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SpatialIndAlgs.cpp
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/**
* GeoDa TM, Copyright (C) 2011-2015 by Luc Anselin - all rights reserved
*
* This file is part of GeoDa.
*
* GeoDa is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* GeoDa is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <math.h>
#include <wx/wx.h>
#include <fstream>
#include <boost/foreach.hpp>
#include <boost/random.hpp>
#include <boost/random/uniform_01.hpp>
#include <boost/random/normal_distribution.hpp>
#include <boost/random/uniform_int_distribution.hpp>
#include <wx/filename.h>
#include <wx/string.h>
#include <wx/stopwatch.h>
#include "PointSetAlgs.h"
#include "GenGeomAlgs.h"
#include "SpatialIndAlgs.h"
#include "VarCalc/NumericTests.h"
#include "ShapeOperations/OGRLayerProxy.h"
#include "Explore/MapLayer.hpp"
#include "Project.h"
#include "GdaException.h"
#include "logger.h"
using namespace std;
void SpatialIndAlgs::to_3d_centroids(const vector<pt_2d>& pt2d,
vector<pt_3d>& pt3d)
{
size_t obs = pt2d.size();
pt3d.resize(obs);
for (size_t i=0; i<obs; ++i) {
pt3d[i] = pt_3d(bg::get<0>(pt2d[i]), bg::get<1>(pt2d[i]), 0);
}
}
void SpatialIndAlgs::to_3d_centroids(const vector<pt_lonlat>& ptll,
vector<pt_3d>& pt3d)
{
size_t obs = ptll.size();
pt3d.resize(obs);
for (size_t i=0; i<obs; ++i) {
double x, y, z;
GenGeomAlgs::LongLatDegToUnit(bg::get<0>(ptll[i]),
bg::get<1>(ptll[i]),
x, y, z);
pt3d[i] = pt_3d(x, y, z);
}
}
void SpatialIndAlgs::default_test()
{
// create the rtree using default constructor
rtree_box_2d_t rtree;
// create some values
for ( unsigned i = 0 ; i < 10 ; ++i ) {
// create a box
box_2d b(pt_2d(i + 0.0f, i + 0.0f), pt_2d(i + 0.5f, i + 0.5f));
// insert new value
rtree.insert(std::make_pair(b, i));
}
// find values intersecting some area defined by a box
box_2d query_box(pt_2d(0, 0), pt_2d(5, 5));
std::vector<box_2d_val> result_s;
rtree.query(bgi::intersects(query_box), std::back_inserter(result_s));
const int k=3;
// find k nearest values to a point
std::vector<box_2d_val> result_n;
rtree.query(bgi::nearest(pt_2d(0, 0), k), std::back_inserter(result_n));
// note: in Boost.Geometry WKT representation of a box is polygon
// display results
stringstream ss;
ss << "spatial query box:" << std::endl;
ss << bg::wkt<box_2d>(query_box) << std::endl;
ss << "spatial query result:" << std::endl;
BOOST_FOREACH(box_2d_val const& v, result_s) {
ss << bg::wkt<box_2d>(v.first) << " - " << v.second << std::endl;
}
ss << k << "-nn query point:" << std::endl;
ss << bg::wkt<pt_2d>(pt_2d(0, 0)) << std::endl;
ss << k << "-nn query result:" << std::endl;
BOOST_FOREACH(box_2d_val const& v, result_n) {
ss << bg::wkt<box_2d>(v.first) << " - " << v.second << std::endl;
}
pt_lonlat sp(0, 45);
ss << "Spherical pt get<0>: " << bg::get<0>(sp) << std::endl;
ss << "Spherical pt get<1>: " << bg::get<1>(sp) << std::endl;
ss << "Spherical pt: " << bg::wkt<pt_lonlat>(sp) << std::endl;
ss << "default_test() END";
}
void SpatialIndAlgs::print_rtree_stats(rtree_box_2d_t& rtree)
{
stringstream ss;
ss << "Rtree stats:" << endl;
ss << " size: " << rtree.size() << endl;
ss << " empty?: " << rtree.empty() << endl;
box_2d bnds = rtree.bounds();
ss << " bounds: " << bg::wkt<box_2d>(bnds);
}
void SpatialIndAlgs::query_all_boxes(rtree_box_2d_t& rtree)
{
int dzero = 0;
int dpos = 0;
int cnt=0;
box_2d bnds = rtree.bounds();
for (rtree_box_2d_t::const_query_iterator it =
rtree.qbegin(bgi::intersects(rtree.bounds()));
it != rtree.qend() ; ++it) { ++cnt; }
cnt = 0;
rtree_box_2d_t::const_query_iterator it;
for (it=rtree.qbegin(bgi::intersects(rtree.bounds())); it != rtree.qend(); ++it)
{
