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Hi Stefan,
Could you please ask future MoveIt! related questions on the moveit-users mailing list: moveit-users@googlegroups.com. Its easier for us to track MoveIt! specific questions there.
Regarding your questions: you can have MoveIt! plan and maintain everything in a different frame: e.g. odom_combined for the PR2 or map. To do this right, you need to have a virtual joint in your SRDF (which can be added through the Setup Assistant) that connects the frame to the root link on your robot: e.g. for the PR2, the corresponding line in the SRDF looks like this:
<virtual_joint name="world_joint" type="planar" parent_frame="odom_combined" child_link="base_footprint"/>
This forces MoveIt! to do everything in the odom_combined frame. It uses TF information to figure out this particular transform. MoveIt! does use transforms outside of those belonging to the robot, it just needs to know about them through the SRDF.