macro "Tiff Converter Plus" {
	s = File.separator;

	lsm = false;
	lif = false;
	tree = false;
	
	//DIALOG
	 rows = 3;
 	 columns = 2;
 	 n = rows*columns;
	 labels = newArray("Z-Project","Composite","RGB-Comp","Brightness/contrast(manual)","Scale bar");//,"blank","blank");
 	 defaults = newArray(0,0,0,0,0);
 	 Dialog.create("options");
 	  Dialog.addMessage("-----------------------------------------------------------------------------------");
	 Dialog.addChoice("Which image types should be affected?", newArray(".lsm", ".lif", "both"));
	 Dialog.addChoice("Where should the processed images be saved?", newArray("input = output", "all in one Folder", "copy Tree"));
	 Dialog.addCheckbox("Overwrite already processed Images? (checked for every processing step)", 1)
	 Dialog.addMessage("-----------------------------------------------------------------------------------");
	 Dialog.addMessage("Processing: ");
	 Dialog.addCheckboxGroup(rows,columns,labels,defaults);
	 Dialog.addMessage("-----------------------------------------------------------------------------------");
	 Dialog.addCheckbox("keep Log?", 1);
	 Dialog.addCheckbox("save Log?", 0);
   	 Dialog.show();
 
 	 //DIALOG VALUES
 	 type = Dialog.getChoice();
 	 sav = Dialog.getChoice();
 	 over = Dialog.getCheckbox();
 	 
 	 zpro = Dialog.getCheckbox();
 	 comp = Dialog.getCheckbox();
 	 Rcom = Dialog.getCheckbox();
 	 InCo = Dialog.getCheckbox();
 	 sbar = Dialog.getCheckbox();
 	 //blan = Dialog.getCheckbox();
 	 //bla2 = Dialog.getCheckbox();

   	 lg = Dialog.getCheckbox();
   	 ls = Dialog.getCheckbox();

   	 //Z- PRojection Intensity
   	 if (zpro) {
 	 	 Dialog.create("Z- Projection");
		 Dialog.addChoice("Intensity:", newArray("Max Intensity", "Average Intensity"));
		 Dialog.show();
		 t= Dialog.getChoice();
 		 if (t=="Max Intensity") protype = "projection=[Max Intensity]";
 		 if (t=="Average Intensity") protype = "projection=[Average Intensity]";
   	 }
 	 //SCALE BAR
 	 if (sbar) {
 	 	 Dialog.create("Scale Bar");
 	 	 Dialog.addNumber("Width:", 25);
 	 	 Dialog.addCheckbox("Overlay?", 1);
 	 	 wi= Dialog.getNumber();
 	 	 ov = Dialog.getCheckbox();
 	 	 if (ov) overlay = "overlay";
 	 	 else overlay = "";
 	 	 
 	 }
 	 
 	 dir = getDirectory("Choose a Directory");
 	 
 	 
 	 print("image types: "+type);
 	 print("save Folder: "+sav);
 	 print("Overwrite? "+over);
 	 print("-----Processing-----");
 	 print("Z-Project: "+zpro);
 	 if (zpro) print("Intensity: "+protype);
 	 print("Composite: "+comp);
 	 print("RGB-composite: "+Rcom);
 	 print("Intensitie/Contrast: "+InCo);
 	 print("----------------------------------------");
 	 
 	 if(type==".lsm") lsm = true;
 	 if(type==".lif") lif = true;
 	 if(type=="both"){
 	 	lsm = true;
 	 	lif = true;
 	 }
	if (sav=="all in one Folder") {
		trgt = getDirectory("Choose a target");
	}
	if (sav=="copy Tree") {
		tree = getDirectory("Choose a target for first Folder");
		clean = tree;
	}
	searchFolder(dir,tree);
	if (sav=="copy Tree") {
		print("cleanup");
		cleanup(clean);
	}
	print("All done");
	if (ls) {
		selectWindow("Log");
		getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
		saveAs("Text", dir+s+"Fiji_Log_"+dayOfMonth+"-"+month+1+"-"+year+" Time_"+hour+"-"+minute+"-"+second);
	}
	if (!lg) {
		wait(2000);
		close("Log");	
	}

	
	function searchFolder(directory,tree){
		
		list = getFileList(directory);
		for (i=0; i<list.length;i++) {
			print("checking object: "+list[i]);
			print(i+1+"/"+list.length + " in Folder");
			hilf = (endsWith(list[i],"/")) || (endsWith(list[i],"\\")); //Ist Ordner?
			if (hilf) {
					
