summaryrefslogtreecommitdiff
path: root/src/Witness_complex/example/strange_sphere.cpp
diff options
context:
space:
mode:
Diffstat (limited to 'src/Witness_complex/example/strange_sphere.cpp')
-rw-r--r--src/Witness_complex/example/strange_sphere.cpp219
1 files changed, 219 insertions, 0 deletions
diff --git a/src/Witness_complex/example/strange_sphere.cpp b/src/Witness_complex/example/strange_sphere.cpp
new file mode 100644
index 00000000..9188bd8e
--- /dev/null
+++ b/src/Witness_complex/example/strange_sphere.cpp
@@ -0,0 +1,219 @@
+/* This file is part of the Gudhi Library. The Gudhi library
+ * (Geometric Understanding in Higher Dimensions) is a generic C++
+ * library for computational topology.
+ *
+ * Author(s): Siargey Kachanovich
+ *
+ * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ * This program 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.
+ *
+ * This program 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/>.
+ */
+#define BOOST_PARAMETER_MAX_ARITY 12
+
+
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Strange_witness_complex.h>
+#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/reader_utils.h>
+#include "output.h"
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <utility>
+#include <string>
+#include <vector>
+
+#include <CGAL/Cartesian_d.h>
+#include <CGAL/Search_traits.h>
+#include <CGAL/Search_traits_adapter.h>
+#include <CGAL/property_map.h>
+#include <CGAL/Epick_d.h>
+#include <CGAL/Orthogonal_incremental_neighbor_search.h>
+#include <CGAL/Kd_tree.h>
+#include <CGAL/Euclidean_distance.h>
+
+#include <CGAL/Kernel_d/Vector_d.h>
+#include <CGAL/point_generators_d.h>
+#include <CGAL/constructions_d.h>
+#include <CGAL/Fuzzy_sphere.h>
+#include <CGAL/Random.h>
+
+
+#include <boost/tuple/tuple.hpp>
+#include <boost/iterator/zip_iterator.hpp>
+#include <boost/iterator/counting_iterator.hpp>
+#include <boost/range/iterator_range.hpp>
+
+
+#include "generators.h"
+
+using namespace Gudhi;
+using namespace Gudhi::witness_complex;
+
+typedef std::vector< Vertex_handle > typeVectorVertex;
+typedef Strange_witness_complex< Simplex_tree<> > WitnessComplex;
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef K::FT FT;
+typedef K::Point_d Point_d;
+typedef CGAL::Search_traits<
+ FT, Point_d,
+ typename K::Cartesian_const_iterator_d,
+ typename K::Construct_cartesian_const_iterator_d> Traits_base;
+typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
+
+typedef CGAL::Search_traits_adapter<
+ std::ptrdiff_t, Point_d*, Traits_base> STraits;
+typedef CGAL::Orthogonal_incremental_neighbor_search<STraits, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>> Neighbor_search;
+typedef Neighbor_search::Tree Tree;
+typedef Neighbor_search::Distance Distance;
+typedef Neighbor_search::iterator KNS_iterator;
+typedef Neighbor_search::iterator KNS_range;
+typedef boost::container::flat_map<int, int> Point_etiquette_map;
+typedef CGAL::Kd_tree<STraits> Tree2;
+typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
+typedef std::vector<Point_d> Point_Vector;
+
+/** Function that chooses landmarks from W and place it in the kd-tree L.
