Code fragments for registering two images

tuboReg_macro.ijm

//20120911
// Kota Miura
// Code fragments for registering two images
// & printing out shift in positions.
// refer to
// http://bigwww.epfl.ch/thevenaz/turboreg/turboRegMacro.txt
// for more examples. 

//using opened image opened and refering their title.

frame1 = "t1.tif"; //  a frame in a sequence
frame2 = "t2.tif";  // next frame in the sequence
 
selectWindow(frame1);
width = getWidth();
height = getWidth();

run("TurboReg ",
   "-align"
   + "-window " + frame1 + " "// Source (window reference).
   + " 0 0 " + (width - 1) + " " + (height - 1)
   + "-window " + frame2 + " "// Target (window reference).
   + " 0 0 " + (width - 1) + " " + (height - 1)
   + " -translation"
   + " " + (width / 2) + " " + (height / 2)
   + " " + (width / 2) + " " + (height / 2)
   + " -hideOutput"
);

sourceX0 = getResult("sourceX", 0); // First line of the table.
sourceY0 = getResult("sourceY", 0);
targetX0 = getResult("targetX", 0);
targetY0 = getResult("targetY", 0);
print(sourceX0, sourceY0, targetX0, targetY0);


// another way accessing image file in the file system. 
// in this case, you should know the image size (width and height)
// by first opeing the file and check its width and height. 
run("TurboReg ",
   "-align"
   + " -file " + sourcePathAndFileName
   + " 0 0 " + (width - 1) + " " + (height - 1)
   + " -file " + targetPathAndFileName
   + " 0 0 " + (width - 1) + " " + (height - 1)
   + " -translation"
   + " " + (width / 2) + " " + (height / 2)
   + " " + (width / 2) + " " + (height / 2)
   + " -hideOutput"
);