Example #1
0
 // Added by Marcel Boeglin 2013.09.22
 private Overlay projectHyperStackRois(Overlay overlay) {
   if (overlay == null) return null;
   int t1 = imp.getFrame();
   int channels = projImage.getNChannels();
   int slices = 1;
   int frames = projImage.getNFrames();
   Overlay overlay2 = new Overlay();
   Roi roi;
   int c, z, t;
   int size = channels * slices * frames;
   for (Roi r : overlay.toArray()) {
     c = r.getCPosition();
     z = r.getZPosition();
     t = r.getTPosition();
     roi = (Roi) r.clone();
     if (size == channels) { // current time frame
       if (z >= startSlice && z <= stopSlice && t == t1 || c == 0) {
         roi.setPosition(c);
         overlay2.add(roi);
       }
     } else if (size == frames * channels) { // all time frames
       if (z >= startSlice && z <= stopSlice) roi.setPosition(c, 1, t);
       else if (z == 0) roi.setPosition(c, 0, t);
       else continue;
       overlay2.add(roi);
     }
   }
   return overlay2;
 }
Example #2
0
 // Added by Marcel Boeglin 2013.09.23
 private Overlay projectStackRois(Overlay overlay) {
   if (overlay == null) return null;
   Overlay overlay2 = new Overlay();
   Roi roi;
   int s;
   for (Roi r : overlay.toArray()) {
     s = r.getPosition();
     roi = (Roi) r.clone();
     if (s >= startSlice && s <= stopSlice || s == 0) {
       roi.setPosition(s);
       overlay2.add(roi);
     }
   }
   return overlay2;
 }
Example #3
0
 private boolean deleteOverlayRoi(ImagePlus imp) {
   if (imp == null) return false;
   Overlay overlay = null;
   ImageCanvas ic = imp.getCanvas();
   if (ic != null) overlay = ic.getShowAllList();
   if (overlay == null) overlay = imp.getOverlay();
   if (overlay == null) return false;
   Roi roi = imp.getRoi();
   for (int i = 0; i < overlay.size(); i++) {
     Roi roi2 = overlay.get(i);
     if (roi2 == roi) {
       overlay.remove(i);
       imp.deleteRoi();
       ic = imp.getCanvas();
       if (ic != null) ic.roiManagerSelect(roi, true);
       return true;
     }
   }
   return false;
 }
Example #4
0
 // Added by Marcel Boeglin 2013.09.22
 private Overlay projectRGBHyperStackRois(Overlay overlay) {
   if (overlay == null) return null;
   int frames = projImage.getNFrames();
   int t1 = imp.getFrame();
   Overlay overlay2 = new Overlay();
   Roi roi;
   int c, z, t;
   for (Roi r : overlay.toArray()) {
     c = r.getCPosition();
     z = r.getZPosition();
     t = r.getTPosition();
     roi = (Roi) r.clone();
     if (z >= startSlice && z <= stopSlice || z == 0 || c == 0 || t == 0) {
       if (frames == 1 && t != t1 && t != 0) // current time frame
       continue;
       roi.setPosition(t);
       overlay2.add(roi);
     }
   }
   return overlay2;
 }