1 files changed, 131 insertions, 33 deletions

diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index 06f31341..0317ea39 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -15,12 +15,13 @@
 #include <gudhi/distance_functions.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Points_off_io.h>
-
-#include "Persistent_cohomology_interface.h"
+#include <gudhi/Flag_complex_edge_collapser.h>
 
 #include <iostream>
 #include <vector>
 #include <utility>  // std::pair
+#include <tuple>
+#include <iterator>  // for std::distance
 
 namespace Gudhi {
 
@@ -33,22 +34,60 @@ 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 Filtered_simplices = std::vector<std::pair<Simplex, Filtration_value>>;
+  using Simplex_and_filtration = std::pair<Simplex, Filtration_value>;
+  using Filtered_simplices = std::vector<Simplex_and_filtration>;
+  using Skeleton_simplex_iterator = typename Base::Skeleton_simplex_iterator;
+  using Complex_simplex_iterator = typename Base::Complex_simplex_iterator;
+  using Extended_filtration_data = typename Base::Extended_filtration_data;
+  using Boundary_simplex_iterator = typename Base::Boundary_simplex_iterator;
+  using Siblings = typename Base::Siblings;
+  using Node = typename Base::Node;
+  typedef bool (*blocker_func_t)(Simplex simplex, void *user_data);
 
  public:
-  bool find_simplex(const Simplex& vh) {
-    return (Base::find(vh) != Base::null_simplex());
+
+  Extended_filtration_data efd;
+  
+  bool find_simplex(const Simplex& simplex) {
+    return (Base::find(simplex) != Base::null_simplex());
   }
 
-  void assign_simplex_filtration(const Simplex& vh, Filtration_value filtration) {
-    Base::assign_filtration(Base::find(vh), filtration);
+  void assign_simplex_filtration(const Simplex& simplex, Filtration_value filtration) {
+    Base::assign_filtration(Base::find(simplex), filtration);
+    Base::clear_filtration();
   }
 
   bool insert(const Simplex& simplex, Filtration_value filtration = 0) {
     Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration);
+    if (result.first != Base::null_simplex())
+      Base::clear_filtration();
     return (result.second);
   }
 
+  void insert_matrix(double* filtrations, int n, int stride0, int stride1, double max_filtration) {
+    // We could delegate to insert_graph, but wrapping the matrix in a graph interface is too much work,
+    // and this is a bit more efficient.
+    auto& rm = this->root()->members_;
+    for(int i=0; i<n; ++i) {
+      char* p = reinterpret_cast<char*>(filtrations) + i * stride0;
+      double fv = *reinterpret_cast<double*>(p + i * stride1);
+      if(fv > max_filtration) continue;
+      auto sh = rm.emplace_hint(rm.end(), i, Node(this->root(), fv));
+      Siblings* children = nullptr;
+      // Should we make a first pass to count the number of edges so we can reserve the right space?
+      for(int j=i+1; j<n; ++j) {
+        double fe = *reinterpret_cast<double*>(p + j * stride1);
+        if(fe > max_filtration) continue;
+        if(!children) {
+          children = new Siblings(this->root(), i);
+          sh->second.assign_children(children);
+        }
+        children->members().emplace_hint(children->members().end(), j, Node(children, fe));
+      }
+    }
+
+  }
+
   // Do not interface this function, only used in alpha complex interface for complex creation
   bool insert_simplex(const Simplex& simplex, Filtration_value filtration = 0) {
     Insertion_result result = Base::insert_simplex(simplex, filtration);
@@ -79,32 +118,15 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
 
   void remove_maximal_simplex(const Simplex& simplex) {
     Base::remove_maximal_simplex(Base::find(simplex));
-    Base::initialize_filtration();
+    Base::clear_filtration();
   }
 
