Exemplo n.º 1
0
  @Override
  protected Collection<? extends ITrace> createProfile(
      final IImageTrace image,
      IRegion region,
      IROI rbs,
      boolean tryUpdate,
      boolean isDrag,
      IProgressMonitor monitor) {

    if (monitor.isCanceled()) return null;
    if (image == null) return null;

    if ((region.getRegionType() != RegionType.BOX)
        && (region.getRegionType() != RegionType.PERIMETERBOX)) return null;

    Dataset slice = createZoom(image, region, rbs, tryUpdate, isDrag, monitor);

    Dataset yData = slice.sum(0);
    yData.setName("Intensity");
    Dataset xData = slice.sum(1);
    xData.setName("Intensity");

    final RectangularROI bounds = (RectangularROI) (rbs == null ? region.getROI() : rbs);
    final Dataset y_indices =
        DatasetFactory.createRange(
            bounds.getPoint()[0], bounds.getPoint()[0] + bounds.getLength(0), 1, Dataset.FLOAT);
    y_indices.setName("X Location");

    topSystem.updatePlot1D(y_indices, Arrays.asList(new IDataset[] {yData}), monitor);
    topSystem.repaint();

    final Dataset x_indices =
        DatasetFactory.createRange(
            bounds.getPoint()[1] + bounds.getLength(1), bounds.getPoint()[1], -1, Dataset.FLOAT);
    x_indices.setName("Y Location");

    final Collection<ITrace> right =
        rightSystem.updatePlot1D(xData, Arrays.asList(new IDataset[] {x_indices}), monitor);
    rightSystem.repaint();

    Display.getDefault()
        .syncExec(
            new Runnable() {

              @Override
              public void run() {
                topSystem.setTitle("");
                rightSystem.setTitle("");

                ILineTrace line = (ILineTrace) right.iterator().next();
                line.setTraceColor(ColorConstants.red);
              }
            });

    return profilePlottingSystem.getTraces();
  }
  protected OperationData process(IDataset input, IMonitor monitor) throws OperationException {

    double d = (2 * Math.PI) / model.getqValue();
    double p = (2 * Math.PI) / (model.getqValue() + model.getqDelta());
    double m = (2 * Math.PI) / (model.getqValue() - model.getqDelta());

    IDiffractionMetadata dm = getFirstDiffractionMetadata(input);
    if (dm == null) throw new OperationException(this, "No calibration information!");

    IParametricROI[] inOut = new IParametricROI[2];

    IParametricROI conic =
        (IParametricROI)
            DSpacing.conicFromDSpacing(
                dm.getDetector2DProperties(), dm.getDiffractionCrystalEnvironment(), d);
    inOut[0] =
        (IParametricROI)
            DSpacing.conicFromDSpacing(
                dm.getDetector2DProperties(), dm.getDiffractionCrystalEnvironment(), m);
    inOut[1] =
        (IParametricROI)
            DSpacing.conicFromDSpacing(
                dm.getDetector2DProperties(), dm.getDiffractionCrystalEnvironment(), p);

    PolylineROI points =
        PeakFittingEllipseFinder.findPointsOnConic(
            DatasetUtils.convertToDataset(input), null, conic, inOut, 256, null);

    double rms = -1;
    double[] semi = new double[2];
    double[] point = new double[2];
    double ang = 0;

    if (points != null && points.getNumberOfPoints() < 3) {

      EllipticalFitROI efroi = PowderRingsUtils.fitAndTrimOutliers(null, points, 2, false);
      rms = efroi.getRMS();
      semi = efroi.getSemiAxes();
      point = efroi.getPoint();
      ang = efroi.getAngleDegrees();
    }

    Dataset r = DatasetFactory.createFromObject(new double[] {rms});
    r.setName("rms");

    Dataset ax = DatasetFactory.createFromObject(semi);
    ax.setName("semi-axes");

    Dataset po = DatasetFactory.createFromObject(point);
    po.setName("centre");

