ArduCopter at the present time does not have a direct energy calculation. I use the logging functions in my Castle ESC’s for that. With the logs from Copter you would have to use mAh or amp-hours, which is not energy (in watt-hours). But the watt-hours could be calculated by taking total amp-hour consumption times average voltage.
You could update your APM Planner2 application for Ubuntu to 2.0.25, which is the latest. For some reason the latest on the firmware site is only there for Mac OSX. I have a build available for either 32 or 64-bit Ubuntu 16.04 here. If you are running an older version of Ubuntu then stick with what you have, as there will be dependency issues. https://drive.google.com/open?id=0B5oLpNzxih4tSzJOUFpIZ1FZWk0