Exemplo n.º 1
0
 void scale(ImageProcessor ip) {
   if (newWindow) {
     Rectangle r = ip.getRoi();
     ImagePlus imp2 = imp.createImagePlus();
     imp2.setProcessor(title, ip.resize(newWidth, newHeight));
     Calibration cal = imp2.getCalibration();
     if (cal.scaled()) {
       cal.pixelWidth *= 1.0 / xscale;
       cal.pixelHeight *= 1.0 / yscale;
     }
     imp2.show();
     imp.trimProcessor();
     imp2.trimProcessor();
     imp2.changes = true;
   } else {
     if (processStack && imp.getStackSize() > 1) {
       Undo.reset();
       StackProcessor sp = new StackProcessor(imp.getStack(), ip);
       sp.scale(xscale, yscale, bgValue);
     } else {
       ip.snapshot();
       Undo.setup(Undo.FILTER, imp);
       ip.setSnapshotCopyMode(true);
       ip.scale(xscale, yscale);
       ip.setSnapshotCopyMode(false);
     }
     imp.killRoi();
     imp.updateAndDraw();
     imp.changes = true;
   }
 }
Exemplo n.º 2
0
 protected void hideRois() {
   if (currentImage == null) return;
   currentImage.killRoi();
   if (currentImage.isVisible()) {
     currentImage.updateAndDraw();
     ImageUtils.removeScrollListener(currentImage, this, this);
   }
   currentImage = null;
 }
Exemplo n.º 3
0
 protected void updateRoi() {
   // System.out.println("image:"+currentImage.getTitle()+ " slice:"+currentImage.getSlice());
   Roi r = currentROIs.get(currentImage.getSlice());
   if (r != null) {
     currentImage.setRoi(r);
   } else {
     currentImage.killRoi();
   }
   currentImage.updateAndDraw();
 }
Exemplo n.º 4
0
 public void run() {
   while (!done) {
     synchronized (this) {
       try {
         wait();
       } catch (InterruptedException e) {
       }
       reset(imp, ip); // GL
       apply(imp, ip); // GL
       imp.updateAndDraw(); // GL
     }
   }
 }
Exemplo n.º 5
0
    public void actionPerformed(ActionEvent e) {
      Button b = (Button) e.getSource();
      if (b == null) return;

      boolean imageThere = checkImage();

      if (imageThere) {
        if (b == originalB) {
          reset(imp, ip);
          filteredB.setEnabled(true);
        } else if (b == filteredB) {
          apply(imp, ip);
        } else if (b == sampleB) {
          reset(imp, ip);
          sample();
          apply(imp, ip);
        } else if (b == stackB) {
          applyStack();
        } else if (b == helpB) {
          IJ.showMessage(
              "Help",
              "Threshold Colour  v1.0\n \n"
                  + "Modification of Bob Dougherty's BandPass2 plugin by G.Landini to\n"
                  + "threshold 24 bit RGB images based on Hue, Saturation and Brightness\n"
                  + "or Red, Green and Blue components.\n \n"
                  + "Pass: Band-pass filter (anything within range is displayed).\n \n"
                  + "Stop: Band-reject filter (anything within range is NOT displayed).\n \n"
                  + "Original: Shows the original image and updates the buffer when\n"
                  + " switching to another image.\n \n"
                  + "Filtered: Shows the filtered image.\n \n"
                  + "Stack: Processes the rest of the slices in the stack (if any)\n"
                  + " using the current settings.\n \n"
                  + "Threshold: Shows the object/background in the foreground and\n"
                  + " background colours selected in the ImageJ toolbar.\n \n"
                  + "Invert: Swaps the fore/background colours.\n \n"
                  + "Sample: (experimental) Sets the ranges of the filters based on the\n"
                  + " pixel value componentd in a rectangular, user-defined, ROI.\n \n"
                  + "HSB RGB: Selects HSB or RGB space and resets all the filters.\n \n"
                  + "Note that the \'thresholded\' image is RGB, not 8 bit grey.");
        }
        updatePlot();
        updateLabels();
        imp.updateAndDraw();
      } else {
        IJ.beep();
        IJ.showStatus("No Image");
      }
      notify();
    }
Exemplo n.º 6
0
 void setStackDisplayRange(ImagePlus imp) {
   ImageStack stack = imp.getStack();
   double min = Double.MAX_VALUE;
   double max = -Double.MAX_VALUE;
   int n = stack.getSize();
   for (int i = 1; i <= n; i++) {
     if (!silentMode) IJ.showStatus("Calculating stack min and max: " + i + "/" + n);
     ImageProcessor ip = stack.getProcessor(i);
     ip.resetMinAndMax();
     if (ip.getMin() < min) min = ip.getMin();
     if (ip.getMax() > max) max = ip.getMax();
   }
   imp.getProcessor().setMinAndMax(min, max);
   imp.updateAndDraw();
 }
Exemplo n.º 7
0
 protected void registerActiveImage() {
   ImagePlus activeImage = WindowManager.getCurrentImage();
   if (activeImage != null
       && activeImage.getProcessor() != null) { // && activeImage.getImageStackSize() > 1
     if (currentImage != null && currentImage.getWindow() != null && currentImage != activeImage) {
       // System.out.println("remove listener:"+currentImage.getTitle());
       ImageUtils.removeScrollListener(currentImage, this, this);
       currentImage.killRoi();
       currentImage.updateAndDraw();
       currentImage = null;
     }
     if (currentImage != activeImage) {
       // System.out.println("add listener:"+activeImage.getTitle());
       ImageUtils.addScrollListener(activeImage, this, this);
       this.currentImage = activeImage;
     }
   }
 }
Exemplo n.º 8
0
 public void mergeSelectedObjects() {
   this.populatingObjects = true;
   HashMap<Integer, ArrayList<Object3DGui>> allObjects = getSplitSelection();
   for (int channelIdx : allObjects.keySet()) {
     ArrayList<Object3DGui> objects = allObjects.get(channelIdx);
     if (objects != null && objects.size() >= 2) {
       Collections.sort(objects);
       Object3DGui o1 = objects.get(0);
       for (int i = objects.size() - 1; i > 0; i--) {
         Object3DGui o2 = objects.get(i);
         o1.merge(o2);
         listModel.removeElement(o2);
         // IJ.log("merge:"+o1.getName()+ "::"+objects.get(i).getName()+ " channel:"+channelIdx);
       }
       o1.getChannel().createObjects();
       if (autoSave) o1.getChannel().saveOutput();
       ImagePlus img = o1.getChannel().getSegmented().getImagePlus();
       if (img.isVisible()) {
         img.updateAndDraw();
       }
     }
   }
   this.populatingObjects = false;
 }
Exemplo n.º 9
0
 public void deleteSelectedObjects() {
   populatingObjects = true;
   try {
     boolean[] modif = new boolean[currentChannels.length];
     for (Object o : this.list.getSelectedValues()) {
       listModel.removeElement(o);
       modif[getChannelRank(((Object3DGui) o).getChannel())] = true;
       ((Object3DGui) o).delete(true);
     }
     for (int i = 0; i < currentChannels.length; i++) {
       if (modif[i]) {
         ImagePlus img = currentChannels[i].getSegmented().getImagePlus();
         if (img.isVisible()) {
           img.updateAndDraw();
         }
         currentChannels[i].createObjects();
         if (autoSave) currentChannels[i].saveOutput();
       }
     }
   } catch (Exception e) {
     exceptionPrinter.print(e, "", Core.GUIMode);
   }
   populatingObjects = false;
 }
Exemplo n.º 10
0
    ImageProcessor setup(ImagePlus imp) {

