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To do this, theres is a sketch in the repository named "MPU6050_calibration". This sketch was written to work with the MPU6050 but it works fine with the 9150 as well.
After you placed the new MPU9150 chip on the copter and added the wireing you need to bring the Quadcopter in a balanced position. Use a water level on the top of the motors to check this.
As soon as the copter is leveled, you upload the calibration sketch to the arduino and start the serial terminal.
Just follow the instructions the sketch is giving to you and after it finished it gives all six offsets as outputs. Integrate these Offsets into the MPUHandler.ino code and you are clear to use the new MPU9150 chip.
During our process it has happened that this sketch stopped during the process for an unknown reason. Just restart the arduino and give it another try.