1 files changed, 0 insertions, 219 deletions
diff --git a/src/Witness_complex/example/strange_sphere.cpp b/src/Witness_complex/example/strange_sphere.cpp
deleted file mode 100644
index 9188bd8e..00000000
--- a/src/Witness_complex/example/strange_sphere.cpp
+++ /dev/null
@@ -1,219 +0,0 @@
-/*    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");
-}