Beispiel #1
0
 void addSelection() {
   ImagePlus imp = IJ.getImage();
   String macroOptions = Macro.getOptions();
   if (macroOptions != null && IJ.macroRunning() && macroOptions.indexOf("remove") != -1) {
     imp.setOverlay(null);
     return;
   }
   Roi roi = imp.getRoi();
   if (roi == null && imp.getOverlay() != null) {
     GenericDialog gd = new GenericDialog("No Selection");
     gd.addMessage("\"Overlay>Add\" requires a selection.");
     gd.setInsets(15, 40, 0);
     gd.addCheckbox("Remove existing overlay", false);
     gd.showDialog();
     if (gd.wasCanceled()) return;
     if (gd.getNextBoolean()) imp.setOverlay(null);
     return;
   }
   if (roi == null) {
     IJ.error("This command requires a selection.");
     return;
   }
   roi = (Roi) roi.clone();
   if (roi.getStrokeColor() == null) roi.setStrokeColor(Toolbar.getForegroundColor());
   int width = Line.getWidth();
   Rectangle bounds = roi.getBounds();
   boolean tooWide = width > Math.max(bounds.width, bounds.height) / 3.0;
   if (roi.getStroke() == null && width > 1 && !tooWide) roi.setStrokeWidth(Line.getWidth());
   Overlay overlay = imp.getOverlay();
   if (overlay != null && overlay.size() > 0 && !roi.isDrawingTool()) {
     Roi roi2 = overlay.get(overlay.size() - 1);
     if (roi.getStroke() == null) roi.setStrokeWidth(roi2.getStrokeWidth());
     if (roi.getFillColor() == null) roi.setFillColor(roi2.getFillColor());
   }
   boolean points = roi instanceof PointRoi && ((PolygonRoi) roi).getNCoordinates() > 1;
   if (points) roi.setStrokeColor(Color.red);
   if (!IJ.altKeyDown() && !(roi instanceof Arrow)) {
     RoiProperties rp = new RoiProperties("Add to Overlay", roi);
     if (!rp.showDialog()) return;
   }
   String name = roi.getName();
   boolean newOverlay = name != null && name.equals("new-overlay");
   if (overlay == null || newOverlay) overlay = new Overlay();
   overlay.add(roi);
   imp.setOverlay(overlay);
   overlay2 = overlay;
   if (points || (roi instanceof ImageRoi) || (roi instanceof Arrow)) imp.killRoi();
   Undo.setup(Undo.OVERLAY_ADDITION, imp);
 }
Beispiel #2
0
 void remove() {
   ImagePlus imp = WindowManager.getCurrentImage();
   if (imp != null) imp.setOverlay(null);
   overlay2 = null;
   RoiManager rm = RoiManager.getInstance();
   if (rm != null) rm.runCommand("show none");
 }
 void showResults() {
   int count = rt.getCounter();
   // if (count==0) return;
   boolean lastSlice = !processStack || slice == imp.getStackSize();
   if ((showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) && slice == 1 && count > 0)
     imp.setOverlay(overlay);
   else if (outlines != null && lastSlice) {
     String title = imp != null ? imp.getTitle() : "Outlines";
     String prefix;
     if (showChoice == MASKS) prefix = "Mask of ";
     else if (showChoice == ROI_MASKS) prefix = "Count Masks of ";
     else prefix = "Drawing of ";
     outlines.update(drawIP);
     outputImage = new ImagePlus(prefix + title, outlines);
     if (inSituShow) {
       if (imp.getStackSize() == 1) Undo.setup(Undo.TRANSFORM, imp);
       imp.setStack(null, outputImage.getStack());
     } else if (!hideOutputImage) outputImage.show();
   }
   if (showResults && !processStack) {
     TextPanel tp = IJ.getTextPanel();
     if (beginningCount > 0 && tp != null && tp.getLineCount() != count) rt.show("Results");
     Analyzer.firstParticle = beginningCount;
     Analyzer.lastParticle = Analyzer.getCounter() - 1;
   } else Analyzer.firstParticle = Analyzer.lastParticle = 0;
 }
Beispiel #4
0
 public void doHyperStackProjection(boolean allTimeFrames) {
   int start = startSlice;
   int stop = stopSlice;
   int firstFrame = 1;
   int lastFrame = imp.getNFrames();
   if (!allTimeFrames) firstFrame = lastFrame = imp.getFrame();
   ImageStack stack = new ImageStack(imp.getWidth(), imp.getHeight());
   int channels = imp.getNChannels();
   int slices = imp.getNSlices();
   if (slices == 1) {
     slices = imp.getNFrames();
     firstFrame = lastFrame = 1;
   }
   int frames = lastFrame - firstFrame + 1;
   increment = channels;
   boolean rgb = imp.getBitDepth() == 24;
   for (int frame = firstFrame; frame <= lastFrame; frame++) {
     for (int channel = 1; channel <= channels; channel++) {
       startSlice = (frame - 1) * channels * slices + (start - 1) * channels + channel;
       stopSlice = (frame - 1) * channels * slices + (stop - 1) * channels + channel;
       if (rgb) doHSRGBProjection(imp);
       else doProjection();
       stack.addSlice(null, projImage.getProcessor());
     }
   }
   projImage = new ImagePlus(makeTitle(), stack);
   projImage.setDimensions(channels, 1, frames);
   if (channels > 1) {
     projImage = new CompositeImage(projImage, 0);
     ((CompositeImage) projImage).copyLuts(imp);
