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What I would suggest is to apply one of the feature detectors on the image that can be found inside the feature2d library:

Basicly use the feature points extracted by SURF, SIFT, ORB, FREAK, BRISK, ... to match both image by searching for matching feature points. The discriptor matching functionality of openCV will help out there. These descriptors create a unique representation of the area around the feature points and try to retrieve them.

By using these feature points, and looking at local features, you do not have to align both images.