694 lines
18 KiB
C++
694 lines
18 KiB
C++
#include "replicateGenerator.hpp"
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#include <cstring>
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#include "omptl/omptl_algorithm"
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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 KDCell<N,ValType,CType> *a, const KDCell<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, typename CellSplitter>
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KDTree<N,ValType,CType,CellSplitter>::~KDTree()
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{
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}
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template<int N, typename ValType, typename CType, typename CellSplitter>
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KDTree<N,ValType,CType,CellSplitter>::KDTree(Cell *cells, NodeIntType Ncells)
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{
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periodic = false;
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base_cell = cells;
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numNodes = Ncells;
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nodes = new Node[numNodes];
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sortingHelper = new Cell *[Ncells];
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for (NodeIntType 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, typename CellSplitter>
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void KDTree<N,ValType,CType,CellSplitter>::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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NodeIntType 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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// Find min and max corner
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for (NodeIntType i = 0; i < activeCells; i++)
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{
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KDCell<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, typename CellSplitter>
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uint32_t KDTree<N,ValType,CType,CellSplitter>::getIntersection(const coords& x, CoordType r,
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KDTree<N,ValType,CType,CellSplitter>::Cell **cells,
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uint32_t numCells)
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{
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RecursionInfoCells<N,ValType,CType> 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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info.distances = 0;
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recursiveIntersectionCells<false>(info, root, 0);
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if (periodic)
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{
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ReplicateGenerator<float, N> r(x, replicate);
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do
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{
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coords x_new;
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r.getPosition(info.x);
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recursiveIntersectionCells<false>(info, root, 0);
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}
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while (r.next());
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}
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return info.currentRank;
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}
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template<int N, typename ValType, typename CType, typename CellSplitter>
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uint32_t KDTree<N,ValType,CType,CellSplitter>::getIntersection(const coords& x, CoordType r,
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Cell **cells,
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CoordType *distances,
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uint32_t numCells)
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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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info.distances = distances;
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recursiveIntersectionCells<false>(info, root, 0);
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if (periodic)
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{
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ReplicateGenerator<float, N> r(x, replicate);
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do
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{
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coords x_new;
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r.getPosition(info.x);
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recursiveIntersectionCells<false>(info, root, 0);
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}
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while (r.next());
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}
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return info.currentRank;
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}
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template<int N, typename ValType, typename CType, typename CellSplitter>
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uint32_t KDTree<N,ValType,CType,CellSplitter>::countCells(const coords& x, CoordType r)
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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 = 0;
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info.currentRank = 0;
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info.numCells = 0;
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info.distances = 0;
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recursiveIntersectionCells<true>(info, root, 0);
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if (periodic)
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{
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ReplicateGenerator<float, N> r(x, replicate);
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do
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{
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coords x_new;
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r.getPosition(info.x);
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recursiveIntersectionCells<true>(info, root, 0);
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}
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while (r.next());
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}
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return info.currentRank;
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}
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template<int N, typename ValType, typename CType, typename CellSplitter>
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template<bool justCount>
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void KDTree<N,ValType,CType,CellSplitter>::recursiveIntersectionCells(RecursionInfoCells<N,ValType,CType>& info,
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Node *node,
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int level)
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{
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int axis = level % N;
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CoordType d2 = 0;
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#if __KD_TREE_ACTIVE_CELLS == 1
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if (node->value->active)
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#endif
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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 (!justCount)
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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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if (info.distances)
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info.distances[info.currentRank] = d2;
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}
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info.currentRank++;
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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<justCount>(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<justCount>(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, typename CType>
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NodeIntType gatherActiveCells(KDCell<N,ValType,CType> **cells,
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NodeIntType Ncells)
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{
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NodeIntType swapId = Ncells-1;
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NodeIntType i = 0;
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#if __KD_TREE_ACTIVE_CELLS == 1
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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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#endif
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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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void KD_default_cell_splitter<N,ValType,CType>::operator()(KDCell<N,ValType,CType> **cells, NodeIntType Ncells,
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NodeIntType& split_index, int axis,
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typename KDDef<N,CType>::KDCoordinates minBound,
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typename KDDef<N,CType>::KDCoordinates maxBound)
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{
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CellCompare<N,ValType,CType> compare(axis);
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omptl::sort(cells,cells+Ncells,compare); // std::sort(cells, cells+Ncells, compare);
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split_index = Ncells/2;
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}
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template<int N, typename ValType, typename CType, typename CellSplitter>
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KDTreeNode<N,ValType,CType> *KDTree<N,ValType,CType,CellSplitter>::buildTree(Cell **cell0,
