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Diffstat (limited to 'geom_bottleneck/bottleneck/src/ann/kd_tree.cpp')
| -rw-r--r-- | geom_bottleneck/bottleneck/src/ann/kd_tree.cpp | 560 |
1 files changed, 560 insertions, 0 deletions
diff --git a/geom_bottleneck/bottleneck/src/ann/kd_tree.cpp b/geom_bottleneck/bottleneck/src/ann/kd_tree.cpp new file mode 100644 index 0000000..ad3a82d --- /dev/null +++ b/geom_bottleneck/bottleneck/src/ann/kd_tree.cpp @@ -0,0 +1,560 @@ +//---------------------------------------------------------------------- +// File: kd_tree.cpp +// Programmer: Sunil Arya and David Mount +// Description: Basic methods for kd-trees. +// Last modified: 01/04/05 (Version 1.0) +//---------------------------------------------------------------------- +// Copyright (c) 1997-2005 University of Maryland and Sunil Arya and +// David Mount. All Rights Reserved. +// +// This software and related documentation is part of the Approximate +// Nearest Neighbor Library (ANN). This software is provided under +// the provisions of the Lesser GNU Public License (LGPL). See the +// file ../ReadMe.txt for further information. +// +// The University of Maryland (U.M.) and the authors make no +// representations about the suitability or fitness of this software for +// any purpose. It is provided "as is" without express or implied +// warranty. +//---------------------------------------------------------------------- +// History: +// Revision 0.1 03/04/98 +// Initial release +// Revision 1.0 04/01/05 +// Increased aspect ratio bound (ANN_AR_TOOBIG) from 100 to 1000. +// Fixed leaf counts to count trivial leaves. +// Added optional pa, pi arguments to Skeleton kd_tree constructor +// for use in load constructor. +// Added annClose() to eliminate KD_TRIVIAL memory leak. +// -------------------------------------------------------------------- +// 2015 - modified by A. Nigmetov to support deletion of points +//---------------------------------------------------------------------- + +#ifdef _WIN32 +#include <ciso646> // make VS more conformal +#endif + +#include "kd_tree.h" // kd-tree declarations +#include "kd_split.h" // kd-tree splitting rules +#include "kd_util.h" // kd-tree utilities +#include <ANN/ANNperf.h> // performance evaluation + +namespace geom_bt { +//---------------------------------------------------------------------- +// Global data +// +// For some splitting rules, especially with small bucket sizes, +// it is possible to generate a large number of empty leaf nodes. +// To save storage we allocate a single trivial leaf node which +// contains no points. For messy coding reasons it is convenient +// to have it reference a trivial point index. +// +// KD_TRIVIAL is allocated when the first kd-tree is created. It +// must *never* deallocated (since it may be shared by more than +// one tree). +//---------------------------------------------------------------------- +static int IDX_TRIVIAL[] = {0}; // trivial point index +ANNkd_leaf *KD_TRIVIAL = NULL; // trivial leaf node + +//---------------------------------------------------------------------- +// Printing the kd-tree +// These routines print a kd-tree in reverse inorder (high then +// root then low). (This is so that if you look at the output +// from the right side it appear from left to right in standard +// inorder.) When outputting leaves we output only the point +// indices rather than the point coordinates. There is an option +// to print the point coordinates separately. +// +// The tree printing routine calls the printing routines on the +// individual nodes of the tree, passing in the level or depth +// in the tree. The level in the tree is used to print indentation +// for readability. +//---------------------------------------------------------------------- + +void ANNkd_split::print( // print splitting node + int level, // depth of node in tree + ostream &out) // output stream +{ + child[ANN_HI]->print(level+1, out); // print high child + out << " "; + for (int i = 0; i < level; i++) // print indentation + out << ".."; + out << "Split cd=" << cut_dim << " cv=" << cut_val; + out << " lbnd=" << cd_bnds[ANN_LO]; + out << " hbnd=" << cd_bnds[ANN_HI]; + out << " np=" << actual_num_points; + out << "\n"; + child[ANN_LO]->print(level+1, out); // print low child +} + +void ANNkd_leaf::print( // print leaf node + int level, // depth of node in tree + ostream &out) // output stream +{ + + out << " "; + for (int i = 0; i < level; i++) // print indentation + out << ".."; + + if (this == KD_TRIVIAL) { // canonical trivial leaf node + out << "Leaf (trivial)\n"; + } + else{ + out << "Leaf n=" << n_pts << " <"; + for (int j = 0; j < n_pts; j++) { + out << bkt[j]; + if (j < n_pts-1) out << ","; + } + out << ">\n"; + } +} + +void ANNkd_tree::Print( // print entire tree + ANNbool with_pts, // print points as well? + ostream &out) // output stream +{ + out << "ANN Version " << ANNversion << "\n"; + if (with_pts) { // print point coordinates + out << " Points:\n"; + for (int i = 0; i < n_pts; i++) { + out << "\t" << i << ": "; + annPrintPt(pts[i], dim, out); + out << "\n"; + } + } + if (root == NULL) // empty tree? + out << " Null tree.\n"; + else { + root->print(0, out); // invoke printing at root + } +} + +//---------------------------------------------------------------------- +// kd_tree statistics (for performance evaluation) +// This routine compute various statistics information for +// a kd-tree. It is used by the implementors for performance +// evaluation of the data structure. +//---------------------------------------------------------------------- + +#define MAX(a,b) ((a) > (b) ? (a) : (b)) + +void ANNkdStats::merge(const ANNkdStats &st) // merge stats from child +{ + n_lf += st.n_lf; n_tl += st.n_tl; + n_spl += st.n_spl; n_shr += st.n_shr; + depth = MAX(depth, st.depth); + sum_ar += st.sum_ar; +} + +//---------------------------------------------------------------------- +// Update statistics for nodes +//---------------------------------------------------------------------- + +const double ANN_AR_TOOBIG = 1000; // too big an aspect ratio + +void ANNkd_leaf::getStats( // get subtree statistics + int dim, // dimension of space + ANNkdStats &st, // stats (modified) + ANNorthRect &bnd_box) // bounding box +{ + st.reset(); + st.n_lf = 1; // count this leaf + if (this == KD_TRIVIAL) st.n_tl = 1; // count trivial leaf + double ar = annAspectRatio(dim, bnd_box); // aspect ratio of leaf + // incr sum (ignore outliers) + st.sum_ar += float(ar < ANN_AR_TOOBIG ? ar : ANN_AR_TOOBIG); +} + +void ANNkd_split::getStats( // get subtree statistics + int dim, // dimension of space + ANNkdStats &st, // stats (modified) + ANNorthRect &bnd_box) // bounding box +{ + ANNkdStats ch_stats; // stats for children + // get stats for low child + ANNcoord hv = bnd_box.hi[cut_dim]; // save box bounds + bnd_box.hi[cut_dim] = cut_val; // upper bound for low child + ch_stats.reset(); // reset + child[ANN_LO]->getStats(dim, ch_stats, bnd_box); + st.merge(ch_stats); // merge them + bnd_box.hi[cut_dim] = hv; // restore bound + // get stats for high child + ANNcoord lv = bnd_box.lo[cut_dim]; // save box bounds + bnd_box.lo[cut_dim] = cut_val; // lower bound for high child + ch_stats.reset(); // reset + child[ANN_HI]->getStats(dim, ch_stats, bnd_box); + st.merge(ch_stats); // merge them + bnd_box.lo[cut_dim] = lv; // restore bound + + st.depth++; // increment depth + st.n_spl++; // increment number of splits +} + +//---------------------------------------------------------------------- +// getStats +// Collects a number of statistics related to kd_tree or +// bd_tree. +//---------------------------------------------------------------------- + +void ANNkd_tree::getStats( // get tree statistics + ANNkdStats &st) // stats (modified) +{ + st.reset(dim, n_pts, bkt_size); // reset stats + // create bounding box + ANNorthRect