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In order to develop the low cost and high precision navigation system of a small unmanned aerial vehicle (UAV), a data fusion method based on the strap-down inertial navigation system (SINS) and the Global Positioning System (GPS), and the algorithms simplified of the Kalman filtering were discussed deeply in the paper. A SINS which adopted an improved attitude-updating algorithm was proposed using the micro-electro-mechanism system inertial measurement unit (MEMS-IMU) and the digital signal processor (DSP). The integration method of the SINS and GPS double-system and the integrated system error sources were analysed in the paper. Then the theory pattern of the SINS and GPS integrated navigation system was designed. The experiment results of the theory pattern showed that the integrated navigation system had the higher positioning and measurement accuracy, the lower cost and better real time. It could meet the navigation and guidance needs of a small low-cost UAV. It provided the effective theoretical basis of the test prototype.