1 files changed, 0 insertions, 156 deletions
diff --git a/utilities/Witness_complex/strong_witness_persistence.cpp b/utilities/Witness_complex/strong_witness_persistence.cpp
deleted file mode 100644
index f386e992..00000000
--- a/utilities/Witness_complex/strong_witness_persistence.cpp
+++ /dev/null
@@ -1,156 +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) 2016 Inria
- *
- *    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/Euclidean_strong_witness_complex.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Points_off_io.h>
-#include <gudhi/pick_n_random_points.h>
-#include <gudhi/choose_n_farthest_points.h>
-
-#include <boost/program_options.hpp>
-
-#include <CGAL/Epick_d.h>
-
-#include <string>
-#include <vector>
-#include <limits>  // infinity
-
-using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
-using Point_d = K::Point_d;
-
-using Point_vector = std::vector<Point_d>;
-using Strong_witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>;
-using SimplexTree = Gudhi::Simplex_tree<>;
-
-using Filtration_value = SimplexTree::Filtration_value;
-
-using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>;
-
-void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag,
-                     Filtration_value& max_squared_alpha, int& p, int& dim_max, Filtration_value& min_persistence);
-
-int main(int argc, char* argv[]) {
-  std::string file_name;
-  std::string filediag;
-  Filtration_value max_squared_alpha;
-  int p, nbL, lim_d;
-  Filtration_value min_persistence;
-  SimplexTree simplex_tree;
-
-  program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence);
-
-  // Extract the points from the file file_name
-  Point_vector witnesses, landmarks;
-  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
-  if (!off_reader.is_valid()) {
-    std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
-    exit(-1);  // ----- >>
-  }
-  witnesses = Point_vector(off_reader.get_point_cloud());
-  std::cout << "Successfully read " << witnesses.size() << " points.\n";
-  std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
-
-  // Choose landmarks (decomment one of the following two lines)
-  // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
-  Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point,
-                                               std::back_inserter(landmarks));
-
-  // Compute witness complex
-  Strong_witness_complex strong_witness_complex(landmarks, witnesses);
-
-  strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d);
-
-  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
-  std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
-
-  // Sort the simplices in the order of the filtration
-  simplex_tree.initialize_filtration();
-
-  // Compute the persistence diagram of the complex
-  Persistent_cohomology pcoh(simplex_tree);
-  // initializes the coefficient field for homology
-  pcoh.init_coefficients(p);
-
-  pcoh.compute_persistent_cohomology(min_persistence);
-
-  // Output the diagram in filediag
-  if (filediag.empty()) {
-    pcoh.output_diagram();
-  } else {
-    std::ofstream out(filediag);
-    pcoh.output_diagram(out);
-    out.close();
-  }
-
-  return 0;
-}
-
-void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag,
-                     Filtration_value& max_squared_alpha, int& p, int& dim_max, Filtration_value& min_persistence) {
-  namespace po = boost::program_options;
-
-  po::options_description hidden("Hidden options");
-  hidden.add_options()("input-file", po::value<std::string>(&file_name),
-                       "Name of file containing a point set in off format.");
-
-  po::options_description visible("Allowed options", 100);
-  Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity();
-  visible.add_options()("help,h", "produce help message")("landmarks,l", po::value<int>(&nbL),
-                                                          "Number of landmarks to choose from the point cloud.")(
-      "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::cout")(
-      "max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
-      "Maximal squared relaxation parameter.")(
-      "field-charac,p", po::value<int>(&p)->default_value(11),
-      "Characteristic p of the coefficient field Z/pZ for computing homology.")(
-      "min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
-      "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
-      "intervals")("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
-                   "Maximal dimension of the strong witness complex we want to compute.");
-
-  po::positional_options_description pos;
-  pos.add("input-file", 1);
-
-  po::options_description all;
-  all.add(visible).add(hidden);
-  po::variables_map vm;
-
-  po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm);
-  po::notify(vm);
-
-  if (vm.count("help") || !vm.count("input-file")) {
-    std::cout << std::endl;
-    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-    std::cout << "of a Strong witness complex defined on a set of input points.\n \n";
-    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
-    std::cout << "   p   dim b d \n";
-    std::cout << "where dim is the dimension of the homological feature,\n";
-    std::cout << "b and d are respectively the birth and death of the feature and \n";
-    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
-    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-    std::cout << visible << std::endl;
-    exit(-1);
-  }
-}