//This macro processes multiple images in a folder, outputting the maximum intensity projections of SIM data to the same or a different folder
//Created by Dr Chidinma Okolo and Thomas Fish
//Diamond Light Source, UK
fileRegex = "^\\d{14}[_\\w\\d]+FL$";

input_directory = getDirectory("Input directory");
output_directory = getDirectory("Output directory");

processFolder(input_directory, output_directory);

function processFolder(input_directory, output_directory) {

	save_images = getBoolean("Do you wish to save the output images?", "Save", "Don't save");
	display_images = getBoolean("Do you wish to display all images after exiting", "Yes", "No");

	file_list = getFileList(input_directory);
	for (i = 0; i < file_list.length; i++) {
		input_path = input_directory + File.separator + file_list[i];
		if(File.isDirectory(input_path)) {
			processFolder(input_path);
		}
		else if(File.isFile(input_path) && matches(list[i], fileRegex)) {
			openFile(input_directory, file_list[i]);
			processFile(file_list[i]);
			if(save_images) {
				saveFile(output_directory, file_list[i]);
			}
		}
	}
	if(display_images) {
		displayFiles(file_list);
	}
	else {
		closeFiles(file_list);
	}
}

function openFile(intput_directory, file_name) {
	input_path = input + File.separator + file;
	run("Bio-Formats Importer", "open=input_path open_all_series windowless=true");
}

function processFile(input, output, file) {
	run("Z Project...", "projection=[Max Intensity]");

}

function saveFile(output, filename) {
	output_path = output + File.separator + file + "_max_intensity_proj";
	saveAs(".tiff", output_path);
}

function displayFiles(file_list) {
	for (i = 0; i < file_list.length; i++) {
		selectWindow(file_list[i]);
		run("Enhance Contrast", "saturated=0.35");
	}
	run("Tile");
}

function closeFiles(file_list) {
	for (i = 0; i < file_list.length; i++) {
		close(file_list[i]);
	}
}