Fix CGAL 4.11 bug and remove old_interface file. Better done with #if

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2774 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9a905b04cfa2718f9d5abc80e14ab1ee26d16279

3 files changed, 25 insertions, 270 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index be23de35..e82ef04c 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -127,15 +127,9 @@ if(CGAL_FOUND)
 
     install(TARGETS weighted_periodic_alpha_complex_3d_persistence DESTINATION bin)
 
-    # On CGAL 4.11, the weighted alpha shape 3 interface was changed - the new interface
-    add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp)
-  else(NOT CGAL_VERSION VERSION_LESS 4.11.0)
-    # On CGAL 4.11, the weighted alpha shape 3 interface was changed - the old interface
-    add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence_old_cgal_interface.cpp)
   endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
 
-  # cf. if (NOT CGAL_VERSION VERSION_LESS 4.11.0) and else(NOT CGAL_VERSION VERSION_LESS 4.11.0)
-  # same target name on purpose
+  add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp)
   target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES})
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
index 92fed4c1..85b0ab34 100644
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -26,11 +26,17 @@
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Points_3D_off_io.h>
 
+#include <CGAL/config.h>
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Regular_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
 #include <CGAL/iterator.h>
 
+// For CGAL < 4.11
+#if CGAL_VERSION_NR < 1041100000
+#include <CGAL/Regular_triangulation_euclidean_traits_3.h>
+#endif  // CGAL_VERSION_NR < 1041100000
+
 #include <fstream>
 #include <cmath>
 #include <string>
@@ -44,17 +50,34 @@
 #include "alpha_complex_3d_helper.h"
 
 using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
+
+// For CGAL < 4.11
+#if CGAL_VERSION_NR < 1041100000
+using Gt = CGAL::Regular_triangulation_euclidean_traits_3<Kernel>;
+using Vb = CGAL::Alpha_shape_vertex_base_3<Gt>;
+using Fb = CGAL::Alpha_shape_cell_base_3<Gt>;
+using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
+using Triangulation_3 = CGAL::Regular_triangulation_3<Gt, Tds>;
+
+// From file type definition
+using Point_3 = Gt::Bare_point;
+using Weighted_point_3 = Gt::Weighted_point;
+
+// For CGAL >= 4.11
+#else  // CGAL_VERSION_NR < 1041100000
 using Rvb = CGAL::Regular_triangulation_vertex_base_3<Kernel>;
 using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel,Rvb>;
 using Rcb = CGAL::Regular_triangulation_cell_base_3<Kernel>;
 using Cb = CGAL::Alpha_shape_cell_base_3<Kernel,Rcb>;
 using Tds = CGAL::Triangulation_data_structure_3<Vb,Cb>;
 using Triangulation_3 = CGAL::Regular_triangulation_3<Kernel,Tds>;
-using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
 
 // From file type definition
 using Point_3 = Triangulation_3::Bare_point;
 using Weighted_point_3 = Triangulation_3::Weighted_point;
+#endif  // CGAL_VERSION_NR < 1041100000
+
+using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
 
