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);
 }
Beispiel #2
0
 private void doRGBProjection(ImageStack stack) {
   ImageStack[] channels = ChannelSplitter.splitRGB(stack, true);
   ImagePlus red = new ImagePlus("Red", channels[0]);
   ImagePlus green = new ImagePlus("Green", channels[1]);
   ImagePlus blue = new ImagePlus("Blue", channels[2]);
   imp.unlock();
   ImagePlus saveImp = imp;
   imp = red;
   color = "(red)";
   doProjection();
   ImagePlus red2 = projImage;
   imp = green;
   color = "(green)";
   doProjection();
   ImagePlus green2 = projImage;
   imp = blue;
   color = "(blue)";
   doProjection();
   ImagePlus blue2 = projImage;
   int w = red2.getWidth(), h = red2.getHeight(), d = red2.getStackSize();
   if (method == SD_METHOD) {
     ImageProcessor r = red2.getProcessor();
     ImageProcessor g = green2.getProcessor();
     ImageProcessor b = blue2.getProcessor();
     double max = 0;
     double rmax = r.getStatistics().max;
     if (rmax > max) max = rmax;
     double gmax = g.getStatistics().max;
     if (gmax > max) max = gmax;
     double bmax = b.getStatistics().max;
     if (bmax > max) max = bmax;
     double scale = 255 / max;
     r.multiply(scale);
     g.multiply(scale);
     b.multiply(scale);
     red2.setProcessor(r.convertToByte(false));
     green2.setProcessor(g.convertToByte(false));
     blue2.setProcessor(b.convertToByte(false));
   }
   RGBStackMerge merge = new RGBStackMerge();
   ImageStack stack2 =
       merge.mergeStacks(w, h, d, red2.getStack(), green2.getStack(), blue2.getStack(), true);
   imp = saveImp;
   projImage = new ImagePlus(makeTitle(), stack2);
 }
Beispiel #3
0
 void enlargeCanvas() {
   imp.unlock();
   if (imp.getStackSize() == 1) Undo.setup(Undo.COMPOUND_FILTER, imp);
   IJ.run("Select All");
   IJ.run("Rotate...", "angle=" + angle);
   Roi roi = imp.getRoi();
   Rectangle r = roi.getBounds();
   if (r.width < imp.getWidth()) r.width = imp.getWidth();
   if (r.height < imp.getHeight()) r.height = imp.getHeight();
   IJ.showStatus("Rotate: Enlarging...");
   IJ.run(
       "Canvas Size...",
       "width="
           + r.width
           + " height="
           + r.height
           + " position=Center "
           + (fillWithBackground ? "" : "zero"));
   IJ.showStatus("Rotating...");
 }
Beispiel #4
0
  public int setup(String arg, ImagePlus imp) {
    // IJ.register(Average_Oversampled.class);

    if (IJ.versionLessThan("1.32c")) return DONE;

    if (this.pre) { // before finding means

      imp.unlock();
      this.imp = imp;
      this.nslices = imp.getNSlices();
      this.width = imp.getWidth();
      this.height = imp.getHeight();
      this.slicecols = new float[nslices][width];
      this.pre = false;
      return (DOES_ALL + DOES_STACKS + FINAL_PROCESSING);

    } else { // find SD after finding means of columns
      float sum; // sum of pixel values column
      float avg; // average pixel value of a column
      double devsum; // sum of deviations
      double devavg; // standard deviation
      double[] columns = new double[width]; // x-axis of plot
      double[] sdevs = new double[width]; // y-axis of plot

      for (int i = 0; i < width; i += 1) {
        sum = 0; // reset with each column
        avg = 0; // reset with each column
        devsum = 0; // reset with each column
        devavg = 0; // reset with each column
        columns[i] = i; // building x-axis

        for (int s = 0; s < nslices; s += 1) { // sum of column means
          sum = sum + slicecols[s][i];
        }
        avg = sum / nslices; // mean of one column across all slices

        for (int s = 0; s < nslices; s += 1) { // standard deviation
          devsum = devsum + Math.pow((slicecols[s][i] - avg), 2); // square diff
        }
        devavg = Math.sqrt(devsum / nslices);

        sdevs[i] = devavg; // building y-axis
      }

      Plot plot = new Plot("Average SD by Column", "Columns", "Standard Deviation", columns, sdevs);
      plot.show();

