1 files changed, 0 insertions, 221 deletions
diff --git a/example/Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp b/example/Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp
deleted file mode 100644
index 34092ef6..00000000
--- a/example/Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp
+++ /dev/null
@@ -1,221 +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
- *
- *    Copyright (C) 2017 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/graph_simplicial_complex.h>
-#include <gudhi/distance_functions.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Points_off_io.h>
-
-#include <CGAL/Epick_d.h>
-#include <CGAL/Min_sphere_of_spheres_d.h>
-#include <CGAL/Min_sphere_of_points_d_traits_d.h>
-
-#include <boost/program_options.hpp>
-
-#include <string>
-#include <vector>
-#include <limits>   // infinity
-#include <utility>  // for pair
-#include <map>
-
-// -------------------------------------------------------------------------------
-// cech_complex_cgal_mini_sphere_3d is an example of each step that is required to
-// build a Cech over a Simplex_tree. Please refer to cech_persistence to see
-// how to do the same thing with the Cech_complex wrapper for less detailed
-// steps.
-// -------------------------------------------------------------------------------
-
-// Types definition
-using Simplex_tree = Gudhi::Simplex_tree<>;
-using Vertex_handle = Simplex_tree::Vertex_handle;
-using Simplex_handle = Simplex_tree::Simplex_handle;
-using Filtration_value = Simplex_tree::Filtration_value;
-using Siblings = Simplex_tree::Siblings;
-using Graph_t = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
-                                      boost::property<Gudhi::vertex_filtration_t, Filtration_value>,
-                                      boost::property<Gudhi::edge_filtration_t, Filtration_value> >;
-using Edge_t = std::pair<Vertex_handle, Vertex_handle>;
-
-using Kernel = CGAL::Epick_d<CGAL::Dimension_tag<3> >;
-using Point = Kernel::Point_d;
-using Traits = CGAL::Min_sphere_of_points_d_traits_d<Kernel, Filtration_value, 3>;
-using Min_sphere = CGAL::Min_sphere_of_spheres_d<Traits>;
-
-using Points_off_reader = Gudhi::Points_off_reader<Point>;
-
-class Cech_blocker {
- public:
-  bool operator()(Simplex_handle sh) {
-    std::vector<Point> points;
-#if DEBUG_TRACES
-    std::cout << "Cech_blocker on [";
-#endif  // DEBUG_TRACES
-    for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) {
-      points.push_back(point_cloud_[vertex]);
-#if DEBUG_TRACES
-      std::cout << vertex << ", ";
-#endif  // DEBUG_TRACES
-    }
-    Min_sphere ms(points.begin(), points.end());
-    Filtration_value radius = ms.radius();
-#if DEBUG_TRACES
-    std::cout << "] - radius = " << radius << " - returns " << (radius > threshold_) << std::endl;
-#endif  // DEBUG_TRACES
-    simplex_tree_.assign_filtration(sh, radius);
-    return (radius > threshold_);
-  }
-  Cech_blocker(Simplex_tree& simplex_tree, Filtration_value threshold, const std::vector<Point>& point_cloud)
-      : simplex_tree_(simplex_tree), threshold_(threshold), point_cloud_(point_cloud) {}
-
- private:
-  Simplex_tree simplex_tree_;
-  Filtration_value threshold_;
-  std::vector<Point> point_cloud_;
-};
-
-template <typename InputPointRange>
-Graph_t compute_proximity_graph(InputPointRange& points, Filtration_value threshold);
-
-void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& threshold, int& dim_max);
-
-int main(int argc, char* argv[]) {
-  std::string off_file_points;
-  Filtration_value threshold;
-  int dim_max;
-
-  program_options(argc, argv, off_file_points, threshold, dim_max);
-
-  // Extract the points from the file filepoints
-  Points_off_reader off_reader(off_file_points);
-
-  // Compute the proximity graph of the points
-  Graph_t prox_graph = compute_proximity_graph(off_reader.get_point_cloud(), threshold);
-
-  // Min_sphere sph1(off_reader.get_point_cloud()[0], off_reader.get_point_cloud()[1], off_reader.get_point_cloud()[2]);
-  // Construct the Rips complex in a Simplex Tree
-  Simplex_tree st;
-  // insert the proximity graph in the simplex tree
-  st.insert_graph(prox_graph);
-  // expand the graph until dimension dim_max
-  st.expansion_with_blockers(dim_max, Cech_blocker(st, threshold, off_reader.get_point_cloud()));
-
-  std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
-  std::cout << "   and has dimension " << st.dimension() << " \n";
-
-  // Sort the simplices in the order of the filtration
-  st.initialize_filtration();
-
-#if DEBUG_TRACES
-  std::cout << "********************************************************************\n";
-  // Display the Simplex_tree - Can not be done in the middle of 2 inserts
-  std::cout << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n";
-  std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n";
-  for (auto f_simplex : st.filtration_simplex_range()) {
-    std::cout << "   "
-              << "[" << st.filtration(f_simplex) << "] ";
-    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
-      std::cout << static_cast<int>(vertex) << " ";
-    }
-    std::cout << std::endl;
-  }
-#endif  // DEBUG_TRACES
-  return 0;
-}
-
-void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& threshold, int& dim_max) {
-  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 an OFF file containing a 3d point set.\n");
-
-  po::options_description visible("Allowed options", 100);
-  visible.add_options()("help,h", "produce help message")(
-      "max-edge-length,r",
-      po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
-      "Maximal length of an edge for the Cech complex construction.")(
-      "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
-      "Maximal dimension of the Cech 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 << "Construct a Cech complex defined on a set of input points.\n \n";
-
-    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-    std::cout << visible << std::endl;
-    exit(-1);
-  }
-}
-
-/** Output the proximity graph of the points.
- *
- * If points contains n elements, the proximity graph is the graph
- * with n vertices, and an edge [u,v] iff the distance function between
- * points u and v is smaller than threshold.
- *
- * The type PointCloud furnishes .begin() and .end() methods, that return
- * iterators with value_type Point.
- */
-template <typename InputPointRange>
-Graph_t compute_proximity_graph(InputPointRange& points, Filtration_value threshold) {
-  std::vector<Edge_t> edges;
-  std::vector<Filtration_value> edges_fil;
-
-  Kernel k;
-  Vertex_handle idx_u, idx_v;
-  Filtration_value fil;
-  idx_u = 0;
-  for (auto it_u = points.begin(); it_u != points.end(); ++it_u) {
-    idx_v = idx_u + 1;
-    for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) {
-      fil = k.squared_distance_d_object()(*it_u, *it_v);
-      // For Cech Complex, threshold is a radius (distance /2)
-      fil = std::sqrt(fil) / 2.;
-      if (fil <= threshold) {
-        edges.emplace_back(idx_u, idx_v);
-        edges_fil.push_back(fil);
-      }
-    }
-    ++idx_u;
-  }
-
-  Graph_t skel_graph(edges.begin(), edges.end(), edges_fil.begin(),
-                     idx_u);  // number of points labeled from 0 to idx_u-1
-
-  auto vertex_prop = boost::get(Gudhi::vertex_filtration_t(), skel_graph);
-
-  boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end;
-  for (std::tie(vi, vi_end) = boost::vertices(skel_graph); vi != vi_end; ++vi) {
-    boost::put(vertex_prop, *vi, 0.);
-  }
-
-  return skel_graph;
-}