Hi,
I think I wasn't clear about what we'd like to do.
Obviously all environment data will end up in the Octomap as usual.
Now, when we have observed an actual object (e.g. a cup), but don't know, what it is yet, we'd like to try to grasp or place it.
We, however, do know that this cluster of points is an object. So this should be removed from the octomap, so that we do not get collisions when interacting with these points. This removal usually happens when you add this as a moveit_msgs/CollisionObject and/or attach this to the end effector.
The goal is to only have this cluster of points as a CollisionObject, but keep all other points integrated in the Octomap to avoid collisions. What we do right now is to put the Octomap in the AllowedCollisionMatrix until we have handled the object, which is obviously dangerous.
So, maybe a reformulation of the question would be: What is the best way to interact with objects represented by point clouds in MoveIt? One possible answer would be: Run surface reconstruction to get a mesh. I'd like to know if someone can confirm/guess that this might be unnecessary as only a meshes vertices are considered.