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Is there any way to choose which branches of the tf tree are being published without modifying the URDF? For example using some argument in the launch file from where we invoke the robot_state_publisher which specifies that some transformations won't be published?

No, there is no support for this.

Or at least: not in the standard (ie: "official") robot_state_publisher node.

Everything in the urdf stored in the robot_description parameter will be considered by the robot_state_publisher.