1 files changed, 0 insertions, 160 deletions
diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
deleted file mode 100644
index 6a3728fb..00000000
--- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
+++ /dev/null
@@ -1,160 +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):       Vincent Rouvreau
- *                     Pawel Dlotko - 2017 - Swansea University, UK
- *
- *    Copyright (C) 2014 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 <boost/program_options.hpp>
-#include <boost/variant.hpp>
-
-#include <gudhi/Alpha_complex_3d.h>
-#include <gudhi/Alpha_complex_3d_options.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Points_3D_off_io.h>
-
-#include <fstream>
-#include <cmath>
-#include <string>
-#include <tuple>
-#include <map>
-#include <utility>
-#include <vector>
-#include <cstdlib>
-
-// gudhi type definition
-using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Periodic_alpha_shapes_3d>;
-using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Filtration_value = Simplex_tree::Filtration_value;
-using Persistent_cohomology =
-    Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp>;
-
-void program_options(int argc, char *argv[], std::string &off_file_points, std::string &cuboid_file,
-                     std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence);
-
-int main(int argc, char **argv) {
-  std::string off_file_points;
-  std::string cuboid_file;
-  std::string output_file_diag;
-  int coeff_field_characteristic;
-  Filtration_value min_persistence;
-
-  program_options(argc, argv, off_file_points, cuboid_file, output_file_diag, coeff_field_characteristic,
-                  min_persistence);
-
-  // Read the OFF file (input file name given as parameter) and triangulate points
-  Gudhi::Points_3D_off_reader<Alpha_complex_3d::Point_3> off_reader(off_file_points);
-  // Check the read operation was correct
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << off_file_points << std::endl;
-    exit(-1);
-  }
-
-  // Read iso_cuboid_3 information from file
-  std::ifstream iso_cuboid_str(cuboid_file);
-  double x_min, y_min, z_min, x_max, y_max, z_max;
-  if (iso_cuboid_str.good()) {
-    iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max;
-  } else {
-    std::cerr << "Unable to read file " << cuboid_file << std::endl;
-    exit(-1);
-  }
-  // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
-  if ((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min)) {
-    std::cerr << "The size of the cuboid in every directions is not the same." << std::endl;
-    exit(-1);
-  }
-
-  Alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), x_min, y_min, z_min, x_max, y_max, z_max);
-
-  Simplex_tree simplex_tree;
-
-  alpha_complex.create_complex(simplex_tree);
-
-  // Sort the simplices in the order of the filtration
-  simplex_tree.initialize_filtration();
-
-  std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
-  // Compute the persistence diagram of the complex
-  Persistent_cohomology pcoh(simplex_tree, true);
-  // initializes the coefficient field for homology
-  pcoh.init_coefficients(coeff_field_characteristic);
-
-  pcoh.compute_persistent_cohomology(min_persistence);
-
-  // Output the diagram in filediag
-  if (output_file_diag.empty()) {
-    pcoh.output_diagram();
-  } else {
-    std::cout << "Result in file: " << output_file_diag << std::endl;
-    std::ofstream out(output_file_diag);
-    pcoh.output_diagram(out);
-    out.close();
-  }
-
-  return 0;
-}
-
-void program_options(int argc, char *argv[], std::string &off_file_points, std::string &cuboid_file,
-                     std::string &output_file_diag, int &coeff_field_characteristic,
-                     Filtration_value &min_persistence) {
-  namespace po = boost::program_options;
-  po::options_description hidden("Hidden options");
-  hidden.add_options()("input-file", po::value<std::string>(&off_file_points),
-                       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ")(
-      "cuboid-file", po::value<std::string>(&cuboid_file),
-      "Name of file describing the periodic domain. Format is: min_hx min_hy min_hz\nmax_hx max_hy max_hz");
-
-  po::options_description visible("Allowed options", 100);
-  visible.add_options()("help,h", "produce help message")(
-      "output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::cout")(
-      "field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11),
-      "Characteristic p of the coefficient field Z/pZ for computing homology.")(
-      "min-persistence,m", po::value<Filtration_value>(&min_persistence),
-      "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
-      "intervals");
-
-  po::positional_options_description pos;
-  pos.add("input-file", 1);
-  pos.add("cuboid-file", 2);
-
-  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") || !vm.count("cuboid-file")) {
-    std::cout << std::endl;
-    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-    std::cout << "of a periodic 3D Alpha 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 cuboid-file" << std::endl << std::endl;
-    std::cout << visible << std::endl;
-    std::abort();
-  }
-}