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NodeIntType 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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Node *node;
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int axis = depth % N;
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NodeIntType mid;
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coords tmpBound;
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NodeIntType nodeId;
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#pragma omp atomic capture
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nodeId = (this->lastNode)++;
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node = &nodes[nodeId];
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// Isolate the environment
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splitter(cell0, Ncells, mid, axis, minBound, maxBound);
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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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#pragma omp task private(tmpBound)
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{
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node->children[0] = buildTree(cell0, mid, depth, minBound, tmpBound);
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}
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memcpy(tmpBound, minBound, sizeof(coords));
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tmpBound[axis] = node->value->coord[axis];
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#pragma omp task private(tmpBound)
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{
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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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}
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#pragma omp taskwait
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#ifdef __KD_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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node->numNodes++;
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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, typename CellSplitter>
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NodeIntType KDTree<N,ValType,CType,CellSplitter>::countActives() const
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{
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NodeIntType numActive = 0;
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for (NodeIntType i = 0; i < lastNode; i++)
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{
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#if __KD_TREE_ACTIVE_CELLS == 1
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if (nodes[i].value->active)
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#endif
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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, typename CellSplitter>
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typename KDDef<N,CType>::CoordType
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KDTree<N,ValType,CType,CellSplitter>::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, typename CellSplitter>
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void
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KDTree<N,ValType,CType,CellSplitter>::recursiveNearest(
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Node *node,
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int level,
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const coords& x,
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CoordType& R2,
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Cell *& best)
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{
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CoordType d2 = 0;
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int axis = level % N;
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Node *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, typename CType, typename CellSplitter>
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KDCell<N,ValType,CType> *
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KDTree<N,ValType,CType,CellSplitter>::getNearestNeighbour(const coords& x)
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{
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CoordType R2 = INFINITY;
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Cell *best = 0;
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recursiveNearest(root, 0, x, R2, best);
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if (periodic)
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{
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ReplicateGenerator<float, N> r(x, replicate);
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do
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{
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coords x_new;
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r.getPosition(x_new);
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recursiveNearest(root, 0, x_new, R2, best);
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}
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while (r.next());
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}
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return best;
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}
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template<int N, typename ValType, typename CType, typename CellSplitter>
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void
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KDTree<N,ValType,CType,CellSplitter>::recursiveMultipleNearest(RecursionMultipleInfo<N,ValType,CType>& info, Node *node,
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int level)
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{
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CoordType d2 = 0;
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int axis = level % N;
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Node *other, *go;
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if (info.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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recursiveMultipleNearest(info, go, level+1);
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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, info.x);
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info.queue.push(node->value, thisR2);
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info.traversed++;
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// if (go == 0)
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// return;
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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 = info.x[axis]-node->value->coord[axis];
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if (delta1*delta1 < info.queue.getMaxPriority())
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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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recursiveMultipleNearest(info, other, level+1);
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}
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}
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}
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template<int N, typename ValType, typename CType, typename CellSplitter>
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void KDTree<N,ValType,CType,CellSplitter>::getNearestNeighbours(const coords& x, uint32_t N2,
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Cell **cells)
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{
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RecursionMultipleInfo<N,ValType> info(x, cells, N2);
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for (int i = 0; i < N2; i++)
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cells[i] = 0;
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recursiveMultipleNearest(info, root, 0);
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if (periodic)
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{
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ReplicateGenerator<float, N> r(x, replicate);
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do
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{
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coords x_new;
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r.getPosition(info.x);
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recursiveMultipleNearest(info, root, 0);
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}
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while (r.next());
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}
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// std::cout << "Traversed = " << info.traversed << std::endl;
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}
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template<int N, typename ValType, typename CType, typename CellSplitter>
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void KDTree<N,ValType,CType,CellSplitter>::getNearestNeighbours(const coords& x, uint32_t N2,
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Cell **cells,
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CoordType *distances)
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{
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RecursionMultipleInfo<N,ValType> info(x, cells, N2);
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for (int i = 0; i < N2; i++)
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cells[i] = 0;
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recursiveMultipleNearest(info, root, 0);
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if (periodic)
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{
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ReplicateGenerator<float, N> r(x, replicate);
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do
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{
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coords x_new;
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r.getPosition(info.x);
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recursiveMultipleNearest(info, root, 0);
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}
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while (r.next());
