//PE AVIs to Hyperstack macro

//Warn abour numerical padding of filenames,
//without which there will be anamlous results...
showMessageWithCancel("Padding of filenames", "NOTE: This script assumes that numerical parts of filenames are padded.\nPerkin-Elmer software generated non-padded names.\nFilenames should have names like XX001XX...XX010XX, not XX1XX....XX010XX. \nOne solution is at:\nhttps://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Pad_Image_Names\nClick 'OK' to continue or 'Cancel' to stop.");

//Create dialog to obtain input from user
path = File.openDialog("Select a file in the directory");
inputDir = File.getDirectory(path);
// Get file list in input directory
//print("Path: " + path);
//print("inputDir: " + inputDir);
images = getFileList(inputDir);
//Check for movie files in the selected directory
//First get the list of AVI names and put into an array
f = 0;

//Need to look at file names to see how many wavelengths; populate some arrays
//Old UltraView supported 5 laser lines and DIC
totalWavelengths = 0;
wavelengthA = newArray("");
wavelengthB = newArray("");
wavelengthC = newArray("");
wavelengthD = newArray("");
wavelengthE = newArray("");
wavelengthF = newArray("");

//There are two ways the data can be output: 
//(1) single AVIs are single time points through space (Z stacks); or
//(2) single AVIs are single focal planes through time
//The latter have "Slice" in the name, which we'll try to detect,
//but to be safe We'll ask... 
foundSliceinName = true;
for (i = 0; i < images.length; i++) {
	if ((indexOf(images[i], ".AVI") > 0) || (indexOf(images[i], ".avi") > 0)) {
		//print("Processing " + inputDir + images[i]);
		if (f == 0 ) {
			firstMovieName = images[i];
			if (indexOf(firstMovieName, "Slice") > 0) {
				//print("Found slice descriptor in filename. Will suggest each AVI is a single slice over time.");
				foundSliceinName = true;
			} else {	
				//print("Did not find  slice descriptor in filename. Will suggest each AVI is a single time point Z stack.");
				foundSliceinName = false;				
			}
		}
		f = f + 1;
		movieName = images[i];
		if ((indexOf(images[i], "WavelengthA")) > 0){
			//print("File name: " + movieName + " Wavelength A");
			wavelengthA = Array.concat(wavelengthA, movieName);
			if (totalWavelengths < 1) {totalWavelengths = totalWavelengths + 1;}
			} 
		else if ((indexOf(images[i], "WavelengthB")) > 0){
			//print("Wavelength B detected");
			//print("File name: " + movieName + " Wavelength B");
			wavelengthB = Array.concat(wavelengthB, movieName);
			if (totalWavelengths < 2) {totalWavelengths = totalWavelengths + 1;}
			}
		else if ((indexOf(images[i], "WavelengthC")) > 0){
			//print("File name: " + movieName + " Wavelength C");
			wavelengthC = Array.concat(wavelengthC, movieName);
			}
		else if ((indexOf(images[i], "WavelengthD")) > 0){
			//print("File name: " + movieName + " Wavelength D");
			wavelengthD = Array.concat(wavelengthD, movieName);
			}
		else if ((indexOf(images[i], "WavelengthE")) > 0){
			//print("File name: " + movieName + " Wavelength E");
			wavelengthE = Array.concat(wavelengthE, movieName);
			}
		else if ((indexOf(images[i], "WavelengthF")) > 0){
			//print("File name: " + movieName + " Wavelength F");
			wavelengthF = Array.concat(wavelengthF, movieName);
			}

		if (f == 1) {
			aviNames = newArray(firstMovieName);
			} else {
				aviNames = Array.concat(aviNames, movieName);
			}
		}
	}

if (f == 0) {
	showMessage("No movie files found.");
	exit;
	}
//showMessage("Total AVIs found: " + f);

//Dialog so user can select data structure; prepopulated with  choice based on file naming.
Dialog.create("Confirm AVI Data Format");
items = newArray("Each AVI is a single time point (Z stack)", "Each AVI is a single slice over time");

if (foundSliceinName) {
	Dialog.addRadioButtonGroup("Confirm AVI data structure:", items, 2, 1, "Each AVI is a single slice over time");
	} else {
	Dialog.addRadioButtonGroup("Confirm AVI data structure:", items, 2, 1, "Each AVI is a single time point (Z stack)");
	}
Dialog.show();
AVIDataOption = Dialog.getRadioButton();
//print("AVI Data option: " + AVIDataOption);
if (AVIDataOption == "Each AVI is a single time point (Z stack)") {
	stacksAreZSlices = true;
	//print("AVIDataString is true");
	} else {
	stacksAreZSlices = false;
	//print("AVIDataString is false");
	}

setBatchMode(true);
//Open the first AVI and get the number of slices
run("AVI...", "avi=[" + inputDir + firstMovieName + "] use");
focalPlanes = nSlices;
//showMessage("Z planes: " + nSlices);
close;
setBatchMode(false);
//print ("First movie name: " + firstMovieName);
//print ("Last movie name: " + movieName);
print("Channels: " + totalWavelengths);
print("Focal planes: " + focalPlanes);
timePoints = f/totalWavelengths;
print("Time points: " + timePoints);"
setBatchMode(true);
print("Concatenating AVIs...");
for (i = 0; i < f; i++) {
	//print(inputDir + aviNames[i]);
	run("AVI...", "avi=[" + inputDir + aviNames[i] + "] use");
}
run("Concatenate...", "all_open");

if (stacksAreZSlices == true) {
	print("Creating hyperstack. Single AVIs are Z stacks...");
	run("Stack to Hyperstack...", "order=xyztc (default) channels=" + totalWavelengths + " slices=" + focalPlanes + " frames=" + timePoints);
	} else {
	print("Creating hyperstack. Single AVIs are single slices through time...");
	run("Stack to Hyperstack...", "order=xytzc channels=" + totalWavelengths + " slices=" + focalPlanes + " frames=" + timePoints);
	}
	
rename("AVIs");
setBatchMode(false);
print("Complete.");