/* Process_Folder_IJM.ijm
 * IJ BAR snippet https://github.com/tferr/Scripts/tree/master/Snippets
 *
 * This macro implements a a reusable batch processor[1] that processes a folder
 * of files of a certain type. It is a more flexible alternative to the IJ1
 * Process>Batch>Macro built-in command.
 *
 * It is composed of four functions:
 *   1. getOutputDirectory(): Sets a destination folder to save processed images
 *   2. validExtension(): Determines which file extension(s) should be processed
 *   3. processFiles(): Applies myRoutines() to each individual image
 *      (Processed images are save as TIFF in output directory)
 *   4. myRoutines(): Container to hold the image processing routines
 *      (In this example, it randomizes the image name to allow blind analysis)
 *
 * Because all the tasks required to iterate through the files are handled by
 * separated functions, only the myRoutines() function needs to be edited, e.g.,
 * with code generated by the Macro Recorder. It can also call macros and scripts
 * saved elsewhere (see http://fiji.sc/BAR#ProcessingFunction)
 *
 * Resources
 * [1] http://fiji.sc/BAR#Batch_Processors
 * https://github.com/tferr/Scripts/tree/master/Snippets#batch-processors
 * https://github.com/tferr/Scripts/tree/master/Snippets#imagej-macro-language
 * http://rsb.info.nih.gov/ij/macros/BatchProcessFolders.txt
 */


// Define input directory
inputDir = getDirectory("Select a source directory");

// Create output directory
outputDir = getOutputDirectory(inputDir);

// Iterate through inputDir (ignoring files with non-specified
// extensions) and save a copy of processed images in outputDir
processFiles(inputDir, outputDir);

// Proudly inform that all the processing is done
if (getBoolean("All done! Reveal output directory?"))
    call("bar.Utils.revealFile", outputDir);


/*
 * This function defines the image manipulation routines. In this example, it
 * renames the active image using a random string. Note that we do not need to
 * worry about opening, closing and saving the image as .tif without overriding
 * the original file. Those operations are already performed by <processFiles()>.
 */
function myRoutines() {

	// We'll first define a new function that generates a random
	// string. See http://fiji.sc/BAR#IJ_Macro_Language for details
	function randomString(length, spacers) {
		template = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ";
		nChars = lengthOf(template);
		string = "";
		for (i=0; i<length; i++) {
			idx = maxOf(0, round(random()*nChars-1));
			string += substring(template, idx, idx+1);
			if (spacers && i%5==0) string += "_";
		}
		return string;
	}

	// Since we'll be logging filename changes to the Results table, we
	// need to keep track of the table's measurement counter. We'll assume
	// that the Results table was closed when myroutines() was first called
	availableRow = maxOf(0, nResults);

	// Log original filename before changing it
	setResult("Original filename", availableRow, getTitle());

	// Rename image and log changes
	rename(randomString(20, true));
	setResult("Randomized filename", availableRow, getTitle());
}

/*
 * This function retrieves the full path to a '_Processed' folder placed at the
 * same location of <input_dir>. For safety, the macro is aborted if <input_dir>
 * is not accessible or if the directory cannot be created, e.g., due to lack of
 * appropriate credentials. It does nothing if such a directory already exists.
 */
function getOutputDirectory(input_dir) {

	// Check if path to input_dir is valid
	if (!File.isDirectory(input_dir)) {
		exit("Macro aborted: The directory\n'"+ input_dir +"'\nwas not found.");
	}

	// Ensure the string defining input_dir does not end in '/' or '\'
	if (endsWith(input_dir, File.separator)) {
		separatorPosition = lengthOf(input_dir);
		input_dir = substring(input_dir, 0, separatorPosition-1);
	}

	// Create output directory (unless it already exists)
	output_dir = input_dir + "_Processed" + File.separator;
	if (!File.isDirectory(output_dir)) {
		File.makeDirectory(output_dir);
		if (!File.isDirectory(output_dir))
			exit("Macro aborted:\n" + output_dir + "\ncould not be created.");
	}
	return output_dir;
}

/*
 * This function returns true if the file extension of the argument <filename>
 * is present in the <extensions> array. Returns false otherwise.
 */
function validExtension(filename) {
	extensions = newArray(".tif", ".stk", ".oib");
	valid = false;
	for (i=0; i<extensions.length; i++) {
		if (endsWith(toLowerCase(filename), extensions[i])) {
			valid = true;
			break;
		}
	}
	return valid;
}

/*
 * This function applies <myRoutines()> to individual files filtered by
 * <validExtension()> in <input_dir> and all of its subdirectories. The
 * argument <output_dir> specifies the directory where a a TIFF copy of
 * each processed image will be saved. It does nothing if <input_dir>
 * does not exist.
 */
function processFiles(input_dir, output_dir) {

	// Do not display images during macro execution
	setBatchMode(true);

	// Get contents of input directory (files and subdirectories)
	files = getFileList(input_dir);

	// Loop through the file list. We will check if input_dir/output_dir
	// exist since that task was already performed by getOutputDirectory()
	for (i=0; i<files.length; i++) {

		// Display progress
		showProgress(i, files.length);

		// Process files of the desired extension
		file_path = input_dir + files[i];
		if (validExtension(file_path)) {

			// Open file. Note that some files may not be handled by
			// IJ directly but by other plugins, such as Bio-Formats
			open(file_path);

			// Apply processing steps
			myRoutines();

			// Save processed image in outDir (enforcing .tif extension)
			image_title = getTitle();
			dot_position = lastIndexOf(image_title, ".");
			if (dot_position!=-1)
				image_title = substring(image_title, 0, dot_position);
			saveAs("tiff", output_dir + image_title + ".tif");
			close();

		// Process subdirectories of input_dir
		} else if (endsWith(file_path, "/")) {
			processFiles(file_path, output_dir);

		// Report unsolicited files
		} else {
			print(i+1, "Skipping "+ file_path +"... not the right file type");
		}
	}
}