Sort_particles.txt

setBatchMode(1);
open(File.openDialog("Open particles file to sort (.tif)"));
title = getTitle();

showStatus("Sorting particles...");
showProgress(0);
max_distance=1000;

selectImage(title);
nresults = getHeight();
nframes = 0;
for (r=round(nresults*0.75);r<nresults;r++)
{
	selectImage(title);
	f = getPixel(13, r)*1000000;
	if (f>nframes) nframes=f;
}

counter = 0;
sorted = newArray(nresults);

first = 0;
last_good_first = 0;
last_good_frame = 0;
for (f=1;f<=nframes;f++)
{
	if (f%100==0)
	{
		p = f/nframes;
		showProgress(p*0.5);
		showStatus("Sorted "+counter+"/"+nresults+" particles... ("+round(p*100)+"% done)");
	}
	if (first-max_distance>0) first = first - max_distance;
	else first = 0;
	
	r=first;
	start=first;
	break = 1;
	last = -1;
	while ((r<nresults) && break)
	{
		selectImage(title);
		if (f==round(getPixel(13,r)*1000000))
		{
			if (first==start)
			{ 
				first = r;
				last_good_first = r;
				last_good_frame = f;
			}
			last=r;
			sorted[counter]=r;
			counter++;
		}
		if ((last!=-1) && (r>(last+max_distance))) break=0;
		else if ((last==-1) && (r>(last_good_first+(f-last_good_frame)*max_distance+max_distance))) break = 0;
		r++;
	}
	if (max_distance<100) max_distance = 100;
	else if (last!=-1) // particles found
		max_distance = round(max_distance * 0.99 + ((last-first)) * 0.01);
	//print(first, last, max_distance);
}

print("Lost particles while sorting: "+(nresults-counter)/nresults*100+"%");
showStatus("Rebuilding particles table...");
copy = "Copy"
newImage(copy, "32-bit Black", 14, counter, 1);
for (r=0;r<counter;r++)
{
	showProgress(r/counter*0.5+0.5);
	for (x=0;x<14;x++)
	{
		selectImage(title);
		v = getPixel(x, sorted[r]);
		selectImage(copy);
		setPixel(x, r, v);
	}
}
showProgress(1);
selectImage(title);
close();
selectImage(copy);
rename(title);
saveAs("tiff");
close();
showStatus("Done...");