//This macro processes multiple images in a folder, outputting the pseudo wide field (PWF) 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 = getDirectory("Input directory");
output = getDirectory("Output directory");

processFolder(input);

function processFolder(input) {
	list = getFileList(input);
	for (i = 0; i < list.length; i++) {
		input_path = input + File.separator + list[i];
		if(File.isDirectory(input_path)) {
			processFolder(input_path);
		}
		else if(File.isFile(input_path) && matches(list[i], fileRegex)) {
			processFile(input, output, list[i]);
		}
	}
}

function processFile(input, output, file) {
	input_path = input + File.separator + file;
	run("Bio-Formats Importer", "open=input_path open_all_series windowless=true");
	run("Raw SI Data to Pseudo-Widefield", "angles=3 phases=5 intensity rescale");
	output_path = output + File.separator + file;
	saveAs(".tif", output_path);

     while (nImages>0) {
     	selectImage(nImages);
        close();
     }
}