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I have an AUV with a 12 inch diameter, 29 inch long capsule. Inside the capsule sits an Intel NUC computer, an NVIDIA Jetson GPU, an Arduino Mega, a Sparton IMU (9 DOF) as well as a custom voltage regulator. Given the noise, would it be practical to attempt to use my magnetometer, even with calibration and filtering? If so, what should I keep in mind regarding the placement of my IMU in the AUV's capsule, given that I have already read this post?

I have tried moving it as far away from the sources of noise as possible but the noise persists. I looked into shielding, but that looks like it would block the Earth's magnetic data as well, which would render the shield pointless.

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Mags are used in almost all UAVs. It will be useful and it will be a unique source of information.

Adding a some shielding between the mag and your computers and power lines will greatly reduced the noise. Noise can be further reduced by twisting all of the wires that carry significant current (wires to motors and ESCs).

Be aware that the measurement will still be noisy. It should be incorporated into your estimated state using a Kalman filter. Look into fusing measurements from the mag with measurements from an IMU . This will give far superior results compared to treating the measurements as your real state.

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As mentioned in the previous answer, many small, low-cost underwater (and aerial) vehicles use a magnetic compass. You need a good procedure for both hard-iron and soft-iron calibration of your magnetometer. Constantly having to calibrate them sucks, but they're way less expensive than a FOG. With good calibration, you should be able to achieve adequate performance with the magnetometer. If you're operating indoors in a tank, you should be able to rely on visual based odometry and other approaches that have limited applicability in the open ocean. DVL-based dead-reckoning has worked just fine, but, if you don't have a DVL, you'll get much better performance with an EKF...but your IMU may provide a KF output (I know the microstrain does). Also, instead of shielding the compass, you might try shielding the external sources of electro-magnetic interference.

Giancarlo Troni's paper on bias calibration is probably worth a read: https://ieeexplore.ieee.org/document/6942597/

If your AUV has a DVL, Giancarlo spent much of his PhD working on DVL-AHRS alignment and calibration: https://ieeexplore.ieee.org/document/6405003/

https://ieeexplore.ieee.org/document/6094942/

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