Package ome.xml.model

Examples of ome.xml.model.Pixels

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        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);
    }
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    final ImageFile imageFile = imageFileDetails.getImageFile();
    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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   */
  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());
      final NonNegativeInteger c = plane.getTheC();
      if (c != null) {
        final int cidx = c.getValue().intValue();
        if (pixels.sizeOfChannelList() > cidx) {
          Channel channel = pixels.getChannel(cidx);
          if (channel != null) {
            putIfNotNull(map, MD_CHANNEL_NAME, channel.getName());
            final PositiveInteger samplesPerPixel = channel.getSamplesPerPixel();
            if (samplesPerPixel != null) {
              final int nSamplesPerPixel = samplesPerPixel.getValue().intValue();
              map.put(MD_COLOR_FORMAT, (nSamplesPerPixel == 1)?MD_MONOCHROME:MD_RGB);
            }
          }
        }
      }
    } else {
      if (pixels != null){
        if (pixels.getSizeC().getValue().intValue() == 1) {
          map.put(MD_COLOR_FORMAT, MD_MONOCHROME);
          Channel channel = pixels.getChannel(0);
          if (channel != null) {
            putIfNotNull(map, MD_CHANNEL_NAME, channel.getName());
          }
        } else if (pixels.sizeOfChannelList() == 1) {
          map.put(MD_COLOR_FORMAT, MD_RGB);
        } else {
          map.put(MD_COLOR_FORMAT, MD_MONOCHROME);
          Channel channel = pixels.getChannel(source.theC());
          if (channel != null) {
            putIfNotNull(map, MD_CHANNEL_NAME, channel.getName());
          }
        }
      } else {
        /*
         * Use the channel within the plane to guess at the format.
         */
        final int channel = source.getChannel();
        switch(channel) {
        case ImagePlane.INTERLEAVED:
          map.put(MD_COLOR_FORMAT, MD_RGB);
          break;
        case ImagePlane.ALWAYS_MONOCHROME:
          map.put(MD_COLOR_FORMAT, MD_MONOCHROME);
          break;
        case ImagePlane.BLUE_CHANNEL:
          map.put(MD_COLOR_FORMAT, MD_MONOCHROME);
          map.put(MD_CHANNEL_NAME, CH_BLUE);
          break;
        case ImagePlane.RED_CHANNEL:
          map.put(MD_COLOR_FORMAT, MD_MONOCHROME);
          map.put(MD_CHANNEL_NAME, CH_RED);
          break;
        case ImagePlane.GREEN_CHANNEL:
          map.put(MD_COLOR_FORMAT, MD_MONOCHROME);
          map.put(MD_CHANNEL_NAME, CH_GREEN);
          break;
        case ImagePlane.ALPHA_CHANNEL:
          map.put(MD_COLOR_FORMAT, MD_MONOCHROME);
          map.put(MD_CHANNEL_NAME, CH_ALPHA);
          break;
        default:
          map.put(MD_COLOR_FORMAT, MD_MONOCHROME);
          break;
        }
      }
      /*
       * Assume it's a movie if there's no plane data and there is more than one frame. The index gives the T.
       */
      if (pixels.getSizeT().getValue().intValue() > 1)
        map.put(MD_T, StringCache.intern(Integer.toString(source.getIndex())));
      else if (pixels.getSizeZ().getValue().intValue() > 1)
        map.put(MD_Z, StringCache.intern(Integer.toString(source.getIndex())));
    }
    return map;
  }
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        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();
            nPlanes = nChannels * pixels.getSizeT().getValue() * pixels.getSizeZ().getValue();
            for (int plane=0; plane<nPlanes; plane++) {
              final ImagePlane imagePlane = new ImagePlane(imageSeries, plane, ImagePlane.ALWAYS_MONOCHROME);
              final ImagePlaneDetails ipd = extract(imagePlane);
              ipd.put(OMEPlaneMetadataExtractor.MD_C, Integer.toString(imagePlane.theC()));
              ipd.put(OMEPlaneMetadataExtractor.MD_T, Integer.toString(imagePlane.theT()));
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   */
  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) {
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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 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);
    setDimensionOrder(this, pixels);
    int nPlanes = 1;
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   * @throws URISyntaxException
   */
  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)));
      }
      final ImageFileDetails ifd = imageFiles.get(uri);
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Related Classes of ome.xml.model.Pixels

  • 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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