bnd_box(dim, bnd_box_lo, bnd_box_hi); + if (root != NULL) { // if nonempty tree + root->getStats(dim, st, bnd_box); // get statistics + st.avg_ar = st.sum_ar / st.n_lf; // average leaf asp ratio + } +} + +//---------------------------------------------------------------------- +// kd_tree destructor +// The destructor just frees the various elements that were +// allocated in the construction process. +//---------------------------------------------------------------------- + +ANNkd_tree::~ANNkd_tree() // tree destructor +{ + if (root != NULL and root != KD_TRIVIAL) delete root; + if (pidx != NULL) delete [] pidx; + if (bnd_box_lo != NULL) annDeallocPt(bnd_box_lo); + if (bnd_box_hi != NULL) annDeallocPt(bnd_box_hi); +} + +//---------------------------------------------------------------------- +// This is called with all use of ANN is finished. It eliminates the +// minor memory leak caused by the allocation of KD_TRIVIAL. +//---------------------------------------------------------------------- +void annClose() // close use of ANN +{ + if (KD_TRIVIAL != NULL) { + delete KD_TRIVIAL; + KD_TRIVIAL = NULL; + } +} + +//---------------------------------------------------------------------- +// kd_tree constructors +// There is a skeleton kd-tree constructor which sets up a +// trivial empty tree. The last optional argument allows +// the routine to be passed a point index array which is +// assumed to be of the proper size (n). Otherwise, one is +// allocated and initialized to the identity. Warning: In +// either case the destructor will deallocate this array. +// +// As a kludge, we need to allocate KD_TRIVIAL if one has not +// already been allocated. (This is because I'm too dumb to +// figure out how to cause a pointer to be allocated at load +// time.) +//---------------------------------------------------------------------- + +void ANNkd_tree::SkeletonTree( // construct skeleton tree + int n, // number of points + int dd, // dimension + int bs, // bucket size + ANNpointArray pa, // point array + ANNidxArray pi) // point indices +{ + dim = dd; // initialize basic elements + n_pts = n; + bkt_size = bs; + pts = pa; // initialize points array + + root = NULL; // no associated tree yet + + if (pi == NULL) { // point indices provided? + pidx = new ANNidx[n]; // no, allocate space for point indices + for (int i = 0; i < n; i++) { + pidx[i] = i; // initially identity + } + } + else { + pidx = pi; // yes, use them + } + + bnd_box_lo = bnd_box_hi = NULL; // bounding box is nonexistent + if (KD_TRIVIAL == NULL) // no trivial leaf node yet? + KD_TRIVIAL = new ANNkd_leaf(0, IDX_TRIVIAL); // allocate it + + // for deletion + pointToLeafVec.clear(); + pointToLeafVec.reserve(n_pts); + for(int k = 0; k < n_pts; ++k) { + pointToLeafVec.push_back(NULL); + } +} + +ANNkd_tree::ANNkd_tree( // basic constructor + int n, // number of points + int dd, // dimension + int bs) // bucket size +{ SkeletonTree(n, dd, bs); } // construct skeleton tree + + + +//---------------------------------------------------------------------- +// rkd_tree - recursive procedure to build a kd-tree +// +// Builds a kd-tree for points in pa as indexed through the +// array pidx[0..n-1] (typically a subarray of the array used in +// the top-level call). This routine permutes the array pidx, +// but does not alter pa[]. +// +// The construction is based on a standard algorithm for constructing +// the kd-tree (see Friedman, Bentley, and Finkel, ``An algorithm for +// finding best matches in logarithmic expected time,'' ACM Transactions +// on Mathematical Software, 3(3):209-226, 1977). The procedure +// operates by a simple divide-and-conquer strategy, which determines +// an appropriate orthogonal cutting plane (see below), and splits +// the points. When the number of points falls below the bucket size, +// we simply store the points in a leaf node's bucket. +// +// One of the arguments is a pointer to a splitting routine, +// whose