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MelchiorSchuhMelchiorSchuh
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Merge pull request #986 from Geode-solutions/feat/implement_dynamic_kdtree
Feat/implement_dynamic_kdtree
2 parents c2aab5d + 16d7a8b commit 743634b

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‎bindings/python/requirements.txt‎

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# This file is autogenerated by pip-compile with Python 3.10
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# by the following command:
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#
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# pip-compile bindings/python/requirements.in
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# pip-compile --pre bindings/python/requirements.in
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#

‎include/geode/geometry/dynamic_nn_search.hpp‎

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/*
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* Copyright (c) 2019 - 2024 Geode-solutions
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*
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*/
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#pragma once
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#include <geode/basic/pimpl.hpp>
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#include <geode/geometry/common.hpp>
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#include <geode/geometry/point.hpp>
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namespace geode
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{
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/*!
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* Given a list of points, this class returns neighboring points.
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*/
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template < index_t dimension >
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class DynamicNNSearch
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{
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OPENGEODE_DISABLE_COPY( DynamicNNSearch );
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public:
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explicit DynamicNNSearch( std::vector< Point< dimension > > points );
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DynamicNNSearch( DynamicNNSearch&& other ) noexcept;
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~DynamicNNSearch();
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index_t nb_points() const;
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const Point< dimension >& point( index_t index ) const;
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void add_point( const Point< dimension >& point );
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/*!
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* Get the neighbors closer than a given distance from the given point
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* or within a sphere
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* @param[in] point The center of the sphere
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* @param[in] threshold_distance The radius of the sphere
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* @return the list of points inside this distance
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*/
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std::vector< index_t > radius_neighbors(
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const Point< dimension >& point, double threshold_distance ) const;
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private:
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IMPLEMENTATION_MEMBER( impl_ );
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};
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ALIAS_2D_AND_3D( DynamicNNSearch );
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} // namespace geode

‎src/geode/geometry/CMakeLists.txt‎

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@@ -38,6 +38,7 @@ add_geode_library(
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"common.cpp"
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"coordinate_system.cpp"
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"distance.cpp"
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"dynamic_nn_search.cpp"
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"frame.cpp"
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"information.cpp"
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"intersection.cpp"
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"common.hpp"
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"coordinate_system.hpp"
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"distance.hpp"
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"dynamic_nn_search.hpp"
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"frame.hpp"
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"information.hpp"
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"intersection.hpp"

