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You can check our new paper about OctoMap (PDF preprint) for a detailed analysis of the performance.

Looking at our outdoor dataset (50m maxrange), it will take about 1.7 seconds to insert 700000 points into the map at 20cm resolution. Most of this time will be spent in the raycasting operation. So I would strongy suggest downsampling the initial clouds, e.g. with a PCL voxel grid first. Something below the OctoMap resolution (5-10cm) should be fine so you don't lose too much detail.

To obtain all obstacles in the map, simply traverse it with a leaf iterator: http://octomap.github.com/octomap/doc/classleaf__iterator.html#details

This is the most efficient way, much faster than looping over all possible coordinates.

For finding connected components, best work on OcTreeKeys directly. You might find some code in the class "OcTreeLUT" useful for neighbor finding, but we're not really using that code anymore (consider it experimental and untested).