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1)

My understanding is that robot_pose_ekf is a deprecated/orphaned package. Considering that, and how active the support for robot_localization is, you should use robot_localization. It does exactly what I think you are asking for and the wiki page is super well documented and there is a lot of discussion here on RA about how to setup and debug the package.

Personally I learned by installing the Clearpath Husky simulator and learning from there. You can see here in the husky_control package how they set up robot_localization to generate the transform from odom to base_link by fusing odom and imu measurements.

2)

Generally, it is my understanding, that the tf tree should be used by every application that needs to understand its location. So in my opinion looking up transforms between things is a good way to find location, but may not translate perfectly into every single specific use case you can imagine.