예제 #1
0
  private IDataset getToggledData(IImageTrace image, IProgressMonitor monitor) {

    if (image.getData() == trans) {
      return orig;
    } else {
      this.orig = image.getData();

      Object[] oa;
      try {
        oa = filter.filter(orig, null);
        this.trans = (IDataset) oa[0];
        return trans;

      } catch (Exception e) {
        e.printStackTrace();
        return orig;
      }
    }
  }
예제 #2
0
  protected Dataset createZoom(
      final IImageTrace image,
      IRegion region,
      IROI rbs,
      boolean tryUpdate,
      boolean isDrag,
      IProgressMonitor monitor) {

    if (!(region.getROI() instanceof RectangularROI)) return null;
    final RectangularROI bounds = (RectangularROI) (rbs == null ? region.getROI() : rbs);
    if (bounds == null) return null;
    if (!region.isVisible()) return null;

    if (monitor.isCanceled()) return null;

    final int yInc = bounds.getPoint()[1] < bounds.getEndPoint()[1] ? 1 : -1;
    final int xInc = bounds.getPoint()[0] < bounds.getEndPoint()[0] ? 1 : -1;

    Dataset im = DatasetUtils.convertToDataset(image.getData());
    Dataset slice = DatasetUtils.convertToDataset(ToolUtils.getClippedSlice(im, bounds));
    slice.setName(region.getName());
    // Calculate axes to have real values not size
    Dataset yLabels = null;
    Dataset xLabels = null;
    if (image.getAxes() != null && image.getAxes().size() > 0) {
      Dataset xl = DatasetUtils.convertToDataset(image.getAxes().get(0));
      if (xl != null) xLabels = ZoomTool.getLabelsFromLabels(xl, bounds, 0);
      Dataset yl = DatasetUtils.convertToDataset(image.getAxes().get(1));
      if (yl != null) yLabels = ZoomTool.getLabelsFromLabels(yl, bounds, 1);
    }

    if (yLabels == null)
      yLabels =
          DatasetFactory.createRange(
              IntegerDataset.class, bounds.getPoint()[1], bounds.getEndPoint()[1], yInc);
    if (xLabels == null)
      xLabels =
          DatasetFactory.createRange(
              IntegerDataset.class, bounds.getPoint()[0], bounds.getEndPoint()[0], xInc);

    final IImageTrace zoom_trace =
        (IImageTrace)
            profilePlottingSystem.updatePlot2D(
                slice, Arrays.asList(new IDataset[] {xLabels, yLabels}), monitor);
    registerTraces(region, Arrays.asList(new ITrace[] {zoom_trace}));
    Display.getDefault()
        .syncExec(
            new Runnable() {
              public void run() {
                zoom_trace.setPaletteData(image.getPaletteData());
              }
            });

    return slice;
  }
예제 #3
0
  public static IROI runConicPeakFit(
      final IProgressMonitor monitor,
      Display display,
      final IPlottingSystem plotter,
      IImageTrace t,
      IParametricROI roi,
      IParametricROI[] innerOuter,
      int nPoints) {

    if (roi == null) return null;

    final ProgressMonitorWrapper mon = new ProgressMonitorWrapper(monitor);
    monitor.subTask("Find POIs near initial ellipse");
    Dataset image = (Dataset) t.getData();
    BooleanDataset mask = (BooleanDataset) t.getMask();
    PolylineROI points;
    monitor.subTask("Fit POIs");

    points = PeakFittingEllipseFinder.findPointsOnConic(image, mask, roi, innerOuter, nPoints, mon);

    if (monitor.isCanceled()) return null;

    if (points == null) return null;

    if (roi instanceof EllipticalROI) {
      if (points.getNumberOfPoints() < 3) {
        throw new IllegalArgumentException("Could not find enough points to trim");
      }

      monitor.subTask("Trim POIs");
      EllipticalFitROI efroi = PowderRingsUtils.fitAndTrimOutliers(mon, points, 5, false);
      logger.debug("Found {}...", efroi);
      monitor.subTask("");
      return efroi;
    }

    return points;
  }