     if (method == SUM_METHOD || method == SD_METHOD)
       ((CompositeImage) projImage).resetDisplayRanges();
   }
   if (frames > 1) projImage.setOpenAsHyperStack(true);
   Overlay overlay = imp.getOverlay();
   if (overlay != null) {
     startSlice = start;
     stopSlice = stop;
     if (imp.getType() == ImagePlus.COLOR_RGB)
       projImage.setOverlay(projectRGBHyperStackRois(overlay));
     else projImage.setOverlay(projectHyperStackRois(overlay));
   }
   IJ.showProgress(1, 1);
 }
Beispiel #5
0
 void hide() {
   ImagePlus imp = IJ.getImage();
   Overlay overlay = imp.getOverlay();
   if (overlay != null) {
     overlay2 = overlay;
     imp.setOverlay(null);
   }
   RoiManager rm = RoiManager.getInstance();
   if (rm != null) rm.runCommand("show none");
 }
Beispiel #6
0
 void fromRoiManager() {
   ImagePlus imp = IJ.getImage();
   RoiManager rm = RoiManager.getInstance();
   if (rm == null) {
     IJ.error("ROI Manager is not open");
     return;
   }
   Roi[] rois = rm.getRoisAsArray();
   if (rois.length == 0) {
     IJ.error("ROI Manager is empty");
     return;
   }
   Overlay overlay = new Overlay();
   for (int i = 0; i < rois.length; i++) overlay.add((Roi) rois[i].clone());
   imp.setOverlay(overlay);
   ImageCanvas ic = imp.getCanvas();
   if (ic != null) ic.setShowAllROIs(false);
   rm.setEditMode(imp, false);
   imp.killRoi();
 }
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 addImage() {
    ImagePlus imp = IJ.getImage();
    int[] wList = WindowManager.getIDList();
    if (wList == null || wList.length < 2) {
      IJ.error("Add Image...", "The command requires at least two open images.");
      return;
    }
    String[] titles = new String[wList.length];
    for (int i = 0; i < wList.length; i++) {
      ImagePlus imp2 = WindowManager.getImage(wList[i]);
      titles[i] = imp2 != null ? imp2.getTitle() : "";
    }
    int x = 0, y = 0;
    Roi roi = imp.getRoi();
    if (roi != null && roi.isArea()) {
      Rectangle r = roi.getBounds();
      x = r.x;
      y = r.y;
    }
    int index = 0;
    if (wList.length == 2) {
      ImagePlus i1 = WindowManager.getImage(wList[0]);
      ImagePlus i2 = WindowManager.getImage(wList[1]);
      if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) index = 1;
    } else if (imp.getID() == wList[0]) index = 1;

    GenericDialog gd = new GenericDialog("Add Image...");
    gd.addChoice("Image to add:", titles, titles[index]);
    gd.addNumericField("X location:", x, 0);
    gd.addNumericField("Y location:", y, 0);
    gd.addNumericField("Opacity (0-100%):", 100, 0);
    gd.addCheckbox("Create image selection", createImageRoi);
    gd.showDialog();
    if (gd.wasCanceled()) return;
    index = gd.getNextChoiceIndex();
    x = (int) gd.getNextNumber();
    y = (int) gd.getNextNumber();
    double opacity = gd.getNextNumber() / 100.0;
    createImageRoi = gd.getNextBoolean();
    ImagePlus overlay = WindowManager.getImage(wList[index]);
    if (wList.length == 2) {
      ImagePlus i1 = WindowManager.getImage(wList[0]);
      ImagePlus i2 = WindowManager.getImage(wList[1]);
      if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) {
        imp = i1;
        overlay = i2;
      }
    }
    if (overlay == imp) {
      IJ.error(
          "Add Image...", "Image to be added cannot be the same as\n\"" + imp.getTitle() + "\".");
      return;
    }
    if (overlay.getWidth() > imp.getWidth() && overlay.getHeight() > imp.getHeight()) {
      IJ.error(
          "Add Image...", "Image to be added cannnot be larger than\n\"" + imp.getTitle() + "\".");
      return;
    }
    if (createImageRoi && x == 0 && y == 0) {
      x = imp.getWidth() / 2 - overlay.getWidth() / 2;
      y = imp.getHeight() / 2 - overlay.getHeight() / 2;
    }
    roi = new ImageRoi(x, y, overlay.getProcessor());
    roi.setName(overlay.getShortTitle());
    if (opacity != 1.0) ((ImageRoi) roi).setOpacity(opacity);
    if (createImageRoi) imp.setRoi(roi);
    else {
      Overlay overlayList = imp.getOverlay();
      if (overlayList == null) overlayList = new Overlay();
      overlayList.add(roi);
      imp.setOverlay(overlayList);
      overlay2 = overlayList;
      Undo.setup(Undo.OVERLAY_ADDITION, imp);
    }
  }
Beispiel #9
0
 void show() {
   ImagePlus imp = IJ.getImage();
   if (overlay2 != null) imp.setOverlay(overlay2);
   RoiManager rm = RoiManager.getInstance();
   if (rm != null) rm.runCommand("show all");
 }
Beispiel #10
0
 /**
  * Performs actual projection using specified method. If handleOverlay, adds stack overlay
  * elements from startSlice to stopSlice to projection
  */
 public void doProjection(boolean handleOverlay) {
   doProjection();
   Overlay overlay = imp.getOverlay();
   if (handleOverlay && overlay != null) projImage.setOverlay(projectStackRois(overlay));
 }