Beispiel #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;
 }
 /**
  * Saves statistics for one particle in a results table. This is a method subclasses may want to
  * override.
  */
 protected void saveResults(ImageStatistics stats, Roi roi) {
   analyzer.saveResults(stats, roi);
   if (recordStarts) {
     rt.addValue("XStart", stats.xstart);
     rt.addValue("YStart", stats.ystart);
   }
   if (addToManager) {
     if (roiManager == null) {
       if (Macro.getOptions() != null && Interpreter.isBatchMode())
         roiManager = Interpreter.getBatchModeRoiManager();
       if (roiManager == null) {
         Frame frame = WindowManager.getFrame("ROI Manager");
         if (frame == null) IJ.run("ROI Manager...");
         frame = WindowManager.getFrame("ROI Manager");
         if (frame == null || !(frame instanceof RoiManager)) {
           addToManager = false;
           return;
         }
         roiManager = (RoiManager) frame;
       }
       if (resetCounter) roiManager.runCommand("reset");
     }
     if (imp.getStackSize() > 1) roi.setPosition(imp.getCurrentSlice());
     if (lineWidth != 1) roi.setStrokeWidth(lineWidth);
     roiManager.add(imp, roi, rt.getCounter());
   }
   if (showResults) rt.addResults();
 }
Beispiel #3
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;
 }
Beispiel #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;
 }