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This paper is concerned with orientation estimation using inertial and magnetic sensors. A new measurement equation is proposed for the quaternion-based indirect Kalman filter. Instead of using magnetic sensor data directly in the measurement equation, the data are modified so that the magnetic sensor data almost do not affect pitch and roll estimation during the measurement update. The proposed algorithms can be used for an application, where pitch and roll estimation is critical and there are large magnetic disturbances. Through an experiment and simulations, the proposed algorithms are compared with the standard method that uses magnetic sensor data for pitch and roll estimation. Using 50 simulation data, it is shown that pitch and roll estimation errors are significantly smaller when there are magnetic disturbances.