#@ File (label = "Input directory", style = "directory") input
#@ File (label = "Output directory", style = "directory") output
#@ String (label = "File suffix", value = ".jpg") suffix

//-- initialise a counting variable with which to output the files
count=1;
zeroPad=4;
setBatchMode(true);
processFolder(input);

// function to scan folders/subfolders/files to find files with correct suffix
function processFolder(input) {
	list = getFileList(input);
	list = Array.sort(list);
	for (i = 0; i < list.length; i++) {
		if(endsWith(list[i], suffix))
			processFile(input, output, list[i]);
	}
}

function processFile(input, output, file) {
	print("Processing: " + input + File.separator + file);
	open(input + File.separator + file);
	saveAs("jpeg", output+File.separator+IJ.pad(count,zeroPad));
	count++	;
	print("Saving to: " + output);
	close("*");
}