BATCH_Select_area_calculate_fraction

//Tested using ImageJ 1.53c
//Opens images and ask user to select ROIs, save area of ROIs and calculate area fraction for each. saves image and results

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

run("Set Measurements...", "area area_fraction redirect=None decimal=6");
processFolder(input);


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

function processFile(input, output, file) {
	open(input+File.separator+list[i]);
	
	
	
	
	//******User varialbes
	rolling_ball = 50;
	gaussian = 2;
	lower_threshold = 60;
	
	//Get image properties
	run("Z Project...", "projection=[Max Intensity]");
	title = getTitle();
	noEXT = File.nameWithoutExtension;
	

	run("Split Channels");
	run("Merge Channels...", "c2=[C2-"+title+"] c3=[C1-"+title+"] create ignore");
	rename(title);
	
	
	//*****Filters
	//Add two slacshes before a filter if you dont want to use it
	run("Gaussian Blur...", "sigma="+gaussian);
	run("Subtract Background...", "rolling="+rolling_ball);
	//Save Filtered Image
	selectImage(title);
	saveAs("tiff", output+File.separator+noEXT+"_FLT.tiff");
	
	//loop over the ROI selection
	calculate=false;
	while (calculate==false) {
		ROISelector(lower_threshold);
		
		Dialog.createNonBlocking("Controls");
		Options = newArray("Make another ROI", "Next Image");
		Dialog.addRadioButtonGroup("Options", Options, 2, 1, "Make another ROI");
		Dialog.show();
		
		next = Dialog.getRadioButton;
	
		row = nResults-1;
		setResult("Cell", row, noEXT);
			
		if (next=="Make another ROI") {
			
		}
		if (next=="Next Image") {
			calculate = true;
			close("*");
			updateResults();
		}
		
	
		
		
	}
	
	saveAs("Results", output+File.separator+"Results.csv");
	
	
	
	//ROI Selection function
	function ROISelector(lower_threshold) { 
		run("Select None");
		waitForUser("Select ROI. Press OK after selection");
		isSelection=is("area");
		if (isSelection==false) {
			run("Select All");
		}
		setOption("BlackBackground", true);
		Stack.setChannel(1);
		run("Duplicate...", "title=ROI_area");
		
		getStatistics(area, mean, min, max, std, histogram);
	  	setThreshold(lower_threshold, max);
		run("Measure");
		close();
		selectImage(noEXT+"_FLT.tiff");
		

	}

}