//(c) Neil M. Kad 2011
// If you publish using this please cite:
// Kad N.M., Wang H., Kennedy G. G., Warshaw D. M., Van Houten B., Collaborative dynamic DNA scanning by nucleotide excision repair proteins investigated by single-molecule imaging of quantum dot labeled proteins. Molecular Cell. 2010. Vol 37 No. 5, 702-13.



setPasteMode("Blend"); 
//x=4; y=-9;
//xg=19; yg=-11;
yes_no = newArray("yes", "no");
answer = "yes";
ex = 25

// run("Duplicate...", "title=[copy] duplicate");
w = getWidth();
h = getHeight();
w1 = w+(2*ex); h1 = h+(2*ex);
rename("copy");

run("Canvas Size...", "width=w1 height=h1 position=Center zero");

	makeRectangle(ex, ex, w, h/3);
	run("Duplicate...", "title=[red] duplicate");

	selectWindow("red");
	run("Red");
	run("RGB Color");

function RedAmberAlign(alignwindow){
	Dialog.create("image nudge");
 	Dialog.addSlider("Left-Right:", -ex, ex,4);
 	Dialog.addSlider("Down-Up:", -ex, ex, -9);
  	Dialog.show();
 	x= Dialog.getNumber();
 	y= Dialog.getNumber();

	

	selectWindow("copy");
	makeRectangle(ex-x , (h/3+y+ex), w , h/3);
	run("Duplicate...", "title=[amber] duplicate");


	selectWindow("amber");
	run("Blue");
	run("RGB Color");
	
imageCalculator("Add create stack", "red","amber");
rename("first combination");


	Dialog.create("image nudge");
 	Dialog.addChoice("Is this OK?", yes_no);
	Dialog.show();
 	answer = Dialog.getChoice();


if (answer=="no") { 
		selectWindow("amber");
		close();
		selectWindow("first combination");
		close();
		RedAmberAlign("amber");
		}
	else {
		selectWindow("amber");
		close();		
		RedAmberAlign2("green");
		print ("red to amber "+x+" , "+y);
}
}

RedAmberAlign("amber");


function RedAmberAlign2(alignwindow){
	Dialog.create("image nudge");
 	Dialog.addSlider("Left-Right:", -ex, ex,19);
 	Dialog.addSlider("Down-Up:", -ex, ex, -11);
  	Dialog.show();
 	xg= Dialog.getNumber();
 	yg= Dialog.getNumber();

	

	selectWindow("copy");
	makeRectangle(ex-xg , (2*h/3+yg+ex), w , h/3);
	run("Duplicate...", "title=[green] duplicate");


	selectWindow("green");
	run("Green");
	run("RGB Color");
	
imageCalculator("Add create stack", "red","green");
rename("second combination");


	Dialog.create("image nudge");
 	Dialog.addChoice("Is this OK?", yes_no);
	Dialog.show();
 	answer = Dialog.getChoice();


if (answer=="no") { 
		selectWindow("green");
		close();
		selectWindow("second combination");
		close();
		RedAmberAlign2("green");
		}
	else {
		selectWindow("second combination");
		close();
		print ("red to green "+xg+" , "+yg);

}
}



imageCalculator("Add create stack", "first combination","green");
rename("final combination");

		selectWindow("green");
		close();
		selectWindow("first combination");
		close();
		selectWindow("red");
		close();
		selectWindow("copy");
		close();