/**
* Calculates a 16-bit grayscale Euclidean Distance Map for a binary 8-bit image. Each foreground
* (nonzero) pixel in the binary image is assigned a value equal to its distance from the nearest
* background (zero) pixel, multiplied by EDM.ONE. For compatibility with previous versions of
* ImageJ only.
*/
public ShortProcessor make16bitEDM(ImageProcessor ip) {
FloatProcessor floatEdm = makeFloatEDM(ip, 0, false);
floatEdm.setMinAndMax(0, 65535. / ONE);
return (ShortProcessor) floatEdm.convertToShort(true);
}
/**
* Computes the geodesic distance function for each pixel in mask, using the given mask. Mask and
* marker should be ImageProcessor the same size and containing float values. The function returns
* a new Float processor the same size as the input, with values greater or equal to zero.
*/
@Override
public FloatProcessor geodesicDistanceMap(ImageProcessor marker, ImageProcessor mask) {
// size of image
width = mask.getWidth();
height = mask.getHeight();
// update mask
this.maskProc = mask;
// create new empty image, and fill it with black
FloatProcessor result = new FloatProcessor(width, height);
result.setValue(0);
result.fill();
// initialize empty image with either 0 (foreground) or Inf (background)
array = result.getFloatArray();
for (int i = 0; i < width; i++) {
for (int j = 0; j < height; j++) {
int val = marker.get(i, j) & 0x00ff;
array[i][j] = val == 0 ? backgroundValue : 0;
}
}
int iter = 0;
do {
modif = false;
// forward iteration
IJ.showStatus("Forward iteration " + iter);
forwardIteration();
// backward iteration
IJ.showStatus("Backward iteration " + iter);
backwardIteration();
// Iterate while pixels have been modified
iter++;
} while (modif);
// Normalize values by the first weight
if (this.normalizeMap) {
for (int i = 0; i < width; i++) {
for (int j = 0; j < height; j++) {
array[i][j] /= this.weights[0];
}
}
}
// Compute max value within the mask
float maxVal = 0;
for (int i = 0; i < width; i++) {
for (int j = 0; j < height; j++) {
if (maskProc.getPixel(i, j) != 0) maxVal = Math.max(maxVal, array[i][j]);
}
}
// update and return resulting Image processor
result.setFloatArray(array);
result.setMinAndMax(0, maxVal);
// Forces the display to non-inverted LUT
if (result.isInvertedLut()) result.invertLut();
return result;
}
/** 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
