Generic KD Tree
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Guilhem Lavaux
parent
de35eeabd8
commit
a6341d3378
122
src/mykdtree.hpp
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122
src/mykdtree.hpp
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#ifndef __HV_KDTREE_HPP
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#define __HV_KDTREE_HPP
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#include <cmath>
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#include "config.hpp"
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namespace CosmoTool {
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template<int N>
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struct NGBDef
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{
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typedef float CoordType;
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typedef float NGBCoordinates[N];
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static const int NumCubes = 1 << (N);
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};
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template<int N, typename ValType>
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struct NGBCell
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{
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bool active;
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ValType val;
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typename NGBDef<N>::NGBCoordinates coord;
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};
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class NotEnoughCells: public Exception
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{
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public:
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NotEnoughCells() : Exception() {}
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~NotEnoughCells() throw () {}
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};
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template<int N, typename ValType>
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struct NGBTreeNode
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{
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NGBCell<N,ValType> *value;
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NGBTreeNode<N,ValType> *children[2];
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typename NGBDef<N>::NGBCoordinates minBound, maxBound;
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};
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template<int N, typename ValType>
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class RecursionInfoCells
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{
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public:
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typename NGBDef<N>::NGBCoordinates x;
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typename NGBDef<N>::CoordType r, r2;
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NGBCell<N, ValType> **cells;
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uint32_t currentRank;
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uint32_t numCells;
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};
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template<int N, typename ValType>
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class NGBTree
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{
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public:
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static const int NumCubes = NGBDef<N>::NumCubes;
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public:
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typedef typename NGBDef<N>::CoordType CoordType;
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typedef typename NGBDef<N>::NGBCoordinates coords;
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typedef typename CosmoQueue<NGBCell<N,ValType>*> NGBQueue;
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NGBTree(NGBCell<N,ValType> *cells, uint32_t Ncells);
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~NGBTree();
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uint32_t getIntersection(const coords& x, CoordType r,
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NGBCell<N, ValType> **cells,
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uint32_t numCells)
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throw (NotEnoughCells);
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NGBCell<N, ValType> *getNearestNeighbour(const coords& x);
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void getNearestNeighbours(const coords& x, uint32_t N,
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NGBCell<N, ValType> **cells);
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NGBTreeNode<N,ValType> *getRoot() { return root; }
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void optimize();
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NGBTreeNode<N,ValType> *getAllNodes() { return nodes; }
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uint32_t getNumNodes() const { return lastNode; }
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uint32_t countActives() const;
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protected:
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NGBTreeNode<N, ValType> *nodes;
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uint32_t numNodes;
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uint32_t lastNode;
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NGBTreeNode<N, ValType> *root;
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NGBCell<N, ValType> **sortingHelper;
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NGBTreeNode<N, ValType> *buildTree(NGBCell<N,ValType> **cell0,
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uint32_t N,
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uint32_t depth,
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coords minBound,
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coords maxBound);
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void recursiveIntersectionCells(RecursionInfoCells<N,ValType>& info,
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NGBTreeNode<N,ValType> *node,
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int level)
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throw (NotEnoughCells);
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CoordType computeDistance(NGBCell<N,ValType> *cell, const coords& x);
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void recursiveNearest(NGBTreeNode<N, ValType> *node,
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int level,
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const coords& x,
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CoordType& R2,
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NGBCell<N,ValType>*& cell);
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void recursiveMultiNearest(NGBTreeNode<N, ValType> *node,
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int level,
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const coords& x,
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NGBQueue& q);
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};
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template<int N, class T>
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uint32_t gatherActiveCells(NGBCell<N,T> **cells, uint32_t numCells);
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};
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#include "mykdtree.tcc"
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#endif
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307
src/mykdtree.tcc
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307
src/mykdtree.tcc
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#include <cstring>
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#include <algorithm>
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#include <limits>
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#include <iostream>
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namespace CosmoTool {
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template<int N, typename ValType>
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class CellCompare
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{
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public:
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CellCompare(int k)
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{
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rank = k;
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}
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bool operator()(const NGBCell<N,ValType> *a, const NGBCell<N,ValType> *b) const
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{
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return (a->coord[rank] < b->coord[rank]);
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}
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protected:
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int rank;