-  Filtered_simplices get_filtration() {
-    Base::initialize_filtration();
-    Filtered_simplices filtrations;
-    for (auto f_simplex : Base::filtration_simplex_range()) {
-      Simplex simplex;
-      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
-        simplex.insert(simplex.begin(), vertex);
-      }
-      filtrations.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
+  Simplex_and_filtration get_simplex_and_filtration(Simplex_handle f_simplex) {
+    Simplex simplex;
+    for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
+      simplex.insert(simplex.begin(), vertex);
     }
-    return filtrations;
-  }
-
-  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)) {
-        simplex.insert(simplex.begin(), vertex);
-      }
-      skeletons.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
-    }
-    return skeletons;
+    return std::make_pair(std::move(simplex), Base::filtration(f_simplex));
   }
 
   Filtered_simplices get_star(const Simplex& simplex) {
@@ -131,9 +153,85 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     return cofaces;
   }
 
-  void create_persistence(Gudhi::Persistent_cohomology_interface<Base>* pcoh) {
-    Base::initialize_filtration();
-    pcoh = new Gudhi::Persistent_cohomology_interface<Base>(*this);
+  void compute_extended_filtration() {
+    this->efd = this->extend_filtration();
+    return;
+  }
+
+  Simplex_tree_interface* collapse_edges(int nb_collapse_iteration) {
+    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)) {
+      if (Base::dimension(sh) == 1) {
+        typename Base::Simplex_vertex_range rg = Base::simplex_vertex_range(sh);
+        auto vit = rg.begin();
+        Vertex_handle v = *vit;
+        Vertex_handle w = *++vit;
+        edges.emplace_back(v, w, Base::filtration(sh));
+      }
+    }
+
+    for (int iteration = 0; iteration < nb_collapse_iteration; iteration++) {
+      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
+    for (Simplex_handle sh : Base::skeleton_simplex_range(0)) {
+      collapsed_stree_ptr->insert({*(Base::simplex_vertex_range(sh).begin())}, Base::filtration(sh));
+    }
+    // Insert remaining edges
+    for (auto remaining_edge : edges) {
+      collapsed_stree_ptr->insert({std::get<0>(remaining_edge), std::get<1>(remaining_edge)}, std::get<2>(remaining_edge));
+    }
+    return collapsed_stree_ptr;
+  }
+
+  void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void *user_data) {
+    Base::expansion_with_blockers(dimension, [&](Simplex_handle sh){
+      Simplex simplex(Base::simplex_vertex_range(sh).begin(), Base::simplex_vertex_range(sh).end());
+      return user_func(simplex, user_data);
+    });
+  }
+
+  // Iterator over the simplex tree
+  Complex_simplex_iterator get_simplices_iterator_begin() {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::complex_simplex_range().begin();
+  }
+
+  Complex_simplex_iterator get_simplices_iterator_end() {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::complex_simplex_range().end();
+  }
+
+  typename std::vector<Simplex_handle>::const_iterator get_filtration_iterator_begin() {
+    // Base::initialize_filtration(); already performed in filtration_simplex_range
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::filtration_simplex_range().begin();
+  }
+
+  typename std::vector<Simplex_handle>::const_iterator get_filtration_iterator_end() {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::filtration_simplex_range().end();
+  }
+
+  Skeleton_simplex_iterator get_skeleton_iterator_begin(int dimension) {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::skeleton_simplex_range(dimension).begin();
+  }
+
+  Skeleton_simplex_iterator get_skeleton_iterator_end(int dimension) {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::skeleton_simplex_range(dimension).end();
+  }
+
+  std::pair<Boundary_simplex_iterator, Boundary_simplex_iterator> get_boundary_iterators(const Simplex& simplex) {
+    auto bd_sh = Base::find(simplex);
+    if (bd_sh == Base::null_simplex())
+      throw std::runtime_error("simplex not found - cannot find boundaries");
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    auto boundary_srange = Base::boundary_simplex_range(bd_sh);
+    return std::make_pair(boundary_srange.begin(), boundary_srange.end());
   }
 };