// Importing High Speed Hyperspectral Raman Timeseries data into hyperstacks

// 		1) Get image directories list (locate, list folders, import CARS&SRS,
// 			rename appropriately)
//		2) Make blank hyperstack
// 		3) Import each timeseries into respective hyperstacks (CARS & SRS)

// Locate image directories
dirpar = getDirectory("Choose a Directory"); // parent folder directory
print("START LOADING:: "+dirpar)
dirlist = getFileList(dirpar)	//List of subdirectories containing all images
filename = File.getName(dirpar)	// Make file name title of the parent directory folder
//Array.print(dirlist)

print("list length = "+dirlist.length)
length = dirlist.length;	//Number of files in directory
firstimg = "ChanA_0001_0001_0001_0001.tif"		//Every MANTIS image is named like this
print("List[0] = "+dirlist[0])
firststack = dirpar+dirlist[0]+firstimg

// Import first image stack (c=0, t = 0-249 frames)
run("Bio-Formats Importer", "open=[&firststack] color_mode=Default rois_import=[ROI manager] split_channels view=[Standard ImageJ] stack_order=Default");
selectWindow("ChanA_0001_0001_0001_0001.tif - C=0")
rename(filename+"_CARS")
CARSstack = getTitle()	//Channel C=0 is PMT channel (usually CARS)
selectWindow("ChanA_0001_0001_0001_0001.tif - C=1")
rename(filename+"_SRS")
SRSstack = getTitle()	// Channel C=1 is the Photodiode channel (Always SRS)

// Loop through file folders. Append to respective stacks
for (i = 0; i<dirlist.length; i++){
	nextstack = dirpar+dirlist[i]+firstimg;
	print("Loading "+nextstack);
	run("Bio-Formats Importer", "open=[&nextstack] color_mode=Default rois_import=[ROI manager] split_channels view=[Standard ImageJ] stack_order=Default");
	run("Concatenate...", "  title=[&CARSstack] open image1=[&CARSstack] image2=[ChanA_0001_0001_0001_0001.tif - C=0] image3=[-- None --]");
	run("Concatenate...", "  title=[&SRSstack] open image1=[&SRSstack] image2=[ChanA_0001_0001_0001_0001.tif - C=1] image3=[-- None --]");
	print("Loaded " + toString(i) + " - " + dirlist[i]);
};	//Output will be a stack for CARS and SRS with all images stacked into a single third dimension

//Convert to hyperstacks. (separate color and time channels). 
// 		every 250 frames is 250 time points. each group of 250 frames comprises 1 color channel.
// 		Permute stacks into a x-y-t-c hyperstack to generate hyperspectral timeseries thats easy to separate out 
print("Stack Loading Complete");

selectWindow(CARSstack);
getDimensions(width, height, channels, slices, frames)
//length = 52;
fms = frames/length;
run("Stack to Hyperstack...", "order=xytcz channels=&length slices=1 frames=&fms display=Grayscale");	// CHANGE FRAME NUMBERS BASED ON YOUR INPUTS
selectWindow(SRSstack);
run("Stack to Hyperstack...", "order=xytcz channels=&length slices=1 frames=&fms display=Grayscale");
print("Stack Reordering Complete");