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Originally Posted by JohnOwens
ChibiVader, I'm afraid I'm going to have to hurt you now. I've finally gotten around to (more) seriously tackling this IRAF stuff, along with the associated ds9, x11iraf, xpa, pgplot, etc. etc., and OUCH!  At least I'm fairly sure now that there's got to be some way within it to do stacking, per se; now I'm wondering how manual or automated the registration of the images is. Just hope I don't go off the deep end and start writing my own registration package for it if/when I find out there isn't one already.
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A few hints:
For stacking of registered images, the command
imcombine is your friend. You can set upper/lower thresholds to ignore, so you keep information and weight it properly where only some of the images cover an area.
Registration - ahhh, ummmm, I haven't found a way that's nearly as automated as one would like. There are some tricks which will let you refine image shifts at the pixel level if you can get within a few pixels manually.
Other general tricks - most IRAF commands can operate on whole lists of images, or use lists either of images or numerical values, and address them with the syntax @filename where a file or file list would normally be given. These can be created on the fly by other IRAF commands.
You might also check out some of the "contributed" IRAF packages - dimsum (dithered image summation) is designed for stacking large numbers of dithered images such as one needs to do in the near-IR, and might posisbly have a better registration technique than the standard packages.