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diff --git a/src/Witness_complex/example/relaxed_witness_persistence.cpp b/src/Witness_complex/example/relaxed_witness_persistence.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) 2016 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 <gudhi/Simplex_tree.h>
-#include <gudhi/Relaxed_witness_complex.h>
-#include <gudhi/Dim_lists.h>
-#include <gudhi/reader_utils.h>
-#include <gudhi/Persistent_cohomology.h>
-#include "Landmark_choice_random_knn.h"
-#include "Landmark_choice_sparsification.h"
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-#include <algorithm>
-#include <set>
-#include <queue>
-#include <iterator>
-#include <string>
-
-#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"
-#include "output.h"
-
-using namespace Gudhi;
-using namespace Gudhi::witness_complex;
-using namespace Gudhi::persistent_cohomology;
-
-typedef std::vector<Point_d> Point_Vector;
-typedef Relaxed_witness_complex< Simplex_tree<> > RelaxedWitnessComplex;
-typedef Simplex_tree<>::Simplex_handle Simplex_handle;
-
-/**
- * \brief Customized version of read_points
- * which takes into account a possible nbP first line
- *
- */
-inline void
-read_points_cust(std::string file_name, std::vector< std::vector< double > > & points) {
- std::ifstream in_file(file_name.c_str(), std::ios::in);
- if (!in_file.is_open()) {
- std::cerr << "Unable to open file " << file_name << std::endl;
- return;
- }
- std::string line;
- double x;
- while (getline(in_file, line)) {
- std::vector< double > point;
- std::istringstream iss(line);
- while (iss >> x) {
- point.push_back(x);
- }
- if (point.size() != 1)
- points.push_back(point);
- }
- in_file.close();
-}
-
-void output_experiment_information(char * const file_name)
-{
- std::cout << "Enter a valid experiment number. Usage: "
- << file_name << " exp_no options\n";
- std::cout << "Experiment description:\n"
- << "0 nbP nbL dim alpha limD mu_epsilon: "
- << "Build persistence diagram on relaxed witness complex "
- << "built from a point cloud on (dim-1)-dimensional sphere "
- << "consisting of nbP witnesses and nbL landmarks. "
- << "The maximal relaxation is alpha and the limit on simplicial complex "
- << "dimension is limD.\n";
- std::cout << "1 file_name nbL alpha limD: "
- << "Build persistence diagram on relaxed witness complex "
- << "build from a point cloud stored in a file and nbL landmarks. "
- << "The maximal relaxation is alpha and the limit on simplicial complex dimension is limD\n";
-}
-
-void rw_experiment(Point_Vector & point_vector, int nbL, FT alpha, int limD, FT mu_epsilon = 0.1)
-{
- clock_t start, end;
- Simplex_tree<> simplex_tree;
-
- // Choose landmarks
- std::vector<std::vector< int > > knn;
- std::vector<std::vector< FT > > distances;
- start = clock();
- //Gudhi::witness_complex::landmark_choice_by_random_knn(point_vector, nbL, alpha, limD, knn, distances);
- std::vector<Point_d> landmarks;
- Gudhi::witness_complex::landmark_choice_by_sparsification(point_vector, nbL, mu_epsilon, landmarks);
- Gudhi::witness_complex::build_distance_matrix(point_vector, // aka witnesses
- landmarks, // aka landmarks
- alpha,
- limD,
- knn,
- distances);
- end = clock();
- double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
- std::cout << "Choice of " << nbL << " landmarks took "
- << time << " s. \n";
- // Compute witness complex
- start = clock();
- RelaxedWitnessComplex rw(distances,
- knn,
- simplex_tree,
- nbL,
- alpha,
- limD);
- end = clock();
- time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
- std::cout << "Relaxed witness complex for " << nbL << " landmarks took "
- << time << " s. \n";
- std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
- // std::cout << simplex_tree << "\n";
-
- // Compute the persistence diagram of the complex
- simplex_tree.set_dimension(limD);
- persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree, true);
- int p = 3;
- pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
- start = clock();
- pcoh.compute_persistent_cohomology( alpha/1000 );
- end = clock();
- time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
- std::cout << "Persistence diagram took "
- << time << " s. \n";
- pcoh.output_diagram();
-
- int chi = 0;
- for (auto sh: simplex_tree.complex_simplex_range())
- chi += 1-2*(simplex_tree.dimension(sh)%2);
- std::cout << "Euler characteristic is " << chi << std::endl;
-
-}
-
-
-int experiment0 (int argc, char * const argv[])
-{
- if (argc != 8) {
- std::cerr << "Usage: " << argv[0]
- << " 0 nbP nbL dim alpha limD mu_epsilon\n";
- return 0;
- }
- /*
- boost::filesystem::path p;
- for (; argc > 2; --argc, ++argv)
- p /= argv[1];
- */
-
- int nbP = atoi(argv[2]);
- int nbL = atoi(argv[3]);
- int dim = atoi(argv[4]);
- double alpha = atof(argv[5]);
- int limD = atoi(argv[6]);
- double mu_epsilon = atof(argv[7]);
-
- // 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";
-
- rw_experiment(point_vector, nbL, alpha, limD);
-}
-
-int experiment1 (int argc, char * const argv[])
-{
- if (argc != 3) {
- std::cerr << "Usage: " << argv[0]
- << " 1 file_name\n";
- return 0;
- }
- /*
- boost::filesystem::path p;
- for (; argc > 2; --argc, ++argv)
- p /= argv[1];
- */
-
- std::string file_name = argv[2];
-
- // Read the point file
- Point_Vector point_vector;
- read_points_cust(file_name, point_vector);
- std::cout << "The file contains " << point_vector.size() << " points.\n";
- std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
-
- bool ok = false;
- int nbL, limD;
- double alpha;
- while (!ok) {
- std::cout << "Relaxed witness complex: parameters nbL, alpha, limD.\n";
- std::cout << "Enter nbL: ";
- std::cin >> nbL;
- std::cout << "Enter alpha: ";
- std::cin >> alpha;
- std::cout << "Enter limD: ";
- std::cin >> limD;
- std::cout << "Start relaxed witness complex...\n";
- rw_experiment(point_vector, nbL, alpha, limD);
- std::cout << "Is the result correct? [y/n]: ";
- char answer;
- std::cin >> answer;
- switch (answer) {
- case 'n':
- ok = false; break;
- default :
- ok = true; break;
- }
- }
- // ok = false;
- // while (!ok) {
- // std::cout << "Rips complex: parameters threshold, limD.\n";
- // std::cout << "Enter threshold: ";
- // std::cin >> alpha;
- // std::cout << "Enter limD: ";
- // std::cin >> limD;
- // std::cout << "Start Rips complex...\n";
- // rips_experiment(point_vector, alpha, limD);
- // std::cout << "Is the result correct? [y/n]: ";
- // char answer;
- // std::cin >> answer;
- // switch (answer) {
- // case 'n':
- // ok = false; break;
- // default :
- // ok = true; break;
- // }
- // }
-}
-
-int main (int argc, char * const argv[])
-{
- if (argc == 1) {
- output_experiment_information(argv[0]);
- return 1;
- }
- switch (atoi(argv[1])) {
- case 0 :
- return experiment0(argc, argv);
- case 1 :
- return experiment1(argc, argv);
- default :
- output_experiment_information(argv[0]);
- return 1;
- }
-}
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