s=File.separator;




Dialog.create("Kymograph Data Management");
Dialog.addCheckbox("Input Directory = Output Directory", true);
items1=newArray("Average Intensity", "Max Intensity", "Min Intensity", "Sum Slices", "Standard Deviation", "Median");
Dialog.addChoice("Projection for ROI:", items1, "Max Intensity");
Dialog.show();

inDisOutD=Dialog.getCheckbox();
Projection=Dialog.getChoice();

inDir=getDirectory("Choose the Raw Data Containing Folder");

if (inDisOutD==true) {
	outDir=inDir;
}
else {
	outDir=getDirectory("Choose Output Folder");
	if ((inDir==outDir) || (startsWith(outDir, inDir))) {
	exit("Input folder must be different from and not within output folder!");
	}
}

inDir1=inDir;
setBatchMode(true);

ProjectionOfLoops(outDir);

setBatchMode(false);

print("Done!");


function ProjectionOfLoops(outDir) {
	list = getFileList(outDir);
	for (i=0; i<list.length; i++) {
		if (endsWith(list[i], "/")) {
			ProjectionOfLoops(outDir+list[i]);	
		}
		else if ((endsWith(list[i], "_Stack_Extr.tif"))&&(!File.exists(replace(outDir+s+list[i], "_Stack_Extr.tif", "_LoopProj.tif")))) {
			open(outDir+list[i]);
			name=File.getName(outDir+list[i]);
			selectWindow(name);
			run("Z Project...", "projection=["+Projection+"] all");
			saveAs("tiff", replace(outDir+s+list[i], "_Stack_Extr.tif", "_LoopProj.zip"));  			  			
     		run("Close All");
     		run("Collect Garbage");
		
		}
	}
}