//4d Viewer to Hyperstack macro
// Create dialog to obtain input from user
inputDir = getDirectory("Select a Directory");
// Get file list in input directory
images = getFileList(inputDir);

//Check for movie files in the selected directory
//The 4d Viewer data structure is a series of movies with the name "FocalPlane" + n, where n is non--added number (")1,2...10...etc.).
f = 0;
for (i = 0; i < images.length; i++) {
	if ((indexOf(images[i], ".mov") > 0) || (indexOf(images[i], ".MOV") > 0)) {
		//print("Processing " + inputDir + images[i]);
		firstMovieName = images[i]; 
		f = f + 1;
		}
	}
if (f == 0) {
	showMessage("No movie files found.");
	exit;
	}
	
//Ordinarily would need to pad filenames and run an array sort here,
//but Bio-Formats is smart about this!
//print("Movie files found: " + f);

/*
 n = 0;
for (i = 0; i < images.length; i++) {
	if ((indexOf(images[i], ".mov") > 0) || (indexOf(images[i], ".MOV") > 0)) {
		run("Bio-Formats Importer", "open=" + inputDir + images[i] + " color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
		print("Processing " + images[i]);
		n = n + 1;
		if (n == 1) {
			selectWindow(images[i]);
			timePoints = nSlices;
			}
		}
}
*/

/*
n = 0;
for (i = 0; i < f; i++) {
	fileName = inputDir + "FocalPlane" + (i+1) + ".mov";
	//print("File name: " + fileName);
	run("Bio-Formats Importer", "open=[" + fileName + "] color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
	print("Processing " + "FocalPlane" + (i+1) + ".mov");
	n = n + 1;
	if (n == 1) {
		selectWindow("FocalPlane" + (i+1) + ".mov");
		timePoints = nSlices;
		}
}

print("Focal planes = " + f);
print("Time points = " + timePoints);
print("Concatenating...");
//run("Concatenate...", "  image1=FocalPlane1.mov image2=FocalPlane2.mov image3=FocalPlane3.mov image4=FocalPlane4.mov image5=FocalPlane5.mov image6=FocalPlane6.mov image7=FocalPlane7.mov image8=FocalPlane8.mov image9=FocalPlane9.mov image10=FocalPlane10.mov image11=FocalPlane11.mov image12=FocalPlane12.mov");
run("Concatenate...", "all_open");
print("Converting to Hyperstack...");
run("Stack to Hyperstack...", "order=xyctz channels=1 slices=" + f + " frames=" + timePoints);
rename("Concatenated 4d");
setBatchMode(false);
print("Complete.");
*/

run("Bio-Formats Importer", "open=" + inputDir + firstMovieName + " color_mode=Default group_files rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT use_virtual_stack dimensions axis_1_number_of_images=" + f + " axis_1_axis_first_image=1 axis_1_axis_increment=1 contains=[] name=" + firstMovieName + "-" + f + ".mov");