// Target and source images (Window name of the color images)
// Note that these are window names and not filenames
target="Baboon.jpg";
source="DeformedBaboon.jpg";

// Filename of the transformation (full path)
// Make sure that the path does not contain any white space
transformation="G:\\HOME_epfl\\plugins\\UnwarpJ\\Help\\GrayOutput_transf.txt";

// No change from here -------------------------------------------------
requires("1.35g");
// Generate separate images for each RGB channel
selectImage(target);
run("RGB Stack");
w=getWidth();
h=getHeight();
setSlice(1); run("Copy");
newImage("TargetRed", "8-bit White", w, h, 1);
run("Paste");
saveAs("Tiff", "TargetRed.tif");
close();
selectImage(target);
setSlice(2); run("Copy");
newImage("TargetGreen", "8-bit White", w, h, 1);
run("Paste");
saveAs("Tiff", "TargetGreen.tif");
close();
selectImage(target);
setSlice(3); run("Copy");
newImage("TargetBlue", "8-bit White", w, h, 1);
run("Paste");
saveAs("Tiff", "TargetBlue.tif");
close();
run("RGB Color");

selectImage(source);
run("RGB Stack");
w=getWidth();
h=getHeight();
setSlice(1); run("Copy");
newImage("SourceRed", "8-bit White", w, h, 1);
run("Paste");
saveAs("Tiff", "SourceRed.tif");
close();
selectImage(source);
setSlice(2); run("Copy");
newImage("SourceGreen", "8-bit White", w, h, 1);
run("Paste");
saveAs("Tiff", "SourceGreen.tif");
close();
selectImage(source);
setSlice(3); run("Copy");
newImage("SourceBlue", "8-bit White", w, h, 1);
run("Paste");
saveAs("Tiff", "SourceBlue.tif");
close();
run("RGB Color");

// Apply transformation 
run("UnwarpJ ","-transform TargetRed.tif SourceRed.tif "+transformation+" RegisteredRed.tif");
run("UnwarpJ ","-transform TargetGreen.tif  SourceGreen.tif "+transformation+" RegisteredGreen.tif");
run("UnwarpJ ","-transform TargetBlue.tif  SourceBlue.tif "+transformation+" RegisteredBlue.tif");

// Form the registered color image
selectImage(target);
run("Duplicate...", "title=RegisteredImage");
run("RGB Stack");

open("RegisteredRed.tif");
run("8-bit");
run("Copy");
selectImage("RegisteredImage");
setSlice(1);
run("Paste");
selectImage("RegisteredRed.tif"); close();

open("RegisteredGreen.tif");
run("8-bit");
run("Copy");
selectImage("RegisteredImage");
setSlice(2);
run("Paste");
selectImage("RegisteredGreen.tif"); close();

open("RegisteredBlue.tif");
run("8-bit");
run("Copy");
selectImage("RegisteredImage");
setSlice(3);
run("Paste");
selectImage("RegisteredBlue.tif"); close();

selectImage("RegisteredImage");
run("RGB Color");

// Delete auxiliary files
File.delete("TargetRed.tif");
File.delete("TargetGreen.tif");
File.delete("TargetBlue.tif");
File.delete("SourceRed.tif");
File.delete("SourceGreen.tif");
File.delete("SourceBlue.tif");
File.delete("RegisteredRed.tif");
File.delete("RegisteredGreen.tif");
File.delete("RegisteredBlue.tif");