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I'm not sure I 100% follow your issue, but if I were to rephrase you can tell me if this is what you mean: you're running SLAM on a robot providing the map->odom transform and your robot is providing the odom->base_link transform via the encoders. When you're doing this in (what it appears to be simulation of a square, featureless room) your space, the robot is jumping around.

From looking at the photo provided, I have also seen this of gmapping when you put it in a regular, featureless environment like a square room with nothing in it. You need to add some features or make the environment not exactly the same to the simulation for gmapping to grab onto things correctly.