    Dataset a = DatasetFactory.createFromObject(new double[] {ang});
    a.setName("angle");

    return new OperationData(input, new Serializable[] {r, ax, po, a});
  }
  @Override
  protected OperationData process(IDataset input, IMonitor monitor) {

    RectangularROI box = model.getBox();

    Dataset in1 =
        BoxSlicerRodScanUtils.rOIBox(input, monitor, box.getIntLengths(), box.getIntPoint());

    if (g2 == null) g2 = new Polynomial2D(model.getFitPower());
    if ((int) Math.pow(model.getFitPower() + 1, 2) != g2.getNoOfParameters())
      g2 = new Polynomial2D(model.getFitPower());

    Dataset[] fittingBackground =
        BoxSlicerRodScanUtils.LeftRightTopBottomBoxes(
            input, monitor, box.getIntLengths(), box.getIntPoint(), model.getBoundaryBox());

    Dataset offset = DatasetFactory.ones(fittingBackground[2].getShape(), Dataset.FLOAT64);

    Dataset intermediateFitTest = Maths.add(offset, fittingBackground[2]);
    Dataset matrix =
        LinearLeastSquaresServicesForSXRD.polynomial2DLinearLeastSquaresMatrixGenerator(
            model.getFitPower(), fittingBackground[0], fittingBackground[1]);

    DoubleDataset test = (DoubleDataset) LinearAlgebra.solveSVD(matrix, intermediateFitTest);
    double[] params = test.getData();

    DoubleDataset in1Background =
        g2.getOutputValues0(
            params, box.getIntLengths(), model.getBoundaryBox(), model.getFitPower());

    IndexIterator it = in1Background.getIterator();

    while (it.hasNext()) {
      double v = in1Background.getElementDoubleAbs(it.index);
      if (v < 0) in1Background.setObjectAbs(it.index, 0);
    }

    Dataset pBackgroundSubtracted = Maths.subtract(in1, in1Background, null);

    pBackgroundSubtracted.setName("pBackgroundSubtracted");

    IndexIterator it1 = pBackgroundSubtracted.getIterator();

    while (it1.hasNext()) {
      double q = pBackgroundSubtracted.getElementDoubleAbs(it1.index);
      if (q < 0) pBackgroundSubtracted.setObjectAbs(it1.index, 0);
    }

    Dataset output = DatasetUtils.cast(pBackgroundSubtracted, Dataset.FLOAT64);

    output.setName("Region of Interest, polynomial background removed");

    return new OperationData(output);
  }
Exemplo n.º 4
0
  @Override
  public DataReductionInfo export(DataReductionSlice drslice) throws Exception {

    final Collection<IRegion> regions = getPlottingSystem().getRegions();

    for (IRegion region : regions) {
      if (!isRegionTypeSupported(region.getRegionType())) continue;

      final RectangularROI bounds = (RectangularROI) region.getROI();
      if (bounds == null) continue;
      if (!region.isVisible()) continue;

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

      final Dataset slice =
          DatasetUtils.convertToDataset(
              drslice
                  .getData()
                  .getSlice(
                      new int[] {(int) bounds.getPoint()[1], (int) bounds.getPoint()[0]},
                      new int[] {(int) bounds.getEndPoint()[1], (int) bounds.getEndPoint()[0]},
                      new int[] {yInc, xInc}));
      slice.setName(region.getName().replace(' ', '_'));

