void doIterations(ImageProcessor ip, String mode) {
if (escapePressed) return;
if (!previewing && iterations > 1) IJ.showStatus(arg + "... press ESC to cancel");
for (int i = 0; i < iterations; i++) {
if (Thread.currentThread().isInterrupted()) return;
if (IJ.escapePressed()) {
escapePressed = true;
ip.reset();
return;
}
if (mode.equals("erode")) ((ByteProcessor) ip).erode(count, background);
else ((ByteProcessor) ip).dilate(count, background);
}
}
// Particle finding routine based on spots enhancement with
// 2D PSF Gaussian approximated convolution/backgrounds subtraction, thresholding
// and particle filtering
void detectParticles(
ImageProcessor ip, SMLDialog fdg, int nFrame, Overlay SpotsPositions_, Roi RoiActive_) {
int nThreshold;
FloatProcessor dupip = null; // duplicate of image
ImageProcessor dushort; // duplicate of image
ByteProcessor dubyte = null; // tresholded image
TypeConverter tc;
dupip = (FloatProcessor) ip.duplicate().convertToFloat();
SMLblur1Direction(
dupip, fdg.dPSFsigma * 0.5, 0.0002, true, (int) Math.ceil(5 * fdg.dPSFsigma * 0.5));
SMLblur1Direction(dupip, fdg.dPSFsigma * 0.5, 0.0002, false, 0);
// new ImagePlus("gassconvoluted", dupip.convertToFloat().duplicate()).show();
// low-pass filtering by gaussian blurring
// lowpassGauss.blurGaussian(dupip, fdg.dPSFsigma*0.5, fdg.dPSFsigma*0.5, 0.0002);
// convolution with gaussian PSF kernel
SMLconvolveFloat(dupip, fConKernel, fdg.nKernelSize, fdg.nKernelSize);
// new ImagePlus("convoluted", dupip.duplicate()).show();
tc = new TypeConverter(dupip, true);
dushort = tc.convertToShort();
// new ImagePlus("convoluted", dushort.duplicate()).show();
// thresholding
// old straightforward thresholding
// imgstat = ImageStatistics.getStatistics(dupip, 22, null); //6 means MEAN + STD_DEV, look at
// ij.measure.Measurements
// nThreshold = (int)(imgstat.mean + 3.0*imgstat.stdDev);
// new smart thresholding
nThreshold = getThreshold(dushort);
dushort.threshold(nThreshold);
// convert to byte
dubyte = (ByteProcessor) dushort.convertToByte(false);
// new ImagePlus("threshold", dubyte.duplicate()).show();
// morphological operations on thresholded image
// dubyte.dilate(2, 0);
// dubyte.erode(2, 0);
// cleaning up image a bit
if (fdg.nKernelSize > 3) {
dubyte.dilate();
// new ImagePlus("dilated", dubyte.duplicate()).show();
dubyte.erode();
// new ImagePlus("erosion", dubyte.duplicate()).show();
}
// dupip.invert();
labelParticles(
dubyte,
ip,
nFrame,
fdg.dPixelSize,
fdg.nAreaCut,
fdg.dPSFsigma,
SpotsPositions_,
fdg.bShowParticles,
RoiActive_); // , fdg.bIgnoreFP);//, fdg.dSymmetry/100);
}