s=File.separator;




Dialog.create("Bruker Data Manager");
//Dialog.addCheckbox("Input Directory = Output Directory", true);
Dialog.addMessage("Extract Mean Gray Values from ROI:");
items=newArray("_C2_Reg", "_C2_to_C1_Reg_C2_Spl", "_BSub");
Dialog.addChoice("Extract From:", items, "_BSub");

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(outDir);

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(inDir+s+list[i], ExtrFrom+".tif", ExtrFrom+"_MeanGray.csv")))) {
			open(inDir+list[i]);
			name=File.nameWithoutExtension;
			selectWindow(name+".tif");
			roiManager("Open", replace(inDir+s+list[i], ExtrFrom+".tif", "_RoiSet.zip"));
			indexes = newArray(roiManager("count")-1);
			for (k = 1; k < roiManager("count"); k++) {
				indexes[k-1] = k;
			}
				//n = getInfo("roi.name");
				//setResult(t, i, t);
			roiManager("select", indexes);
				//roiManager("Select", i);
			roiManager("Multi Measure");
			selectWindow("Results");
			if (inDisOutD==true) savepath = inDir+name+"_MeanGray.csv";
			else savepath = outDir+name+"_MeanGray.csv";
			saveAs("Results", savepath);			
			close("Results");
			//roiManager("Select", 0);
			//roiManager("Delete");
			//roiManager("Select", 0);
			//roiManager("Delete");
			close(name);
			run("Close");
		run("Close All");
		
		}
	}
}