/*
 * IJ script to pull measurements from an Ilastik Simple Segmentation Output with 3 labels
 */

#@ File (label = "Input directory", style = "directory") input
#@ String (label = "File suffix", value = "Segmentation.tif") suffix

//-- pre
setBatchMode(true);
run("Clear Results");
saveSettings();
run("Set Measurements...", "area limit display redirect=None decimal=0");

//-- run
processFolder(input);

//-- post
restoreSettings();
print("done");


function processFolder(input) {
	list = getFileList(input);
	list = Array.sort(list);
	for (i = 0; i < list.length; i++) {
		if(endsWith(list[i], suffix))
			processFile(input, list[i]);
	}
}

function processFile(input, file) {
print("Processing: " + input + File.separator + file);
open(input + File.separator + file);

for (labels=1;labels<4;labels++){
setThreshold(labels, labels);
run("Measure");
}
resetThreshold();
close("*");
}