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};
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template<int N, typename ValType>
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NGBTree<N,ValType>::~NGBTree()
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{
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}
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template<int N, typename ValType>
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NGBTree<N,ValType>::NGBTree(NGBCell<N,ValType> *cells, uint32_t Ncells)
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{
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numNodes = Ncells;
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nodes = new NGBTreeNode<N,ValType>[numNodes];
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sortingHelper = new NGBCell<N,ValType> *[Ncells];
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for (uint32_t i = 0; i < Ncells; i++)
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sortingHelper[i] = &cells[i];
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optimize();
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}
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template<int N, typename ValType>
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void NGBTree<N,ValType>::optimize()
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{
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coords absoluteMin, absoluteMax;
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std::cout << "Optimizing the tree..." << std::endl;
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uint32_t activeCells = gatherActiveCells(sortingHelper, numNodes);
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std::cout << " number of active cells = " << activeCells << std::endl;
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lastNode = 0;
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for (int i = 0; i < N; i++)
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{
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absoluteMin[i] = -std::numeric_limits<typeof (absoluteMin[0])>::max();
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absoluteMax[i] = std::numeric_limits<typeof (absoluteMax[0])>::max();
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}
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std::cout << " rebuilding the tree..." << std::endl;
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root = buildTree(sortingHelper, activeCells, 0, absoluteMin, absoluteMax);
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std::cout << " done." << std::endl;
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}
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template<int N, typename ValType>
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uint32_t NGBTree<N,ValType>::getIntersection(const coords& x, CoordType r,
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NGBCell<N, ValType> **cells,
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uint32_t numCells)
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throw (NotEnoughCells)
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{
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RecursionInfoCells<N,ValType> info;
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memcpy(info.x, x, sizeof(x));
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info.r = r;
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info.r2 = r*r;
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info.cells = cells;
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info.currentRank = 0;
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info.numCells = numCells;
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recursiveIntersectionCells(info, root, 0);
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return info.currentRank;
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}
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template<int N, typename ValType>
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void NGBTree<N,ValType>::recursiveIntersectionCells(RecursionInfoCells<N,ValType>& info,
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NGBTreeNode<N,ValType> *node,
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int level)
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throw (NotEnoughCells)
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{
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int axis = level % N;
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CoordType d2 = 0;
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if (node->value->active)
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{
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for (int j = 0; j < 3; j++)
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{
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CoordType delta = info.x[j]-node->value->coord[j];
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d2 += delta*delta;
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}
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if (d2 < info.r2)
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{
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if (info.currentRank == info.numCells)
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throw NotEnoughCells();
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info.cells[info.currentRank++] = node->value;
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}
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}
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// The hypersphere intersects the left child node
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if (((info.x[axis]+info.r) > node->minBound[axis]) &&
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((info.x[axis]-info.r) < node->value->coord[axis]))
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{
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if (node->children[0] != 0)
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recursiveIntersectionCells(info, node->children[0],
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level+1);
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}
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if (((info.x[axis]+info.r) > node->value->coord[axis]) &&
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((info.x[axis]-info.r) < node->maxBound[axis]))
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{
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if (node->children[1] != 0)
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recursiveIntersectionCells(info, node->children[1],
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level+1);
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}
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}
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template<int N, typename ValType>
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uint32_t gatherActiveCells(NGBCell<N,ValType> **cells,
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uint32_t Ncells)
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{
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uint32_t swapId = Ncells-1;
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uint32_t i = 0;
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while (!cells[swapId]->active && swapId > 0)
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swapId--;
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while (i < swapId)
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{
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if (!cells[i]->active)
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{
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std::swap(cells[i], cells[swapId]);
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while (!cells[swapId]->active && swapId > i)
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{
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swapId--;
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}
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}
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i++;
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}
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return swapId+1;
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}
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template<int N, typename ValType>
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NGBTreeNode<N, ValType> *NGBTree<N,ValType>::buildTree(NGBCell<N,ValType> **cell0,
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uint32_t Ncells,
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uint32_t depth,
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coords minBound,
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coords maxBound)
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{
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if (Ncells == 0)
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return 0;
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int axis = depth % N;
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NGBTreeNode<N,ValType> *node = &nodes[lastNode++];