prototype is: +// +// void split( +// ANNpointArray pa, // complete point array +// ANNidxArray pidx, // point array (permuted on return) +// ANNorthRect &bnds, // bounds of current cell +// int n, // number of points +// int dim, // dimension of space +// int &cut_dim, // cutting dimension +// ANNcoord &cut_val, // cutting value +// int &n_lo) // no. of points on low side of cut +// +// This procedure selects a cutting dimension and cutting value, +// partitions pa about these values, and returns the number of +// points on the low side of the cut. +//---------------------------------------------------------------------- + +ANNkd_ptr rkd_tree( // recursive construction of kd-tree + ANNpointArray pa, // point array + ANNidxArray pidx, // point indices to store in subtree + int n, // number of points + int dim, // dimension of space + int bsp, // bucket space + ANNorthRect &bnd_box, // bounding box for current node + ANNkd_splitter splitter, // splitting routine + vector<ANNkd_leaf*>* ppointToLeafVec) +{ + if (n <= bsp) { // n small, make a leaf node + if (n == 0) // empty leaf node + return KD_TRIVIAL; // return (canonical) empty leaf + else { // construct the node and return + ANNkd_leaf* res = new ANNkd_leaf(n, pidx); + if ( 1 == bsp) { + (*ppointToLeafVec)[*pidx] = res; + } + return res; + } + } + else { // n large, make a splitting node + int cd; // cutting dimension + ANNcoord cv; // cutting value + int n_lo; // number on low side of cut + ANNkd_node *lo, *hi; // low and high children + + // invoke splitting procedure + (*splitter)(pa, pidx, bnd_box, n, dim, cd, cv, n_lo); + + ANNcoord lv = bnd_box.lo[cd]; // save bounds for cutting dimension + ANNcoord hv = bnd_box.hi[cd]; + + bnd_box.hi[cd] = cv; // modify bounds for left subtree + lo = rkd_tree( // build left subtree + pa, pidx, n_lo, // ...from pidx[0..n_lo-1] + dim, bsp, bnd_box, splitter, ppointToLeafVec); + bnd_box.hi[cd] = hv; // restore bounds + + bnd_box.lo[cd] = cv; // modify bounds for right subtree + hi = rkd_tree( // build right subtree + pa, pidx + n_lo, n-n_lo,// ...from pidx[n_lo..n-1] + dim, bsp, bnd_box, splitter, ppointToLeafVec); + bnd_box.lo[cd] = lv; // restore bounds + + // create the splitting node + ANNkd_split *ptr = new ANNkd_split(cd, cv, lv, hv, lo, hi); + if (lo != KD_TRIVIAL) + lo->setParent(ptr); + if (hi != KD_TRIVIAL) + hi->setParent(ptr); + ptr->setNumPoints(lo->getNumPoints() + hi->getNumPoints()); + + return ptr; // return pointer to this node + } +} + +// for kd-trees with deletion +/* +ANNkd_ptr rkd_tree_wd( // recursive construction of kd-tree + ANNpointArray pa, // point array + ANNidxArray pidx, // point indices to store in subtree + int n, // number of points + int dim, // dimension of space + int bsp, // bucket space + ANNorthRect &bnd_box, // bounding box for current node + ANNkd_splitter_wd splitter) // splitting routine +{ + ANNidx cut_pt_idx; + if (n <= bsp) { // n small, make a leaf node + if (n == 0) // empty leaf node + return KD_TRIVIAL; // return (canonical) empty leaf + else // construct the node and return + return new ANNkd_leaf(n, pidx); + } + else { // n large, make a splitting node + int cd; // cutting dimension + ANNcoord cv; // cutting value + int n_lo; // number on low side of cut + ANNkd_node *lo, *hi; // low and high children + + // invoke splitting procedure + (*splitter)(pa, pidx, bnd_box, n, dim, cd, cv, n_lo, cut_pt_idx); + + ANNcoord lv = bnd_box.lo[cd]; // save bounds for cutting dimension + ANNcoord hv = bnd_box.hi[cd]; + + bnd_box.hi[cd] = cv; // modify bounds for left subtree + lo = rkd_tree_wd( // build left subtree + pa, pidx, n_lo, // ...from pidx[0..n_lo-1] + dim, bsp, bnd_box, splitter); + bnd_box.hi[cd] = hv; // restore bounds + + bnd_box.lo[cd] = cv; // modify bounds for right subtree + hi = rkd_tree_wd( // build right subtree + pa, pidx + n_lo, n-n_lo,// ...from pidx[n_lo..n-1] + dim, bsp, bnd_box, splitter); + bnd_box.lo[cd] = lv; // restore