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The three bullet points under moveit integration can be addressed by sticking to URDF + xacro. You can have a URDF for each model, and xacro to configure the URDFs differently. The URDF files can be loaded into Gazebo and into ROS for use with MoveIt.

I don't know much about moveit planning scenes. Can they be generated from sensor data, does it require URDF, or is it a special format?

Could you explaing your last bullet point "What to push to TF..."? I'm not sure what your question is.