void applyStack() {
   // int minKeepH = minHue, maxKeepH = maxHue; //GL not needed?
   // int minKeepS = minSat, maxKeepS = maxSat;
   // int minKeepB = minBri, maxKeepB = maxBri;
   for (int i = 1; i <= numSlices; i++) {
     imp.setSlice(i);
     if (!checkImage()) {
       IJ.beep();
       IJ.showStatus("No Image");
       return;
     }
     //	minHue = minKeepH;
     //	maxHue = maxKeepH;
     //	minSat = minKeepS;
     //	maxSat = maxKeepS;
     //	minBri = minKeepB;
     //	maxBri = maxKeepB;
     apply(imp, ip);
   }
 }
Example #2
0
  public void showRois3D() {
    registerActiveImage();
    if (currentImage == null) return;
    // verifier que l'image active a les memes dimentions
    Object[] os = this.list.getSelectedValues();

    if (os.length == 1) {
      mcib3d.geom.Object3D o = ((Object3DGui) os[0]).getObject3D();
      currentImage.setSlice((o.getZmax() + o.getZmin()) / 2 + 1);
    }
    int nSlices = currentImage.getNSlices();

    currentROIs = new HashMap<Integer, Roi>(nSlices);
    // stores the roi mask to save memory..
    if (roiMask == null || !roiMask.sameDimentions(currentImage)) {
      roiMask = new ImageByte("mask", currentImage.getWidth(), currentImage.getHeight(), nSlices);
    } else {
      roiMask.erase();
    }
    ImageStack maskStack = roiMask.getImageStack();
    Object3DGui obj;
    for (Object o : os) {
      obj = (Object3DGui) o;
      obj.getObject3D().draw(maskStack, 255);
    }
    // roiMask.show();

    for (int i = 1; i <= nSlices; i++) {
      ImagePlus im = new ImagePlus("mask", maskStack.getProcessor(i));
      im.getProcessor().setThreshold(1, 255, ImageProcessor.NO_LUT_UPDATE);
      ThresholdToSelection tts = new ThresholdToSelection();
      tts.setup("", im);
      tts.run(im.getProcessor());
      Roi r = im.getRoi();
      if (r != null) currentROIs.put(i, r);
    }
    updateRoi();
  }
Example #3
0
  public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
    if (IJ.isMacOSX()) IJ.wait(50);
    Calibration cal = imp.getCalibration();
    width = gd.getNextNumber();
    height = gd.getNextNumber();
    xRoi = gd.getNextNumber();
    yRoi = gd.getNextNumber();
    if (stackSize > 1) iSlice = (int) gd.getNextNumber();
    oval = gd.getNextBoolean();
    square = gd.getNextBoolean();
    centered = gd.getNextBoolean();
    if (cal.scaled()) scaledUnits = gd.getNextBoolean();
    if (gd.invalidNumber() || width <= 0 || height <= 0) return false;
    //
    Vector numFields = gd.getNumericFields();
    Vector checkboxes = gd.getCheckboxes();
    boolean newWidth = false, newHeight = false, newXY = false;
    if (e != null && e.getSource() == checkboxes.get(SQUARE) && square) {
      width = 0.5 * (width + height); // make square: same width&height
      height = width;
      newWidth = true;
      newHeight = true;
    }
    if (e != null && e.getSource() == checkboxes.get(CENTERED)) {
      double shiftBy = centered ? 0.5 : -0.5; // 'centered' changed:
      xRoi += shiftBy * width; // shift x, y to keep roi the same
      yRoi += shiftBy * height;
      newXY = true;
    }
    if (square && width != height && e != null) { // in 'square' mode, synchronize width&height
      if (e.getSource() == numFields.get(WIDTH)) {
        height = width;
        newHeight = true;
      } else if (e.getSource() == numFields.get(HEIGHT)) {
        width = height;
        newWidth = true;
      }
    }
    if (e != null && cal.scaled() && e.getSource() == checkboxes.get(SCALED_UNITS)) {
      double xFactor = scaledUnits ? cal.pixelWidth : 1. / cal.pixelWidth;
      double yFactor = scaledUnits ? cal.pixelHeight : 1. / cal.pixelHeight;
      width *= xFactor; // transform everything to keep roi the same
      height *= yFactor;
      xRoi *= xFactor;
      yRoi *= yFactor;
      newWidth = true;
      newHeight = true;
      newXY = true;
    }
    int digits = (scaledUnits || (int) width != width) ? 2 : 0;
    if (newWidth) ((TextField) (numFields.get(WIDTH))).setText(IJ.d2s(width, digits));
    if (newHeight) ((TextField) (numFields.get(HEIGHT))).setText(IJ.d2s(height, digits));
    digits = (scaledUnits || (int) xRoi != xRoi || (int) yRoi != yRoi) ? 2 : 0;
    if (newXY) {
      ((TextField) (numFields.get(X_ROI))).setText(IJ.d2s(xRoi, digits));
      ((TextField) (numFields.get(Y_ROI))).setText(IJ.d2s(yRoi, digits));
    }

    if (stackSize > 1 && iSlice > 0 && iSlice <= stackSize) imp.setSlice(iSlice);
    if (!newWidth && !newHeight && !newXY) // don't draw if an update will come immediately
    drawRoi();
    return true;
  }