public void run(ImageProcessor ip) {
if (enlarge && gd.wasOKed())
synchronized (this) {
if (!isEnlarged) {
enlargeCanvas();
isEnlarged = true;
}
}
if (isEnlarged) { // enlarging may have made the ImageProcessor invalid, also for the parallel
// threads
int slice = pfr.getSliceNumber();
if (imp.getStackSize() == 1) ip = imp.getProcessor();
else ip = imp.getStack().getProcessor(slice);
}
ip.setInterpolationMethod(interpolationMethod);
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) ip.setBackgroundValue(ip.getBestIndex(bgc));
else if (bitDepth == 24) ip.setBackgroundValue(bgc.getRGB());
} else ip.setBackgroundValue(0);
ip.rotate(angle);
if (!gd.wasOKed()) drawGridLines(gridLines);
if (isEnlarged && imp.getStackSize() == 1) {
imp.changes = true;
imp.updateAndDraw();
Undo.setup(Undo.COMPOUND_FILTER_DONE, imp);
}
}
/** 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