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Found where the problem was by looking through the rxconsole printouts:

[WARN]    Could not transform imu message from IMU to base_footprint. Imu will not be activated yet.

Turns out that the frame_id when I published the /imu/data was not set to gyro_link to match the URDF. That's why robot_pose_ekf could not work properly.

For those of you reading this who are just starting out ROS/navigation stack, it would be good to remember the difference between "topic" and "frame", and the need to connect the two when publishing the topic.