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(1) On the wiki tutorial page, it states that you can run an instance of ekf_localization_node. That will output the message type you need. This is the same instance of ekf_localization_node that is taking in the output of navsat_transform_node. Yes, the data path is circular, but necessary: if you drive a robot around inside a building and fuse only IMU and wheel encoder odometry, and then drive outside, you need to know where the robot thought it was so that the transform from lat/long to your world frame is consistent.

(2) Where are you getting velocity information? The filter doesn't take wheel encoder data. It takes twist (velocity) data, which is usually generated from wheel encoders. In any case, yes, fuse all those things into an instance of ekf_localization_node and then pass that in as the third (missing) input from (1) above.

(3) Not sure what you mean here. Try searching for other r_l GPS integration questions, as there are many on ROS Answers, though I admit that the search functionality doesn't always produce the results you'd expect.