//Teil unter Schleife der Reference Funktion wird zu oft aufgerufen
//Bessere Unterteilung benötigt
//
macro "NEW_Segmentaion" {
	s = File.separator;
	count = 0;
	zahl = 1;
	Ritems = newArray("multiple KCs","single KC");

	Dialog.create("Segmentation");
	Dialog.addRadioButtonGroup("", Ritems, 1, 2, "multiple KCs")
	//Dialog.addCheckbox("Input Directory = Output Directory", true);
	Dialog.addMessage("Extract Mean Gray Values from ROI:");
	items = newArray("_C2_Reg","_C1_Reg","_C2_to_C1_Reg_C2_Spl","_C2_to_C1_Reg_C1_Spl","_C1_to_C2_Reg_C2_Spl","_C1_to_C2_Reg_C1_Spl","_Stack_Extr_C2_Spl","_Stack_Extr_C1_Spl");
	Dialog.addChoice("Extract From:", items, "_C2_to_C1_Reg_C2_Spl");
	items1 = newArray("Maximum Intensity", "Average Intensity");
	Dialog.addChoice("Projection for ROI:", items1, "Average Intensity");
	Dialog.addSlider("ROI diameter", 2, 16, 8);
	Dialog.addCheckbox("Search active Cells in Reference?", 1);
	//Dialog.addMessage("Delete Files:");
	Dialog.show();
	KC = Dialog.getRadioButton();
	//inDisOutD=Dialog.getCheckbox();
	ExtrFrom=Dialog.getChoice();
	Projection=Dialog.getChoice();
	GR = Dialog.getNumber();
	red = Dialog.getCheckbox();
	if (red) {
		Dialog.create("Red Reference");

		items=newArray("Stack_Extr", "C2_to_C1_Reg", "C1_to_C2_Reg");
		Dialog.addChoice("", items, "C1_Reg.tif");
		items = newArray("C1", "C2");
		Dialog.addMessage("Which Channel is Reference?");
		Dialog.addRadioButtonGroup("", items, 1, 2, "C2");
		Dialog.addSlider("Active Tolerance", 2, 16, 8);
		Dialog.show();
		ExtrFrom2 = Dialog.getChoice();
		keep = Dialog.getRadioButton();
		T = Dialog.getNumber();
	}

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

	inDisOutD=true;
	outDir=inDir;
	/*
	if (red) {
		SchActive = Reference(inDir);
		//print(SchActive);
		//array.show(SchActive);
	}
	
	else {
		Active = false;
	
	}
*/
	if (KC == "single KC") {
	MeanGrayValueExtraction(inDir);
	}
	else {
		//install
		multipleKCSegmentation(inDir);
	}
	close("Results");
	close("ROI Manager");
	function MeanGrayValueExtraction(inDir) {
	list = getFileList(inDir);
	for (i=0; i<list.length; i++) {
		if (endsWith(list[i], "/")) {
			MeanGrayValueExtraction(inDir+list[i]);	
		}
		else if ((endsWith(list[i], ExtrFrom+".tif"))&&(!File.exists(replace(outDir+s+list[i], ExtrFrom+".tif", ExtrFrom+"_RoiSet.zip")))) {
			open(inDir+list[i]);
			name=File.getName(inDir+list[i]);
			selectWindow(name);
			run("Z Project...", "projection=["+Projection+"]");
			//selectWindow("AVG_"+name);
			run("Duplicate...", "title=Mask");
			selectWindow("Mask");
			run("Make Binary");
			setTool("wand");
			run("ROI Manager...");
			
			waitForUser("Select the Cell/ROI please");
			
			roiManager("Add");
			roiManager("Select", 0);
			roiManager("Rename", "Cell");
			run("Make Inverse");
			roiManager("Add");
			roiManager("Select", 1);
			roiManager("Rename", "Background");
			roiManager("Select", newArray(0,1));
			roiManager("Save", inDir+s+File.nameWithoutExtension+"_Roiset.zip");//replace(inDir+s+list[i], ExtrFrom+".tif", ExtrFrom+"_RoiSet.zip"));						
			selectWindow(name);
			close(name);
			close("Results");
			roiManager("Select", newArray(0,1));
			roiManager("Delete");
			run("Close");
		run("Close All");
		
		}
	}
}
	
	function multipleKCSegmentation(inDir) {
		
		list = getFileList(inDir);
		for (i=0; i<list.length; i++) {
		
		ex = replace(list[i], "^..?_","");
		
