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By themselves, SIFT and other keypoint-descriptors matching methods do not cope well with multiple instances of the same object on an image. Some authors tackled the problem : http://www.cmu.edu/qolt/Research/publications/2009Pubs/collet_icra09_final.pdf
But I have no code implementation of their method.
Oh, there are some quick explanation in section IV-C of the paper on why it doesn't normally work without a special way to address it.