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}
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memcpy(distances, info.queue.getPriorities(), sizeof(CoordType)*N2);
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}
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#ifdef __KD_TREE_SAVE_ON_DISK
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#define KDTREE_DISK_SIGNATURE "KDTREE"
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#define KDTREE_DISK_SIGNATURE_LEN 7
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template<int N, typename CType>
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struct KDTreeOnDisk
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{
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long cell_id;
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long children_node[2];
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typename KDDef<N, CType>::KDCoordinates minBound, maxBound;
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};
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struct KDTreeHeader
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{
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char id[KDTREE_DISK_SIGNATURE_LEN];
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long nodesUsed, numCells;
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long rootId;
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};
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template<int N, typename ValType, typename CType, typename CellSplitter>
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void KDTree<N,ValType,CType,CellSplitter>::saveTree(std::ostream& o) const
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{
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KDTreeHeader h;
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strncpy(h.id, KDTREE_DISK_SIGNATURE, KDTREE_DISK_SIGNATURE_LEN);
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h.nodesUsed = lastNode;
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h.numCells = numNodes;
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h.rootId = root - nodes;
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o.write((char*)&h, sizeof(h));
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for (long i = 0; i < lastNode; i++)
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{
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KDTreeOnDisk<N,CType> node_on_disk;
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node_on_disk.cell_id = nodes[i].value - base_cell;
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if (nodes[i].children[0] == 0)
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node_on_disk.children_node[0] = -1L;
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else
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node_on_disk.children_node[0] = nodes[i].children[0] - nodes;
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assert((node_on_disk.children_node[0] == -1) || ((node_on_disk.children_node[0] >= 0) && (node_on_disk.children_node[0] < lastNode)));
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if (nodes[i].children[1] == 0)
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node_on_disk.children_node[1] = -1L;
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else
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node_on_disk.children_node[1] = nodes[i].children[1] - nodes;
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assert((node_on_disk.children_node[1] == -1) || ((node_on_disk.children_node[1] >= 0) && (node_on_disk.children_node[1] < lastNode)));
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memcpy(node_on_disk.minBound, nodes[i].minBound, sizeof(coords));
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memcpy(node_on_disk.maxBound, nodes[i].maxBound, sizeof(coords));
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o.write((char *)&node_on_disk, sizeof(node_on_disk));
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}
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}
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template<int N, typename ValType, typename CType, typename CellSplitter>
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KDTree<N,ValType,CType,CellSplitter>::KDTree(std::istream& in, Cell *cells, NodeIntType Ncells)
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{
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KDTreeHeader h;
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if (!in)
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throw InvalidOnDiskKDTree();
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in.read((char *)&h, sizeof(h));
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if (!in || strncmp(h.id, KDTREE_DISK_SIGNATURE, KDTREE_DISK_SIGNATURE_LEN) != 0)
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{
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std::cerr << "KDTree Signature invalid" << std::endl;
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throw InvalidOnDiskKDTree();
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}
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if (h.numCells != Ncells || h.nodesUsed < 0) {
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std::cerr << "The number of cells has changed (" << h.numCells << " != " << Ncells << ") or nodesUsed=" << h.nodesUsed << std::endl;
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throw InvalidOnDiskKDTree();
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}
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base_cell = cells;
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nodes = new Node[h.nodesUsed];
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lastNode = h.nodesUsed;
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numNodes = Ncells;
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for (long i = 0; i < lastNode; i++)
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{
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KDTreeOnDisk<N,CType> node_on_disk;
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in.read((char *)&node_on_disk, sizeof(node_on_disk));
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if (!in) {
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std::cerr << "End-of-file reached" << std::endl;
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delete[] nodes;
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throw InvalidOnDiskKDTree();
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}
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if (node_on_disk.cell_id > numNodes || node_on_disk.cell_id < 0 ||
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node_on_disk.children_node[0] > lastNode || node_on_disk.children_node[0] < -1 ||
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node_on_disk.children_node[1] > lastNode || node_on_disk.children_node[1] < -1)
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{
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delete[] nodes;
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std::cerr << "Invalid cell id or children node id invalid" << std::endl;
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std::cerr << node_on_disk.cell_id << std::endl << node_on_disk.children_node[0] << std::endl << node_on_disk.children_node[1] << std::endl;
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throw InvalidOnDiskKDTree();
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}
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nodes[i].value = base_cell + node_on_disk.cell_id;
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if (node_on_disk.children_node[0] == -1)
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nodes[i].children[0] = 0;
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else
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nodes[i].children[0] = nodes + node_on_disk.children_node[0];
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if (node_on_disk.children_node[1] == -1)
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nodes[i].children[1] = 0;
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else
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nodes[i].children[1] = nodes + node_on_disk.children_node[1];
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memcpy(nodes[i].minBound, node_on_disk.minBound, sizeof(coords));
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memcpy(nodes[i].maxBound, node_on_disk.maxBound, sizeof(coords));
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int c;
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for (c = 0; c < N; c++)
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if (nodes[i].value->coord[c] < nodes[i].minBound[c] ||
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nodes[i].value->coord[c] > nodes[i].maxBound[c])
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break;
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if (c != N)
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{
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delete[] nodes;
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std::cerr << "Coordinates of the cell inconsistent with the boundaries" << std::endl
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<< " X=" << nodes[i].value->coord[0] << " B=[" << nodes[i].minBound[0] << "," << nodes[i].maxBound[0] << "]" << std::endl
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<< " Y=" << nodes[i].value->coord[1] << " B=[" << nodes[i].minBound[1] << "," << nodes[i].maxBound[1] << "]" << std::endl
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<< " Z=" << nodes[i].value->coord[2] << " B=[" << nodes[i].minBound[2] << "," << nodes[i].maxBound[2] << "]" << std::endl;
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throw InvalidOnDiskKDTree();
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}
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}
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root = &nodes[h.rootId];
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sortingHelper = new Cell *[Ncells];
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for (NodeIntType i = 0; i < Ncells; i++)
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sortingHelper[i] = &cells[i];
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}
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#endif
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};
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