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You might wanna give the mapstitch package (http:// www.ros.org/wiki/mapstitch) a try.

It uses opencv's estimateRigidTransform method to calculate rotation and translation between two maps. The estimation works best the larger the maps are, that's why mapstitch actually needs three topics of published maps: map, world and align. The map on the align topic will be rotated/translated to the world map and this transformation will be published whenever the map topic gets updated.

We aligned maps after they have been completely build (which was enough in our use case), while replaying the original dataset. It might however also work in a setup with incomplete maps.