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I don't get it why you are stop/starting move base, if you can clarify that, I could give you better options. That is quite aggressive an I would avoid doing it.

What I can suggest now is:

1 - you can call a move_base service to clear layers (http://wiki.ros.org/move_base#Services)

2 - the layers have a dynamic reconfigurable parameter enabled , so you can (de)activate a single layer

3 - you can add recovery behaviour that clear a specific layer if your robot is stuck, you can choose what layer to clear and from what distance to begin clearing, but they will only be triggered if the plan fails or by oscillation conditions (check http://wiki.ros.org/move_base#Parameters).

3 - I've never used it, but it may suit you: https://github.com/DLu/decaying_obstacle_layer