weighted_alpha_complex_3d_persistence.cpp using Alpha_complex_3d new module

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3639 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b7e5f4674a56bef537ba5f4dda62e6605bf8c249

1 files changed, 13 insertions, 168 deletions

diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
index cdeeabfc..56fd6a7c 100644
--- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
@@ -23,23 +23,12 @@
 #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 <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/Alpha_shape_cell_base_3.h>
-#include <CGAL/Alpha_shape_vertex_base_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>
@@ -51,58 +40,12 @@
 
 #include "alpha_complex_3d_helper.h"
 
-// Alpha_shape_3 templates type definitions
-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>;
-
-// 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;
-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::vector<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 Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
+using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Weighted_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<ST, Gudhi::persistent_cohomology::Field_Zp>;
+    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 &weight_file,
                      std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence);
@@ -118,131 +61,33 @@ int main(int argc, char **argv) {
                   min_persistence);
 
   // Read the OFF file (input file name given as parameter) and triangulate points
-  Gudhi::Points_3D_off_reader<Point_3> off_reader(off_file_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 OFF file " << off_file_points << std::endl;
     exit(-1);
   }
 
-  // Retrieve the points
-  std::vector<Point_3> lp = off_reader.get_point_cloud();
-
   // Read weights information from file
   std::ifstream weights_ifstr(weight_file);
-  std::vector<Weighted_point_3> wp;
+  std::vector<double> weights;
   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 " << weight_file << std::endl;
-      exit(-1);
+    while (weights_ifstr >> weight) {
+      weights.push_back(weight);
     }
   } else {
     std::cerr << "Unable to read weights file " << weight_file << std::endl;
     exit(-1);
   }
 
-  // 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;
+  Alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights);
 
-  // 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();
-  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++;
-    } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
-      vertex_list = from_facet<Vertex_list, Facet>(*facet);
-      count_facets++;
-    } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
-      vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
-      count_edges++;
-    } 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;
-    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.push_back(vertex);
-        map_cgal_simplex_tree.emplace(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.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
-    simplex_tree.insert_simplex(the_simplex, 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 simplex_tree;
 
-#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;
+  alpha_complex.create_complex(simplex_tree);
 
-  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() << " ";
-#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();