Adjust per-particle defocus of subparticles in volume alignment tools?

I guess it depends on the format of alignments3D/pose … docs for the scipy transformation are here: from_rotvec — SciPy v1.14.0 Manual

This is also where in the docs for CS tools, it would be useful to have a detailed description of all the data structures in CS, in addition to a description of the modules - a description of e.g. how pose is specified would be helpful (maybe it is there already, I just couldn’t find it at a glance)

From here: It's time I admit I don't know what Rodrigues vectors are - #3 by DanielAsarnow

Pose is specified in axis-angle representation, which is what from_rotvec is expecting by default, and printing alignments3d/pose during the script looks consistent with that. What I don’t quite understand is whether something is going wrong when applying that transformation to the recentering vector - that is all I can think of as the issue, but can’t figure out why that would be the case…

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