bounds + + // create the splitting node + ANNkd_split *ptr = new ANNkd_split(cd, cv, lv, hv, lo, hi, cut_pt_idx); + + return ptr; // return pointer to this node + } +} +*/ + +//---------------------------------------------------------------------- +// kd-tree constructor +// This is the main constructor for kd-trees given a set of points. +// It first builds a skeleton tree, then computes the bounding box +// of the data points, and then invokes rkd_tree() to actually +// build the tree, passing it the appropriate splitting routine. +//---------------------------------------------------------------------- + +ANNkd_tree::ANNkd_tree( // construct from point array + ANNpointArray pa, // point array (with at least n pts) + int n, // number of points + int dd, // dimension + int bs, // bucket size + ANNsplitRule split) // splitting method +{ + SkeletonTree(n, dd, bs); // set up the basic stuff + pts = pa; // where the points are + actual_num_points = n; + if (n == 0) return; // no points--no sweat + + ANNorthRect bnd_box(dd); // bounding box for points + annEnclRect(pa, pidx, n, dd, bnd_box);// construct bounding rectangle + // copy to tree structure + bnd_box_lo = annCopyPt(dd, bnd_box.lo); + bnd_box_hi = annCopyPt(dd, bnd_box.hi); + + switch (split) { // build by rule + case ANN_KD_STD: // standard kd-splitting rule + root = rkd_tree(pa, pidx, n, dd, bs, bnd_box, kd_split, &pointToLeafVec); + break; + case ANN_KD_MIDPT: // midpoint split + root = rkd_tree(pa, pidx, n, dd, bs, bnd_box, midpt_split, &pointToLeafVec); + break; + case ANN_KD_FAIR: // fair split + root = rkd_tree(pa, pidx, n, dd, bs, bnd_box, fair_split, &pointToLeafVec); + break; + case ANN_KD_SUGGEST: // best (in our opinion) + case ANN_KD_SL_MIDPT: // sliding midpoint split + root = rkd_tree(pa, pidx, n, dd, bs, bnd_box, sl_midpt_split, &pointToLeafVec); + break; + case ANN_KD_SL_FAIR: // sliding fair split + root = rkd_tree(pa, pidx, n, dd, bs, bnd_box, sl_fair_split, &pointToLeafVec); + break; + // for kd-trees with deletion + /* + //case ANN_KD_SUGGEST: + case ANN_KD_STD_WD: + root = rkd_tree_wd(pa, pidx, n, dd, bs, bnd_box, kd_split_wd); + break; + case ANN_KD_MIDPT_WD: + root = rkd_tree_wd(pa, pidx, n, dd, bs, bnd_box, kd_split_wd); + break; + case ANN_KD_SL_MIDPT_WD: + root = rkd_tree_wd(pa, pidx, n, dd, bs, bnd_box, kd_split_wd); + break; + */ + default: + annError("Illegal splitting method", ANNabort); + } +} + + +// deletion code +// +// +// +// +// +void ANNkd_tree::delete_point(const int point_idx) +{ + // range check + assert(0 <= point_idx and point_idx < n_pts); + assert(actual_num_points > 0); + // if this is the first deletion, + // initialize isDeleted vector + if (isDeleted.empty()) { + isDeleted.reserve(n_pts); + for(size_t k = 0; k < n_pts; ++k) { + isDeleted.push_back(false); + } + } + // points shouldn't be deleted twice + assert(!isDeleted[point_idx]); + assert(root != NULL); + ANNkd_leaf* leafWithPoint = pointToLeafVec.at(point_idx); + assert(leafWithPoint != NULL); + // if leafWithPoint != root, + // its parent will delete the leaf + pointToLeafVec.at(point_idx)->delete_point(point_idx, leafWithPoint != root); + if (leafWithPoint == root) { + // we had only one point, + // so the tree must delete it + root = KD_TRIVIAL; + delete leafWithPoint; + } + isDeleted[point_idx] = true; + actual_num_points--; +} + +void ANNkd_leaf::delete_point(const int point_idx, const bool killYourself) +{ + assert(n_pts == 1); + assert(bkt[0] == point_idx); + ANNkd_split* myPar = parent; + while(myPar != NULL) { + myPar->decNumPoints(); + myPar = myPar->getParent(); + } + if (parent != NULL) + parent->delete_leaf(this); + if (killYourself) + delete this; +} + +void ANNkd_split::delete_leaf(ANNkd_leaf* childToDelete) +{ + assert(child[ANN_LO] == childToDelete or child[ANN_HI] == childToDelete); + if (child[ANN_LO] == childToDelete) + child[ANN_LO] = KD_TRIVIAL; + else + child[ANN_HI] = KD_TRIVIAL; +} +} |