Shack-Hartmann sensing with arbitrarily shaped pupil

The measurements of Shack-Hartmann wavefront sensors in adaptive microscopy can be affected by missing or ill-formed spots behind the subapertures. This may change dynamically during operation, so an updatable control method is required. We provide a protocol along with Python code to update the wavefront corrector control matrix and command vector while performing Shack-Hartmann sensing with an arbitrarily shaped pupil for both zonal and modal control methods.