Split functions into multiple less complex ones

[ddundo]

Many functions/methods are way too long and very hard to follow. For example, run in run_calibration.py is over 1400 lines long.

We should introduce new functions or even new modules (e.g. #64) to take over some of the functionality.

[drounce]

Agreed. We've discussed restructuring the if/elif format concerning the calibration options. Certainly there are opportunities to break these down even further.