Merge branch 'master' into insert

3 files changed, 51 insertions, 37 deletions

diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h
index 671af4a4..469b91ce 100644
--- a/src/python/include/Alpha_complex_interface.h
+++ b/src/python/include/Alpha_complex_interface.h
@@ -57,6 +57,16 @@ class Alpha_complex_interface {
       alpha_ptr_->create_simplex_tree(simplex_tree, max_alpha_square, default_filtration_value);
   }
 
+  static void set_float_relative_precision(double precision) {
+    // cf. Exact_alpha_complex_dD kernel type in Alpha_complex_factory.h
+    CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>::FT::set_relative_precision_of_to_double(precision);
+  }
+
+  static double get_float_relative_precision() {
+    // cf. Exact_alpha_complex_dD kernel type in Alpha_complex_factory.h
+    return CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>::FT::get_relative_precision_of_to_double();
+  }
+
  private:
   std::unique_ptr<Abstract_alpha_complex> alpha_ptr_;
 };
diff --git a/src/python/include/Persistent_cohomology_interface.h b/src/python/include/Persistent_cohomology_interface.h
index e5a3dfba..945378a0 100644
--- a/src/python/include/Persistent_cohomology_interface.h
+++ b/src/python/include/Persistent_cohomology_interface.h
@@ -12,6 +12,8 @@
 #define INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
 
 #include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Simplex_tree.h>  // for Extended_simplex_type
+
 
 #include <cstdlib>
 #include <vector>
@@ -223,6 +225,44 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
     return out;
   }
 
+  using Filtration_value = typename FilteredComplex::Filtration_value;
+  using Birth_death = std::pair<Filtration_value, Filtration_value>;
+  using Persistence_subdiagrams = std::vector<std::vector<std::pair<int, Birth_death>>>;
+
+  Persistence_subdiagrams compute_extended_persistence_subdiagrams(Filtration_value min_persistence){
+    Persistence_subdiagrams pers_subs(4);
+    auto const& persistent_pairs = Base::get_persistent_pairs();
+    for (auto pair : persistent_pairs) {
+      std::pair<Filtration_value, Extended_simplex_type> px = stptr_->decode_extended_filtration(stptr_->filtration(get<0>(pair)),
+                                                                                                        stptr_->efd);
+      std::pair<Filtration_value, Extended_simplex_type> py = stptr_->decode_extended_filtration(stptr_->filtration(get<1>(pair)),
+                                                                                                        stptr_->efd);
+      std::pair<int, Birth_death> pd_point = std::make_pair(stptr_->dimension(get<0>(pair)),
+                                                            std::make_pair(px.first, py.first));
+      if(std::abs(px.first - py.first) > min_persistence){
+        //Ordinary
+        if (px.second == Extended_simplex_type::UP && py.second == Extended_simplex_type::UP){
+          pers_subs[0].push_back(pd_point);
+        }
+        // Relative
+        else if (px.second == Extended_simplex_type::DOWN && py.second == Extended_simplex_type::DOWN){
+          pers_subs[1].push_back(pd_point);
+        }
+        else{
+          // Extended+
+          if (px.first < py.first){
+            pers_subs[2].push_back(pd_point);
+          }
+          //Extended-
+          else{
+            pers_subs[3].push_back(pd_point);
+          }
+        }
+      }
+    }
+    return pers_subs;
+  }
+
  private:
   // A copy
   FilteredComplex* stptr_;
diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index b93ccfff..0317ea39 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -15,9 +15,7 @@
 #include <gudhi/distance_functions.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Points_off_io.h>
-#ifdef GUDHI_USE_EIGEN3
 #include <gudhi/Flag_complex_edge_collapser.h>
-#endif
 
 #include <iostream>
 #include <vector>
@@ -160,38 +158,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     return;
   }
 
-  std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> compute_extended_persistence_subdiagrams(const std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>& dgm, Filtration_value min_persistence){
-    std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> new_dgm(4);
-    for (unsigned int i = 0; i < dgm.size(); i++){
-      std::pair<Filtration_value, Extended_simplex_type> px = this->decode_extended_filtration(dgm[i].second.first, this->efd);
-      std::pair<Filtration_value, Extended_simplex_type> py = this->decode_extended_filtration(dgm[i].second.second, this->efd);
-      std::pair<int, std::pair<Filtration_value, Filtration_value>> pd_point = std::make_pair(dgm[i].first, std::make_pair(px.first, py.first));
-      if(std::abs(px.first - py.first) > min_persistence){
-        //Ordinary
-        if (px.second == Extended_simplex_type::UP && py.second == Extended_simplex_type::UP){
-          new_dgm[0].push_back(pd_point);
-        }
-        // Relative
-        else if (px.second == Extended_simplex_type::DOWN && py.second == Extended_simplex_type::DOWN){
-          new_dgm[1].push_back(pd_point);
-        }
-        else{
-          // Extended+
-          if (px.first < py.first){
-            new_dgm[2].push_back(pd_point);
-          }
-          //Extended-
-          else{
-            new_dgm[3].push_back(pd_point);
-          }
-        }
-      }
-    }
-    return new_dgm;
-  }
-
   Simplex_tree_interface* collapse_edges(int nb_collapse_iteration) {
-#ifdef GUDHI_USE_EIGEN3
     using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>;
     std::vector<Filtered_edge> edges;
     for (Simplex_handle sh : Base::skeleton_simplex_range(1)) {
@@ -205,7 +172,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     }
 
     for (int iteration = 0; iteration < nb_collapse_iteration; iteration++) {
-      edges = Gudhi::collapse::flag_complex_collapse_edges(edges);
+      edges = Gudhi::collapse::flag_complex_collapse_edges(std::move(edges));
     }
     Simplex_tree_interface* collapsed_stree_ptr = new Simplex_tree_interface();
     // Copy the original 0-skeleton
@@ -217,9 +184,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
       collapsed_stree_ptr->insert({std::get<0>(remaining_edge), std::get<1>(remaining_edge)}, std::get<2>(remaining_edge));
     }
     return collapsed_stree_ptr;
-#else
-    throw std::runtime_error("Unable to collapse edges as it requires Eigen3 >= 3.1.0.");
-#endif
   }
 
   void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void *user_data) {