const box_2d_val& v = *it;
pt_2d c;
boost::geometry::centroid(v.first, c);
vector<box_2d_val> q;
rtree.query(bgi::intersects(v.first), std::back_inserter(q));
int qcnt=0;
BOOST_FOREACH(box_2d_val const& w, q) {
if (w.second == v.second)
continue;
++cnt;
++qcnt;
}
}
}
void SpatialIndAlgs::knn_query(const rtree_pt_2d_t& rtree, int nn)
{
int cnt=0;
box_2d bnds = rtree.bounds();
rtree_pt_2d_t::const_query_iterator it;
for (it= rtree.qbegin(bgi::intersects(rtree.bounds())); it != rtree.qend(); ++it)
{
++cnt;
}
cnt = 0;
const int k=nn+1;
for (it= rtree.qbegin(bgi::intersects(rtree.bounds())); it != rtree.qend(); ++it)
{
const pt_2d_val& v = *it;
vector<pt_2d_val> q;
rtree.query(bgi::nearest(v.first, k), std::back_inserter(q));
BOOST_FOREACH(pt_2d_val const& w, q) {
if (w.second == v.second) {
continue;
}
++cnt;
}
}
}
GwtWeight* SpatialIndAlgs::knn_build(const vector<double>& x,
const vector<double>& y,
int nn,
bool is_arc, bool is_mi,
bool is_inverse, double power,
const wxString& kernel,
double bandwidth,
bool adaptive_bandwidth,
bool use_kernel_diagnals)
{
size_t nobs = x.size();
GwtWeight* gwt = 0;
if (is_arc) {
rtree_pt_3d_t rtree;
{
vector<pt_3d> pts;
{
vector<pt_lonlat> ptll(nobs);
for (int i=0; i<nobs; ++i) ptll[i] = pt_lonlat(x[i], y[i]);
to_3d_centroids(ptll, pts);
}
fill_pt_rtree(rtree, pts);
}
gwt = knn_build(rtree, nn, true, is_mi, is_inverse, power, kernel, bandwidth, adaptive_bandwidth, use_kernel_diagnals);
} else {
rtree_pt_2d_t rtree;
{
vector<pt_2d> pts(nobs);
for (int i=0; i<nobs; ++i) pts[i] = pt_2d(x[i], y[i]);
fill_pt_rtree(rtree, pts);
}
gwt = knn_build(rtree, nn, is_inverse, power, kernel, bandwidth, adaptive_bandwidth, use_kernel_diagnals);
}
return gwt;
}
void SpatialIndAlgs::apply_kernel(const GwtWeight* Wp, const wxString& kernel, bool use_kernel_diagnals)
{
// apply kernel
double gaussian_const = pow(M_PI * 2.0, -0.5);
for (int i=0; i<Wp->num_obs; i++) {
GwtElement& e = Wp->gwt[i];
GwtNeighbor* nbrs = e.dt();
for (int j=0; j<e.Size(); j++) {
if (!use_kernel_diagnals && i==nbrs[j].nbx) {
nbrs[j].weight = 1.0;
continue;
}
// functions follow Anselin and Rey (2010) table 5.4
if (kernel.IsSameAs("triangular",false)) {
nbrs[j].weight = 1 - nbrs[j].weight;
} else if (kernel.IsSameAs("uniform", false)) {
nbrs[j].weight = 0.5;
} else if (kernel.IsSameAs("epanechnikov", false)) {
nbrs[j].weight = (3.0 / 4.0) * (1.0 - pow(nbrs[j].weight,2.0));
} else if (kernel.IsSameAs("quartic", false)) {
nbrs[j].weight = (15.0 / 16.0) * pow((1.0 - pow(nbrs[j].weight,2.0)), 2.0);
} else if (kernel.IsSameAs("gaussian", false)) {
nbrs[j].weight = gaussian_const * exp( -pow(nbrs[j].weight, 2.0) / 2.0 );
}
}
}
}
GwtWeight* SpatialIndAlgs::knn_build(const rtree_pt_2d_t& rtree, int nn, bool is_inverse, double power, const wxString& kernel, double bandwidth_, bool adaptive_bandwidth_, bool use_kernel_diagnals)
{
GwtWeight* Wp = new GwtWeight;
Wp->num_obs = rtree.size();
Wp->is_symmetric = false;
Wp->symmetry_checked = true;
Wp->gwt = new GwtElement[Wp->num_obs];
int cnt=0;
const int k=nn+1;
double bandwidth = bandwidth_;
bool adaptive_bandwidth = adaptive_bandwidth_;
for (rtree_pt_2d_t::const_query_iterator it =
rtree.qbegin(bgi::intersects(rtree.bounds()));
it != rtree.qend() ; ++it)
{
const pt_2d_val& v = *it;
size_t obs = v.second;
// each point "v" with index "obs"
vector<pt_2d_val> q;
rtree.query(bgi::nearest(v.first, k), std::back_inserter(q));
GwtElement& e = Wp->gwt[obs];
e.alloc(q.size());
double local_bandwidth = 0;
BOOST_FOREACH(pt_2d_val const& w, q) {
if (kernel.IsEmpty() && w.second == v.second)
continue;
GwtNeighbor neigh;
neigh.nbx = w.second;
double d = bg::distance(v.first, w.first);