      // calculate CTN
      double ctn;
      double sdevssum = 0;
      for (double sd : sdevs) {
        sdevssum = sdevssum + sd;
      }
      ctn = sdevssum / width;

      // display CTN on results table
      ResultsTable rt = ResultsTable.getResultsTable();
      // rt.incrementCounter();
      rt.addValue("Column Temporal Noise", ctn);
      rt.show("Results");

      this.pre = false;

      return DONE;
    }
  }
    public BandAdjuster() {

      super("Threshold Colour");
      if (instance != null) {
        instance.toFront();
        return;
      }
      imp = WindowManager.getCurrentImage();
      if (imp == null) {
        IJ.beep();
        IJ.showStatus("No image");
        return;
      }
      IJ.run("Select None");
      thread = new Thread(this, "BandAdjuster");
      WindowManager.addWindow(this);
      instance = this;
      IJ.register(PasteController.class);

      ij = IJ.getInstance();
      Font font = new Font("SansSerif", Font.PLAIN, 10);
      GridBagLayout gridbag = new GridBagLayout();
      GridBagConstraints c = new GridBagConstraints();
      setLayout(gridbag);

      int y = 0;
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      labelh = new Label("Hue", Label.CENTER);
      add(labelh, c);

      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(7, 0, 0, 0);
      labelf = new Label("Filter type", Label.RIGHT);
      add(labelf, c);

      // plot
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.fill = c.BOTH;
      c.anchor = c.CENTER;
      c.insets = new Insets(0, 5, 0, 0);
      add(plot, c);

      // checkboxes
      panelh = new Panel();
      filterTypeH = new CheckboxGroup();
      bandPassH = new Checkbox("Pass");
      bandPassH.setCheckboxGroup(filterTypeH);
      bandPassH.addItemListener(this);
      panelh.add(bandPassH);
      bandStopH = new Checkbox("Stop");
      bandStopH.setCheckboxGroup(filterTypeH);
      bandStopH.addItemListener(this);
      panelh.add(bandStopH);
      bandPassH.setState(true);
      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(5, 0, 0, 0);
      add(panelh, c);

      // minHue slider
      minSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 90 : 100;
      c.fill = c.HORIZONTAL;
      c.insets = new Insets(5, 5, 0, 0);

      add(minSlider, c);
      minSlider.addAdjustmentListener(this);
      minSlider.setUnitIncrement(1);

      // minHue slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 10 : 0;
      c.insets = new Insets(5, 0, 0, 0);
      label1 = new Label("       ", Label.LEFT);
      label1.setFont(font);
      add(label1, c);

      // maxHue sliderHue
      maxSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.weightx = 100;
      c.insets = new Insets(5, 5, 0, 0);
      add(maxSlider, c);
      maxSlider.addAdjustmentListener(this);
      maxSlider.setUnitIncrement(1);

      // maxHue slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.gridy = y++;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      label2 = new Label("       ", Label.LEFT);
      label2.setFont(font);
      add(label2, c);

      // =====
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(10, 0, 0, 0);
      labels = new Label("Saturation", Label.CENTER);
      add(labels, c);

      // plot
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.fill = c.BOTH;
      c.anchor = c.CENTER;
      c.insets = new Insets(0, 5, 0, 0);
      add(splot, c);

      // checkboxes
      panels = new Panel();
      filterTypeS = new CheckboxGroup();
      bandPassS = new Checkbox("Pass");
      bandPassS.setCheckboxGroup(filterTypeS);
      bandPassS.addItemListener(this);
      panels.add(bandPassS);
      bandStopS = new Checkbox("Stop");
      bandStopS.setCheckboxGroup(filterTypeS);
      bandStopS.addItemListener(this);
      panels.add(bandStopS);
      bandPassS.setState(true);
      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(5, 0, 0, 0);
      add(panels, c);

      // minSat slider
      minSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 90 : 100;
      c.fill = c.HORIZONTAL;
      c.insets = new Insets(5, 5, 0, 0);
      add(minSlider2, c);
      minSlider2.addAdjustmentListener(this);
      minSlider2.setUnitIncrement(1);

      // minSat slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 10 : 0;
      c.insets = new Insets(5, 0, 0, 0);
      label3 = new Label("       ", Label.LEFT);
      label3.setFont(font);
      add(label3, c);

