3 files changed, 91 insertions, 9 deletions

diff --git a/src/cython/include/Nerve_gic_interface.h b/src/cython/include/Nerve_gic_interface.h
new file mode 100644
index 00000000..aa71e2a6
--- /dev/null
+++ b/src/cython/include/Nerve_gic_interface.h
@@ -0,0 +1,61 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2018 Inria
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef INCLUDE_NERVE_GIC_INTERFACE_H_
+#define INCLUDE_NERVE_GIC_INTERFACE_H_
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/GIC.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <iostream>
+#include <vector>
+#include <string>
+
+namespace Gudhi {
+
+namespace cover_complex {
+
+class Nerve_gic_interface : public Cover_complex<std::vector<double>> {
+ public:
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree) {
+    create_complex(*simplex_tree);
+    simplex_tree->initialize_filtration();
+  }
+  void set_cover_from_Euclidean_Voronoi(int m) {
+    set_cover_from_Voronoi(Gudhi::Euclidean_distance(), m);
+  }
+  double set_graph_from_automatic_euclidean_rips(int N) {
+    return set_graph_from_automatic_rips(Gudhi::Euclidean_distance(), N);
+  }
+  void set_graph_from_euclidean_rips(double threshold) {
+    set_graph_from_rips(threshold, Gudhi::Euclidean_distance());
+  }
+};
+
+}  // namespace cover_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_NERVE_GIC_INTERFACE_H_
diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h
index a86b1187..8cf71a4e 100644
--- a/src/cython/include/Persistent_cohomology_interface.h
+++ b/src/cython/include/Persistent_cohomology_interface.h
@@ -85,6 +85,32 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
     return persistence;
   }
 
+  std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs() {
+    auto pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::get_persistent_pairs();
+
+    std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs;
+    persistence_pairs.reserve(pairs.size());
+    for (auto pair : pairs) {
+      std::vector<int> birth;
+      if (get<0>(pair) != stptr_->null_simplex()) {
+        for (auto vertex : stptr_->simplex_vertex_range(get<0>(pair))) {
+          birth.push_back(vertex);
+        }
+      }
+
+      std::vector<int> death;
+      if (get<1>(pair) != stptr_->null_simplex()) {
+        for (auto vertex : stptr_->simplex_vertex_range(get<1>(pair))) {
+          death.push_back(vertex);
+        }
+      }
+
+      persistence_pairs.push_back(std::make_pair(birth, death));
+    }
+    return persistence_pairs;
+  }
+
  private:
   // A copy
   FilteredComplex* stptr_;
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 2772460a..71418886 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -45,24 +45,19 @@ class Tangential_complex_interface {
   using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>;
 
  public:
-  Tangential_complex_interface(const std::vector<std::vector<double>>& points) {
+  Tangential_complex_interface(int intrisic_dim, const std::vector<std::vector<double>>& points) {
     Dynamic_kernel k;
-    unsigned intrisic_dim = 0;
-    if (points.size() > 0)
-      intrisic_dim = points[0].size() - 1;
 
     tangential_complex_ = new TC(points, intrisic_dim, k);
     tangential_complex_->compute_tangential_complex();
     num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
   }
 
-  Tangential_complex_interface(const std::string& off_file_name, bool from_file = true) {
-    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
+  Tangential_complex_interface(int intrisic_dim, const std::string& off_file_name, bool from_file = true) {
     Dynamic_kernel k;
-    unsigned intrisic_dim = 0;
+
+    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
     std::vector<Point_d> points = off_reader.get_point_cloud();
-    if (points.size() > 0)
-      intrisic_dim = points[0].size() - 1;
 
     tangential_complex_ = new TC(points, intrisic_dim, k);
     tangential_complex_->compute_tangential_complex();