//Egeblad lab's:
//  ______          _ _                       
// |___  /         | (_)                      
//    / /_____ __ _| |_  __ _ _ __   ___ _ __ 
//   / /______/ _` | | |/ _` | '_ \ / _ \ '__|
//  / /__    | (_| | | | (_| | | | |  __/ |   
// /_____|    \__,_|_|_|\__, |_| |_|\___|_|   
//                       __/ |                
//                      |___/                 

//Please, install requirementes prior to usage:
//TemplateMatching: add this to the update site list: http://sites.imagej.net/Template_Matching/

Dialog.create("Egeblad lab's Z-aligner");
Dialog.addChoice("What kind of alignment?", newArray("SIFT", "TemplateMatching"));
Dialog.addChoice("What algorithm (for SIFT)?", newArray("Translation", "Rigid", "Similarity", "Affine"));
Dialog.show();
choice = Dialog.getChoice();
alg = Dialog.getChoice();

waitForUser("Attention", "In the next dialog, choose the folder where you want to save your results.");
path = getDirectory("Choose where to save the results");
indivpath = path+File.separator+"indiv_files";
if (File.exists(indivpath)==false) {
			File.makeDirectory(indivpath);
}

print("You chose algorithm: "+alg);

if (choice == "TemplateMatching") {
	choice=0;
	}
	
else {
	choice=1;
	}

rename("origin");

Stack.getDimensions(width, height, channels, slices, frames); 
rectx1 = width*5/100;
rectx2 = width-((width*5/100)*2);
recty1 = height*5/100;
recty2 = height-((height*5/100)*2);

for (i = 1; i < (frames+1); i++) {
	print("-------------------------------");
	print("Processing frame "+i+" of "+frames);
	print("-------------------------------");
	selectWindow("origin");
	run("Duplicate...", "duplicate frames="+i+"-"+i);
	if (choice == 0) {
		print("I'm going to do TemplateMatching");
		makeRectangle(rectx1, recty1, rectx2, recty2);
		run("Align slices in stack...", "method=5 windowsizex="+parseInt(rectx2)+" windowsizey="+parseInt(recty2)+" x0="+parseInt(rectx1)+" y0="+parseInt(recty1)+" swindow=0 subpixel=false itpmethod=0 ref.slice=1 show=true");	
	}
	
	else {
		print("I'm going to do SIFT");
		run("Linear Stack Alignment with SIFT", "initial_gaussian_blur=1.60 steps_per_scale_octave=3 minimum_image_size=64 maximum_image_size=1024 feature_descriptor_size=4 feature_descriptor_orientation_bins=8 closest/next_closest_ratio=0.92 maximal_alignment_error=25 inlier_ratio=0.05 expected_transformation="+alg+" interpolate");
		run("Stack to Hyperstack...", "order=xyczt(default) channels=1 slices="+slices+" frames=1 display=Grayscale");
		selectWindow("origin-1");
		close();
	}
	
	saveAs("Tiff", indivpath+File.separator+"frame_"+i+".tif");

}

selectWindow("origin");
saveAs("Tiff", path+File.separator+"original.tif");
close();
run("Concatenate...", "all_open open");

saveAs("Tiff", path+File.separator+"processed.tif");

print("Done.");