	//	ex2 = replace(ex, "_~_.*_.*"+ExtrFrom+".tif", "_RoiSet.zip");
		ex2 = replace(ex, "_~_.*_.*"+ExtrFrom+".tif", "_RoiSet.zip");
		//print(ExtrFrom);
		//print(ex2);
		
		
		
		hilf=(File.exists(inDir+ex2));
		hilf2 = (endsWith(list[i],ExtrFrom+".tif"));
		//print("File exists?: "+hilf);
		//print("endet mit "+ExtrFrom+".tif :"+hilf2);
		if (endsWith(list[i], "/")) {
			multipleKCSegmentation(inDir+list[i]);
		}
		else if ((endsWith(list[i], ExtrFrom+".tif"))&&(!File.exists(inDir+ex2))) {
			if (red) {
			Active = Reference(inDir);
			}
			count++;
			//File.makeDirectory(outDir+s+"Test");
			open(inDir+list[i]);
			name=File.getName(inDir+list[i]);
			selectWindow(name);					//Background first
			run("Z Project...", "projection=["+Projection+"]");
			run("Duplicate...", "title=Enhanced_Contrast");
			selectWindow("Enhanced_Contrast");		
			run("Enhance Contrast", "saturated=2.00");
			close("\\Others");
			//run("Duplicate...", "title=Background");
			//run("Options...", "iterations=50 count=4 do=Nothing");
			//run("Make Binary");
			run("In [+]");
			run("In [+]");
			setTool("freehand");
			makeRectangle(0, 0, 0, 0);
			while (selectionType() == -1) {
				waitForUser("Outline non- Background");
			}
			
			run("Make Inverse");
			roiManager("add");
			roiManager("select", 0);
			roiManager("rename", "Background");
			makeRectangle(1, 1, 0, 0);
			roiManager("deselect");
			

			
			
			selectWindow("Enhanced_Contrast");		
			
			setTool("Seg Tool");
			//setTool("multipoint");
			waitForUser("Click on the Cells");
			z = roiManager("count");
			//wait(3000);
			for (c = 1; c < z; c++) {
				roiManager("select", c);
				//wait(3000);
			//	run("Set Measurements...", "stack redirect=None decimal=3");
				run("Set Measurements...", "area mean standard modal min centroid center perimeter bounding fit shape feret's integrated median skewness kurtosis area_fraction stack redirect=None decimal=3");
				roiManager("measure");
				//wait(5000);
				x = getResult("X", 0);
				y = getResult("Y", 0);
				makeOval(x-(GR/2), y-(GR/2), GR, GR);
				//wait(3000);
				roiManager("add & draw");
				//wait(3000);
				close("Results");
				
			}
			for (c = 1; c < z; c++) {
				print("Delete");
				print(c);
				print(roiManager("count"));
				print("-----------------");
				roiManager("select", 1);
				//wait(3000);
				roiManager("delete");
				//wait(3000);
			}
			for (c = 1; c < z; c++) {
				close("Results");
				print("Rename");
				act = false;
				print("Begin: "+act);
				print("c: "+c);
				print("Count: "+roiManager("count"));
				roiManager("select", c);
				//wait(3000);
				
				if (red) {
				roiManager("measure");
				x = getResult("X", 0);
				y = getResult("Y", 0);
				print("x:  "+x+"     y:  "+y);
				
				//if (ActiveX.length>0) {
				//for (k = 0; k < L; k++){
				
					ActiveX = Array.slice(Active,0,Active.length/2);
					ActiveY = Array.slice(Active,Active.length/2,Active.length);
					for (k = 0; k < ActiveX.length; k++) {
					print("k: "+k);
					print("ActiveX: "+ActiveX[k]+"x: "+x);
					print((ActiveX[k]-x)+"        "+(ActiveY[k]-y));
					hilfX = abs(ActiveX[k]-x) < 6;
					hilfY = abs(ActiveY[k] -y) < 6;
					print("hilfX:  "+hilfX+"  hilfY:  "+hilfY);
					if ((abs(ActiveX[k]-x)< T+1) && (abs(ActiveY[k] -y)<T+1))   {
						act = true;
						print("IF :"+act);
						}
					
					}
					print("Act: "+act);
					if (act) {
						roiManager("rename", "Cell"+c+" ~CAMEL");
					}else {
						roiManager("rename","Cell"+c );
					}
				}else {
					roiManager("rename","Cell"+c );
				}
				
			}
			if (red) {
				setColor(255, 0, 255);
					for (o = 0; o < ActiveX.length; o++) {
						xDraw = ActiveX[o];
						yDraw = ActiveY[o];
						for (u = -T; u <= T ; u++) {
							makePoint(xDraw+u, yDraw, "small yellow dot");
							fill();
							makePoint(xDraw, yDraw+u, "small yellow dot");
							fill();
							
