I have been following the usual steps for configuring Pixhawk for a quadcopter. I have tried both QGroundControl and MissionPlanner with both ArduCopter 3.3. and PX4 flight stacks. I don't have the ESCs connected but instead I am monitoring the PWM outputs on a scope. The servo rail is powered at 5V from an external Power Supply. When I use ArduCopter there is no signal at all on the "MAIN OUT" PWM outputs and there is a 1000us signal on "AUX OUT" outputs. With PX4 firmware there is 1000us singal on "MAIN OUT" and 2000us signal on "AUX OUT". In both cases I successfully armed the pixhawk but when I increase throttle nothing on the output changes (RC is definitely configured properly as I can see inputs changing in both Mission Planner and QGroundControl).
I have a feeling I am missing some configuration settings? Please help!
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That usually means that you haven't pressed the safety switch (or haven't disabled it in the parameters)
If you were able to arm the copter the it should have created a flight log which will contain the PWM output to each of the pins. Try checking the log with mission planner and look for RCout. As far as I can tell it should be working.