if (bandwidth_ ==0 && d > bandwidth) bandwidth = d;
if (d > local_bandwidth) local_bandwidth = d;
if (is_inverse) d = pow(d, power);
neigh.weight = d;
e.Push(neigh);
++cnt;
}
if (adaptive_bandwidth && local_bandwidth > 0 && !kernel.IsEmpty()) {
GwtNeighbor* nbrs = e.dt();
for (int j=0; j<e.Size(); j++) {
nbrs[j].weight = nbrs[j].weight / local_bandwidth;
}
}
}
if (!adaptive_bandwidth && bandwidth > 0 && !kernel.IsEmpty()) {
// use max knn distance as bandwidth
for (int i=0; i<Wp->num_obs; i++) {
GwtElement& e = Wp->gwt[i];
GwtNeighbor* nbrs = e.dt();
for (int j=0; j<e.Size(); j++) {
nbrs[j].weight = nbrs[j].weight / bandwidth;
}
}
}
if (!kernel.IsEmpty()) {
apply_kernel(Wp, kernel, use_kernel_diagnals);
}
return Wp;
}
GwtWeight* SpatialIndAlgs::knn_build(const rtree_pt_3d_t& rtree, int nn,
bool is_arc, bool is_mi, bool is_inverse, double power, const wxString& kernel, double bandwidth_, bool adaptive_bandwidth_, bool use_kernel_diagnals)
{
wxStopWatch sw;
using namespace GenGeomAlgs;
GwtWeight* Wp = new GwtWeight;
Wp->num_obs = rtree.size();
Wp->is_symmetric = false;
Wp->symmetry_checked = true;
Wp->gwt = new GwtElement[Wp->num_obs];
int cnt=0;
const int k=nn+1;
double bandwidth = bandwidth_;
bool adaptive_bandwidth = adaptive_bandwidth_;
// if not set, use max knn distance as bandwidth
for (rtree_pt_3d_t::const_query_iterator it =
rtree.qbegin(bgi::intersects(rtree.bounds()));
it != rtree.qend() ; ++it)
{
const pt_3d_val& v = *it;
size_t obs = v.second;
vector<pt_3d_val> q;
rtree.query(bgi::nearest(v.first, k), std::back_inserter(q));
GwtElement& e = Wp->gwt[obs];
e.alloc(q.size());
double lon_v, lat_v;
double x_v, y_v;
if (is_arc) {
UnitToLongLatDeg(bg::get<0>(v.first), bg::get<1>(v.first),
bg::get<2>(v.first), lon_v, lat_v);
} else {
x_v = bg::get<0>(v.first);
y_v = bg::get<1>(v.first);
}
double local_bandwidth = 0;
BOOST_FOREACH(pt_3d_val const& w, q) {
if (kernel.IsEmpty() && w.second == v.second)
continue;
GwtNeighbor neigh;
neigh.nbx = w.second;
if (is_arc) {
double lon_w, lat_w;
UnitToLongLatDeg(bg::get<0>(w.first), bg::get<1>(w.first),
bg::get<2>(w.first), lon_w, lat_w);
if (is_mi) {
neigh.weight = ComputeArcDistMi(lon_v, lat_v, lon_w, lat_w);
} else {
neigh.weight = ComputeArcDistKm(lon_v, lat_v, lon_w, lat_w);
}
} else {
//neigh.weight = bg::distance(v.first, w.first);
neigh.weight = ComputeEucDist(x_v, y_v,
bg::get<0>(w.first),
bg::get<1>(w.first));
}
if (is_inverse) neigh.weight = pow(neigh.weight, power);
if (bandwidth_ == 0 && neigh.weight > bandwidth)
bandwidth = neigh.weight;
if (neigh.weight > local_bandwidth)
local_bandwidth = neigh.weight;
e.Push(neigh);
++cnt;
}
if (adaptive_bandwidth && local_bandwidth > 0 && !kernel.IsEmpty()) {
GwtNeighbor* nbrs = e.dt();
for (int j=0; j<e.Size(); j++) {
nbrs[j].weight = nbrs[j].weight / local_bandwidth;
}
}
}
if (!adaptive_bandwidth && bandwidth > 0 && !kernel.IsEmpty()) {
// use max knn distance as bandwidth
for (int i=0; i<Wp->num_obs; i++) {
GwtElement& e = Wp->gwt[i];
GwtNeighbor* nbrs = e.dt();
for (int j=0; j<e.Size(); j++) {
nbrs[j].weight = nbrs[j].weight / bandwidth;
}
}
}
if (!kernel.IsEmpty()) {
apply_kernel(Wp, kernel, use_kernel_diagnals);
}
stringstream ss;
ss << "Time to create 3D " << (is_arc ? " arc " : "")
<< nn << "-NN GwtWeight "
<< "with " << cnt << " total neighbors in ms : " << sw.Time();
return Wp;
}
double SpatialIndAlgs::est_thresh_for_num_pairs(const rtree_pt_2d_t& rtree,
double num_pairs)
{
double nobs_d = (double) rtree.size();
if (num_pairs >= (nobs_d*(nobs_d-1.0))/2.0) {
return bg::distance(rtree.bounds().min_corner(), rtree.bounds().max_corner());
}
// Need roughly double since pairs are visited twice.
