Beispiel #1
0
  /** Generate output image whose type is same as input image. */
  private ImagePlus makeOutputImage(ImagePlus imp, FloatProcessor fp, int ptype) {
    int width = imp.getWidth();
    int height = imp.getHeight();
    float[] pixels = (float[]) fp.getPixels();
    ImageProcessor oip = null;

    // Create output image consistent w/ type of input image.
    int size = pixels.length;
    switch (ptype) {
      case BYTE_TYPE:
        oip = imp.getProcessor().createProcessor(width, height);
        byte[] pixels8 = (byte[]) oip.getPixels();
        for (int i = 0; i < size; i++) pixels8[i] = (byte) pixels[i];
        break;
      case SHORT_TYPE:
        oip = imp.getProcessor().createProcessor(width, height);
        short[] pixels16 = (short[]) oip.getPixels();
        for (int i = 0; i < size; i++) pixels16[i] = (short) pixels[i];
        break;
      case FLOAT_TYPE:
        oip = new FloatProcessor(width, height, pixels, null);
        break;
    }

    // Adjust for display.
    // Calling this on non-ByteProcessors ensures image
    // processor is set up to correctly display image.
    oip.resetMinAndMax();

    // Create new image plus object. Don't use
    // ImagePlus.createImagePlus here because there may be
    // attributes of input image that are not appropriate for
    // projection.
    return new ImagePlus(makeTitle(), oip);
  }
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);
 }
    void setHistogram(ImagePlus imp, int j) {
      ImageProcessor ip = imp.getProcessor();
      ImageStatistics stats = ImageStatistics.getStatistics(ip, AREA + MODE, null);
      int maxCount2 = 0;
      histogram = stats.histogram;
      for (int i = 0; i < stats.nBins; i++)
        if ((histogram[i] > maxCount2) && (i != stats.mode)) maxCount2 = histogram[i];
      hmax = stats.maxCount;
      if ((hmax > (maxCount2 * 1.5)) && (maxCount2 != 0)) { // GL 1.5 was 2
        hmax = (int) (maxCount2 * 1.1); // GL 1.1 was 1.5
        histogram[stats.mode] = hmax;
      }
      os = null;
      ColorModel cm = ip.getColorModel();
      if (!(cm instanceof IndexColorModel)) return;
      IndexColorModel icm = (IndexColorModel) cm;
      int mapSize = icm.getMapSize();
      if (mapSize != 256) return;
      byte[] r = new byte[256];
      byte[] g = new byte[256];
      byte[] b = new byte[256];
      icm.getReds(r);
      icm.getGreens(g);
      icm.getBlues(b);
      hColors = new Color[256];