      // maxSat slider
      maxSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 100;
      c.insets = new Insets(5, 5, 0, 0);
      add(maxSlider2, c);
      maxSlider2.addAdjustmentListener(this);
      maxSlider2.setUnitIncrement(1);

      // maxSat slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      label4 = new Label("       ", Label.LEFT);
      label4.setFont(font);
      add(label4, c);

      // =====
      c.gridx = 0;
      c.gridwidth = 1;
      c.gridy = y++;
      c.weightx = 0;
      c.insets = new Insets(10, 0, 0, 0);
      labelb = new Label("Brightness", Label.CENTER);
      add(labelb, c);

      c.gridx = 0;
      c.gridwidth = 1;
      c.gridy = y;
      c.fill = c.BOTH;
      c.anchor = c.CENTER;
      c.insets = new Insets(0, 5, 0, 0);
      add(bplot, c);

      // checkboxes
      panelb = new Panel();
      filterTypeB = new CheckboxGroup();
      bandPassB = new Checkbox("Pass");
      bandPassB.setCheckboxGroup(filterTypeB);
      bandPassB.addItemListener(this);
      panelb.add(bandPassB);
      bandStopB = new Checkbox("Stop");
      bandStopB.setCheckboxGroup(filterTypeB);
      bandStopB.addItemListener(this);
      panelb.add(bandStopB);
      bandPassB.setState(true);
      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(5, 0, 0, 0);
      add(panelb, c);

      // minBri slider
      minSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 90 : 100;
      c.fill = c.HORIZONTAL;
      c.insets = new Insets(5, 5, 0, 0);
      add(minSlider3, c);
      minSlider3.addAdjustmentListener(this);
      minSlider3.setUnitIncrement(1);

      // minBri slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 10 : 0;
      c.insets = new Insets(5, 0, 0, 0);
      label5 = new Label("       ", Label.LEFT);
      label5.setFont(font);
      add(label5, c);

      // maxBri slider
      maxSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 100;
      c.insets = new Insets(5, 5, 0, 0);
      add(maxSlider3, c);
      maxSlider3.addAdjustmentListener(this);
      maxSlider3.setUnitIncrement(1);

      // maxBri slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      label6 = new Label("       ", Label.LEFT);
      label6.setFont(font);
      add(label6, c);

      // =====
      panelt = new Panel();
      threshold = new Checkbox("Threshold");
      threshold.addItemListener(this);
      panelt.add(threshold);

      invert = new Checkbox("Invert");
      invert.addItemListener(this);
      panelt.add(invert);

      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(0, 0, 0, 0);
      add(panelt, c);

      // buttons
      panel = new Panel();
      // panel.setLayout(new GridLayout(2, 2, 0, 0));
      originalB = new Button("Original");
      originalB.setEnabled(false);
      originalB.addActionListener(this);
      originalB.addKeyListener(ij);
      panel.add(originalB);

      filteredB = new Button("Filtered");
      filteredB.setEnabled(false);
      filteredB.addActionListener(this);
      filteredB.addKeyListener(ij);
      panel.add(filteredB);

      stackB = new Button("Stack");
      stackB.addActionListener(this);
      stackB.addKeyListener(ij);
      panel.add(stackB);

      helpB = new Button("Help");
      helpB.addActionListener(this);
      helpB.addKeyListener(ij);
      panel.add(helpB);

      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(0, 0, 0, 0);
      add(panel, c);

      panelMode = new Panel();

      sampleB = new Button("Sample");
      sampleB.addActionListener(this);
      sampleB.addKeyListener(ij);
      panelMode.add(sampleB);

      colourMode = new CheckboxGroup();
      hsb = new Checkbox("HSB");
      hsb.setCheckboxGroup(colourMode);
      hsb.addItemListener(this);
      panelMode.add(hsb);
      hsb.setState(true);
      rgb = new Checkbox("RGB");
      rgb.setCheckboxGroup(colourMode);
      rgb.addItemListener(this);
      panelMode.add(rgb);

      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(0, 0, 0, 0);
      add(panelMode, c);

      addKeyListener(ij); // ImageJ handles keyboard shortcuts
      pack();
      GUI.center(this);
      setVisible(true);

      ip = setup(imp);
      if (ip == null) {
        imp.unlock();
        IJ.beep();
        IJ.showStatus("RGB image cannot be thresholded");
        return;
      }
      thread.start();
    }
Beispiel #6
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;
  }