Ejemplo n.º 1
0
 /**
  * Do watershed segmentation based on the EDM of the foreground objects (nonzero pixels) in an
  * 8-bit image. Particles are segmented by their shape; segmentation lines added are background
  * pixels (value = 0);
  */
 public void toWatershed(ImageProcessor ip) {
   FloatProcessor floatEdm = makeFloatEDM(ip, 0, false);
   ByteProcessor maxIp =
       maxFinder.findMaxima(
           floatEdm,
           MAXFINDER_TOLERANCE,
           ImageProcessor.NO_THRESHOLD,
           MaximumFinder.SEGMENTED,
           false,
           true);
   if (maxIp != null) ip.copyBits(maxIp, 0, 0, Blitter.AND);
 }
Ejemplo n.º 2
0
 /**
  * Called by the PlugInFilterRunner after setup. Asks the user in case of a stack and prepares a
  * separate ouptut stack if required
  */
 public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
   this.pfr = pfr;
   int width = imp.getWidth();
   int height = imp.getHeight();
   // ask whether to process all slices of stack & prepare stack
   // (if required) for writing into it in parallel threads
   flags = IJ.setupDialog(imp, flags);
   if ((flags & DOES_STACKS) != 0 && outImageType != BYTE_OVERWRITE) {
     outStack = new ImageStack(width, height, imp.getStackSize());
     maxFinder.setNPasses(imp.getStackSize());
   }
   return flags;
 } // public int showDialog
Ejemplo n.º 3
0
 /**
  * Prepare the progress bar. Without calling it or if nPasses=0, no progress bar will be shown.
  *
  * @param nPasses Number of images that this EDM will process.
  */
 public void setNPasses(int nPasses) {
   this.nPasses = nPasses;
   progressDone = 0;
   if (USES_MAX_FINDER[processType]) maxFinder.setNPasses(nPasses);
 }
Ejemplo n.º 4
0
  /** Called by the PlugInFilterRunner to process the image or one frame of a stack */
  public void run(ImageProcessor ip) {
    if (interrupted) return;
    int width = ip.getWidth();
    int height = ip.getHeight();

    int backgroundValue =
        (processType == VORONOI)
            ? (background255 ? 0 : (byte) 255)
            : // Voronoi needs EDM of the background
            (background255 ? (byte) 255 : 0); // all others do EDM of the foreground
    if (USES_WATERSHED[processType]) nPasses = 0; // watershed has its own progress bar
    FloatProcessor floatEdm = makeFloatEDM(ip, backgroundValue, false);

    ByteProcessor maxIp = null;
    if (USES_MAX_FINDER[processType]) {
      if (processType == VORONOI) floatEdm.multiply(-1); // Voronoi starts from minima of EDM
      int maxOutputType =
          USES_WATERSHED[processType] ? MaximumFinder.SEGMENTED : MaximumFinder.SINGLE_POINTS;
      boolean isEDM = processType != VORONOI;
      maxIp =
          maxFinder.findMaxima(
              floatEdm,
              MAXFINDER_TOLERANCE,
              ImageProcessor.NO_THRESHOLD,
              maxOutputType,
              false,
              isEDM);
      if (maxIp == null) { // segmentation cancelled by user?
        interrupted = true;
        return;
      } else if (processType != WATERSHED) {
        if (processType == VORONOI) floatEdm.multiply(-1);
        resetMasked(floatEdm, maxIp, processType == VORONOI ? -1 : 0);
      }
    }

    ImageProcessor outIp = null;
    if (processType == WATERSHED) {
      if (background255) maxIp.invert();
      ip.copyBits(maxIp, 0, 0, Blitter.COPY);
      ip.setBinaryThreshold();
    } else
      switch (outImageType) { // for all these, output contains the values of the EDM
        case FLOAT:
          outIp = floatEdm;
          break;
        case SHORT:
          floatEdm.setMinAndMax(0., 65535.);
          outIp = floatEdm.convertToShort(true);
          break;
        case BYTE:
          floatEdm.setMinAndMax(0., 255.);
          outIp = floatEdm.convertToByte(true);
          break;
        case BYTE_OVERWRITE:
          ip.setPixels(0, floatEdm);
          if (floatEdm.getMax() > 255.) ip.resetMinAndMax(); // otherwise we have max of floatEdm
      }

    if (outImageType != BYTE_OVERWRITE) { // new output image
      if (outStack == null) {
        outImp = new ImagePlus(TITLE_PREFIX[processType] + imp.getShortTitle(), outIp);
      } else outStack.setPixels(outIp.getPixels(), pfr.getSliceNumber());
    }
  } // public void run