Add insert_simplex in Alpha_complex_3d.h

Modify periodic_alpha_complex_3d_persistence.cpp with new module


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3636 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 271e55ce7363a1af991fb107896307887827df65

2 files changed, 28 insertions, 164 deletions

diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
index ff6eb3e6..58364802 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
@@ -225,16 +225,17 @@ public:
                 (z_max - z_min == y_max - y_min),
                 std::invalid_argument("The size of the cuboid in every directions is not the same."));
 
-#ifdef GUDHI_DEBUG
-    // Defined in GUDHI_DEBUG to avoid unused variable warning
-    double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min);
-#endif
-
     using Weighted_point_3 = typename AlphaComplex3dOptions::Weighted_point_3;
     std::vector<Weighted_point_3> weighted_points_3;
 
     std::size_t index = 0;
     weighted_points_3.reserve(points.size());
+
+#ifdef GUDHI_DEBUG
+    // Defined in GUDHI_DEBUG to avoid unused variable warning for GUDHI_CHECK
+    double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min);
+#endif
+
     while ((index < weights.size()) && (index < points.size())) {
       GUDHI_CHECK((weights[index] < maximal_possible_weight) || (weights[index] >= 0),
                   std::invalid_argument("Invalid weight at line" + std::to_string(index + 1) +
@@ -325,7 +326,9 @@ public:
 #endif  // DEBUG_TRACES
           vertex_list.push_back((*cell)->vertex(i));
         }
+#ifdef DEBUG_TRACES
         count_cells++;
+#endif  // DEBUG_TRACES
       } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
           for (auto i = 0; i < 4; i++) {
             if ((*facet).second != i) {
@@ -335,7 +338,9 @@ public:
               vertex_list.push_back((*facet).first->vertex(i));
             }
           }
+#ifdef DEBUG_TRACES
         count_facets++;
+#endif  // DEBUG_TRACES
       } else if (const Edge *edge = CGAL::object_cast<Edge>(&object_iterator)) {
             for (auto i : {(*edge).second, (*edge).third}) {
 #ifdef DEBUG_TRACES
@@ -343,13 +348,15 @@ public:
 #endif  // DEBUG_TRACES
               vertex_list.push_back((*edge).first->vertex(i));
             }
+#ifdef DEBUG_TRACES
         count_edges++;
+#endif  // DEBUG_TRACES
       } else if (const Alpha_vertex_handle *vertex = CGAL::object_cast<Alpha_vertex_handle>(&object_iterator)) {
-        count_vertices++;
 #ifdef DEBUG_TRACES
-              std::cout << "from vertex=" << (*vertex)->point() << std::endl;
+        count_vertices++;
+        std::cout << "from vertex=" << (*vertex)->point() << std::endl;
 #endif  // DEBUG_TRACES
-              vertex_list.push_back((*vertex));
+        vertex_list.push_back((*vertex));
       }
       // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
       Simplex_tree_vector_vertex the_simplex;
@@ -378,11 +385,10 @@ public:
         AlphaComplex3dOptions::template value_from_iterator<Filtration_value,
                                                             typename std::vector<Alpha_value_type>::iterator>
                                                               (the_alpha_value_iterator);
-      //Filtration_value filtr = CGAL::to_double(the_alpha_value_iterator->exact());
 #ifdef DEBUG_TRACES
       std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
-      //complex.insert_simplex(the_simplex, static_cast<Filtration_value>(filtr));
+      complex.insert_simplex(the_simplex, static_cast<Filtration_value>(filtr));
       GUDHI_CHECK(the_alpha_value_iterator != alpha_values_.end(), "CGAL provided more simplices than values");
       ++the_alpha_value_iterator;
     }
diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
index 42f3ddcb..6a3728fb 100644
--- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
@@ -24,18 +24,12 @@
 #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/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h>
-#include <CGAL/Periodic_3_Delaunay_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>
-
 #include <fstream>
 #include <cmath>
 #include <string>
@@ -45,45 +39,12 @@
 #include <vector>
 #include <cstdlib>
 
-#include "alpha_complex_3d_helper.h"
-
-// Traits
-using K = CGAL::Exact_predicates_inexact_constructions_kernel;
-using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>;
-// Vertex type
-using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>;
-using Vb = CGAL::Triangulation_vertex_base_3<PK, DsVb>;
-using AsVb = CGAL::Alpha_shape_vertex_base_3<PK, Vb>;
-// Cell type
-using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>;
-using Cb = CGAL::Triangulation_cell_base_3<PK, DsCb>;
-using AsCb = CGAL::Alpha_shape_cell_base_3<PK, Cb>;
-using Tds = CGAL::Triangulation_data_structure_3<AsVb, AsCb>;
-using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3<PK, Tds>;
-using Alpha_shape_3 = CGAL::Alpha_shape_3<P3DT3>;
-using Point_3 = PK::Point_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::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<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 &cuboid_file,
                      std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence);
@@ -99,10 +60,10 @@ 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;
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << off_file_points << std::endl;
     exit(-1);
   }
 
@@ -121,114 +82,11 @@ int main(int argc, char **argv) {
     exit(-1);
   }
 
-  // Retrieve the points
-  std::vector<Point_3> lp = off_reader.get_point_cloud();
-
-  // Define the periodic cube
-  P3DT3 pdt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
-  // Heuristic for inserting large point sets (if pts is reasonably large)
-  pdt.insert(lp.begin(), lp.end(), true);
-  // As pdt won't be modified anymore switch to 1-sheeted cover if possible
-  if (pdt.is_triangulation_in_1_sheet()) {
-    pdt.convert_to_1_sheeted_covering();
-  } else {
-    std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl;
-    exit(-1);
-  }
-  std::cout << "Periodic Delaunay computed." << std::endl;
-
-  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
-  // Maybe need to set it to GENERAL mode
-  Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL);
+  Alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), x_min, y_min, z_min, x_max, y_max, z_max);
 
-  // filtration with alpha values from alpha shape
-  std::vector<Object> the_objects;
-  std::vector<Alpha_value_type> the_alpha_values;
+  Simplex_tree simplex_tree;
 
-  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();
-  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;
-  }
-
-#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() << " ";
-#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
+  alpha_complex.create_complex(simplex_tree);
 
   // Sort the simplices in the order of the filtration
   simplex_tree.initialize_filtration();