New kd tree type for count in range
This commit is contained in:
Guilhem Lavaux
parent
a194f1f00b
commit
1290fdb54c
@ -1,5 +1,5 @@
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SHLIBS= libCosmoTool.so
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SOURCES= loadRamses.cpp yorick.cpp miniargs.cpp fortran.cpp interpolate.cpp load_data.cpp powerSpectrum.cpp octTree.cpp
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SOURCES= loadRamses.cpp yorick.cpp miniargs.cpp fortran.cpp interpolate.cpp load_data.cpp powerSpectrum.cpp octTree.cpp
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LIBS= -lnetcdf_c++ -lnetcdf -lgsl -lgslcblas -lm
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include config.mk
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105
src/kdtree_leaf.hpp
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105
src/kdtree_leaf.hpp
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#ifndef __LEAF_KDTREE_HPP
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#define __LEAF_KDTREE_HPP
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#include <cmath>
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#include "config.hpp"
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#include "bqueue.hpp"
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namespace CosmoTool {
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template<int N, typename CType = ComputePrecision>
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struct KDLeafDef
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{
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typedef CType CoordType;
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typedef float KDLeafCoordinates[N];
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};
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template<int N, typename ValType, typename CType = ComputePrecision>
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struct KDLeafCell
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{
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bool active;
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ValType val;
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typename KDLeafDef<N,CType>::KDLeafCoordinates 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, typename CType = ComputePrecision>
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struct KDLeafTreeNode
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{
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bool leaf;
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union {
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KDLeafCell<N,ValType,CType> *value;
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KDLeafTreeNode<N,ValType,CType> *children[2];
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};
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typename KDLeafDef<N,CType>::KDLeafCoordinates minBound, maxBound;
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#ifdef __KDLEAF_TREE_NUMNODES
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uint32_t numNodes;
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#endif
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};
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template<int N, typename ValType, typename CType = ComputePrecision>
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class KDLeafTree
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{
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public:
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typedef typename KDLeafDef<N,CType>::CoordType CoordType;
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typedef typename KDLeafDef<N>::KDLeafCoordinates coords;
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typedef KDLeafCell<N,ValType,CType> Cell;
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typedef KDLeafTreeNode<N,ValType,CType> Node;
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KDLeafTree(Cell *cells, uint32_t Ncells);
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~KDLeafTree();
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Node *getRoot() { return root; }
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void optimize();
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Node *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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CoordType computeDistance(const Cell *cell, const coords& x) const;
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#ifdef __KDLEAF_TREE_NUMNODES
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uint32_t getNumberInNode(const Node *n) const { return n->numNodes; }
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#else
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uint32_t getNumberInNode(const Node *n) const {
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if (n == 0)
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return 0;
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return 1+getNumberInNode(n->children[0])+getNumberInNode(n->children[1]);
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}
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#endif
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double countInRange(CType sLo, CType sHi, Node *root1 = 0, Node *root2 = 0) const;
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protected:
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Node *nodes;
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uint32_t numNodes, numCells;
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uint32_t lastNode;
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Node *root;
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Cell **sortingHelper;
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Node *buildTree(Cell **cell0,
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uint32_t NumCells,
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uint32_t depth,
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coords minBound,
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coords maxBound);
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double recursiveCountInRange(Node *na, Node *nb, CType sLo, CType sHi) const;
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};
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template<int N, typename T, typename CType>
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uint32_t gatherActiveCells(KDLeafCell<N,T,CType> **cells, uint32_t numCells);
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};
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#include "kdtree_leaf.tcc"
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#endif
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308
src/kdtree_leaf.tcc
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308
src/kdtree_leaf.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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#include <cassert>
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namespace CosmoTool {
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template<int N, typename ValType, typename CType>
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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 KDLeafCell<N,ValType,CType> *a, const KDLeafCell<N,ValType,CType> *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, typename CType>
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KDLeafTree<N,ValType,CType>::~KDLeafTree()
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{
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}
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template<int N, typename ValType, typename CType>
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KDLeafTree<N,ValType,CType>::KDLeafTree(Cell *cells, uint32_t Ncells)
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{
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numNodes = Ncells*3;
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numCells = Ncells;
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nodes = new Node[numNodes];
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sortingHelper = new Cell *[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, typename CType>
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void KDLeafTree<N,ValType,CType>::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, numCells);
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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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// Find min and max corner
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for (uint32_t i = 0; i < activeCells; i++)
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{
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KDLeafCell<N,ValType,CType> *cell = sortingHelper[i];
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for (int k = 0; k < N; k++) {
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if (cell->coord[k] < absoluteMin[k])
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absoluteMin[k] = cell->coord[k];
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if (cell->coord[k] > absoluteMax[k])
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absoluteMax[k] = cell->coord[k];
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}
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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, typename CType>
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uint32_t gatherActiveCells(KDLeafCell<N,ValType,CType> **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, typename CType>
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KDLeafTreeNode<N,ValType,CType> *
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KDLeafTree<N,ValType,CType>::buildTree(Cell **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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assert(lastNode != numNodes);
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Node *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,CType> compare(axis);
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std::sort(cell0, cell0+Ncells, compare);
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}
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node->leaf = false;
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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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if (Ncells == 1)
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{