double avg_n = (num_pairs / nobs_d)*2.0;
// To avoid the use of a hash table, we just allow pairs
// to be counted twice each bin is just an average. Although
// distances will be calculated twice, the cost should be offset
// by the faster performance of no hash table inserts / lookups.
double thresh = est_thresh_for_avg_num_neigh(rtree, avg_n);
return thresh;
}
double SpatialIndAlgs::est_thresh_for_avg_num_neigh(const rtree_pt_2d_t& rtree,
double avg_n)
{
// Use a binary search to estimate threshold to acheive average num neighbors
wxStopWatch sw;
using namespace GenGeomAlgs;
int max_iters = 20;
int iters = 0;
double lower = 0;
double lower_avg = 0;
box_2d bnds(rtree.bounds());
double upper = bg::distance(bnds.min_corner(), bnds.max_corner());
double upper_avg = (double) rtree.size();
double guess = upper;
double guess_avg = upper_avg;
double th = guess;
bool was_improvement = true;
for (iters=0; iters<max_iters && was_improvement; ++iters) {
guess = lower + (upper-lower)/2.0;
guess_avg = est_avg_num_neigh_thresh(rtree, guess);
{
stringstream ss;
ss << "\niter: " << iters << " target avg: " << avg_n << endl;
ss << " lower: " << lower << ", lower_avg: " << lower_avg << endl;
ss << " guess: " << guess << ", guess_avg: " << guess_avg << endl;
ss << " upper: " << upper << ", upper_avg: " << upper_avg;
}
if (guess_avg == avg_n) {
//LOG_MSG("new guess was exact!");
// this will never happen, but put case here for completeness
th = guess;
was_improvement = false;
} else if (guess_avg <= lower_avg) {
//LOG_MSG("new guess below lower bound");
was_improvement = false;
} else if (guess_avg >= upper_avg) {
//LOG_MSG("new guess above lower bound");
was_improvement = false;
} else if (guess_avg < avg_n) {
//LOG_MSG("increase lower bound");
lower = guess;
lower_avg = guess_avg;
} else { // guess_avg > avg_n
//LOG_MSG("decrease upper bound");
upper = guess;
upper_avg = guess_avg;
}
if (was_improvement) {
th = guess;
}
}
stringstream ss;
ss << "Estimated " << th << " threshold for average "
<< "number neighbors " << avg_n << "." << endl;
ss << "Calculation time to peform " << iters << " iterations: "
<< sw.Time() << " ms.";
LOG_MSG("Exiting est_thresh_for_avg_num_neigh");
return th;
}
double SpatialIndAlgs::est_avg_num_neigh_thresh(const rtree_pt_2d_t& rtree,
double th, size_t trials)
{
wxStopWatch sw;
using namespace GenGeomAlgs;
vector<pt_2d_val> query_pts;
rtree.query(bgi::intersects(rtree.bounds()), back_inserter(query_pts));
// Mersenne Twister random number generator, randomly seeded
// with current time in seconds since Jan 1 1970.
