//qFunctions
function montageMaker(dir)	{
	// check how many slices/channels
	Stack.getDimensions(width, height, channels, slices, frames);
	getPixelSize(unit, pixelWidth, pixelHeight);
// checks now happen before this is called
//	if (channels * slices * frames == 1) exit ("Need more than one channel or slice or frame");
	run("Stack to Images");
	numImages = nImages;
	imgArray = newArray(numImages);
	colArray = newArray(numImages);
	mArray = newArray(numImages + 1);
	mArray[0] = "*None*";
	grayChoiceArray = newArray(numImages);
	for (i=0; i<numImages; i++)	{
		selectImage(i+1);
		run("Grays");
		imgArray[i] = getImageID();
		title = getTitle();
		colArray[i] = title;
		mArray[i+1] = title;
		grayChoiceArray[i] = d2s(i+1,0);
	}
	// give the option of making up to 2 merges
	Dialog.create("Montage Choice");
	Dialog.addMessage("How many grayscale panels?");
	Dialog.addChoice("I'd like...", grayChoiceArray);
	Dialog.addMessage("How many merge panels?");
	Dialog.addChoice("I'd like...", newArray("0","1","2"));
	Dialog.addCheckbox("Vertical montage?", false);
	Dialog.show();
	gPanels = Dialog.getChoice();
	mPanels = Dialog.getChoice();
	vChoice = Dialog.getCheckbox();
	// if vertical montage, rotate all images left
	if (vChoice == true) {
		for (i = 0; i < numImages; i ++)	{
			selectImage(i+1);
			run("Rotate 90 Degrees Left");
		}
	}
	// Image choices
	gVar = parseInt(gPanels);
	mVar = parseInt(mPanels);
	// Make arrays to hold image choices
	gNameArray = newArray(gVar);
	if (mVar == 1) {
		m1NameArray = newArray(7);
	}
	else if (mVar == 2) {
		m1NameArray = newArray(7);
		m2NameArray = newArray(7);
	}