+ * Note: nbL hould be removed if the code moves to Witness_complex
+ */
+void landmark_choice(Point_Vector &W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
+{
+ std::cout << "Enter landmark choice to kd tree\n";
+ //std::vector<Point_d> landmarks;
+ int chosen_landmark;
+ //std::pair<Point_etiquette_map::iterator,bool> res = std::make_pair(L_i.begin(),false);
+ Point_d* p;
+ CGAL::Random rand;
+ for (int i = 0; i < nbL; i++)
+ {
+ // while (!res.second)
+ // {
+ do chosen_landmark = rand.get_int(0,nbP);
+ while (std::find(landmarks_ind.begin(), landmarks_ind.end(), chosen_landmark) != landmarks_ind.end());
+ //rand++;
+ //std::cout << "Chose " << chosen_landmark << std::endl;
+ p = &W[chosen_landmark];
+ //L_i.emplace(chosen_landmark,i);
+ // }
+ landmarks.push_back(*p);
+ landmarks_ind.push_back(chosen_landmark);
+ //std::cout << "Added landmark " << chosen_landmark << std::endl;
+ }
+ }
+
+void landmarks_to_witness_complex(Point_Vector &W, int nbL)
+{
+ //********************Preface: origin point
+ unsigned D = W[0].size();
+ std::vector<FT> orig_vector;
+ for (unsigned i = 0; i < D; i++)
+ orig_vector.push_back(0);
+ Point_d origin(orig_vector);
+ //Distance dist;
+ //dist.transformed_distance(0,1);
+ //******************** Constructing a WL matrix
+ int nbP = W.size();
+ Point_Vector landmarks;
+ std::vector<int> landmarks_ind;
+ landmark_choice(W, nbP, nbL, landmarks, landmarks_ind);
+
+
+ STraits traits(&(landmarks[0]));
+ Euclidean_distance ed;
+ std::vector< std::vector <int> > WL(nbP);
+ std::vector< std::vector< typename std::vector<int>::iterator > > ope_limits(nbP);
+ Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
+ boost::counting_iterator<std::ptrdiff_t>(nbL),
+ typename Tree::Splitter(),
+ traits);
+
+ std::cout << "Enter (D+1) nearest landmarks\n";
+ //std::cout << "Size of the tree is " << L.size() << std::endl;
+ for (int i = 0; i < nbP; i++) {
+ //std::cout << "Entered witness number " << i << std::endl;
+ Point_d& w = W[i];
+ std::queue< typename std::vector<int>::iterator > ope_queue; // queue of points at (1+epsilon) distance to current landmark
+ Neighbor_search search(L, w, FT(0), true, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(landmarks[0])));
+ Neighbor_search::iterator search_it = search.begin();
+
+ //Incremental search and filling WL
+ while (WL[i].size() < D)
+ WL[i].push_back((search_it++)->first);
+ }
+ write_wl("WL.txt", WL); //!
+ //******************** Constructng a witness complex
+ std::cout << "Entered witness complex construction\n";
+
+ Simplex_tree<> simplex_tree;
+ WitnessComplex(WL, simplex_tree, nbL, W[0].size()-1);
+ //std::cout << simplex_tree << "\n"; //!
+ write_witness_mesh(W, landmarks_ind, simplex_tree, false, true);
+}
+
+
+
+/** Write a gnuplot readable file.
+ * Data range is a random access range of pairs (arg, value)
+ */
+template < typename Data_range >
+void write_data(Data_range & data, std::string filename) {
+ std::ofstream ofs(filename, std::ofstream::out);
+ for (auto entry : data)
+ ofs << entry.first << ", " << entry.second << "\n";
+ ofs.close();
+}
+
+
+
+int main(int argc, char * const argv[]) {
+ if (argc != 4) {
+ std::cerr << "Usage: " << argv[0]
+ << " nbP nbL dim\n";
+ return 0;
+ }
+
+ int nbP = atoi(argv[1]);
+ int nbL = atoi(argv[2]);
+ int dim = atoi(argv[3]);
+ clock_t start, end;
+
+ // Construct the Simplex Tree
+ Simplex_tree<> simplex_tree;
+
+ std::vector< std::pair<int, double> > l_time;
+
+ // Read the point file
+ Point_Vector point_vector;
+ generate_points_sphere(point_vector, nbP, dim);
+ std::cout << "Successfully generated " << point_vector.size() << " points.\n";
+ std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
+
+ // Choose landmarks
+ start = clock();
+ std::vector<std::vector< int > > knn;
+
+ landmarks_to_witness_complex(point_vector, nbL);
+
+ end = clock();
+ double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
+ std::cout << "Witness complex for " << nbL << " landmarks took "
+ << time << " s. \n";
+ l_time.push_back(std::make_pair(nbP, time));
+ //write_data(l_time, "w_time.dat");
+}