s=File.separator;




Dialog.create("Bruker Data Manager");
//Dialog.addCheckbox("Input Directory = Output Directory", true);
Dialog.addMessage("Substract Background From:");
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");

Dialog.show();

//inDisOutD=Dialog.getCheckbox();
ExtrFrom=Dialog.getChoice();

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

inDisOutD=true;
outDir=inDir;



inDir1=inDir;


//setBatchMode(true);
MeanGrayValueExtraction(inDir);
//setBatchMode(false);


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+"_BSub.tif")))) {
			open(inDir+list[i]);
			name=File.nameWithoutExtension;
			selectWindow(name+".tif");
			N=nSlices;
			
			ex = replace(list[i], "^..?_","");
			ex2 = replace(ex, "_~_.*_.*"+ExtrFrom+".tif", "_RoiSet.zip");
			
			roiManager("Open", inDir+ex2);//replace(inDir+s+list[i], ExtrFrom+".tif", "_RoiSet.zip"));
			
			roiManager("Select", 0);
			run("Set Measurements...", "area mean feret's redirect=None decimal=3");
			roiManager("Multi Measure");
			
			roiManager("Delete");
			
			selectWindow(name+".tif");
			
			for (k=1; k<=N; k++) {
				
				Background=getResult("Mean(Background)", k-1);
				Stack.setSlice(k);
				run("Subtract...", "value="+Background+" slice");
				}
			
			roiManager("Delete");	
						
			selectWindow(name+".tif");
			if (inDisOutD==true) savepath = inDir+name+"_BSub.tif";
			else savepath = outDir+name+"_BSub.tif";
			saveAs("Tiff", savepath);
			
			close(name);
			//roiManager("Select", 0);
			//roiManager("Delete");
			close("Results");
			run("Close");
		run("Close All");		
		}
	}
}