My actual problem is that the hugin suite alone offers at least a dozen or so command (align_image_stack, cpclean, deghosting_mask, geocpset, hugin_hdrm, pto_merge, verdandi, and whatnot), plus there's panotools (with a big overlap, because hugin uses panotools). And I don't know which of these are relevant. Of those relevant, I don't know which of them are redundant and which complement each other. (E.g. align_image_stack would be pretty near to what I need, but it assumes all images are the same size, which I don't know how to do in an automated manner and which is also an indicator that align_image_stack isn't actually what I want.)
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