// Time_Profiles macro by Christophe Leterrier

macro "Time Profiles" {

//	Save Settings
	saveSettings();

//	Default values for the Options Panel

	ROIS_EXT = "_ROIs.zip";
/*
	SUBTRACT_DEF = false;
	BG_DEF = false;
	UM_DEF = false;
	NORM_DEF = false;
	NORM_SNR_DEF = 2; // SNR for the Normalize_Movie macro
	STABILIZE_DEF = true;
	FTIM_DEF = false;
	FINT_DEF = 1;
*/

//*************** Dialog 1 : get the input images folder path ***************

//	Get the folder name
	INPUT_DIR = getDirectory("Select the input stacks directory");
	print("\n\n\n*** Filter Timelapse Log ***");
	print("INPUT_DIR :" + INPUT_DIR);

//*************** Dialog 2 : options ***************

//	Creation of the dialog box
/*	
  	Dialog.create("Time Profiles Options");
	Dialog.addCheckbox("Running subtraction", SUBTRACT_DEF);
	Dialog.addCheckbox("Subtract background", BG_DEF);
	Dialog.addCheckbox("Unsharp Mask", UM_DEF);
	Dialog.addCheckbox("Normalize Intensity", NORM_DEF);
	Dialog.addNumber("Normalize SNR", NORM_SNR_DEF);
	Dialog.addCheckbox("Stabilize", STABILIZE_DEF);
	Dialog.addCheckbox("Force time interval", FTIM_DEF);
	Dialog.addNumber("Interval", FINT_DEF, 5, 3, "sec");
	Dialog.show();

//	Feeding variables from dialog choices
	SUBTRACT = Dialog.getCheckbox();
	BG = Dialog.getCheckbox();
	UM = Dialog.getCheckbox();
	NORM = Dialog.getCheckbox();
	NORM_SNR = Dialog.getNumber();
	STABILIZE = Dialog.getCheckbox();
	FTIM = Dialog.getCheckbox();
	FINT = Dialog.getNumber();
*/

//*********************************************

//	Get all file names
	ALL_NAMES = getFileList(INPUT_DIR);
	Array.sort(ALL_NAMES);
	PARENT_DIR = File.getParent(INPUT_DIR);


//	Loop on all .tif extensions
	for (n = 0; n < ALL_NAMES.length; n++) {

		FILE_NAME = ALL_NAMES[n];
		FILE_EXT = substring(FILE_NAME, lastIndexOf(FILE_NAME, "."), lengthOf(FILE_NAME));

		if (FILE_EXT == ".tif") {
//			Get the file path
			FILE_PATH = INPUT_DIR + FILE_NAME;

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

			open(FILE_PATH);
			// Store file name without extension and extension
			FILE_SHORTNAME = File.nameWithoutExtension;

			STACK_ID = getImageID();
			Stack.getDimensions(IM_W, IM_H, STACK_CH, STACK_SLICES, STACK_FRAMES);
			getPixelSize(pixelUnit, pixelWidth, pixelHeight);
			TIME_INT = Stack.getFrameInterval();
			Stack.getUnits(X, Y, Z, timeUnit, Value);
			STACK_TITLE = getTitle();

			// Open ROIset for this movie
			ROIS_NAME = FILE_SHORTNAME + ROIS_EXT;
			ROIS_PATH = INPUT_DIR + ROIS_NAME;
			print("ROIs_path: " + ROIS_PATH);
			ROINUMBER = roiManager("count");
			if (ROINUMBER >0) {
				roiManager("Deselect");
				roiManager("Delete");
			}
			roiManager("Open", ROIS_PATH);
			ROINUMBER = roiManager("count");

			for (i = 0; i < ROINUMBER; i++) {
				selectImage(STACK_ID);
				roiManager("select", i);
				imTitle = getTitle();
				imNumber = getSliceNumber();		
				roiTitle = getInfo("selection.name");
				RoiSplit = split(roiTitle, "-");
		
				if (RoiSplit.length > 3) {
					Roi.setProperty("TracingType", RoiSplit[3]);
					Roi.setProperty("TypeName", RoiSplit[4]);
				}
				
				roiType = Roi.getProperty("TracingType");
				roiTypeName = Roi.getProperty("TypeName");

				ProfileName = imTitle + "-" + roiTitle;
				run("Plot Z-axis Profile");
				rename(ProfileName);
			}
			selectImage(STACK_ID);
			close();
		}// end of IF loop on tif extensions
	}// end of FOR loop on all files

	if (ROINUMBER >0) {
		roiManager("Deselect");
		roiManager("Delete");
	}
	
	run("Images to Stack", "name=[Profiles Stack] use");
	save(INPUT_DIR + "Profiles.tif");

	print("");
	print("*** Time Profiles end ***");
	showStatus("Time Profiles finished");
}