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diff --git a/src/Witness_complex/example/witness_complex_knn_landmarks.cpp b/src/Witness_complex/example/witness_complex_knn_landmarks.cpp
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--- a/src/Witness_complex/example/witness_complex_knn_landmarks.cpp
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-/* 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/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-//#include <stdlib.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/reader_utils.h"
-#include "generators.h"
-#include "output.h"
-//#include <boost/filesystem.hpp>
-
-//#include <CGAL/Delaunay_triangulation.h>
-#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_k_neighbor_search.h>
-
-#include <boost/tuple/tuple.hpp>
-#include <boost/iterator/zip_iterator.hpp>
-#include <boost/iterator/counting_iterator.hpp>
-#include <boost/range/iterator_range.hpp>
-
-using namespace Gudhi;
-//using namespace boost::filesystem;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-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::Search_traits_adapter<
- std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-typedef CGAL::Orthogonal_k_neighbor_search<STraits> K_neighbor_search;
-typedef K_neighbor_search::Tree Tree;
-typedef K_neighbor_search::Distance Distance;
-typedef K_neighbor_search::iterator KNS_iterator;
-typedef K_neighbor_search::iterator KNS_range;
-typedef boost::container::flat_map<int, int> Point_etiquette_map;
-
-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_to_tree(Point_Vector &W, int nbP, Point_etiquette_map &L_i, int nbL, std::vector< std::vector <int> > &WL)
-{
- 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;
- srand(24660);
- for (int i = 0; i < nbL; i++)
- {
- // while (!res.second)
- // {
- chosen_landmark = rand()%nbP;
- p = &W[chosen_landmark];
- //L_i.emplace(chosen_landmark,i);
- // }
- landmarks.push_back(*p);
- //std::cout << "Added landmark " << chosen_landmark << std::endl;
- }
- Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
- boost::counting_iterator<std::ptrdiff_t>(nbL),
- typename Tree::Splitter(),
- STraits((Point_d*)&(landmarks[0])));
- /*}
-
-
-void d_nearest_landmarks(Point_Vector &W, Tree &L, Point_etiquette_map &L_i, std::vector< std::vector <int> > &WL)
-{*/
- std::cout << "Enter (D+1) nearest landmarks\n";
- std::cout << "Size of the tree is " << L.size() << std::endl;
-//int nbP = W.size();
- int D = W[0].size();
- for (int i = 0; i < nbP; i++)
- {
- //std::cout << "Entered witness number " << i << std::endl;
- Point_d& w = W[i];
- //std::cout << "Safely constructed a point\n";
- //Search D+1 nearest neighbours from the tree of landmarks L
- K_neighbor_search search(L, w, D+1, FT(0), true,
- CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,CGAL::Euclidean_distance<Traits_base>>((Point_d*)&(landmarks[0])) );
- //std::cout << "Safely found nearest landmarks\n";
- for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
- {
- //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
- //Point_etiquette_map::iterator itm = L_i.find(it->first);
- //assert(itm != L_i.end());
- //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
- WL[i].push_back(it->first);
- //std::cout << i << " " << it->first << ": " << it->second << std::endl;
- }
- }
-}
-
-int main (int argc, char * const argv[])
-{
- if (argc != 3)
- {
- std::cerr << "Usage: " << argv[0]
- << " path_to_point_file nbL \n";
- return 0;
- }
- /*
- boost::filesystem::path p;
-
- for (; argc > 2; --argc, ++argv)
- p /= argv[1];
- */
- std::string file_name = argv[1];
- int nbL = atoi(argv[2]);
-
- clock_t start, end;
- //Construct the Simplex Tree
- Witness_complex<> witnessComplex;
-
- std::cout << "Let the carnage begin!\n";
- Point_Vector point_vector;
- read_points_cust(file_name, point_vector);
- //std::cout << "Successfully read the points\n";
- witnessComplex.setNbL(nbL);
- // witnessComplex.witness_complex_from_points(point_vector);
- int nbP = point_vector.size();
- std::vector<std::vector< int > > WL(nbP);
- //std::set<int> L;
- Tree L;
- Point_etiquette_map L_i;
- start = clock();
- //witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
- landmark_choice_to_tree(point_vector, nbP, L_i, nbL, WL);
- //d_nearest_landmarks(point_vector, L, L_i, WL);
- end = clock();
- std::cout << "Landmark choice took "
- << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
- // Write the WL matrix in a file
- mkdir("output", S_IRWXU);
- const size_t last_slash_idx = file_name.find_last_of("/");
- if (std::string::npos != last_slash_idx)
- {
- file_name.erase(0, last_slash_idx + 1);
- }
- std::string out_file = "output/"+file_name+"_"+argv[2]+".wl";
- write_wl(out_file,WL);
- start = clock();
- witnessComplex.witness_complex(WL);
- //
- end = clock();
- std::cout << "Howdy world! The process took "
- << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
- /*
- char buffer[100];
- int i = sprintf(buffer,"%s_%s_result.txt",argv[1],argv[2]);
- if (i >= 0)
- {
- std::string out_file = (std::string)buffer;
- std::ofstream ofs (out_file, std::ofstream::out);
- witnessComplex.st_to_file(ofs);
- ofs.close();
- }
- */
-
- out_file = "output/"+file_name+"_"+argv[2]+".stree";
- std::ofstream ofs (out_file, std::ofstream::out);
- witnessComplex.st_to_file(ofs);
- ofs.close();
-
- out_file = "output/"+file_name+"_"+argv[2]+".badlinks";
- std::ofstream ofs2(out_file, std::ofstream::out);
- //witnessComplex.write_bad_links(ofs2);
- ofs2.close();
-}
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