1 files changed, 0 insertions, 276 deletions
diff --git a/example/Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp b/example/Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
deleted file mode 100644
index 290a9d9b..00000000
--- a/example/Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
+++ /dev/null
@@ -1,276 +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) 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 <gudhi/Simplex_tree.h>
-#include <gudhi/Points_3D_off_io.h>
-
-#include <boost/variant.hpp>
-
-#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/Delaunay_triangulation_3.h>
-#include <CGAL/Alpha_shape_3.h>
-#include <CGAL/Alpha_shape_vertex_base_3.h>
-#include <CGAL/Alpha_shape_cell_base_3.h>
-#include <CGAL/iterator.h>
-
-#include <fstream>
-#include <cmath>
-#include <string>
-#include <tuple>  // for tuple<>
-#include <map>
-#include <utility>  // for pair<>
-#include <list>
-#include <vector>
-
-// Alpha_shape_3 templates type definitions
-typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel;
-typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb;
-typedef CGAL::Alpha_shape_cell_base_3<Kernel> Fb;
-typedef CGAL::Triangulation_data_structure_3<Vb, Fb> Tds;
-typedef CGAL::Delaunay_triangulation_3<Kernel, Tds> Triangulation_3;
-typedef CGAL::Alpha_shape_3<Triangulation_3> Alpha_shape_3;
-
-// From file type definition
-typedef Kernel::Point_3 Point;
-
-// filtration with alpha values needed type definition
-typedef Alpha_shape_3::FT Alpha_value_type;
-typedef CGAL::Object Object;
-typedef CGAL::Dispatch_output_iterator<
-CGAL::cpp11::tuple<Object, Alpha_value_type>,
-CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
-    std::back_insert_iterator< std::vector<Alpha_value_type> > > > Dispatch;
-typedef Alpha_shape_3::Cell_handle Cell_handle;
-typedef Alpha_shape_3::Facet Facet;
-typedef Alpha_shape_3::Edge Edge;
-typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
-
-// gudhi type definition
-typedef Gudhi::Simplex_tree<> Simplex_tree;
-typedef Simplex_tree::Vertex_handle Simplex_tree_vertex;
-typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map;
-typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
-typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex;
-
-Vertex_list from(const Cell_handle& ch) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-#ifdef DEBUG_TRACES
-    std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-    the_list.push_back(ch->vertex(i));
-  }
-  return the_list;
-}
-
-Vertex_list from(const Facet& fct) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-    if (fct.second != i) {
-#ifdef DEBUG_TRACES
-      std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-      the_list.push_back(fct.first->vertex(i));
-    }
-  }
-  return the_list;
-}
-
-Vertex_list from(const Edge& edg) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-    if ((edg.second == i) || (edg.third == i)) {
-#ifdef DEBUG_TRACES
-      std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-      the_list.push_back(edg.first->vertex(i));
-    }
-  }
-  return the_list;
-}
-
-Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) {
-  Vertex_list the_list;
-#ifdef DEBUG_TRACES
-  std::cout << "from vertex=" << vh->point() << std::endl;
-#endif  // DEBUG_TRACES
-  the_list.push_back(vh);
-  return the_list;
-}
-
-int main(int argc, char * const argv[]) {
-  // program args management
-  if (argc != 2) {
-    std::cerr << "Usage: " << argv[0]
-        << " path_to_off_file \n";
-    return 0;
-  }
-
-  // Read points from file
-  std::string offInputFile(argv[1]);
-  // Read the OFF file (input file name given as parameter) and triangulate points
-  Gudhi::Points_3D_off_reader<Point> off_reader(offInputFile);
-  // Check the read operation was correct
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << argv[1] << std::endl;
-    return 0;
-  }
-  // Retrieve the triangulation
-  std::vector<Point> lp = off_reader.get_point_cloud();
-
-  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
-  Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
-#ifdef DEBUG_TRACES
-  std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
-#endif  // DEBUG_TRACES
-
-  // filtration with alpha values from alpha shape
-  std::vector<Object> the_objects;
-  std::vector<Alpha_value_type> the_alpha_values;
-
-  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
-      std::back_inserter(the_alpha_values));
-
-  as.filtration_with_alpha_values(disp);
-#ifdef DEBUG_TRACES
-  std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