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node->leaf = true;
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node->value = *cell0;
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#ifdef __KDLEAF_TREE_NUMNODES
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node->numNodes = 1;
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#endif
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return node;
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}
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memcpy(tmpBound, maxBound, sizeof(coords));
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tmpBound[axis] = (*(cell0+mid))->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] = (*(cell0+mid))->coord[axis];
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node->children[1] = buildTree(cell0+mid, Ncells-mid, depth,
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tmpBound, maxBound);
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#ifdef __KDLEAF_TREE_NUMNODES
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node->numNodes = (node->children[0] != 0) ? node->children[0]->numNodes : 0;
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node->numNodes += (node->children[1] != 0) ? node->children[1]->numNodes : 0;
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#endif
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return node;
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}
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template<int N, typename ValType, typename CType>
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uint32_t KDLeafTree<N,ValType,CType>::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, typename CType>
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typename KDLeafDef<N,CType>::CoordType
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KDLeafTree<N,ValType,CType>::computeDistance(const Cell *cell, const coords& x) const
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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, typename CType>
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double KDLeafTree<N,ValType,CType>::countInRange(CType sLo, CType sHigh, Node *root1, Node *root2) const
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{
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double result = recursiveCountInRange((root1 == 0) ? root : root1,
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(root2 == 0) ? root : root2,
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sLo*sLo, sHigh*sHigh);
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return result;
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}
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template<int N, typename ValType, typename CType>
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double KDLeafTree<N,ValType,CType>::recursiveCountInRange(Node *na, Node *nb,
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CType sLo, CType sHi) const
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{
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assert(nb != 0);
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if (na == 0)
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{
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return 0;
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}
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uint32_t numNa = getNumberInNode(na);
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uint32_t numNb = getNumberInNode(nb);
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double Cleft, Cright;
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CType minDist, maxDist;
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if (numNa == 1 && numNb == 1)
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{
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assert(na->leaf && nb->leaf);
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CType ab_dist = computeDistance(na->value, nb->value->coord);
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if (ab_dist >= sLo && ab_dist < sHi)
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return 1;
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else
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return 0;
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}
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assert(numNa > 1 || numNb > 1);
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bool overlapping_a = true, overlapping_b = true;
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for (int k = 0; k < N; k++)
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{
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bool min_a_in_B =
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((na->minBound[k] >= nb->minBound[k] &&
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na->minBound[k] <= nb->maxBound[k]));
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bool max_a_in_B =
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((na->maxBound[k] >= nb->minBound[k] &&
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na->maxBound[k] <= nb->maxBound[k]));
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bool min_b_in_A =
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((nb->minBound[k] >= na->minBound[k] &&
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nb->minBound[k] <= na->maxBound[k]));
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bool max_b_in_A =
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((nb->maxBound[k] >= na->minBound[k] &&
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nb->maxBound[k] <= na->maxBound[k]));
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if (!min_a_in_B && !max_a_in_B)
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overlapping_a = false;
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if (!min_b_in_A && !max_b_in_A)
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overlapping_b = false;
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}
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if (overlapping_a || overlapping_b)
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{
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minDist = 0;
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maxDist = 0;
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for (int k = 0; k < N; k++)
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{
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CType delta = max(nb->maxBound[k]-na->minBound[k],na->maxBound[k]-nb->minBound[k]);
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maxDist += delta*delta;
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}
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}
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else
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{
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minDist = maxDist = 0;
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for (int k = 0; k < N; k++)
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{
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CType delta2;
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delta2 = max(nb->maxBound[k]-na->minBound[k],
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na->maxBound[k]-nb->minBound[k]);
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maxDist += delta2*delta2;
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}
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// mins and maxs
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CType minmax[N][2];
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for (int k = 0; k < N; k++)
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{
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if (na->minBound[k] < nb->minBound[k])
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{
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minmax[k][1] = na->maxBound[k];
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minmax[k][0] = nb->minBound[k];
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}
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else
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{
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minmax[k][1] = nb->maxBound[k];
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minmax[k][0] = na->minBound[k];
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}
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}
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for (int k = 0; k < N; k++)
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{
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CType delta = max(minmax[k][0]-minmax[k][1], 0.);
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minDist += delta*delta;
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}
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}
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if (minDist >= sHi)
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return 0;
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if (maxDist < sLo)
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return 0;
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if (sLo <= minDist && maxDist < sHi)
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return ((double)numNa)*numNb;
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if (numNa < numNb)
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{
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assert(!nb->leaf);
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Cleft = recursiveCountInRange(nb->children[0], na, sLo, sHi);
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Cright = recursiveCountInRange(nb->children[1], na, sLo, sHi);
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}
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else
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{
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assert(!na->leaf);
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Cleft = recursiveCountInRange(na->children[0], nb, sLo, sHi);
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Cright = recursiveCountInRange(na->children[1], nb, sLo, sHi);
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}
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return Cleft+Cright;
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}
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};
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