Exemplo n.º 1
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;
  }
  private int getTotalWork(
      CheckWizardPage options, IPlottingSystem system, final IFunctionService funcService) {

    try {
      int ret = 1;
      if (options.is(PersistWizardConstants.ORIGINAL_DATA)) {
        Collection<ITrace> traces = system.getTraces();
        ret += traces != null ? traces.size() : 0;
      }
      if (options.is(PersistWizardConstants.IMAGE_HIST)) {
        final IToolPageSystem tsystem = (IToolPageSystem) system.getAdapter(IToolPageSystem.class);
        final IToolPage tool = tsystem.getActiveTool();
        if (tool != null
            && tool.getToolId().equals("org.dawb.workbench.plotting.tools.imageCompareTool")) {
          final Map<String, IDataset> data = (Map<String, IDataset>) tool.getToolData();
          if (data != null && !data.isEmpty()) {
            ret += data.size();
          }
        }
      }

      final ITrace trace = system.getTraces().iterator().next();
      if (options.is(PersistWizardConstants.MASK) && trace instanceof IImageTrace) {
        IImageTrace image = (IImageTrace) trace;
        final String name = options.getString(PersistWizardConstants.MASK);
        if (image.getMask() != null) {
          ret += 1;
        }
      }

      final Collection<IRegion> regions = system.getRegions();
      if (options.is(PersistWizardConstants.REGIONS) && regions != null && !regions.isEmpty()) {
        ret += regions.size();
      }

      if (options.is(PersistWizardConstants.DIFF_META)) {
        if (trace != null && trace instanceof IImageTrace && trace.getData() != null) {
          ret += 1;
        }
      }

      if (options.is(PersistWizardConstants.FUNCTIONS)) {
        if (funcService != null) {
          Map<String, IFunction> functions = funcService.getFunctions();
          if (functions != null) ret += functions.size();
        }
      }

      return ret;
    } catch (Exception ne) {
      logger.error("Cannot estimate work, assuming 100 things to do!", ne);
      return 100;
    }
  }
Exemplo n.º 3
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;
      }
    }
  }
Exemplo n.º 4
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;
  }