static boost::mt19937 rng(std::time(0));
static boost::random::uniform_int_distribution<> X(0, query_pts.size()-1);
size_t tot_neigh = 0;
for (size_t i=0; i<trials; ++i) {
const pt_2d_val& v = query_pts[X(rng)];
double x = v.first.get<0>();
double y = v.first.get<1>();
box_2d b(pt_2d(x-th, y-th), pt_2d(x+th, y+th));
vector<pt_2d_val> q;
rtree.query(bgi::intersects(b), std::back_inserter(q));
BOOST_FOREACH(const pt_2d_val& w, q) {
if (w.second != v.second && bg::distance(v.first, w.first) <= th)
{
++tot_neigh;
}
}
}
double avg = ((double) tot_neigh) / ((double) trials);
stringstream ss;
ss << "Estimated " << avg << " neighbors on average for "
<< "threshold " << th << "." << endl;
ss << "Time to perform " << trials << " random trials: "
<< sw.Time() << " ms.";
//LOG_MSG(ss.str());
return avg;
}
double SpatialIndAlgs::est_mean_distance(const std::vector<double>& x,
const std::vector<double>& y,
bool is_arc, size_t max_iters)
{
wxStopWatch sw;
using namespace GenGeomAlgs;
const size_t pts_sz = x.size();
const size_t all_pairs_sz = (pts_sz*(pts_sz-1))/2;
if (x.size() != y.size() || x.size() == 0 || y.size() == 0) { return -1; }
double sum = 0;
double smp_cnt = 0;
if (all_pairs_sz <= max_iters) {
for (size_t i=0; i<pts_sz; ++i) {
for (size_t j=i+1; j<pts_sz; ++j) {
sum += (is_arc ? ComputeArcDistRad(x[i], y[i], x[j], y[j]) :
ComputeEucDist(x[i], y[i], x[j], y[j]));
}
}
smp_cnt = (double) all_pairs_sz;
} else {
// Mersenne Twister random number generator, randomly seeded
// with current time in seconds since Jan 1 1970.
static boost::mt19937 rng(std::time(0));
static boost::random::uniform_int_distribution<> X(0, pts_sz-1);
for (size_t t=0; t<max_iters; ++t) {
size_t i=X(rng);
size_t j=X(rng);
sum += (is_arc ? ComputeArcDistRad(x[i], y[i], x[j], y[j]) :
ComputeEucDist(x[i], y[i], x[j], y[j]));
}
smp_cnt = max_iters;
}
stringstream ss;
ss << "est_mean_distance finished in " << sw.Time() << " ms.";
return sum/smp_cnt;
}
double SpatialIndAlgs::est_median_distance(const std::vector<double>& x,
const std::vector<double>& y,
bool is_arc, size_t max_iters)
{
wxStopWatch sw;
using namespace GenGeomAlgs;
if (x.size() != y.size() || x.size() == 0 || y.size() == 0) { return -1; }
const size_t pts_sz = x.size();
const size_t all_pairs_sz = (pts_sz*(pts_sz-1))/2;
vector<double> v;
if (all_pairs_sz <= max_iters) {
v.resize((pts_sz*(pts_sz-1))/2);
size_t t=0;
for (size_t i=0; i<pts_sz; ++i) {
for (size_t j=i+1; j<pts_sz; ++j) {
v[t] = (is_arc ? ComputeArcDistRad(x[i], y[i], x[j], y[j]) :
ComputeEucDist(x[i], y[i], x[j], y[j]));
++t;
}
}
} else {
v.resize(max_iters);
// Mersenne Twister random number generator, randomly seeded
// with current time in seconds since Jan 1 1970.
static boost::mt19937 rng(std::time(0));
static boost::random::uniform_int_distribution<> X(0, pts_sz-1);
size_t cnt=0;
for (size_t t=0; t<max_iters; ++t) {
size_t i=X(rng);
size_t j=X(rng);
//if (i==j) continue;
v[t] = (is_arc ? ComputeArcDistRad(x[i], y[i], x[j], y[j]) :
ComputeEucDist(x[i], y[i], x[j], y[j]));
if (!Gda::is_finite(v[t]) || Gda::is_nan(v[t])) {
stringstream ss;
ss << "d(i="<<i<<",j="<<j<<"): "<<v[t];
}
}
}
sort(v.begin(), v.end());
stringstream ss;
ss << "est_median_distance finished in " << sw.Time() << " ms.";
return v[v.size()/2];
}
GwtWeight* SpatialIndAlgs::thresh_build(const std::vector<double>& x,
