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With the limitations of airborne sensors configuration of conventional miniature UAVs, this paper proposes a practical real-time algorithm which can integrate barometric height and GPS altitude. This algorithm uses the GPS altitude to calibrate baro-altimeter on-line, without considering the motion model and maneuverability of carrier. Tests showed that the fusion algorithm has significantly improved measurement results of altitude information, combining short-term and dynamic performance of barometric height with long-term stability of GPS altitude. On this basis, the height controller was designed for miniature UAVs, and successfully applied to the flight control system of a small unmanned aerial vehicle for polar research, with the control error less than 10m during cruise stage.