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The collision detection of planning_environment ( http://wiki.ros.org/planning_environment ) seems to be using the collision checker of ODE (open dynamics engine). The codes are not available online now, but they are:
Anyway, unless fixing this bug, collision detection between two cylinder models does not work.
Hence, a better solution is using other collision detection library, such as:
Though MoveIt! is an integrated planning tool, we can use it as a collision detection library (and it is easy to use on ROS).
The following videos are the similar situations where we are using MoveIt! as a collision checker. No problem is happening in the collision detection between two cylinder models case.