT;
          break;
        case XYZCT:
          z = i % d.sizeZ;
          c = (i / d.sizeZ) % d.sizeC;
          t = i / d.sizeC / d.sizeZ;
          break;
        case XYZTC:
          z = i % d.sizeZ;
          t = (i / d.sizeZ) % d.sizeT;
          c = i / d.sizeT / d.sizeZ;
          break;
        }
        Plane plane = new Plane();
        plane.setTheC(new NonNegativeInteger(c));
        plane.setTheZ(new NonNegativeInteger(z));
        plane.setTheT(new NonNegativeInteger(t));
        pixels.addPlane(plane);
      }
      image.setPixels(pixels);
      sample.linkImage(image);
      ome.addImage(image);
    }
    imageFile.setXMLDocument(ome);
    return imageFile;
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  /* (non-Javadoc)
   * @see org.cellprofiler.imageset.MetadataExtractor#extract(java.lang.Object)
   */
  public Map<String, String> extract(ImagePlane source) {
    Plane plane = source.getOMEPlane();
    final Image image = source.getSeries().getOMEImage();
    if (image == null) return emptyMap;
    Pixels pixels = image.getPixels();
    HashMap<String, String> map = new HashMap<String, String>();
    if (plane != null) {
      putIfNotNull(map, MD_C, plane.getTheC().toString());
      putIfNotNull(map, MD_T, plane.getTheT().toString());
      putIfNotNull(map, MD_Z, plane.getTheZ().toString());
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      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) {
            // The planes aren't populated - need to infer from size{C / Z / T}
            int nChannels = pixels.sizeOfChannelList();
            if (nChannels == 0) nChannels = pixels.getSizeC().getValue();
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      if (result != 0) return result;
      final ImageSeries seriesA = planeA.getSeries();
      final ImageSeries seriesB = planeB.getSeries();
      result = seriesA.getSeries() - seriesB.getSeries();
      if (result != 0) return result;
      final Image omeImageA = seriesA.getOMEImage();
      final Image omeImageB = seriesB.getOMEImage();
      if (omeImageA == null) return (omeImageA==null)?0:-1;
      if (omeImageB == null) return 1;
      return compare(planeA, planeB);
    }
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  /* (non-Javadoc)
   * @see org.cellprofiler.imageset.MetadataExtractor#extract(java.lang.Object)
   */
  public Map<String, String> extract(ImageSeries source) {
    final Map<String, String> map = new HashMap<String, String>();
    Image image = source.getOMEImage();
    if (image != null) {
      Pixels pixels = image.getPixels();
      putIfNotNull(map, MD_SIZE_X, pixels.getSizeX());
      putIfNotNull(map, MD_SIZE_Y, pixels.getSizeY());
      putIfNotNull(map, MD_SIZE_C, pixels.getSizeC());
      putIfNotNull(map, MD_SIZE_T, pixels.getSizeT());
      putIfNotNull(map, MD_SIZE_Z, pixels.getSizeZ());
      if (image.sizeOfLinkedWellSampleList() == 1) {
        final WellSample wellSample = image.getLinkedWellSample(0);
        putIfNotNull(map, MD_SITE, wellSample.getIndex());
        final Well well = wellSample.getWell();
        if (well != null) {
          map.put(MD_WELL, getWellName(well.getRow().getValue(), well.getColumn().getValue()));
          Plate plate = well.getPlate();
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  /**
   * @return this plane's Plane element in the OME XML model
   */
  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);
  }
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   *
   * @param ome root of OME schema
   * @param id the ID to use to name the stack.
   */
  public void addToOME(OME ome, final String id) {
    final Image image = new Image();
    image.setID(id);
    final Pixels pixels = new Pixels();
    image.setPixels(pixels);
    ome.addImage(image);
    pixels.setID(String.format("Pixels:%s", id));
    final ImagePlaneDetails firstIPD = iterator().next();
    final Image srcImage = firstIPD.getImagePlane().getSeries().getOMEImage();
    PositiveInteger xSize = new PositiveInteger(1);
    PositiveInteger ySize = new PositiveInteger(1);
    if (srcImage != null) {
      final Pixels srcPixels = srcImage.getPixels();
      xSize = srcPixels.getSizeX();
      ySize = srcPixels.getSizeY();
    }
    pixels.setSizeX(xSize);
    pixels.setSizeY(ySize);
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   * @param id the ID of the Image node to load from 
   * @throws URISyntaxException
   */
  public void loadFromOME(OME ome, String id) throws URISyntaxException {
    for (int i=0; i<ome.sizeOfImageList(); i++) {
      Image omeImage = ome.getImage(i);
      if (omeImage.getID().equals(id)) {
        loadFromOMEImage(omeImage);
        return;
      }
    }
    throw new IndexOutOfBoundsException(String.format("Could not find image, \"%s\" in OME-XML", id));
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Related Classes of ome.xml.model.Image

  • org.cellprofiler.imageset.ChannelFilter$OrderingBase
  • org.cellprofiler.imageset.ImagePlane
  • org.cellprofiler.imageset.ImagePlaneDetailsStack
  • org.cellprofiler.imageset.ImagePlaneMetadataExtractor
  • org.cellprofiler.imageset.Mocks
  • org.cellprofiler.imageset.OMEPlaneMetadataExtractor
  • org.cellprofiler.imageset.OMESeriesMetadataExtractor
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