 // filtration with alpha values needed type definition
 using Alpha_value_type = Alpha_shape_3::FT;
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence_old_cgal_interface.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence_old_cgal_interface.cpp
deleted file mode 100644
index e2c48755..00000000
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence_old_cgal_interface.cpp
+++ /dev/null
@@ -1,262 +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 <boost/variant.hpp>
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Points_3D_off_io.h>
-
-#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/Regular_triangulation_euclidean_traits_3.h>
-#include <CGAL/Regular_triangulation_3.h>
-#include <CGAL/Alpha_shape_3.h>
-#include <CGAL/iterator.h>
-
-#include <fstream>
-#include <cmath>
-#include <string>
-#include <tuple>
-#include <map>
-#include <utility>
-#include <list>
-#include <vector>
-#include <cstdlib>
-
-#include "alpha_complex_3d_helper.h"
-
-// Traits
-using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
-using Gt = CGAL::Regular_triangulation_euclidean_traits_3<Kernel>;
-using Vb = CGAL::Alpha_shape_vertex_base_3<Gt>;
-using Fb = CGAL::Alpha_shape_cell_base_3<Gt>;
-using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
-using Triangulation_3 = CGAL::Regular_triangulation_3<Gt, Tds>;
-using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
-
-// From file type definition
-using Point_3 = Gt::Bare_point;
-using Weighted_point_3 = Gt::Weighted_point;
-
-// filtration with alpha values needed type definition
-using Alpha_value_type = Alpha_shape_3::FT;
-using Object = CGAL::Object;
-using Dispatch =
-    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> > > >;
-using Cell_handle = Alpha_shape_3::Cell_handle;
-using Facet = Alpha_shape_3::Facet;
-using Edge_3 = Alpha_shape_3::Edge;
-using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
-
-// gudhi type definition
-using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Filtration_value = ST::Filtration_value;
-using Simplex_tree_vertex = ST::Vertex_handle;
-using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
-using Persistent_cohomology =
-    Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
-
-void usage(char* const progName) {
-  std::cerr << "Usage: " << progName << " path_to_file_graph path_to_weight_file coeff_field_characteristic[integer > "
-                                        "0] min_persistence[float >= -1.0]\n";
-  exit(-1);
-}
-
-int main(int argc, char* const argv[]) {
-  // program args management
-  if (argc != 5) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
-    usage(argv[0]);
-  }
-
-  int coeff_field_characteristic = atoi(argv[3]);
-  Filtration_value min_persistence = strtof(argv[4], nullptr);
-
-  // 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_3> off_reader(offInputFile);
-  // Check the read operation was correct
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << offInputFile << std::endl;
-    usage(argv[0]);
-  }
-
-  // Retrieve the triangulation
-  std::vector<Point_3> lp = off_reader.get_point_cloud();
-
-  // Read weights information from file
-  std::ifstream weights_ifstr(argv[2]);
-  std::vector<Weighted_point_3> wp;
-  if (weights_ifstr.good()) {
-    double weight = 0.0;
-    std::size_t index = 0;
-    wp.reserve(lp.size());
-    // Attempt read the weight in a double format, return false if it fails
-    while ((weights_ifstr >> weight) && (index < lp.size())) {
-      wp.push_back(Weighted_point_3(lp[index], weight));
-      index++;
-    }
-    if (index != lp.size()) {
-      std::cerr << "Bad number of weights in file " << argv[2] << std::endl;
-      usage(argv[0]);
-    }
-  } else {
-    std::cerr << "Unable to read file " << argv[2] << std::endl;
-    usage(argv[0]);
-  }
-
-  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
-  Alpha_shape_3 as(wp.begin(), wp.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;
-  ST 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();
-  int dim_max = 0;
-  Filtration_value filtration_max = 0.0;
-  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<Vertex_list, Cell_handle>(*cell);
-      count_cells++;
-      if (dim_max < 3) {
-        // Cell is of dim 3
-        dim_max = 3;
-      }
-    } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
-      vertex_list = from_facet<Vertex_list, Facet>(*facet);
-      count_facets++;
-      if (dim_max < 2) {
-        // Facet is of dim 2
-        dim_max = 2;
-      }
-    } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
-      vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
-      count_edges++;
-      if (dim_max < 1) {
-        // Edge_3 is of dim 1
-        dim_max = 1;
-      }
-    } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
-      count_vertices++;
-      vertex_list = from_vertex<Vertex_list, Vertex_handle>(*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 " << vertex << std::endl;
-#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
-    Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator);
-#ifdef DEBUG_TRACES
-    std::cout << "filtration = " << filtr << std::endl;
-#endif  // DEBUG_TRACES
-    if (filtr > filtration_max) {
-      filtration_max = filtr;
-    }
-    simplex_tree.insert_simplex(the_simplex_tree, filtr);
-    if (the_alpha_value_iterator != the_alpha_values.end())
-      ++the_alpha_value_iterator;
-    else
-      std::cout << "This shall not happen" << std::endl;
-  }
-  simplex_tree.set_filtration(filtration_max);
-  simplex_tree.set_dimension(dim_max);
-
-#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: " << std::endl;
-  std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
-  std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
-  std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
-  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
-#endif  // DEBUG_TRACES
-
-#ifdef DEBUG_TRACES
-  std::cout << "Iterator on vertices: " << std::endl;
-  for (auto vertex : simplex_tree.complex_vertex_range()) {
-    std::cout << vertex << " ";
-  }
-#endif  // DEBUG_TRACES
-
-  // 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);
-
-  pcoh.output_diagram();
-
-  return 0;
-}