Merge branch 'master' into persistence_intervals_numpy_arrays_vincent

2 files changed, 12 insertions, 23 deletions

diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index 1a6e2477..40aff299 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -54,23 +54,17 @@ class Rips_complex_interface {
   }
 
   void init_points_sparse(const std::vector<std::vector<double>>& points, double threshold, double epsilon) {
-    sparse_rips_complex_.emplace(points, Gudhi::Euclidean_distance(), epsilon);
-    threshold_ = threshold;
+    sparse_rips_complex_.emplace(points, Gudhi::Euclidean_distance(), epsilon, -std::numeric_limits<double>::infinity(), threshold);
   }
   void init_matrix_sparse(const std::vector<std::vector<double>>& matrix, double threshold, double epsilon) {
-    sparse_rips_complex_.emplace(matrix, epsilon);
-    threshold_ = threshold;
+    sparse_rips_complex_.emplace(matrix, epsilon, -std::numeric_limits<double>::infinity(), threshold);
   }
 
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) {
     if (rips_complex_)
       rips_complex_->create_complex(*simplex_tree, dim_max);
-    else {
+    else
       sparse_rips_complex_->create_complex(*simplex_tree, dim_max);
-      // This pruning should be done much earlier! It isn't that useful for sparse Rips,
-      // but it would be inconsistent not to do it.
-      simplex_tree->prune_above_filtration(threshold_);
-    }
     simplex_tree->initialize_filtration();
   }
 
@@ -79,7 +73,6 @@ class Rips_complex_interface {
   // Anyway, storing a graph would make more sense. Or changing the interface completely so there is no such storage.
   boost::optional<Rips_complex<Simplex_tree_interface<>::Filtration_value>> rips_complex_;
   boost::optional<Sparse_rips_complex<Simplex_tree_interface<>::Filtration_value>> sparse_rips_complex_;
-  double threshold_;
 };
 
 }  // namespace rips_complex
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index 3481eeff..ca98517d 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -45,7 +45,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   using Simplex_handle = typename Base::Simplex_handle;
   using Insertion_result = typename std::pair<Simplex_handle, bool>;
   using Simplex = std::vector<Vertex_handle>;
-  using Complex = std::vector<std::pair<Simplex, Filtration_value>>;
+  using Filtered_simplices = std::vector<std::pair<Simplex, Filtration_value>>;
 
  public:
   bool find_simplex(const Simplex& vh) {
@@ -94,9 +94,9 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     Base::initialize_filtration();
   }
 
-  Complex get_filtration() {
+  Filtered_simplices get_filtration() {
     Base::initialize_filtration();
-    Complex filtrations;
+    Filtered_simplices filtrations;
     for (auto f_simplex : Base::filtration_simplex_range()) {
       Simplex simplex;
       for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
@@ -107,8 +107,8 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     return filtrations;
   }
 
-  Complex get_skeleton(int dimension) {
-    Complex skeletons;
+  Filtered_simplices get_skeleton(int dimension) {
+    Filtered_simplices skeletons;
     for (auto f_simplex : Base::skeleton_simplex_range(dimension)) {
       Simplex simplex;
       for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
@@ -119,29 +119,25 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     return skeletons;
   }
 
-  Complex get_star(const Simplex& simplex) {
-    Complex star;
+  Filtered_simplices get_star(const Simplex& simplex) {
+    Filtered_simplices star;
     for (auto f_simplex : Base::star_simplex_range(Base::find(simplex))) {
       Simplex simplex_star;
       for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
-        std::cout << vertex << " ";
         simplex_star.insert(simplex_star.begin(), vertex);
       }
-      std::cout << std::endl;
       star.push_back(std::make_pair(simplex_star, Base::filtration(f_simplex)));
     }
     return star;
   }
 
-  Complex get_cofaces(const Simplex& simplex, int dimension) {
-    Complex cofaces;
+  Filtered_simplices get_cofaces(const Simplex& simplex, int dimension) {
+    Filtered_simplices cofaces;
     for (auto f_simplex : Base::cofaces_simplex_range(Base::find(simplex), dimension)) {
       Simplex simplex_coface;
       for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
-        std::cout << vertex << " ";
         simplex_coface.insert(simplex_coface.begin(), vertex);
       }
-      std::cout << std::endl;
       cofaces.push_back(std::make_pair(simplex_coface, Base::filtration(f_simplex)));
     }
     return cofaces;