const std::vector<double>& y,
double th, double power,
bool is_arc, bool is_mi,
const wxString& kernel,
bool use_kernel_diagnals)
{
using namespace GenGeomAlgs;
size_t nobs = x.size();
GwtWeight* gwt = 0;
if (is_arc) {
double r_th = is_mi ? EarthMiToRad(th) : EarthKmToRad(th);
double u_th = RadToUnitDist(r_th);
rtree_pt_3d_t rtree;
{
vector<pt_3d> pts;
{
vector<pt_lonlat> ptll(nobs);
for (int i=0; i<nobs; ++i) ptll[i] = pt_lonlat(x[i], y[i]);
to_3d_centroids(ptll, pts);
}
fill_pt_rtree(rtree, pts);
}
gwt = thresh_build(rtree, u_th, power, is_mi, kernel, use_kernel_diagnals);
} else {
rtree_pt_2d_t rtree;
{
vector<pt_2d> pts(nobs);
for (int i=0; i<nobs; ++i) {
pts[i] = pt_2d(x[i], y[i]);
}
fill_pt_rtree(rtree, pts);
}
gwt = thresh_build(rtree, th, power, kernel, use_kernel_diagnals);
}
return gwt;
}
GwtWeight* SpatialIndAlgs::thresh_build(const rtree_pt_2d_t& rtree, double th, double power, const wxString& kernel, bool use_kernel_diagnals)
{
wxStopWatch sw;
GwtWeight* Wp = new GwtWeight;
Wp->num_obs = rtree.size();
Wp->is_symmetric = false;
Wp->symmetry_checked = true;
int num_obs = Wp->num_obs;
Wp->gwt = new GwtElement[num_obs];
int cnt=0;
bool ignore_too_large_compute = false;
rtree_pt_2d_t::const_query_iterator it;
for (it = rtree.qbegin(bgi::intersects(rtree.bounds()));
it != rtree.qend() ; ++it)
{
const pt_2d_val& v = *it;
double x = v.first.get<0>();
double y = v.first.get<1>();
box_2d b(pt_2d(x-th, y-th), pt_2d(x+th, y+th));
size_t obs = v.second;
vector<pt_2d_val> q;
rtree.query(bgi::intersects(b), std::back_inserter(q));
size_t lcnt = 0;
list<pt_2d_val> l;
BOOST_FOREACH(pt_2d_val const& w, q) {
if (w.second != v.second &&
bg::distance(v.first, w.first) <= th)
{
l.push_front(w);
++lcnt;
}
}
if (lcnt > 200 && ignore_too_large_compute == false) {
wxString msg = _("You can try to proceed but the current threshold distance value might be too large to compute. If it fails, please input a smaller distance band (which might leave some observations neighborless) or use other weights (e.g. KNN).");
wxMessageDialog dlg(NULL, msg, "Do you want to continue?", wxYES_NO | wxYES_DEFAULT);
if (dlg.ShowModal() != wxID_YES) {
// clean up memory
delete Wp;
throw GdaException(msg.mb_str());
}
else {
ignore_too_large_compute = true;
}
}
GwtElement& e = Wp->gwt[obs];
if (!kernel.IsEmpty()) lcnt += 1;
e.alloc(lcnt);
BOOST_FOREACH(pt_2d_val const& w, l) {
GwtNeighbor neigh;
neigh.nbx = w.second;
double w_val = bg::distance(v.first, w.first);
if (power != 1) w_val = pow(w_val, power);
if (!kernel.IsEmpty()) w_val = w_val / th;
neigh.weight = w_val;
e.Push(neigh);
++cnt;
}
if (!kernel.IsEmpty()) {
// add diagonal item: ii
GwtNeighbor neigh;
neigh.nbx = obs;
neigh.weight = 1;
e.Push(neigh);
}
}
if (!kernel.IsEmpty()) {
apply_kernel(Wp, kernel, use_kernel_diagnals);
}
stringstream ss;
ss << "Time to create " << th << " threshold GwtWeight,"
<< endl << " with " << cnt << " total neighbors in ms : "
<< sw.Time();
return Wp;
}
double SpatialIndAlgs::est_avg_num_neigh_thresh(const rtree_pt_3d_t& rtree,
double th, size_t trials)
{
wxStopWatch sw;
using namespace GenGeomAlgs;
vector<pt_3d_val> query_pts;
rtree.query(bgi::intersects(rtree.bounds()), back_inserter(query_pts));
// Mersenne Twister random number generator, randomly seeded
// with current time in seconds since Jan 1 1970.
