I have a pair of images which I want to align. They are not a panorama, but 
rather they are images of the same object, one in natural light, one in 
fluorescent light.  They were taken with a point-and-shoot camera with a 
cheap tripod and some changeover setup required, so they are not perfectly 
aligned.

After Googling around a bit, I gather that Hugin can help with this, even 
though I don't care about ending up with a combined image.  I just want to 
apply the geometric transformations required to align my pair of images, 
getting a pair of modified JPEGs or TIFFs which are aligned.

I'm generating all the control points manually, and I think I've done a 
reasonable job with that. However, I am at a loss about how to use Hugin to 
get what I want.  

I tried a few different settings in the optimizer and stitcher windows, but 
I don't really know what I'm doing.  With all the default settings I got a 
very tiny canvas size, and adjusted that, but the images weren't aligned. I 
don't really understand which checkboxes on the stitcher tab (or other 
pages) are the important ones for this use case.

Thanks for any help.

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