	// Next dialog
	grout=8;
	Dialog.create("Pick your panels");
	Dialog.addMessage("Select order for grayscale");
	// variations based on number of files
	if (gVar==1)	{
		Dialog.addChoice("Gray Panel 1", colArray);
	}
	else if (gVar==2)	{
		Dialog.addChoice("Gray Panel 1", colArray);
		Dialog.addChoice("Gray Panel 2", colArray);
	}
	else if (gVar==3)	{
		Dialog.addChoice("Gray Panel 1", colArray);
		Dialog.addChoice("Gray Panel 2", colArray);
		Dialog.addChoice("Gray Panel 3", colArray);
	}
	else if (gVar==4)	{
		Dialog.addChoice("Gray Panel 1", colArray);
		Dialog.addChoice("Gray Panel 2", colArray);
		Dialog.addChoice("Gray Panel 3", colArray);
		Dialog.addChoice("Gray Panel 4", colArray);
	}
	else if (gVar==5)	{
		Dialog.addChoice("Gray Panel 1", colArray);
		Dialog.addChoice("Gray Panel 2", colArray);
		Dialog.addChoice("Gray Panel 3", colArray);
		Dialog.addChoice("Gray Panel 4", colArray);
		Dialog.addChoice("Gray Panel 5", colArray);
	}
	else if (gVar==6)	{
		Dialog.addChoice("Gray Panel 1", colArray);
		Dialog.addChoice("Gray Panel 2", colArray);
		Dialog.addChoice("Gray Panel 3", colArray);
		Dialog.addChoice("Gray Panel 4", colArray);
		Dialog.addChoice("Gray Panel 5", colArray);
		Dialog.addChoice("Gray Panel 6", colArray);
	}
	else if (gVar==7)	{
		Dialog.addChoice("Gray Panel 1", colArray);
		Dialog.addChoice("Gray Panel 2", colArray);
		Dialog.addChoice("Gray Panel 3", colArray);
		Dialog.addChoice("Gray Panel 4", colArray);
		Dialog.addChoice("Gray Panel 5", colArray);
		Dialog.addChoice("Gray Panel 6", colArray);
		Dialog.addChoice("Gray Panel 7", colArray);
	}
	// variations based on merges
	if (mVar==0)	{
	}
	else if (mVar==1)	{
		Dialog.addMessage("Select channels for merge");
		Dialog.addChoice("Red", mArray);
		Dialog.addChoice("Green", mArray);
		Dialog.addChoice("Blue", mArray);
		Dialog.addChoice("Gray", mArray);
		Dialog.addChoice("Cyan", mArray);
		Dialog.addChoice("Magenta", mArray);
		Dialog.addChoice("Yellow", mArray);
	}
	else if (mVar==2)	{
		Dialog.addMessage("Select channels for 1st merge");
		Dialog.addChoice("Red", mArray);
		Dialog.addChoice("Green", mArray);
		Dialog.addChoice("Blue", mArray);
		Dialog.addChoice("Gray", mArray);
		Dialog.addChoice("Cyan", mArray);
		Dialog.addChoice("Magenta", mArray);
		Dialog.addChoice("Yellow", mArray);
		Dialog.addMessage("Select channels for 2nd merge");
		Dialog.addChoice("Red", mArray);
		Dialog.addChoice("Green", mArray);
		Dialog.addChoice("Blue", mArray);
		Dialog.addChoice("Gray", mArray);
		Dialog.addChoice("Cyan", mArray);
		Dialog.addChoice("Magenta", mArray);
		Dialog.addChoice("Yellow", mArray);
	}
	Dialog.addNumber("Grout size (pixels):", 8);
	Dialog.addNumber("d.p.i.", 300);
	Dialog.addCheckbox("Scale bar?", false);
	Dialog.addNumber("Scale bar size (µm):", 10);
	Dialog.addNumber("1 px is how many µm?", pixelWidth);
	Dialog.show();
	// variations based on channels
	if (gVar==1)	{
		gNameArray[0] = Dialog.getChoice();
	}
	else if (gVar==2)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
	}
	else if (gVar==3)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
	}
	else if (gVar==4)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
	}
	else if (gVar==5)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
		gNameArray[4] = Dialog.getChoice();
	}
	else if (gVar==6)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
		gNameArray[4] = Dialog.getChoice();
		gNameArray[5] = Dialog.getChoice();
	}
	else if (gVar==7)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
		gNameArray[4] = Dialog.getChoice();
		gNameArray[5] = Dialog.getChoice();
		gNameArray[6] = Dialog.getChoice();
	}
	// variations based on merges
	if (mVar==0)	{
	}
	else if (mVar==1)	{
		m1NameArray[0] = Dialog.getChoice();
		m1NameArray[1] = Dialog.getChoice();
		m1NameArray[2] = Dialog.getChoice();
		m1NameArray[3] = Dialog.getChoice();
		m1NameArray[4] = Dialog.getChoice();
		m1NameArray[5] = Dialog.getChoice();
		m1NameArray[6] = Dialog.getChoice();
	}
	else if (mVar==2)	{
		m1NameArray[0] = Dialog.getChoice();
		m1NameArray[1] = Dialog.getChoice();
		m1NameArray[2] = Dialog.getChoice();
		m1NameArray[3] = Dialog.getChoice();
		m1NameArray[4] = Dialog.getChoice();
		m1NameArray[5] = Dialog.getChoice();
		m1NameArray[6] = Dialog.getChoice();
		m2NameArray[0] = Dialog.getChoice();
		m2NameArray[1] = Dialog.getChoice();
		m2NameArray[2] = Dialog.getChoice();
		m2NameArray[3] = Dialog.getChoice();
		m2NameArray[4] = Dialog.getChoice();
		m2NameArray[5] = Dialog.getChoice();
		m2NameArray[6] = Dialog.getChoice();
	}
	grout = Dialog.getNumber();
	res = Dialog.getNumber();
	sbchoice = Dialog.getCheckbox();
	sblen = Dialog.getNumber();
	mag = Dialog.getNumber();
	// decisions collected
	setBatchMode(true);

	// collect details from images
	win = getTitle(); // could change this so that name is something more logical
	newName = "mtg" + safeName(win);
	len = gVar + mVar;
	newImage(newName, "RGB", ((width*len)+(grout*(len-1))), height, 1);

	// paste in grayscales
	for (i = 0; i < gVar; i++)   {
		wName = gNameArray[i];
		selectImage(wName);
		run("Copy");
		selectImage(newName);
		makeRectangle((width*i)+(grout*i), 0, width, height);
		run("Paste");
	}

	// build mergeString(s)
	merge1String = "";
	merge2String = "";

	for (i = 0; i < 7; i++)   {
		merge1String += "c" + d2s(i+1,0) + "=[" + m1NameArray[i] + "] ";
		if (mVar == 2)
			merge2String += "c" + d2s(i+1,0) + "=[" + m2NameArray[i] + "] ";
	}
	merge1String += "keep";
	merge2String += "keep";
	// make array to hold merge names
	mImgArray = newArray("merge1","merge2");

	// paste in the merge(s)
	for (i = 0; i < mVar; i++)   {
		if (i == 0) {
			run("Merge Channels...", merge1String);
			rename("merge1");
		}
		else {
			run("Merge Channels...", merge2String);
			rename("merge2");
		}
		selectImage(mImgArray[i]);
		run("Copy");
		selectImage(newName);
		makeRectangle(((width*gVar)+(grout*gVar-1))+((width*i)+(grout*i)), 0, width, height);
		run("Paste");
	}

	selectImage(newName);
		// rotate right?
	if (vChoice == true)
		run("Rotate 90 Degrees Right");