static boost::mt19937 rng(std::time(0));
static boost::random::uniform_int_distribution<> X(0, query_pts.size()-1);
size_t tot_neigh = 0;
for (size_t i=0; i<trials; ++i) {
const pt_3d_val& v = query_pts[X(rng)];
double x = v.first.get<0>();
double y = v.first.get<1>();
double z = v.first.get<2>();
box_3d b(pt_3d(x-th, y-th, z-th), pt_3d(x+th, y+th, z+th));
vector<pt_3d_val> q;
rtree.query(bgi::intersects(b), std::back_inserter(q));
BOOST_FOREACH(const pt_3d_val& w, q) {
if (w.second != v.second && bg::distance(v.first, w.first) <= th)
{
++tot_neigh;
}
}
}
double avg = ((double) tot_neigh) / ((double) trials);
stringstream ss;
ss << "Estimated " << avg << " neighbors on average for "
<< "threshold " << th << "." << endl;
ss << "Time to perform " << trials << " random trials: "
<< sw.Time() << " ms.";
return avg;
}
/** threshold th is the radius of intersection sphere with
respect to the unit shpere of the 3d point rtree */
GwtWeight* SpatialIndAlgs::thresh_build(const rtree_pt_3d_t& rtree, double th, double power, bool is_mi, const wxString& kernel, bool use_kernel_diagnals)
{
wxStopWatch sw;
using namespace GenGeomAlgs;
GwtWeight* Wp = new GwtWeight;
Wp->num_obs = rtree.size();
Wp->is_symmetric = false;
Wp->symmetry_checked = true;
Wp->gwt = new GwtElement[Wp->num_obs];
{
stringstream ss;
ss << "In thresh_build for unit sphere" << endl;
ss << "th : " << th << endl;
ss << "Input th (unit sphere secant distance): " << th << endl;
double r = UnitDistToRad(th);
ss << "Input th (unit sphere rad): " << r << endl;
ss << "Input th (earth km): " << EarthRadToKm(r) << endl;
ss << "Input th (earth mi): " << EarthRadToMi(r);
}
int cnt=0;
for (rtree_pt_3d_t::const_query_iterator it =
rtree.qbegin(bgi::intersects(rtree.bounds()));
it != rtree.qend() ; ++it)
{
const pt_3d_val& v = *it;
double vx = v.first.get<0>();
double vy = v.first.get<1>();
double vz = v.first.get<2>();
double lon_v, lat_v;
UnitToLongLatDeg(vx, vy, vz, lon_v, lat_v);
box_3d b(pt_3d(vx-th, vy-th, vz-th), pt_3d(vx+th, vy+th, vz+th));
size_t obs = v.second;
vector<pt_3d_val> q;
rtree.query(bgi::intersects(b), std::back_inserter(q));
size_t lcnt = 0;
list<pt_3d_val> l;
BOOST_FOREACH(pt_3d_val const& w, q) {
if (w.second != v.second &&
bg::distance(v.first, w.first) <= th)
{
l.push_front(w);
++lcnt;
}
}
GwtElement& e = Wp->gwt[obs];
if (!kernel.IsEmpty()) lcnt += 1;
e.alloc(lcnt);
BOOST_FOREACH(pt_3d_val const& w, l) {
GwtNeighbor neigh;
neigh.nbx = w.second;
double wx = w.first.get<0>();
double wy = w.first.get<1>();
double wz = w.first.get<2>();
double lon_w, lat_w;
double d;
UnitToLongLatDeg(wx, wy, wz, lon_w, lat_w);
if (is_mi) {
d = ComputeArcDistMi(lon_v, lat_v, lon_w, lat_w);
} else {
d = ComputeArcDistKm(lon_v, lat_v, lon_w, lat_w);
}
if (power!=1) d = pow(d, power);
if (!kernel.IsEmpty()) d = d / th;
neigh.weight = d;
e.Push(neigh);
++cnt;
}
if (!kernel.IsEmpty()) {
// add diagonal item: ii
GwtNeighbor neigh;
neigh.nbx = obs;
neigh.weight = 1;
e.Push(neigh);
}
}
stringstream ss;
ss << "Time to create arc " << th << " threshold GwtWeight,"
<< endl << " with " << cnt << " total neighbors in ms : "
<< sw.Time();
if (!kernel.IsEmpty()) {
apply_kernel(Wp, kernel, use_kernel_diagnals);
}
return Wp;
}
double SpatialIndAlgs::find_max_1nn_dist(const std::vector<double>& x,
const std::vector<double>& y,
bool is_arc, bool is_mi)
{
using namespace GenGeomAlgs;
size_t nobs = x.size();
double min_d_1nn, max_d_1nn, mean_d_1nn, median_d_1nn, d;
if (is_arc) {
rtree_pt_3d_t rtree;
{
vector<pt_3d> pts;
{
vector<pt_lonlat> ptll(nobs);
for (int i=0; i<nobs; ++i) ptll[i] = pt_lonlat(x[i], y[i]);