      if (isRGB) {
        if (j == 0) {
          for (int i = 0; i < 256; i++) hColors[i] = new Color(i & 255, 0 & 255, 0 & 255);
        } else if (j == 1) {
          for (int i = 0; i < 256; i++) hColors[i] = new Color(0 & 255, i & 255, 0 & 255);
        } else if (j == 2) {
          for (int i = 0; i < 256; i++) hColors[i] = new Color(0 & 255, 0 & 255, i & 255);
        }
      } else {
        if (j == 0) {
          for (int i = 0; i < 256; i++) hColors[i] = new Color(r[i] & 255, g[i] & 255, b[i] & 255);
        } else if (j == 1) {
          for (int i = 0; i < 256; i++)
            // hColors[i] = new Color(127-i/2&255, 127+i/2&255, 127-i/2&255);
            hColors[i] = new Color(192 - i / 4 & 255, 192 + i / 4 & 255, 192 - i / 4 & 255);
        } else if (j == 2) {
          for (int i = 0; i < 256; i++) hColors[i] = new Color(i & 255, i & 255, 0 & 255);
        }
      }
    }
Beispiel #4
0
 public void run(String arg) {
   imp = IJ.getImage();
   Roi roi = imp.getRoi();
   if (roi != null && !roi.isArea()) imp.killRoi(); // ignore any line selection
   ImageProcessor ip = imp.getProcessor();
   if (!showDialog(ip)) return;
   if (ip.getWidth() > 1 && ip.getHeight() > 1) ip.setInterpolate(interpolate);
   else ip.setInterpolate(false);
   ip.setBackgroundValue(bgValue);
   imp.startTiming();
   try {
     if (newWindow && imp.getStackSize() > 1 && processStack) createNewStack(imp, ip);
     else scale(ip);
   } catch (OutOfMemoryError o) {
     IJ.outOfMemory("Scale");
   }
   IJ.showProgress(1.0);
 }
Beispiel #5
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);
 }
 protected void setDrawingColor(int ox, int oy, boolean setBackground) {
   // IJ.log("setDrawingColor: "+setBackground+this);
   int type = imp.getType();
   int[] v = imp.getPixel(ox, oy);
   switch (type) {
     case ImagePlus.GRAY8:
       {
         if (setBackground) setBackgroundColor(getColor(v[0]));
         else setForegroundColor(getColor(v[0]));
         break;
       }
     case ImagePlus.GRAY16:
     case ImagePlus.GRAY32:
       {
         double min = imp.getProcessor().getMin();
         double max = imp.getProcessor().getMax();
         double value = (type == ImagePlus.GRAY32) ? Float.intBitsToFloat(v[0]) : v[0];
         int index = (int) (255.0 * ((value - min) / (max - min)));
         if (index < 0) index = 0;
         if (index > 255) index = 255;
         if (setBackground) setBackgroundColor(getColor(index));
         else setForegroundColor(getColor(index));
         break;
       }
     case ImagePlus.COLOR_RGB:
     case ImagePlus.COLOR_256:
       {
         Color c = new Color(v[0], v[1], v[2]);
         if (setBackground) setBackgroundColor(c);
         else setForegroundColor(c);
         break;
       }
   }
   Color c;
   if (setBackground) c = Toolbar.getBackgroundColor();
   else {
     c = Toolbar.getForegroundColor();
     imp.setColor(c);
   }
   IJ.showStatus("(" + c.getRed() + ", " + c.getGreen() + ", " + c.getBlue() + ")");
 }
    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;
    }
 Color getColor(int index) {
   IndexColorModel cm = (IndexColorModel) imp.getProcessor().getColorModel();
   // IJ.write(""+index+" "+(new Color(cm.getRGB(index))));
   return new Color(cm.getRGB(index));
 }
  /*------------------------------------------------------------------*/
  public void run(String arg) {
    ImagePlus imp = WindowManager.getCurrentImage();
    this.imp = imp;
    if (imp == null) {
      IJ.noImage();
      return;
    }
    if ((1 < imp.getStackSize()) && (imp.getType() == imp.COLOR_256)) {
      IJ.error("Stack of color images not supported (use grayscale)");
      return;
    }
    if (1 < imp.getStackSize()) {
      if (imp.getStack().isRGB()) {
        IJ.error("RGB color images not supported (use grayscale)");
        return;
      }
    }
    if (1 < imp.getStackSize()) {
      if (imp.getStack().isHSB()) {
        IJ.error("HSB color images not supported (use grayscale)");
        return;
      }
    }
    if (imp.getType() == imp.COLOR_256) {
      IJ.error("Indexed color images not supported (use grayscale)");
      return;
    }
    if (imp.getType() == imp.COLOR_RGB) {
      IJ.error("Color images not supported (use grayscale)");
      return;
    }

    differentialsDialog dialog =
        new differentialsDialog(IJ.getInstance(), "Differentials", true, operation);
    GUI.center(dialog);
    dialog.setVisible(true);
    cancel = dialog.getCancel();
    operation = dialog.getOperation();
    dialog.dispose();
    if (cancel) {
      return;
    }

    imp.startTiming();
    if (1 < imp.getStackSize()) {
      if (!(imp.getProcessor().getPixels() instanceof float[])) {
        new StackConverter(imp).convertToGray32();
      }
    } else {
      if (!(imp.getProcessor().getPixels() instanceof float[])) {
        new ImageConverter(imp).convertToGray32();
      }
    }
    ImageStack stack = imp.getStack();
    stackSize = stack.getSize();
    Undo.reset();

    setupProgressBar();
    resetProgressBar();

    for (int i = 1; (i <= stackSize); i++) {
      ImageProcessor ip = stack.getProcessor(i);
      doIt(ip);
      imp.getProcessor().resetMinAndMax();
      imp.setSlice(i);
      imp.updateAndRepaintWindow();
    }
    imp.getProcessor().resetMinAndMax();
    imp.setSlice(1);
    imp.updateAndRepaintWindow();
    cleanUpProgressBar();
    IJ.showTime(imp, imp.getStartTime(), "Differentials: ");
    ImageWindow win = imp.getWindow();
    if (win != null) {
      win.running = false;
    }
  } /* end run */
Beispiel #10
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;
  }