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It turns out that the biggest issue was that the robot was not able to perform all the turns indicated by move_base cmd_vel. In fact it seems that the robot was only able to move in a straight line or take sharp left / right turns.
Not being able to turn slightly it cause the robot inabilty to steer smoothly and this was confusing the planner and thus having to first move into an area where it could potentially take a sharp turn. By refining the code which converts cmd_vel to odom and cmd_vel to motor signals and testing by comparing actual movements with the ones projected on RViz I was able to improve the navigation drastically and now the robot is able to perform better trajectories.