-#endif  // DEBUG_TRACES
-
-  Alpha_shape_3::size_type count_vertices = 0;
-  Alpha_shape_3::size_type count_edges = 0;
-  Alpha_shape_3::size_type count_facets = 0;
-  Alpha_shape_3::size_type count_cells = 0;
-
-  // Loop on objects vector
-  Vertex_list vertex_list;
-  Simplex_tree simplex_tree;
-  Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
-  std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
-  for (auto object_iterator : the_objects) {
-    // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
-      vertex_list = from(*cell);
-      count_cells++;
-    } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
-      vertex_list = from(*facet);
-      count_facets++;
-    } else if (const Edge * edge = CGAL::object_cast<Edge>(&object_iterator)) {
-      vertex_list = from(*edge);
-      count_edges++;
-    } else if (const Alpha_shape_3::Vertex_handle * vertex =
-              CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
-      count_vertices++;
-      vertex_list = from(*vertex);
-    }
-    // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
-    Simplex_tree_vector_vertex the_simplex_tree;
-    for (auto the_alpha_shape_vertex : vertex_list) {
-      Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
-      if (the_map_iterator == map_cgal_simplex_tree.end()) {
-        // alpha shape not found
-        Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
-#ifdef DEBUG_TRACES
-        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert_simplex " << vertex << "\n";
-#endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
-        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
-      } else {
-        // alpha shape found
-        Simplex_tree_vertex vertex = the_map_iterator->second;
-#ifdef DEBUG_TRACES
-        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
-#endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
-      }
-    }
-    // Construction of the simplex_tree
-#ifdef DEBUG_TRACES
-    std::cout << "filtration = " << *the_alpha_value_iterator << std::endl;
-#endif  // DEBUG_TRACES
-    simplex_tree.insert_simplex(the_simplex_tree, std::sqrt(*the_alpha_value_iterator));
-    if (the_alpha_value_iterator != the_alpha_values.end())
-      ++the_alpha_value_iterator;
-    else
-      std::cerr << "This shall not happen" << std::endl;
-  }
-#ifdef DEBUG_TRACES
-  std::cout << "vertices \t\t" << count_vertices << std::endl;
-  std::cout << "edges \t\t" << count_edges << std::endl;
-  std::cout << "facets \t\t" << count_facets << std::endl;
-  std::cout << "cells \t\t" << count_cells << std::endl;
-
-
-  std::cout << "Information of the Simplex Tree:\n";
-  std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
-  std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
-#endif  // DEBUG_TRACES
-
-#ifdef DEBUG_TRACES
-  std::cout << "Iterator on vertices: \n";
-  for (auto vertex : simplex_tree.complex_vertex_range()) {
-    std::cout << vertex << " ";
-  }
-#endif  // DEBUG_TRACES
-
-  std::cout << simplex_tree << std::endl;
-
-#ifdef DEBUG_TRACES
-  std::cout << std::endl << std::endl << "Iterator on simplices:\n";
-  for (auto simplex : simplex_tree.complex_simplex_range()) {
-    std::cout << "   ";
-    for (auto vertex : simplex_tree.simplex_vertex_range(simplex)) {
-      std::cout << vertex << " ";
-    }
-    std::cout << std::endl;
-  }
-#endif  // DEBUG_TRACES
-#ifdef DEBUG_TRACES
-  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:\n";
-  for (auto f_simplex : simplex_tree.filtration_simplex_range()) {
-    std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
-    for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) {
-      std::cout << vertex << " ";
-    }
-    std::cout << std::endl;
-  }
-#endif  // DEBUG_TRACES
-#ifdef DEBUG_TRACES
-  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, and their boundary simplices:\n";
-  for (auto f_simplex : simplex_tree.filtration_simplex_range()) {
-    std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
-    for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) {
-      std::cout << vertex << " ";
-    }
-    std::cout << std::endl;
-
-    for (auto b_simplex : simplex_tree.boundary_simplex_range(f_simplex)) {
-      std::cout << "      " << "[" << simplex_tree.filtration(b_simplex) << "] ";
-      for (auto vertex : simplex_tree.simplex_vertex_range(b_simplex)) {
-        std::cout << vertex << " ";
-      }
-      std::cout << std::endl;
-    }
-  }
-#endif  // DEBUG_TRACES
-
-  return 0;
-}