/** Produce a binary image based on the current confidence matrix */
private void createBinaryMask() {
if (null != confMatrix) {
final ByteProcessor result = (ByteProcessor) confMatrix.convertToByte(false);
result.multiply(255);
// Set background color based on the Process > Binary > Options
if (!Prefs.blackBackground) result.invert();
new ImagePlus("Mask", result).show();
}
}
/** 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