      ImageProcessor ip;
      int type = imp.getType();
      if (type != ImagePlus.COLOR_RGB) return null;
      ip = imp.getProcessor();
      int id = imp.getID();
      int slice = imp.getCurrentSlice();

      if ((id != previousImageID) | (slice != previousSlice) | (flag)) {
        flag = false; // if true, flags a change from HSB to RGB or viceversa
        numSlices = imp.getStackSize();
        stack = imp.getStack();
        width = stack.getWidth();
        height = stack.getHeight();
        numPixels = width * height;

        hSource = new byte[numPixels];
        sSource = new byte[numPixels];
        bSource = new byte[numPixels];

        // restore = (int[])ip.getPixelsCopy(); //This runs into trouble sometimes, so do it the
        // long way:
        int[] temp = (int[]) ip.getPixels();
        restore = new int[numPixels];
        for (int i = 0; i < numPixels; i++) restore[i] = temp[i];

        fillMask = new int[numPixels];

        // Get hsb or rgb from image.
        ColorProcessor cp = (ColorProcessor) ip;
        IJ.showStatus("Gathering data");

        if (isRGB) cp.getRGB(hSource, sSource, bSource);
        else cp.getHSB(hSource, sSource, bSource);

        IJ.showStatus("done");

        // Create a spectrum ColorModel for the Hue histogram plot.
        Color c;
        byte[] reds = new byte[256];
        byte[] greens = new byte[256];
        byte[] blues = new byte[256];
        for (int i = 0; i < 256; i++) {
          c = Color.getHSBColor(i / 255f, 1f, 1f);

          reds[i] = (byte) c.getRed();
          greens[i] = (byte) c.getGreen();
          blues[i] = (byte) c.getBlue();
        }
        ColorModel cm = new IndexColorModel(8, 256, reds, greens, blues);

        // Make an image with just the hue from the RGB image and the spectrum LUT.
        // This is just for a hue histogram for the plot.  Do not show it.
        // ByteProcessor bpHue = new ByteProcessor(width,height,h,cm);
        ByteProcessor bpHue = new ByteProcessor(width, height, hSource, cm);
        ImagePlus impHue = new ImagePlus("Hue", bpHue);
        // impHue.show();

        ByteProcessor bpSat = new ByteProcessor(width, height, sSource, cm);
        ImagePlus impSat = new ImagePlus("Sat", bpSat);
        // impSat.show();

        ByteProcessor bpBri = new ByteProcessor(width, height, bSource, cm);
        ImagePlus impBri = new ImagePlus("Bri", bpBri);
        // impBri.show();

        plot.setHistogram(impHue, 0);
        splot.setHistogram(impSat, 1);
        bplot.setHistogram(impBri, 2);

        updateLabels();
        updatePlot();
        updateScrollBars();
        imp.updateAndDraw();
      }
      previousImageID = id;
      previousSlice = slice;
      return ip;
    }