I am using Pixhawk on a fix wing airplane and very often I don't empty the battery in a single flight. The problem is if I restart the plane, the battery percent meter will start from 100% again.

Since I use normal batteries and no smart batteries like the solo or phantoms' I understand the pixhawk can't know how much battery is left.

Is there any way I can tell the software that the battery is not full?

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  • Just use battery voltage alarm, not capacity alarm.
    Get alarmed using a onboard buzzer, telemetry, (mavlink), frsky telemetry, or graupner HoTT
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