Bug fixes

dev.ipynb

dev.pyx

docs/index.rst

docs/reference/api.rst

docs/reference/classes/log_protocol.rst

docs/reference/cxi_ref.rst

docs/reference/log_ref.rst

pyrost/aberrations_fit.py

pyrost/bin/simulation.pxd

pyrost/bin/simulation.pyx

pyrost/config/ms_parameters.ini

pyrost/cxi_protocol.py

pyrost/data_processing.py

pyrost/include/st_utils.c

pyrost/include/st_utils.h

pyrost/log_protocol.py

pyrost/simulation/ms_parameters.py

pyrost/simulation/mslice.py

pyrost/simulation/st_sim.py