‎src/geode/geometry/dynamic_nn_search.cpp‎

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/*
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* Copyright (c) 2019 - 2024 Geode-solutions
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*
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*/
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#include <geode/geometry/dynamic_nn_search.hpp>
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#include <nanoflann.hpp>
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#include <absl/algorithm/container.h>
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#include <geode/basic/logger.hpp>
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#include <geode/basic/pimpl_impl.hpp>
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namespace geode
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{
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template < index_t dimension >
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class DynamicNNSearch< dimension >::Impl
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{
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public:
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explicit Impl( std::vector< Point< dimension > > points )
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: cloud_{ std::move( points ) },
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dynamic_nn_tree_{ dimension, cloud_ }
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{
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}
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const Point< dimension >& point( const index_t index ) const
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{
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return cloud_.points.at( index );
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}
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index_t nb_points() const
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{
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return cloud_.kdtree_get_point_count();
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}
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std::vector< index_t > radius_neighbors(
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const Point< dimension >& point,
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const double threshold_distance ) const
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{
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std::vector< nanoflann::ResultItem< index_t, double > > results;
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nanoflann::RadiusResultSet< double, index_t > resultSet(
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threshold_distance * threshold_distance, results );
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dynamic_nn_tree_.findNeighbors( resultSet, &copy( point )[0] );
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absl::c_sort( results, nanoflann::IndexDist_Sorter() );
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std::vector< index_t > indices;
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indices.reserve( results.size() );
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for( const auto& result : results )
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{
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indices.emplace_back( result.first );
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}
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return indices;
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}
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void add_point( const Point< dimension >& point )
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{
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const auto nb_points = cloud_.kdtree_get_point_count();
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cloud_.points.emplace_back( point );
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dynamic_nn_tree_.addPoints( nb_points, nb_points );
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}
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private:
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std::array< double, dimension > copy(
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const Point< dimension >& point ) const
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{
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std::array< double, dimension > result;
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for( const auto i : LRange{ dimension } )
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{
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result[i] = point.value( i );
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}
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return result;
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}
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struct PointCloud
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{
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std::vector< Point< dimension > > points;
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size_t kdtree_get_point_count() const
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{
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return points.size();
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}
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double kdtree_get_pt( size_t idx, size_t dim ) const
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{
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return points[idx].value( dim );
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}
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// Optional bounding-box computation: return false to default to a
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// standard bbox computation loop.
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// Return true if the BBOX was already computed by the class and
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// returned in "bb" so it can be avoided to redo it again. Look at
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// bb.size() to find out the expected dimensionality (e.g. 2 or 3
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// for point clouds)
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template < class BBOX >
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bool kdtree_get_bbox( BBOX& /* bb */ ) const
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{
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return false;
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}
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};
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private:
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PointCloud cloud_;
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nanoflann::KDTreeSingleIndexDynamicAdaptor<
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nanoflann::L2_Simple_Adaptor< double, PointCloud >,
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PointCloud,
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dimension,
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index_t >
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dynamic_nn_tree_;
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};
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template < index_t dimension >
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DynamicNNSearch< dimension >::DynamicNNSearch(
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std::vector< Point< dimension > > points )
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: impl_{ std::move( points ) }
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{
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}
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template < index_t dimension >
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DynamicNNSearch< dimension >::DynamicNNSearch(
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DynamicNNSearch&& ) noexcept = default;
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template < index_t dimension >
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DynamicNNSearch< dimension >::~DynamicNNSearch() = default;
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template < index_t dimension >
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const Point< dimension >& DynamicNNSearch< dimension >::point(
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index_t index ) const
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{
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return impl_->point( index );
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}
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template < index_t dimension >
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index_t DynamicNNSearch< dimension >::nb_points() const
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{
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return impl_->nb_points();
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}
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template < index_t dimension >
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std::vector< index_t > DynamicNNSearch< dimension >::radius_neighbors(
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const Point< dimension >& point, double threshold_distance ) const
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{
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return impl_->radius_neighbors( point, threshold_distance );
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}
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template < index_t dimension >
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void DynamicNNSearch< dimension >::add_point(
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const Point< dimension >& point )
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{
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return impl_->add_point( point );
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}
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template class opengeode_geometry_api DynamicNNSearch< 2 >;
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template class opengeode_geometry_api DynamicNNSearch< 3 >;
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} // namespace geode

‎src/geode/geometry/points_sort.cpp‎

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* the two halves
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*/
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template < typename Compare >
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itr split( const itr& begin, const itr& end, const Compare& cmp )
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itr split_container( const itr& begin, const itr& end, const Compare& cmp )
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{
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if( begin >= end )
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{
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const auto m0 = begin;
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const auto m8 = end;
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const auto m4 = split( m0, m8, compX );
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const auto m2 = split( m0, m4, compY );
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const auto m1 = split( m0, m2, compZ );
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const auto m3 = split( m2, m4, compZ );
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const auto m6 = split( m4, m8, compY );
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const auto m5 = split( m4, m6, compZ );
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const auto m7 = split( m6, m8, compZ );
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const auto m4 = split_container( m0, m8, compX );
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const auto m2 = split_container( m0, m4, compY );
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const auto m1 = split_container( m0, m2, compZ );
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const auto m3 = split_container( m2, m4, compZ );
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const auto m6 = split_container( m4, m8, compY );
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const auto m5 = split_container( m4, m6, compZ );
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const auto m7 = split_container( m6, m8, compZ );
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morton_mapping< COORDZ >( points, m0, m1 );
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morton_mapping< COORDY >( points, m1, m2 );
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morton_mapping< COORDY >( points, m2, m3 );
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const auto m0 = begin;
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const auto m4 = end;
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const auto m2 = split( m0, m4, compX );
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const auto m1 = split( m0, m2, compY );
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const auto m3 = split( m2, m4, compY );
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const auto m2 = split_container( m0, m4, compX );
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const auto m1 = split_container( m0, m2, compY );
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const auto m3 = split_container( m2, m4, compY );
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morton_mapping< COORDY >( points, m0, m1 );
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morton_mapping< COORDX >( points, m1, m2 );
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morton_mapping< COORDX >( points, m2, m3 );

‎tests/geometry/CMakeLists.txt‎

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${PROJECT_NAME}::basic
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${PROJECT_NAME}::geometry
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)
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add_geode_test(
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SOURCE "test-dynamic-nnsearch.cpp"
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DEPENDENCIES
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${PROJECT_NAME}::basic
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${PROJECT_NAME}::geometry
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)
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add_geode_test(
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SOURCE "test-intersection.cpp"
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DEPENDENCIES

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