				if (sav=="copy Tree") {								//Ordner dem Baum folgend erstellen		
					fname = File.getName(directory+list[i]);
					File.makeDirectory(tree+s+"TIF_"+fname)
					}
				print("Folder: checking contents");
				print("----------------------------------------");
				searchFolder(""+directory+list[i],""+tree+"TIF_"+list[i]);
			}
			else {
				h = (endsWith(list[i],".lsm") && lsm ==true) || (endsWith(list[i],".lif") && lif ==true);
				if (h)  {
					print("opening...");
					if (endsWith(list[i],".lsm")) open(directory+list[i]);
					else {
						file=directory+list[i];
						run("Bio-Formats Windowless Importer", "open=[file]");			//lif dateien werden mit Importer zu den zuletzt verwendeten einstellungen importiert
					}
					print("process...");
					process(directory+list[i]);
					close("*");
					print("----------------------------------------");
			}
				else {
					print("FIle ignored - wrong data type");
					print("----------------------------------------");
				}
		}
			
			
				
			}
	}
	function process(file){
		suffix="";
		if (zpro) {
			
			run("Z Project...", protype);
			if (t== "Max Intensity") suffix = suffix +"_MAX";
			if (t== "Average Intensity") suffix = suffix + "_AVG";
			speichern();
			
			
		}
		if (comp) {
			run("Make Composite");
			suffix = suffix + "_Comp";
			speichern();
		}
		if (InCo){
			run("Brightness/Contrast...");
			//run("Channels Tool...");
			waitForUser("Please adjust brightness and Contrast \n for every Channel and apply before clicking OK");
			//run("Apply LUT");
			close("B&C");
			//close("Channels");
			suffix = suffix + "_br";
			speichern();
		}
		if (Rcom) {
			run("Stack to RGB", "slices keep");
			
			suffix = suffix + "_RGB";
			
			speichern();
		}
		if (sbar) {
				getPixelSize(unit, pw, ph, pd);
				run("Set Scale...","distance="+1/pw+" known=1 pixel=1 unit="+unit);
				run("Scale Bar...","width="+wi+" height=8 font=28 color=White background=None location=[Lower Right] "+overlay);
				suffix = suffix +"_scaleb";
				speichern();
			}
	}
		//SPEICHERN
	function speichern(){
		if(sav == "input = output") {
			if (over) {
				
				saveAs("Tiff",directory+s+File.nameWithoutExtension+suffix);
			}
			else {
				exist = File.exists(directory+s+File.nameWithoutExtension+suffix+".tif");
				print("File exist: "+exist);
				if (exist ==false) {
					saveAs("Tiff",directory+s+File.nameWithoutExtension+suffix);
				}
				else print("file found - not overwritten");
			}		
			
		}
		if(sav == "all in one Folder"){
			if (over) {
				File.makeDirectory(trgt +s+"processed_Tiff_Files");
				saveAs("Tiff",trgt +s+"processed_Tiff_Files"+s+File.nameWithoutExtension+suffix);
			}
			else {
				exist = File.exists(trgt +s+"processed_Tiff_Files"+s+File.nameWithoutExtension+suffix+".tif");
				print("File exist: "+exist);
				if (exist ==false) {
					File.makeDirectory(trgt +s+"processed_Tiff_Files");
					saveAs("Tiff",trgt +s+"processed_Tiff_Files"+s+File.nameWithoutExtension+suffix);
				}
				else print("file found - not overwritten");
			}
		}
		if(sav == "copy Tree"){
			if (over) {
				
				saveAs("Tiff",tree+s+File.nameWithoutExtension+suffix);
			}
			else {
				exist = File.exists(tree+s+File.nameWithoutExtension+suffix+".tif");
				print("File exist: "+exist);
				if (exist ==false) {
					saveAs("Tiff",tree+s+File.nameWithoutExtension+suffix);
				}
				else print("file found - not overwritten");
			}		
			
			
		}
		
		print("image processed");
	}

	function cleanup(start){
		hilf2 = (endsWith(start,"/")) || (endsWith(start,"\\"));
		if (hilf2) {
			print("Ordner");
			list = getFileList(start);
			for (i = 0; i <list.length; i++) { 
				print("lauf: "+i);
				hilf3 = (endsWith(list[i],"/")) || (endsWith(list[i],"\\"));
				if (hilf3) {
					print("neuer durchlauf");
					print(start+list[i]);
					cleanup(start+list[i]);
			}}
			File.delete(start);
		}}