/**
* 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);
}
/**
* 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
/**
* 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);
}
/** 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