// Batch processing of ROIs, frontloaded
// Build arrays of files tabulated 
//====================================

// Get file directory from user input
dir = getDirectory("Navigate to the folder to be processed");
print("STARTING file extraction: "+dir);

filelist = getFileList(dir);
Array.show(filelist);

// Loop through each folder in the parent directory

//for (i = 0; i < 1; i++) {			// for debugging one folder at a time
for (i = 0; i < filelist.length; i++) {
    // only open folders, not files in the parent direcory
    if (endsWith(filelist[i], "/")) {  
    	
		// List image files in sub folder
		sublist = getFileList(filelist[i]);				 
		firsttif = dir+filelist[i]+"ChanA_001_001_001_001.tif";
		
		// If folder has images in it, 
		if (File.exists(firsttif)) {
			// Import image using Bioformats to preserve metadata. 
			// Uses virtual stacks for speed and RAM, especially on server
			run("Bio-Formats Importer", "open=[&firsttif] color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT use_virtual_stack");

			// Rename all of the files once imported (assumes MANTIS)
			runMacro("SicLab_imgrename_ext.ijm");
			
			// Save in parent directory and close all of the images
			wins = getList("image.titles");
			
			// DO PROCESSING IN HERE
			for (j = 0; j < wins.length; j++) {
				selectWindow(wins[j]);
				//save(dir+wins[j]+".tif");
				n_avg = 50;
				run("Z Project...", "stop=&n_avg projection=[Average Intensity]");
				avgip = getTitle(); 
				run("Enhance Contrast", "saturated=0.35");
				save(dir+wins[0]+"_avgip.tif");
				
			// Step 2: Prompt user for ROIs
				setTool("ellipse");
				waitForUser("Draw ROIs on image. Press 'T' to add them to the ROI manager");
				
				roiManager("show all with labels");
				roiManager("save", dir+"\\"+wins[0]+"_roi.zip");
				
			// Close out of window
				close("*");
			}
			// Print progress once images are extracted
			print(filelist[i]+" COMPLETE");
		} // end of 'file exist' if stmt

    } // end of title folder if statment
   
} // end of image folder for loop
print(dir+" COMPLETE");