Calculation of the offset of the phase

[mirichard-S]

Hi Jérôme,

Can you remind me how the offset of the phase is calculated?
Is the phase equal to zero at the voxel corresponding to the center of mass of the reconstructed modulus?
Or is the phase offset equal to the mean of the phase inside the support?

Best,

[carnisj]

In postprocessing.process_scan:

The parameters are already described in the example config file and docstrings:

offset_method: 'mean' or 'com' (center of mass). This phase value is subtracted to the phase
phase_offset_origin: pixel coordinates or None. If None, the phase origin is determined by phase_offset
phase_offset: use this to offset manually the origin of the phase to the desired value

[carnisj]

I will clean up a bit the function remove_offset and its docstring, but in principle one should be able to get the desired behavior with the existing parameters, correct?