public void splitRGB(ImagePlus imp) {
   boolean keepSource = IJ.altKeyDown();
   String title = imp.getTitle();
   Calibration cal = imp.getCalibration();
   int pos = imp.getCurrentSlice();
   ImageStack[] channels = splitRGB(imp.getStack(), keepSource);
   if (!keepSource) {
     imp.unlock();
     imp.changes = false;
     imp.close();
   }
   ImagePlus rImp = new ImagePlus(title + " (red)", channels[0]);
   rImp.setCalibration(cal);
   rImp.show();
   rImp.setSlice(pos);
   if (IJ.isMacOSX()) IJ.wait(500);
   ImagePlus gImp = new ImagePlus(title + " (green)", channels[1]);
   gImp.setCalibration(cal);
   gImp.show();
   gImp.setSlice(pos);
   if (IJ.isMacOSX()) IJ.wait(500);
   ImagePlus bImp = new ImagePlus(title + " (blue)", channels[2]);
   bImp.setCalibration(cal);
   bImp.show();
   bImp.setSlice(pos);
 }
Example #2
0
 void checkForCalibrationConflict(ImagePlus imp, Calibration cal) {
   Calibration gcal = imp.getGlobalCalibration();
   if (gcal == null || !showConflictMessage || IJ.isMacro()) return;
   if (cal.pixelWidth == gcal.pixelWidth && cal.getUnit().equals(gcal.getUnit())) return;
   GenericDialog gd = new GenericDialog(imp.getTitle());
   gd.addMessage("The calibration of this image conflicts\nwith the current global calibration.");
   gd.addCheckbox("Disable_Global Calibration", true);
   gd.addCheckbox("Disable_these Messages", false);
   gd.showDialog();
   if (gd.wasCanceled()) return;
   boolean disable = gd.getNextBoolean();
   if (disable) {
     imp.setGlobalCalibration(null);
     imp.setCalibration(cal);
     WindowManager.repaintImageWindows();
   }
   boolean dontShow = gd.getNextBoolean();
   if (dontShow) showConflictMessage = false;
 }
 /** Splits the specified image into separate channels. */
 public static ImagePlus[] split(ImagePlus imp) {
   if (imp.getType() == ImagePlus.COLOR_RGB) {
     ImageStack[] stacks = splitRGB(imp.getStack(), true);
     ImagePlus[] images = new ImagePlus[3];
     images[0] = new ImagePlus("red", stacks[0]);
     images[1] = new ImagePlus("green", stacks[1]);
     images[2] = new ImagePlus("blue", stacks[2]);
     return images;
   }
   int width = imp.getWidth();
   int height = imp.getHeight();
   int channels = imp.getNChannels();
   int slices = imp.getNSlices();
   int frames = imp.getNFrames();
   int bitDepth = imp.getBitDepth();
   int size = slices * frames;
   Vector images = new Vector();
   HyperStackReducer reducer = new HyperStackReducer(imp);
   for (int c = 1; c <= channels; c++) {
     ImageStack stack2 = new ImageStack(width, height, size); // create empty stack
     stack2.setPixels(
         imp.getProcessor().getPixels(), 1); // can't create ImagePlus will null 1st image
     ImagePlus imp2 = new ImagePlus("C" + c + "-" + imp.getTitle(), stack2);
     stack2.setPixels(null, 1);
     imp.setPosition(c, 1, 1);
     imp2.setDimensions(1, slices, frames);
     imp2.setCalibration(imp.getCalibration());
     reducer.reduce(imp2);
     if (imp.isComposite() && ((CompositeImage) imp).getMode() == IJ.GRAYSCALE)
       IJ.run(imp2, "Grays", "");
     if (imp2.getNDimensions() > 3) imp2.setOpenAsHyperStack(true);
     images.add(imp2);
   }
   ImagePlus[] array = new ImagePlus[images.size()];
   return (ImagePlus[]) images.toArray(array);
 }
Example #4
0
  public void run(String arg) {
    imp = IJ.getImage();
    int stackSize = imp.getStackSize();
    if (imp == null) {
      IJ.noImage();
      return;
    }

    //  Make sure input image is a stack.
    if (stackSize == 1) {
      IJ.error("Z Project", "Stack required");
      return;
    }

    //  Check for inverting LUT.
    if (imp.getProcessor().isInvertedLut()) {
      if (!IJ.showMessageWithCancel("ZProjection", lutMessage)) return;
    }

    // Set default bounds.
    int channels = imp.getNChannels();
    int frames = imp.getNFrames();
    int slices = imp.getNSlices();
    isHyperstack =
        imp.isHyperStack()
            || (ij.macro.Interpreter.isBatchMode()
                && ((frames > 1 && frames < stackSize) || (slices > 1 && slices < stackSize)));
    boolean simpleComposite = channels == stackSize;
    if (simpleComposite) isHyperstack = false;
    startSlice = 1;
    if (isHyperstack) {
      int nSlices = imp.getNSlices();
      if (nSlices > 1) stopSlice = nSlices;
      else stopSlice = imp.getNFrames();
    } else stopSlice = stackSize;

    // Build control dialog
    GenericDialog gd = buildControlDialog(startSlice, stopSlice);
    gd.showDialog();
    if (gd.wasCanceled()) return;

    if (!imp.lock()) return; // exit if in use
    long tstart = System.currentTimeMillis();
    setStartSlice((int) gd.getNextNumber());
    setStopSlice((int) gd.getNextNumber());
    method = gd.getNextChoiceIndex();
    Prefs.set(METHOD_KEY, method);
    if (isHyperstack) {
      allTimeFrames = imp.getNFrames() > 1 && imp.getNSlices() > 1 ? gd.getNextBoolean() : false;
      doHyperStackProjection(allTimeFrames);
    } else if (imp.getType() == ImagePlus.COLOR_RGB) doRGBProjection(true);
    else doProjection(true);

    if (arg.equals("") && projImage != null) {
      long tstop = System.currentTimeMillis();
      projImage.setCalibration(imp.getCalibration());
      if (simpleComposite) IJ.run(projImage, "Grays", "");
      projImage.show("ZProjector: " + IJ.d2s((tstop - tstart) / 1000.0, 2) + " seconds");
    }

    imp.unlock();
    IJ.register(ZProjector.class);
    return;
  }