communicating with the Pixhawk

On my Recent project, I am trying to do image processing with my quad.
I have Pixhawk with 3DR radios for telemetry. I the image detection I running on my laptop. I am live streaming the Video from the quad in HD and trying to do the analysis on my laptop. now I wanted to know the ways to communicate with the quadcopter. since I have the 3dr radios, can I send the commands through the 3dr radios from y laptop in MAVproxy directly? I wanted to know if there is a better way for that.

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