						}}
					waitForUser("Check Rois");
				}
				//roiManager("rename", "Cell"+c);
				//wait(3000);
			//}
			roisave= replace(File.nameWithoutExtension, "_~_.*_.*"+ExtrFrom, "")+"_RoiSet.zip";
			roisave= replace(roisave,"^..?_","");
			roiManager("Save", inDir+s+roisave);
			print("Once");
			zahl = 1;
			close("*");
			roiManager("reset");
			
			
			
			
			
			
			
			
			
		}
		if ((File.exists(inDir+ex2)))//&&(zahl<19)) {
			//roicheck= replace(File.nameWithoutExtension, "_~_.*_.*"+ExtrFrom, "")+"_RoiSet.zip";
			//roicheck= replace(roicheck,"^..?_","");
			if (endsWith(list[i], ExtrFrom+".tif")) {
				suf = replace(list[i], ".tif", "");
				print(zahl);
				zahl++;
				File.copy(inDir+s+ex2,inDir+s+suf+"_RoiSet.zip");
				//print("Probe: "+inDir+s+ex2,inDir+s+suf+"_RoiSet.zip");
				print(inDir+s+suf+"_RoiSet.zip");
			}
		}
		




				
	}
	function Reference(inDir) {
	Weiter = false;
	print("Reference started");
	list = getFileList(inDir);
	for (i=0; i<list.length; i++) {
		if ((endsWith(list[i], ExtrFrom2+".tif"))&&(!File.exists(replace(inDir+s+list[i], ExtrFrom2, ExtrFrom2+"_"+keep+"_Spl.tif")))) {
				Reference2(inDir);
				Weiter = true;
				print("HIE§");
		}}
				
					if (Weiter) {
					print("Testestestestestes");
					run("Images to Stack", "name=Teststack title=C2");
					print("Teststack");
					selectWindow("Teststack");
					print("Teststack 2");
					close("\\Others");
					print("Teststack 3");
					setTool("Seg Tool");
					print("Teststack 4");
					waitForUser("Select active Cells");
					print("Teststack 5");
					//savepath = inDir+name+"_MeanGrayReference.csv";
					//saveAs("Results", savepath);
					L = roiManager("count");
					print("Teststack 6");
					ActiveX = newArray( L );
					print("Teststack 7");
					ActiveY = newArray( L );
					print("Teststack 8");	
					for (l = 0; l < roiManager("count"); l++) {
						roiManager("select", l);
						print("Teststack iteration 1");
						roiManager("rename", "CAMEL"+l+1);
						roiManager("measure");
						print("Teststack iteration 2");
						ActiveX[l] = getResult("X",l);
						ActiveY[l] = getResult("Y",l);
					}
					
					print("Teststack ende");
					//roiManager("reset");
					Active2 = newArray(0);
					print("");
					Active2  = Array.concat(Active2,ActiveX);
					print("");
					Active2  = Array.concat(Active2,ActiveY);
					//Array.show(Active);
					print("");
					print("Returned");
					Weiter = false;
					close("ROI Manager");
					close("Results");
					Active3 = newArray(1,2,3,4,5,6);
					//Array.show(Active2);
					return Active2;
					}
					}
function Reference2(inDir) {
				open(inDir+list[i]);
				name=File.getName(inDir+list[i]);
				selectWindow(name);
				run("Split Channels");
				selectWindow(keep+"-"+name);
				//close();
				for (t = 0; t < list.length; t++) {
					hilf = (startsWith(list[t],substring(list[i], 0, 1))) && (endsWith(list[t],"RoiSet.zip"));
					//print(hilf);
					if (hilf)  {
						filepath = inDir+list[t];
						//print(filepath);
						print("Weiter:  "+Weiter);
				}}
				
				//roiManager("open", filepath);
				
				
				run("Z Project...", "projection=[Average Intensity]");
				run("Enhance Contrast", "saturated=1.00");
				//close("\\Others");
				//run("In [+]");
				//run("In [+]");
				//roiManager("show all with labels");
				//setTool("rectangle");
				
				//waitForUser("Check ROIs");
				//selectWindow("AVG_"+keep+"-"+name);
				
				
					
					
				
				//roiManager("Multi Measure");
				//roiManager("reset");
				//selectWindow("Results");
				//savepath = inDir+name+"_MeanGrayReference.csv";
				//saveAs("Results", savepath);			
				//close("Results");
				//close("*");
				
		}}