//Prompts user to select folders....
numdir = getDirectory("Select Folder Containing Numerator Image Files");
dendir = getDirectory("Select Folder Containing Denominator Image Files");
outdir =  getDirectory("Select Folder For Output Images");

numlist = getFileList(numdir);
denlist = getFileList(dendir);

if (numlist != denlist) {
	print("Error: Folders must contain the same number of files");
}



// ---------------------------Dialog box 1--------------------------------
Dialog.create("Create Intensity Modulated Display...");

Dialog.addCheckbox("Smooth prior to division? ", true);
Dialog.show();
smooth = Dialog.getCheckbox();

//Open the files ins the folders....
for (i=0; i<numlist.length; i++) {  //Safe since both folders contain the same number of files

	showProgress((i+1)/numlist.length); //progress bar

	numpath = numdir+numlist[i];
	denpath = dendir+denlist[i];

	open(numpath);
	open(denpath);	

	process();
	
}


function process () {

//Creates ratio image...
if (smooth == true) {

	selectWindow(numlist[i]);
	run("8-bit");
	run("Gaussian Blur...", "sigma=1 stack");
	selectWindow(denlist[i]);
	run("8-bit");
	run("Gaussian Blur...", "sigma=1 stack");

	setBatchMode(true);
	imageCalculator("Divide create 32-bit stack", numlist[i], denlist[i]);

	ratioimg = getTitle();
	
	selectWindow(numlist[i]); //Keep denom image to use for brightness
	close();

}

if (smooth == false) {
 
	selectWindow(numlist[i]);
	run("8-bit");
	selectWindow(denlist[i]);
	run("8-bit");
	
	setBatchMode(true);
	imageCalculator("Divide create 32-bit stack", numlist[i], denlist[i]);

	ratioimg = getTitle();

	selectWindow(numlist[i]);  //Keep denom image to use for brightness
	close();
	
}


// ---------------------------Dialog box 2--------------------------------

//Finds the max value in the ratio image in the middle of the stack...
selectWindow(ratioimg);
getDimensions(ratioimgwidth, ratioimgheight, channels, ratioimgslices, frames);
setSlice(floor(ratioimgslices/2)); //picks the middle slice

run("Enhance Contrast", "saturated=0.1");
getMinAndMax(min, absmax);
//Suggest a max value to display in the ratio image based on its histogram.... 
run("Enhance Contrast", "saturated=1.00");
getMinAndMax(min, sugmax);

Dialog.create("Set Scale...");
Dialog.addSlider("Set maximum displayed value in ratio image: ", 0, absmax, sugmax);
Dialog.addSlider("Set % saturation in denominator image: ", 0.5, 5, 1);
Dialog.show();

usermax = Dialog.getNumber();
usersat = Dialog.getNumber();

selectWindow(ratioimg);
setMinAndMax(0, usermax);  // max as selected by user
run("8-bit");
run("Invert", "stack");  //Makes high ratios hot and low ratios cool  (inherently, red hue = 0 -> blue hue = 170)
run("Multiply...", "value=0.666 stack");  // Contstrains hues from 0-170 to match calibration bar (so only red->blue colors are shown)

selectWindow(denlist[i]);
run("Enhance Contrast", "saturated="+usersat+" process_all");  // as selected by user
run("8-bit");

//----------------------Creates HSB Image -------------------------------------

setBatchMode(true);

//Creates a Saturation (constant) stack image
newImage("Sat", "8-bit white", ratioimgwidth, ratioimgheight, ratioimgslices);

//Initializes the final IMD stack image
newImage(numlist[i]+"IMD_Stack", "RGB black", ratioimgwidth, ratioimgheight,  ratioimgslices);

for (j=0; j<ratioimgslices; j++) {

//IJ DOES NOT SUPPORT HSB HYPERSTACKS.... HSB IMAGES MUST BE 2D.
//Creates an HSB image... THIS IS THE ONLY WAY TO DO IT!!
	newImage("HSB", "RGB black", ratioimgwidth, ratioimgheight, 1);
	run("HSB Stack"); // A 2D image with the 3 HSB channels

//COPIES THE HUE IMAGE
	selectWindow(ratioimg);
	setSlice(j+1);
	run("Select All");
	run("Copy");

	selectWindow("HSB");
	Stack.setChannel(1);
	Stack.setSlice(j+1); 
	run("Paste");

//COPIES THE SATURATION IMAGE
	selectWindow("Sat");
	setSlice(j+1);
	run("Select All");
	run("Copy");

	selectWindow("HSB");
	Stack.setChannel(2);
	Stack.setSlice(j+1); 
	run("Paste");

//COPIES THE BRIGHTNESS IMAGE
	selectWindow(denlist[i]);
	setSlice(j+1);
	run("Select All");
	run("Copy");
	
	selectWindow("HSB");
	Stack.setChannel(3);
	Stack.setSlice(j+1); 
	run("Paste");

//Turns the HSB values into an RGB image and copies it into the final stack..
	selectWindow("HSB");
	run("RGB Color");
	run("Select All");
	run("Copy");
	close();		

	selectWindow(numlist[i]+"IMD_Stack");
	setSlice(j+1);
	run("Select All");
	run("Paste");

	showProgress( (j+1)/ratioimgslices); //progress bar

} // EO FOR

selectWindow(ratioimg); 
run("Close"); // Closes the ratio image stack

selectWindow("Sat"); 
run("Close"); // Closes the sat image stack

selectWindow(denlist[i]);
run("Close"); // Closes the denom image stack

selectWindow(numlist[i]+"IMD_Stack"); //Make IMD stack the active window.  Then exits batch mode to show this image.
run("Select None");
saveAs("tiff", outdir+numlist[i]+"IMD");
close();


} // EO process

showStatus("IMD Finished!!!");