to_3d_centroids(ptll, pts);
}
fill_pt_rtree(rtree, pts);
}
get_pt_rtree_stats(rtree, min_d_1nn, max_d_1nn, mean_d_1nn, median_d_1nn);
d = is_mi ? EarthRadToMi(max_d_1nn) : EarthRadToKm(max_d_1nn);
} else {
rtree_pt_2d_t rtree;
{
vector<pt_2d> pts(nobs);
for (int i=0; i<nobs; ++i) pts[i] = pt_2d(x[i], y[i]);
fill_pt_rtree(rtree, pts);
}
get_pt_rtree_stats(rtree, min_d_1nn, max_d_1nn, mean_d_1nn, median_d_1nn);
d = max_d_1nn;
}
return d;
}
void SpatialIndAlgs::get_pt_rtree_stats(const rtree_pt_2d_t& rtree,
double& min_d_1nn, double& max_d_1nn,
double& mean_d_1nn, double& median_d_1nn)
{
wxStopWatch sw;
const int k=2;
size_t obs = rtree.size();
vector<double> d(obs);
for (rtree_pt_2d_t::const_query_iterator it =
rtree.qbegin(bgi::intersects(rtree.bounds()));
it != rtree.qend() ; ++it)
{
const pt_2d_val& v = *it;
vector<pt_2d_val> q;
rtree.query(bgi::nearest(v.first, k), std::back_inserter(q));
BOOST_FOREACH(pt_2d_val const& w, q) {
if (w.second == v.second) continue;
d[v.second] = bg::distance(v.first, w.first);
}
}
sort(d.begin(), d.end());
min_d_1nn = d[0];
max_d_1nn = d[d.size()-1];
median_d_1nn = d[(d.size()-1)/2];
double s=0;
for (size_t i=0; i<obs; ++i) s += d[i];
mean_d_1nn = s / (double) obs;
stringstream ss;
ss << "Euclidean points stats:" << endl;
ss << " min_d_1nn: " << min_d_1nn << endl;
ss << " max_d_1nn: " << max_d_1nn << endl;
ss << " median_d_1nn: " << median_d_1nn << endl;
ss << " mean_d_1nn: " << mean_d_1nn << endl;
ss << " running time in ms: " << sw.Time();
}
/** results returned in radians */
void SpatialIndAlgs::get_pt_rtree_stats(const rtree_pt_3d_t& rtree,
double& min_d_1nn, double& max_d_1nn,
double& mean_d_1nn, double& median_d_1nn)
{
wxStopWatch sw;
using namespace GenGeomAlgs;
size_t obs = rtree.size();
vector<double> d(obs);
for (rtree_pt_3d_t::const_query_iterator it =
rtree.qbegin(bgi::intersects(rtree.bounds()));
it != rtree.qend() ; ++it)
{
const pt_3d_val& v = *it;
vector<pt_3d_val> q;
rtree.query(bgi::nearest(v.first, 2), std::back_inserter(q));
BOOST_FOREACH(pt_3d_val const& w, q) {
if (w.second == v.second) continue;
double lonv, latv, lonw, latw;
UnitToLongLatRad(v.first.get<0>(), v.first.get<1>(),
v.first.get<2>(), lonv, latv);
UnitToLongLatRad(w.first.get<0>(), w.first.get<1>(),
w.first.get<2>(), lonw, latw);
d[v.second] = LonLatRadDistRad(lonv, latv, lonw, latw);
}
}
sort(d.begin(), d.end());
min_d_1nn = d[0];
max_d_1nn = d[d.size()-1];
median_d_1nn = d[(d.size()-1)/2];
double s=0;
for (size_t i=0; i<obs; ++i) s += d[i];
mean_d_1nn = s / (double) obs;
stringstream ss;
ss << "Long / Lat points stats:" << endl;
ss << " min_d_1nn: " << min_d_1nn << " rad, "
<< RadToDeg(min_d_1nn) << " deg, "
<< EarthRadToKm(min_d_1nn) << " km, "
<< EarthRadToMi(min_d_1nn) << " mi" << endl;
ss << " max_d_1nn: " << max_d_1nn << " rad, "
<< RadToDeg(max_d_1nn) << " deg, "
<< EarthRadToKm(max_d_1nn) << " km, "
<< EarthRadToMi(max_d_1nn) << " mi" << endl;
ss << " median_d_1nn: " << median_d_1nn << " rad, "
<< RadToDeg(median_d_1nn) << " deg, "
<< EarthRadToKm(median_d_1nn) << " km, "
<< EarthRadToMi(median_d_1nn) << " mi" << endl;
ss << " mean_d_1nn: " << mean_d_1nn << " rad, "
<< RadToDeg(mean_d_1nn) << " deg, "
<< EarthRadToKm(mean_d_1nn) << " km, "
<< EarthRadToMi(mean_d_1nn) << " mi" << endl;
ss << " running time in ms: " << sw.Time();
}
GwtWeight* SpatialIndAlgs::knn_build(const rtree_pt_lonlat_t& rtree, int nn)
{
GwtWeight* Wp = new GwtWeight;
Wp->num_obs = rtree.size();
Wp->is_symmetric = false;
Wp->symmetry_checked = true;
Wp->gwt = new GwtElement[Wp->num_obs];