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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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