s=File.separator;




Dialog.create("Kymograph Data Management");
Dialog.addCheckbox("Input Directory = Output Directory", true);
items1=newArray("Average", "Median", "Min", "Max", "Sum");
Dialog.addChoice("Projection of Timepoints to Line:", items1, "Average");
items2=newArray("_Ch1Spl.tif", "_Ch2Spl.tif", "_OneCh_Reg.tif", "_LoopProj.tif", "_Stack_Extr.tif");
Dialog.addChoice("Create Kymograph From:", items2, "Ch1Spl.tif");
Dialog.show();

inDisOutD=Dialog.getCheckbox();
Method=Dialog.getChoice();
KymoFrom=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);

SplitChannels(outDir);

setBatchMode(false);

print("Done!");


function SplitChannels(outDir) {
	list = getFileList(outDir);
	for (i=0; i<list.length; i++) {
		if (endsWith(list[i], "/")) {
			SplitChannels(outDir+list[i]);	
		}
		else if ((endsWith(list[i], KymoFrom))&&(!File.exists(replace(outDir+s+list[i], KymoFrom, KymoFrom+"_Kymo.tif")))) {
			open(outDir+list[i]);
			name=File.getName(outDir+list[i]);
			selectWindow(name);
			nSlc=nSlices;
			height=getHeight();
			run("Bin...", "x=1 y="+height+" z=1 bin="+Method+"");
			
			for (j=1; j<nSlc; j++) {
				if (j==1) {
					selectWindow(name);
					setSlice(j);
					run("Duplicate...", "title="+j+"");
				}
				else if (j==2) {
					selectWindow(name);
					setSlice(j);
					run("Duplicate...", "title="+j+"");
					run("Combine...", "stack1=["+j-1+"] stack2=["+j+"] combine");
				}
				else {
					selectWindow(name);
					setSlice(j);
					run("Duplicate...", "title="+j+"");
					run("Combine...", "stack1=[Combined Stacks] stack2=["+j+"] combine");
				}
			}
			
			selectWindow("Combined Stacks");
			resetMinAndMax();			
			saveAs("tiff", replace(outDir+s+list[i], KymoFrom, KymoFrom+"_Kymo.tif"));			  			
     		run("Close All");
     		run("Collect Garbage");		
		}
	}
}