Beispiel #1
0
 void addToRoiManager(ImagePlus imp) {
   if (IJ.macroRunning() && Interpreter.isBatchModeRoiManager())
     IJ.error("run(\"Add to Manager\") may not work in batch mode macros");
   Frame frame = WindowManager.getFrame("ROI Manager");
   if (frame == null) IJ.run("ROI Manager...");
   if (imp == null) return;
   Roi roi = imp.getRoi();
   if (roi == null) return;
   frame = WindowManager.getFrame("ROI Manager");
   if (frame == null || !(frame instanceof RoiManager)) IJ.error("ROI Manager not found");
   RoiManager rm = (RoiManager) frame;
   boolean altDown = IJ.altKeyDown();
   IJ.setKeyUp(IJ.ALL_KEYS);
   if (altDown && !IJ.macroRunning()) IJ.setKeyDown(KeyEvent.VK_SHIFT);
   if (roi.getState() == Roi.CONSTRUCTING) { // wait (up to 2 sec.) until ROI finished
     long start = System.currentTimeMillis();
     while (true) {
       IJ.wait(10);
       if (roi.getState() != Roi.CONSTRUCTING) break;
       if ((System.currentTimeMillis() - start) > 2000) {
         IJ.beep();
         IJ.error("Add to Manager", "Selection is not complete");
         return;
       }
     }
   }
   rm.runCommand("add");
   IJ.setKeyUp(IJ.ALL_KEYS);
 }
 /**
  * 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
 void createMask(ImagePlus imp) {
   Roi roi = imp.getRoi();
   boolean useInvertingLut = Prefs.useInvertingLut;
   Prefs.useInvertingLut = false;
   if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT)) {
     createMaskFromThreshold(imp);
     Prefs.useInvertingLut = useInvertingLut;
     return;
   }
   ImagePlus maskImp = null;
   Frame frame = WindowManager.getFrame("Mask");
   if (frame != null && (frame instanceof ImageWindow))
     maskImp = ((ImageWindow) frame).getImagePlus();
   if (maskImp == null) {
     ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
     if (!Prefs.blackBackground) ip.invertLut();
     maskImp = new ImagePlus("Mask", ip);
     maskImp.show();
   }
   ImageProcessor ip = maskImp.getProcessor();
   ip.setRoi(roi);
   ip.setValue(255);
   ip.fill(ip.getMask());
   maskImp.updateAndDraw();
   Prefs.useInvertingLut = useInvertingLut;
 }
 void updateSliceSummary() {
   int slices = imp.getStackSize();
   float[] areas = rt.getColumn(ResultsTable.AREA);
   if (areas == null) areas = new float[0];
   String label = imp.getTitle();
   if (slices > 1) {
     label = imp.getStack().getShortSliceLabel(slice);
     label = label != null && !label.equals("") ? label : "" + slice;
   }
   String aLine = null;
   double sum = 0.0;
   int start = areas.length - particleCount;
   if (start < 0) return;
   for (int i = start; i < areas.length; i++) sum += areas[i];
   int places = Analyzer.getPrecision();
   Calibration cal = imp.getCalibration();
   String total = "\t" + ResultsTable.d2s(sum, places);
   String average = "\t" + ResultsTable.d2s(sum / particleCount, places);
   String fraction = "\t" + ResultsTable.d2s(sum * 100.0 / totalArea, 1);
   aLine = label + "\t" + particleCount + total + average + fraction;
   aLine = addMeans(aLine, areas.length > 0 ? start : -1);
   if (slices == 1) {
     Frame frame = WindowManager.getFrame("Summary");
     if (frame != null && (frame instanceof TextWindow) && summaryHdr.equals(prevHdr))
       tw = (TextWindow) frame;
   }
   if (tw == null) {
     String title = slices == 1 ? "Summary" : "Summary of " + imp.getTitle();
     tw = new TextWindow(title, summaryHdr, aLine, 450, 300);
     prevHdr = summaryHdr;
   } else tw.append(aLine);
 }
 void addToRoiManager(ImagePlus imp) {
   if (IJ.macroRunning() && Interpreter.isBatchModeRoiManager())
