I am trying to align an image according to a base image and according to the position of 2 circles on the left of each page.
The link for base image: http://tinypic.com/view.php?pic=nmi053&s=6
The link for unregistered image: http://tinypic.com/view.php?pic=2zsbmuu&s=6
The code I have so far is listed below but the only thing I have a problem with is how to use imtransfrom function to register the image.
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Have you tried imregister()? It will condense all that code down into a single line of code. Go ahead, make it easy on yourself.
Here's a modification of the original approach using ABSOR, available here
[LI, numI] = bwlabel( imfill(BWIremove,'holes') );
[LJ, numJ] = bwlabel( imfill(BWJremove,'holes') );
centroidsI = regionprops(LI,'Centroid');
centroidsJ = regionprops(LJ,'Centroid');
% Create a transformation structure for an affine % transformation.
S=absor(cJ.', cI.'); t_concord=maketform('affine', S.M(1:2,:).');
registered = imtransform(IMJ,t_concord,....);
Because you're only using 2 landmarks to perform the registration, the alignment will probably not be as perfect as with imregister, although as I've said, I have my doubts about how well imregister would work across a larger population of questionnaires.
There are things you could do to improve the tilt angle estimate though, like find more landmarks, or use regionprops(...,'Orientation') on the answer boxes.