Drone's body/fixed frame

I am doing a research concerning quadcopters, and I am facing an issue that I couldn't solve yet. I controlling my drone by sending the commands to the Android phone mounted on it and connected to its controller. Using this phone, I can also measure many quantities, thanks to the embedded sensors in the phone. 

So my issue is, how can I estimate the offset between the frame of the phone ( defined here), and the body frame of the drone? i.e. I can command the motors to generate a specific torque, but this is in the phone's frame because the measurements where done in the phone's frame not the drone's body frame (unless the origin of the phone's frame coincides with the drone's frame, which is almost impossible to happen per hand ).

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