// Batch process macro template by Christophe Leterrier
// 14/09/2023
//
//This takes an input folder, process each file that has a certain extension, an saves the resulting files in an output folder next to the input folder.
//
// Folder Structure:
//
// •Experiment folder
// |–•Input folder
// |-•Output folder (created from the input folder by this macro)



macro "Batch_Macro" {

//*************** Initialization ***************

	// Defulat parameters for the batch macro
	MACRO_NAME = "Batch Macro";
	EXT = ".tif"; // extension to identify the files to process inside the input folder
	BATCH = true; // use the batch mode when looping on images
	SHORTEN_FOLDER = false; // shorten the input folder name to generate the output folder name, leaving only the first "word"
	FOLDER_SUFFIX = "processed"; // Suffix to add to the output folder

	// Default values for the Options Panel
	LUTS_DEF = false;
	CHAN_DEF = "0,1,2,3";

	// Get the input folder name
	INPUT_DIR=getDirectory("Select the input images directory");

	print("\n\n\n*** " + MACRO_NAME + " Log ***");
	print("");
	print("INPUT_DIR :" + INPUT_DIR);


//*************** Dialog ***************

	// Creation of the dialog box
	Dialog.create(MACRO_NAME + " Options");
	
	Dialog.addCheckbox("Use colored LUTs", LUTs_DEF);
	Dialog.addString("Overlay channels #", CHAN_DEF, 15);
	
	Dialog.show();

	// Feeding variables from dialog choices
	LUTS = Dialog.getCheckbox();
	CHAN = Dialog.getString();

	// Get all file names
	ALL_NAMES=getFileList(INPUT_DIR);
	Array.sort(ALL_NAMES);
	N_LENGTH = ALL_NAMES.length;
	ALL_EXT=newArray(N_LENGTH);
	// Create extensions array
	for (i = 0; i < N_LENGTH; i++) {
	//	print(ALL_NAMES[i]);
		ALL_NAMES_PARTS = getFileExtension(ALL_NAMES[i]);
		ALL_EXT[i] = ALL_NAMES_PARTS[1];
	}


//*************** Prepare processing ***************

	if (BATCH == true) setBatchMode(true);

	// Create the output folder (by default it is a folder next to the input folder)

	OUTPUT_DIR = File.getParent(INPUT_DIR);
	OUTPUT_NAME = File.getName(INPUT_DIR);
	
	// Shorten input folder name (optional)
	if ( SHORTEN_FOLDER == true) {
		OUTPUT_SHORTA = split(OUTPUT_NAME, " ");
		OUTPUT_SHORT = OUTPUT_SHORTA[0];
	}	
	else OUTPUT_SHORT = OUTPUT_NAME;
	
	OUTPUT_DIR = OUTPUT_DIR + File.separator + OUTPUT_SHORT + " " + FOLDER_SUFFIX + File.separator;
	if (File.isDirectory(OUTPUT_DIR) == false) {
		File.makeDirectory(OUTPUT_DIR);
	}


	OUTPUT_PARENT_DIR=File.getParent(OUTPUT_DIR);

	print("OUTPUT_DIR: " + OUTPUT_DIR);
	print("OUTPUT_PARENT_DIR: " + OUTPUT_PARENT_DIR);


//*************** Processing  ***************

	// Loop on all chosen extensions
	for (n=0; n<N_LENGTH; n++) {
		if (ALL_EXT[n]== EXT) {

			// Get the file path
			FILE_PATH=INPUT_DIR+ALL_NAMES[n];

			// Store components of the file name
			FILE_NAME=File.getName(FILE_PATH);
			FILE_DIR = File.getParent(FILE_PATH);
			FILE_SEP = getFileExtension(FILE_NAME);
			FILE_SHORTNAME = FILE_SEP[0];
			FILE_EXT = FILE_SEP[1];

			print("");
			print("INPUT_PATH:", FILE_PATH);
	//		print("FILE_NAME:", FILE_NAME);
	//		print("FILE_DIR:", FILE_DIR);
	//		print("FILE_EXT:", FILE_EXT);
	//		print("FILE_SHORTNAME:", FILE_SHORTNAME);

			// Open input file
			open(FILE_PATH);
			IN_ID = getImageID();

			
			// Processing
			
			
			

			// Close input file
			selectImage(IN_ID);
			close();

			// Create output file path and save the output file
			selectImage(OUT_ID);
			OUTPUT_PATH = OUTPUT_DIR + FILE_NAME;
			save(OUTPUT_PATH);
			print("OUTPUT_PATH: " + OUTPUT_PATH);

			// Close output file if checked
			close();



		}// end of IF loop on extensions
	}// end of FOR loop on all files



	if (BATCH == true setBatchMode("exit and display");
	print("");
	print("*** " + MACRO_NAME + " end ***");
	showStatus(MACRO_NAME + " finished");
}


//*************** Functions ***************

function getFileExtension(Name) {
	nameparts = split(Name, ".");
	shortname = nameparts[0];
	if (nameparts.length > 2) {
		for (k = 1; k < nameparts.length - 1; k++) {
			shortname += "." + nameparts[k];
		}
	}
	extname = "." + nameparts[nameparts.length - 1];
	namearray = newArray(shortname, extname);
	return namearray;
}