Truncating the sensor image turned out not to be the nightmare I thought it would be, so removing shadowed spots from the slope calculation seems to work pretty well. The classical controller seems to do a pretty good job flattening the phase, here's a before and after comparison of the reconstructed phase:
The norm of the wavefront slope error isn't really reduced much, <10 percent usually, but I think this is because the reference wavefront is already pretty flat. Right now I'm playing around with deliberately adding a strong focus bias by moving a lens to see if the controller can still compensate.
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