     IJ.error("run(\"Add to Manager\") may not work in batch mode macros");
   Frame frame = WindowManager.getFrame("ROI Manager");
   if (frame == null) IJ.run("ROI Manager...");
   if (imp == null) return;
   Roi roi = imp.getRoi();
   if (roi == null) return;
   frame = WindowManager.getFrame("ROI Manager");
   if (frame == null || !(frame instanceof RoiManager)) IJ.error("ROI Manager not found");
   RoiManager rm = (RoiManager) frame;
   boolean altDown = IJ.altKeyDown();
   IJ.setKeyUp(IJ.ALL_KEYS);
   if (altDown && !IJ.macroRunning()) IJ.setKeyDown(KeyEvent.VK_SHIFT);
   rm.runCommand("add");
   IJ.setKeyUp(IJ.ALL_KEYS);
 }
Beispiel #6
0
 void saveWindowLocations() {
   Frame frame = WindowManager.getFrame("B&C");
   if (frame != null) Prefs.saveLocation(ContrastAdjuster.LOC_KEY, frame.getLocation());
   frame = WindowManager.getFrame("Threshold");
   if (frame != null) Prefs.saveLocation(ThresholdAdjuster.LOC_KEY, frame.getLocation());
   frame = WindowManager.getFrame("Results");
   if (frame != null) {
     Prefs.saveLocation(TextWindow.LOC_KEY, frame.getLocation());
     Dimension d = frame.getSize();
     Prefs.set(TextWindow.WIDTH_KEY, d.width);
     Prefs.set(TextWindow.HEIGHT_KEY, d.height);
   }
   frame = WindowManager.getFrame("Log");
   if (frame != null) {
     Prefs.saveLocation(TextWindow.LOG_LOC_KEY, frame.getLocation());
     Dimension d = frame.getSize();
     Prefs.set(TextWindow.LOG_WIDTH_KEY, d.width);
     Prefs.set(TextWindow.LOG_HEIGHT_KEY, d.height);
   }
 }
Beispiel #7
0
 void toRoiManager() {
   ImagePlus imp = IJ.getImage();
   Overlay overlay = imp.getOverlay();
   if (overlay == null) {
     IJ.error("Overlay required");
     return;
   }
   RoiManager rm = RoiManager.getInstance();
   if (rm == null) {
     if (Macro.getOptions() != null && Interpreter.isBatchMode())
       rm = Interpreter.getBatchModeRoiManager();
     if (rm == 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)) return;
       rm = (RoiManager) frame;
     }
   }
   rm.runCommand("reset");
   for (int i = 0; i < overlay.size(); i++) rm.add(imp, overlay.get(i), i);
   rm.setEditMode(imp, true);
   if (rm.getCount() == overlay.size()) imp.setOverlay(null);
 }
Beispiel #8
0
 void createMask(ImagePlus imp) {
   Roi roi = imp.getRoi();
   boolean useInvertingLut = Prefs.useInvertingLut;
   Prefs.useInvertingLut = false;
   boolean selectAll =
       roi != null
           && roi.getType() == Roi.RECTANGLE
           && roi.getBounds().width == imp.getWidth()
           && roi.getBounds().height == imp.getHeight()
           && imp.isThreshold();
   if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT) || selectAll) {
     createMaskFromThreshold(imp);
     Prefs.useInvertingLut = useInvertingLut;
     return;
   }
   ImagePlus maskImp = null;
   Frame frame = WindowManager.getFrame("Mask");
   if (frame != null && (frame instanceof ImageWindow))
     maskImp = ((ImageWindow) frame).getImagePlus();
   if (maskImp == null) {
     ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
     if (!Prefs.blackBackground) ip.invertLut();
     maskImp = new ImagePlus("Mask", ip);
     maskImp.show();
   }
   ImageProcessor ip = maskImp.getProcessor();
   ip.setRoi(roi);
   ip.setValue(255);
   ip.fill(ip.getMask());
   Calibration cal = imp.getCalibration();
   if (cal.scaled()) {
     Calibration cal2 = maskImp.getCalibration();
     cal2.pixelWidth = cal.pixelWidth;
     cal2.pixelHeight = cal.pixelHeight;
     cal2.setUnit(cal.getUnit());
   }
   maskImp.updateAndRepaintWindow();
   Prefs.useInvertingLut = useInvertingLut;
 }