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uint32_t mid = Ncells/2;
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coords tmpBound;
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// Isolate the environment
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{
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CellCompare<N,ValType> compare(axis);
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std::sort(cell0, cell0+Ncells, compare);
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}
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node->value = *(cell0+mid);
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memcpy(&node->minBound[0], &minBound[0], sizeof(coords));
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memcpy(&node->maxBound[0], &maxBound[0], sizeof(coords));
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memcpy(tmpBound, maxBound, sizeof(coords));
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tmpBound[axis] = node->value->coord[axis];
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depth++;
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node->children[0] = buildTree(cell0, mid, depth, minBound, tmpBound);
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memcpy(tmpBound, minBound, sizeof(coords));
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tmpBound[axis] = node->value->coord[axis];
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node->children[1] = buildTree(cell0+mid+1, Ncells-mid-1, depth,
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tmpBound, maxBound);
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return node;
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}
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template<int N, typename ValType>
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uint32_t NGBTree<N,ValType>::countActives() const
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{
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uint32_t numActive = 0;
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for (uint32_t i = 0; i < lastNode; i++)
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{
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if (nodes[i].value->active)
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numActive++;
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}
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return numActive;
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}
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template<int N, typename ValType>
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typename NGBDef<N>::CoordType
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NGBTree<N,ValType>::computeDistance(NGBCell<N, ValType> *cell, const coords& x)
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{
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CoordType d2 = 0;
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for (int i = 0; i < N; i++)
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{
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CoordType delta = cell->coord[i] - x[i];
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d2 += delta*delta;
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}
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return d2;
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}
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template<int N, typename ValType>
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void
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NGBTree<N,ValType>::recursiveNearest(
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NGBTreeNode<N,ValType> *node,
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int level,
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const coords& x,
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CoordType& R2,
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NGBCell<N,ValType> *& best)
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{
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CoordType d2 = 0;
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int axis = level % N;
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NGBTreeNode<N,ValType> *other, *go;
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if (x[axis] < node->value->coord[axis])
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{
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// The best is potentially in 0.
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go = node->children[0];
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other = node->children[1];
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}
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else
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{
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// If not it is in 1.
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go = node->children[1];
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other = node->children[0];
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if (go == 0)
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{
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go = other;
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other = 0;
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}
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}
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if (go != 0)
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{
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recursiveNearest(go, level+1,
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x, R2,best);
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}
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else
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{
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CoordType thisR2 = computeDistance(node->value, x);
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if (thisR2 < R2)
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{
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R2 = thisR2;
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best = node->value;
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}
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return;
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}
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// Check if current node is not the nearest
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CoordType thisR2 =
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computeDistance(node->value, x);
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if (thisR2 < R2)
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{
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R2 = thisR2;
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best = node->value;
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}
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// Now we found the best. We check whether the hypersphere
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// intersect the hyperplane of the other branch
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CoordType delta1;
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delta1 = x[axis]-node->value->coord[axis];
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if (delta1*delta1 < R2)
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{
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// The hypersphere intersects the hyperplane. Try the
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// other branch
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if (other != 0)
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{
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recursiveNearest(other, level+1, x, R2, best);
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}
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}
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}
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template<int N, typename ValType>
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NGBCell<N, ValType> *
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NGBTree<N,ValType>::getNearestNeighbour(const coords& x)
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{
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CoordType R2 = INFINITY;
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NGBCell<N,ValType> *best = 0;
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recursiveNearest(root, 0, x, R2, best);
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return best;
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}
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template<int N, typename ValType>
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void NGBTree<N,ValType>::getNearestNeighbours(const coords& x, uint32_t N2,
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NGBCell<N, ValType> **cells)
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{
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}
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};
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