	//add scale bar (height is same as grout)
	if (sbchoice==true)	{
		getDimensions(w, h, c, slices, frames);
		setColor(255,255,255);
		fillRect(w-(grout+(sblen/mag)), h-(2*grout), sblen/mag, grout);
	}
	//specify dpi default is 300 dpi
	run("Set Scale...", "distance=res known=1 unit=inch");
	run("Select None");

	//save montage
	saveAs("TIFF", dir + newName);
	setBatchMode(false);
	// close originals
	for (i = 0; i < imgArray.length; i ++)	{
		selectImage(imgArray[i]);
		close();
	}
}

function mtgcomp()	{
	imgArray = newArray(nImages);
	rowArray = newArray(nImages);
	nameArray = newArray(nImages);
	widthArray = newArray(nImages);
	heightArray = newArray(nImages);
	print("\\Clear");
	for (i = 0; i < nImages; i ++)	{
		selectImage(i + 1);
		imgArray[i] = getImageID();
		title = getTitle();
		rowArray[i] = title;
		getDimensions(ww, hh, cc, ss, ff);
		widthArray[i] = ww;
		heightArray[i] = hh;
	}
	// check the widths are the same;
	Array.getStatistics(widthArray, min, max, mean, stdDev);
	if (stdDev != 0) exit ("Images have unequal widths");
	theWidth = mean;
	// check the widths are the same;
	Array.getStatistics(heightArray, min, max, mean, stdDev);
	if (stdDev != 0) exit ("Images have unequal heights");
	theHeight = mean;
	// vChoice is vert if we will do horizontal array
	vChoice = "";
	if (theHeight > theWidth) vChoice = "vert";
	len = imgArray.length;

	// Standard sizes
	grout = 16;
	res = 300;
	sblen = 10;
	mag = 0.069;
	// Make dialog box
	Dialog.create("Compile the montages");
	// variations based on number of files
	if (vChoice == "vert")	{
		Dialog.addMessage("Select order for your compilation, left to right");
	}
	else {
		Dialog.addMessage("Select order for your compilation, top to bottom");
	}
	for (i = 0; i < len; i ++)	{
		labStr = d2s(i+1,0);
		Dialog.addChoice(labStr, rowArray);
	}
	Dialog.addNumber("Row gap (px, default = 2 x grout):", 16);
	Dialog.addNumber("d.p.i.", 300);
	Dialog.addCheckbox("Scale bar?", false);
	Dialog.addNumber("Scale bar size (µm):", 10);
	Dialog.addNumber("1 px is how many µm?", 0.069);
	Dialog.show();
	// variations based on number of files
	for (i = 0; i < len; i ++)	{
		nameArray[i] = Dialog.getChoice();
	}
	grout = Dialog.getNumber();
	res = Dialog.getNumber();
	sbchoice = Dialog.getCheckbox();
	sblen = Dialog.getNumber();
	mag = Dialog.getNumber();
	// decisions collected
	setBatchMode(true);

	// setup for save
	win = getTitle();
	dir1 = getDirectory("image");
	newName = "cmp" + len + win;

	// get dimensions
	wArray = newArray(len);
	hArray = newArray(len);
	hPosArray = newArray(len+1);
	hPosArray[0] = 0;
	height = 0;
	for (i=0; i<len; i++)   {
		selectImage(nameArray[i]);
		if (vChoice == "vert")
			run("Rotate 90 Degrees Right");
		getDimensions(w, h, c, slices, frames);
		wArray[i] = w;
		hArray[i] = h;
		hPosArray[i+1] = hPosArray[i] + h;
		width = width + w;
		height = height + h;
	}
	// check widths are the same
	if (width / len != w)	{
		print("Check widths");
	}
	newImage(newName, "RGB", w,(height)+(grout*(len-1)), 1);
	for (i=0; i<len; i++)   {
		selectImage(nameArray[i]);
		run("Select All");
		run("Copy");
		close();
		selectImage(newName);
		makeRectangle(0, (hPosArray[i])+(grout*i), wArray[i], hArray[i]);
		run("Paste");
	}
	// now put back?
	if (vChoice == "vert")
		run("Rotate 90 Degrees Left");
	//add scale bar (height is same as grout)
	if (sbchoice==true)	{
		getDimensions(w, h, c, slices, frames);
		setColor(255,255,255);
		fillRect(w-((grout/2)+(sblen/mag)), h-(2*(grout/2)), sblen/mag, grout/2);
	}
	//specify dpi default is 300 dpi
	run("Set Scale...", "distance=res known=1 unit=inch");
	run("Select None");
	//save montage
	saveAs("TIFF", dir1+newName);
	setBatchMode(false);
}

function safeName(s)	{
	// need to replace some characters to allow save to work properly
	s = replace(s,"c:","");
	s = replace(s,"/","");
	s = replace(s,"\\(","");
	s = replace(s,"\\)","");
	s = replace(s,".tif","");
	s = replace(s," ","_");
	return s;
}