Administrator
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Stack aligner currently only supports image translation in x,y direction to align images, but not image rotation. If you are running photometry, instead of aligning images, use the multi-aperture setup panel option to place apertures using RA/Dec (if your images are plate-solved) and the images will not need to be aligned. If your entire stack is not plate solved, then plate-solve at least the first image in the stack, and then the first image after meridian flip (but be sure in this case that the option in multi-aperture setup panel "halt processing on WCS or centroid error" is disabled).
If you are coadding images for other purposes, you'd need to load two separate stacks, rotate one of the stacks using the flip and rotate options in the Image Display > Process menu. Once they are in the same orientation, then you can use Image Display > Process > "combine stacks into single stack" to join the two. Then you can run stack aligner to align the resulting images using translation. However, if your images do not rotate exactly 180 degrees at meridian flip, or support image rotation throughout the stack, the stack aligner tool and AIJ may not currently be the best option to coadd your images (plus you and the alternate tool will need to deal with how to resample the discrete pixels when the images are rotated).
Karen
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