Examples of ome.xml.model.primitives.NonNegativeInteger

ome.xml.model.primitives.NonNegativeInteger

      in.skipBytes(34);


      String roiID = MetadataTools.createLSID("ROI", i);
      String shapeID = MetadataTools.createLSID("Shape", i, 0);


      NonNegativeInteger fontSize = FormatTools.getFontSize(fontHeight);


      switch (type) {
        case TEXT:
          double x = in.readDouble();
          double y = in.readDouble();

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          break;
        }
      }
      if (well == null) {
        well = new Well();
        well.setRow(new NonNegativeInteger(row));
        well.setColumn(new NonNegativeInteger(col));
        well.setExternalDescription(d.well);
        plate.addWell(well);
      }
      while (well.sizeOfWellSampleList() <= d.site) {
        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);

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    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();

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    pixels.addPlane(destPlane);
    int series = 0;
    int channel = ImagePlane.ALWAYS_MONOCHROME;
    final TiffData location = new TiffData();
    final UUID uuid = new UUID();
    location.setPlaneCount(new NonNegativeInteger(1));
    if (ipd != null) {
      final ImagePlane imagePlane = ipd.getImagePlane();
      series = imagePlane.getSeries().getSeries();
      channel = imagePlane.getChannel();
      location.setIFD(new NonNegativeInteger(imagePlane.getIndex()));
      uuid.setFileName(imagePlane.getImageFile().getURI().toString());
      final Plane omePlane = imagePlane.getOMEPlane();
      if (omePlane != null) {
        location.setFirstC(omePlane.getTheC());
        location.setFirstT(omePlane.getTheT());
        location.setFirstZ(omePlane.getTheZ());
      } else {
        location.setFirstC(NNI_ZERO);
        location.setFirstT(NNI_ZERO);
        location.setFirstZ(NNI_ZERO);
        
      }
    } else {
      // A missing plane.
      // This retrieves a URI placeholder for it.
      uuid.setFileName(new ImageFile(xSize.getValue(), ySize.getValue()).getURI().toString());
      location.setIFD(NNI_ZERO);
      location.setFirstC(NNI_ZERO);
      location.setFirstT(NNI_ZERO);
      location.setFirstZ(NNI_ZERO);
    }
    location.setUUID(uuid);
    pixels.addTiffData(location);
    destPlane.setTheC(new NonNegativeInteger(c));
    destPlane.setTheZ(new NonNegativeInteger(z));
    destPlane.setTheT(new NonNegativeInteger(t));
    if (series > 0) {
      addLongAnnotationToPlane(ome, destPlane, SERIES_ANNOTATION_DESCRIPTION, series);
    }
    if (channel != ImagePlane.ALWAYS_MONOCHROME)
      addLongAnnotationToPlane(ome, destPlane, CHANNEL_ANNOTATION_DESCRIPTION, channel);

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Related Classes of ome.xml.model.primitives.NonNegativeInteger

loci.formats.in.ZeissLSMReader

org.cellprofiler.imageset.ImagePlaneDetailsStack

org.cellprofiler.imageset.Mocks

org.cellprofiler.imageset.OMEPlaneMetadataExtractor

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