I have several collections of 400 or so photos that I took using interval shooting. Sometimes the camera moves very slightly while shooting. My goal is to align all the images at full resolution so that I can combine them into a single image. (The combining will be done in software I wrote myself.)
Usually I use Photoshop's auto-align feature for aligning images, which produces excellent results, but with this many images it seems either to not work or to be extremely slow. Photoshop stopped responding and was still taking 100% CPU days later when I killed it. I tried changing it to perspective transform only (rather than auto) but it didn't seem to help.
From a bit of google searching some people say you can do the aligning in Photoshop in batches. However, as far as I can tell this is not possible. If I align the first twenty images separately from the next twenty, then the two sets of images won't be aligned with each other. Unless there is a way to speed up Photoshop's auto-align feature, I'm looking for software that's designed for the task of aligning this many images.
One option I've tried is
align_image_stack, which is part of Hugin. However, this had problems of its own. On my most recent try, it took days to run and didn't correctly align the images; it also saves the files in an inconvenient format. (See the edit history for details.) I suspect that both Hugin and Photoshop are optimised for aligning a few dozen images at most and aren't really designed for large batches.
These are RAW files straight out of my Pentax K50 and they're about 14-15Mb each, so it's a lot of data when you put all of them together - they can't all fit into memory, and I'm looking for a tool that's designed with this in mind.
I should mention also that I'm on a Mac.