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Hi there. I don't know if you still have the question (probably not...).
I have some experience on this problem. Here are some suggestions:
write a code with octomap library to load the ot file, and to extract xyz from it (like the xyz of occupied grids). Here is a hint:
https://github.com/OctoMap/octomap/blob/v1.8-fixes/octomap/src/octree2pointcloud.cpp
Look at line 86 to 93
you can get xyz through "getCoordinate"
In quadcopter navigation area, there is another type of map: tsdf, here are some useful links from ETHZ ASL on it.
simulator:
https://github.com/GimpelZhang/rotors_simulator
to get ground truth of the map:
https://github.com/ethz-asl/voxblox_ground_truth