      drslice.appendData(slice);
    }
    return new DataReductionInfo(Status.OK_STATUS);
  }
Exemplo n.º 5
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;
  }
Exemplo n.º 6
0
  /**
   * Perform a two-dimensional interpolation
   *
   * @param oldx an IDataset containing a 1D array of X-values, sorted in increasing order,
   *     corresponding to the first dimension of <code>oldxy</code>
   * @param oldy an IDataset containing a 1D array of Y-values, sorted in increasing order,
   *     corresponding to the second dimension of <code>oldxy</code>
   * @param oldxy an IDataset containing a 2D grid of interpolation points
   * @param newx an IDataset containing a 1D array of X-values that will be sent to the
   *     interpolating function
   * @param newy an IDataset containing a 1D array of Y-values that will be sent to the
   *     interpolating function
   * @param interpolator an instance of {@link
   *     org.apache.commons.math3.analysis.interpolation.BivariateGridInterpolator}
   * @param output_type an {@link BicubicInterpolationOutput} that will determine how <code>newx
   *     </code> and <code>newy</code> will be interpreted, and therefore whether a 1D or 2D Dataset
   *     will be returned.
   * @return rank 1 or 2 Dataset, depending on <code>output_type}</code>
   * @throws NonMonotonicSequenceException
   * @throws NumberIsTooSmallException
   */
  public static Dataset interpolate(
      IDataset oldx,
      IDataset oldy,
      IDataset oldxy,
      IDataset newx,
      IDataset newy,
      BivariateGridInterpolator interpolator,
      BicubicInterpolationOutput output_type)
      throws NonMonotonicSequenceException, NumberIsTooSmallException {

    // check shapes
    if (oldx.getRank() != 1) throw new IllegalArgumentException("oldx Shape must be 1D");
    if (oldy.getRank() != 1) throw new IllegalArgumentException("oldy Shape must be 1D");
    if (oldxy.getRank() != 2) throw new IllegalArgumentException("oldxy Shape must be 2D");
    if (oldx.getShape()[0] != oldxy.getShape()[0])
      throw new IllegalArgumentException("oldx Shape must match oldxy Shape[0]");
    if (oldy.getShape()[0] != oldxy.getShape()[1])
      throw new IllegalArgumentException("oldy Shape must match oldxy Shape[1]");
    if (newx.getRank() != 1) throw new IllegalArgumentException("newx Shape must be 1D");
    if (newy.getRank() != 1) throw new IllegalArgumentException("newx Shape must be 1D");
    if (output_type == BicubicInterpolationOutput.ONED && newy.getSize() != newx.getSize())
      throw new IllegalArgumentException(
          "newx and newy Size must be identical when expecting a rank 1 dataset result");

    DoubleDataset oldx_dd = (DoubleDataset) DatasetUtils.cast(oldx, Dataset.FLOAT64);
    DoubleDataset oldy_dd = (DoubleDataset) DatasetUtils.cast(oldy, Dataset.FLOAT64);
    DoubleDataset oldxy_dd = (DoubleDataset) DatasetUtils.cast(oldxy, Dataset.FLOAT64);

    // unlike in Interpolation1D, we will not be sorting here, as it just too complicated
    // the user will be responsible for ensuring the arrays are properly sorted

    // oldxy_dd needs to be transformed into a double[][] array
    // this call may throw an exception that needs handling by the calling method
    BivariateFunction func =
        interpolator.interpolate(
            oldx_dd.getData(), oldy_dd.getData(), convertDoubleDataset2DtoPrimitive(oldxy_dd));

    Dataset rv = null;

    if (output_type == BicubicInterpolationOutput.ONED) {
      rv = DatasetFactory.zeros(new int[] {newx.getSize()}, Dataset.FLOAT64);

      for (int i = 0; i < newx.getSize(); i++) {
        double val = 0.0;
        try {
          val = func.value(newx.getDouble(i), newy.getDouble(i));
          rv.set(val, i);
        } catch (OutOfRangeException e) {
          rv.set(0.0, i);
        }
      }
    } else if (output_type == BicubicInterpolationOutput.TWOD) {
      rv = DatasetFactory.zeros(new int[] {newx.getSize(), newy.getSize()}, Dataset.FLOAT64);

      for (int i = 0; i < newx.getSize(); i++) {
        for (int j = 0; j < newy.getSize(); j++) {
          double val = 0.0;
          try {
            val = func.value(newx.getDouble(i), newy.getDouble(j));
            rv.set(val, i, j);
          } catch (OutOfRangeException e) {
            rv.set(0.0, i, j);
          }
        }
      }
    }

    rv.setName(oldxy.getName() + "_interpolated");

    return rv;
  }