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While Miura's answer wasn't a solution per-se it pointed me in the right direction (thanks!).

I just found out that if you make this call:

rosservice call /rtabmap/publish_map true false false

rtabmap will successively publish all local maps on the above topic (including headers with origin), hence giving me a chance to capture them, merge them, and republish in merged form using map_server or similar. This is still not the ideal solution but to anyone facing the same issue it gets one unblocked.