I think we're passing variance wrong to SFFT

[rknop]

See Pipeline.align_and_preconvolve — it passes the noise images to the SpaceSFFT_CupyFlow constructor. But, if you look at the docstring on the latter, at the slots where the noise images are going, it has variables named with "Var" and that document them as the variance.

I think we probably need to square these noise images.

Try this, see what else it fixes!