Пример #1
0
  /** Refine segmentation with ADD/SUB regions of interests */
  private synchronized void refine() {
    if (controlPanel.status != ControlJPanel.SEGMENTATED_STATUS) return;

    if (controlPanel.addJRadioButton.isSelected()) addRoi = imp.getRoi();
    else subRoi = imp.getRoi();

    if (null != addRoi) {
      final float alpha = controlPanel.addThreshold.getValue() / 100.0f;
      final Shape shape = ShapeRoiHelper.getShape(new ShapeRoi(addRoi));
      final AffineTransform trans = new AffineTransform();
      trans.translate(addRoi.getBounds().getX(), addRoi.getBounds().getY());
      final Area area = new Area(shape);
      area.transform(trans);
      siox.subpixelRefine(area, SioxSegmentator.ADD_EDGE, alpha, (float[]) confMatrix.getPixels());
    }
    if (null != subRoi) {
      final float alpha = controlPanel.subThreshold.getValue() / 100.0f;
      final Shape shape = ShapeRoiHelper.getShape(new ShapeRoi(subRoi));
      final AffineTransform trans = new AffineTransform();
      trans.translate(subRoi.getBounds().getX(), subRoi.getBounds().getY());
      final Area area = new Area(shape);
      area.transform(trans);
      siox.subpixelRefine(area, SioxSegmentator.SUB_EDGE, alpha, (float[]) confMatrix.getPixels());
    }

    updateResult();
  }
Пример #2
0
  /** Segment image based on the current foreground and background ROIs */
  private synchronized void segment() {
    if (controlPanel.bgJRadioButton.isSelected()) backgroundRoi = imp.getRoi();
    else foregroundRoi = imp.getRoi();

    if (foregroundRoi == null) {
      IJ.error("Siox Segmentation", "ERROR: no foreground selected!");
      return;
    }

    // Create confidence matrix and initialize to unknown region of confidence
    confMatrix = new FloatProcessor(imp.getWidth(), imp.getHeight());
    final float[] imgData = (float[]) confMatrix.getPixels();
    confMatrix.add(SioxSegmentator.UNKNOWN_REGION_CONFIDENCE);

    // Set foreground ROI
    if (foregroundRoi != null) {
      confMatrix.setValue(SioxSegmentator.CERTAIN_FOREGROUND_CONFIDENCE);
      confMatrix.fill(foregroundRoi);
    }

    // Set background ROI
    if (backgroundRoi != null) {
      confMatrix.setValue(SioxSegmentator.CERTAIN_BACKGROUND_CONFIDENCE);
      confMatrix.fill(backgroundRoi);
    } else {
      // Workaround: select border pixels which are not foreground as background if no background
      // was specified.
      int w = imp.getWidth(), h = imp.getHeight();
      for (int i = 0; i < w; i++) {
        if (imgData[i] < 0.8f) imgData[i] = 0;
        if (imgData[i + w * (h - 1)] < 0.8f) imgData[i + w * (h - 1)] = 0;
      }
      for (int i = 0; i < h; i++) {
        if (imgData[w * i] < 0.8f) imgData[w * i] = 0;
        if (imgData[w - 1 + w * i] < 0.8f) imgData[w - 1 + w * i] = 0;
      }
    }

    // Call SIOX segmentation method
    int[] pixels = (int[]) ip.getPixels();

    final int smoothes = controlPanel.smoothness.getValue();

    siox = new SioxSegmentator(imp.getWidth(), imp.getHeight(), null);
    boolean success =
        siox.segmentate(pixels, imgData, smoothes, controlPanel.multipart.isSelected() ? 4 : 0);

    if (!success) IJ.error("Siox Segmentation", "The segmentation failed!");

    updateResult();

    // Set status flag to segmented
    controlPanel.status = ControlJPanel.SEGMENTATED_STATUS;
    controlPanel.updateComponentEnabling();

    roiOverlay.setComposite(transparency100);

    // Set up next panel components
    controlPanel.subJRadioButton.setSelected(true);
    controlPanel.addJRadioButton.setSelected(false);
    lastButton = controlPanel.subJRadioButton;
  }