Remove small clusters from a CGAL::Point_set_3

small_cluster_removal.cpp

template < typename Iterable_t >
static std::map<int, int>
compute_cluster_size(const Iterable_t& cluster_map) {
    std::map<int, int> cluster_size;

    for ( const auto& idx : cluster_map ) {
        if ( cluster_size.find(idx) == cluster_size.end() ) {
            // New idx.
            cluster_size[idx] = 1;
        } else {
            // Existing cluster.
            cluster_size[idx]++;
        }
    }

    return cluster_size;
}

// sr::PointSet_t is CGAL::Point_set_3.
void sr::compute_and_remove_small_clusters( 
    sr::PointSet_t& cloud, 
    double avg_spacing, 
    int size_limit, 
    std::ostream& os ) {
    sr::PointSet_t::Property_map<int> cluster_map;

    // Reset or create a new property map.
    if ( cloud.has_property_map<int>("cluster") ) {
        boost::tie( cluster_map, boost::tuples::ignore ) = 
            cloud.property_map<int>("cluster");

        cloud.remove_property_map(cluster_map);
    }

    bool success = false;
    boost::tie( cluster_map, success ) = 
        cloud.add_property_map<int>("cluster", -1);

    if ( !success ) {
        os << "Cannot add cluster property map. \n";
        return;
    }

    // Clustering.
    CGAL::Real_timer rt; rt.start();
    std::size_t n_clusters = 
        CGAL::cluster_point_set(
            cloud,
            cluster_map,
            cloud.parameters().neighbor_radius(avg_spacing)
        );
    rt.stop();
    os << "Find " << n_clusters << " clusters in " << rt.time() << " seoncds. \n";

    // Compute the cluster size.
    std::map<int, int> cluster_size = compute_cluster_size( cluster_map );

    // Remove small clusters.
    for ( auto it = cloud.begin(); it != cloud.end(); ++it ) {
        // Get the cluster index.
        const auto c_idx = cluster_map[*it];

        // Get the cluster size.
        const auto c_size = cluster_size[c_idx];

        if ( c_size <= size_limit ) cloud.remove(it);
    }

    cloud.collect_garbage();
}

I misread the documentation as well, so I thought the code would work as written when downloaded. It did not. Once I added the decrement to the "it" loop counter it worked great. I embedded your call into my program, so I cannot just push a commit. I have pasted the corrected code below. It shows my counters to check that everything added up correctly while debugging, but really only one line of your code (i.e., it--;) changed.

num_pnts = 0;
size_t num_rmvd = 0,num_kept = 0;
for ( auto it = wall_points.begin(); it != wall_points.end(); ++it ) 
{
    num_pnts++;
    if ( rmv_point.at(*it) ) 
    {
        wall_points.remove(it);
        it--;
        num_rmvd ++;
    }
    else
       num_kept ++;
}    
std::cout << num_pnts << " were processed with "<<num_rmvd<<" removed and "<<num_kept<<" kept\n\n"<<std::endl;
wall_points.collect_garbage();