Pixhawk board and PID tuning loop

hi, all, I’m new in this community, and I have some problems on the project that I’m trying to do.
Okay, I’m trying to implement a PID tuning loop on Pixhawk Board in the first place.
For that, I fund this paper http://calhoun.nps.edu/handle/10945/47258 that use PX4 firmware with the Pixhawk board but the problem is that he uses an RC to control the copter and in my case, I want to use dronekit-Python or onboard computer to control the copter.
can you please give your advice, should I use the PX4 or the APM firmware with my pixHawk and what should I do exactly to get the result that I’m looking for