s=File.separator;




Dialog.create("Kymograph Data Management");
Dialog.addCheckbox("Input Directory = Output Directory", true);
Dialog.addMessage("Quantification Parameters:");
Dialog.addNumber("n of Stationary ---", 2);
Dialog.addNumber("n of Anteriograde -->", 2);
Dialog.addNumber("n of Retrograde <--", 2);
//Dialog.addMessage("Video Propperties:");
//Dialog.addNumber("Pixelsize [um]", 5);
//Dialog.addNumber("Framerate [Hz]/fps", 5);
Dialog.show();

inDisOutD=Dialog.getCheckbox();
nStat=Dialog.getNumber();
nAnterio=Dialog.getNumber();
nRetro=Dialog.getNumber();
//PixSize=Dialog.getNumber();
//Framerate=Dialog.getNumber();

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);

KymoAnalysis(outDir);

//setBatchMode(false);

print("Done!");


function KymoAnalysis(outDir) {
	list = getFileList(outDir);
	for (i=0; i<list.length; i++) {
		if (endsWith(list[i], "/")) {
			KymoAnalysis(outDir+list[i]);	
		}
		else if ((endsWith(list[i], "_Kymo.tif"))&&(!File.exists(replace(outDir+s+list[i], "_Kymo.tif", "_Measurements.csv")))) {
			open(outDir+list[i]);
			name=File.getName(outDir+list[i]);
			selectWindow(name);
			setTool("line");
			run("ROI Manager...");
			roiManager("Show All");
			selectWindow(name);
			nLines=roiManager("count");
			do {
				waitForUser("Axonal Transport Analysis", "Draw "+nStat+" indepentent lines on Stationary Vesicles and add them to the ROI manager");
				roiManager("add");
				nLines=roiManager("count");
				roiManager("select", (nLines-1));
				roiManager("rename", "Stationary "+nLines);
			} while (nLines<nStat);
			do {
				waitForUser("Axonal Transport Analysis", "Draw "+nAnterio+" indepentent lines on Anteriograde Transported Vesicles and add them to the ROI manager");
				roiManager("add");
				nLines=roiManager("count"); 
				roiManager("select", (nLines-1));
				roiManager("rename", "Retrograde "+(nLines-nStat));	
			} while (nLines<(nStat+nAnterio));
			do {
				waitForUser("Axonal Transport Analysis", "Draw "+nAnterio+" indepentent lines on Retrograde Transported Vesicles and add them to the ROI manager");
				roiManager("add");
				nLines=roiManager("count"); 
				roiManager("select", (nLines-1));
				roiManager("rename", "Anteriograde "+(nLines-nStat-nAnterio));	
			} while (nLines<(nStat+nAnterio+nRetro));
			roiManager("List");
			selectWindow("Overlay Elements"); 
			saveAs("Results", replace(outDir+s+list[i], "_Kymo.tif", "_Measurements.csv"));
			roiManager("Select", newArray(0,(nLines-1)));
			roiManager("Save", replace(outDir+s+list[i], "_Kymo.tif", "_Lines.zip"));	
			roiManager("reset")
			close(replace(list[i], "_Kymo.tif", "_Measurements.csv"));			  			
     		run("Close All");
     		run("Collect Garbage");	
		}
	}
}