The top plot is the reconstructed phase with zero command (dac=180), while the bottom is with the steady-state control value. Clearly the end result has more phase variation in the center, even though the slope norm is minimized. I think the problem is at the corners. Physically, the WFS has a long barrel opening before the image plane, and this is causing some corner sub-apertures to be shadowed. Currently, my code just sets the slopes at these these locations to zero, and I think that's causing the reconstructed phase surface to dive at the corners like that.
The result is this artificial bowl shape, and this causes a large projection into the focus DM mode even though most of the reference wavefront is pretty flat. It looks like the controller is attempting to compensate for this by depressing the center. Touching, but ultimately wrong. Note that this wasn't a problem in generating the poke matrix, since in that case I was subtracting out the reference wavefront from each measurement. Here I'm attempting to reduce the total wavefront.
To solve this I'll have to change my code to exclude those slope measurements from the corners, rather than just set them to zero. This isn't as easy as it sounds, since the indexing there and in the phase reconstructor is gnarly. If it doesn't drive me insane I'll hopefully have that done Monday.
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