Fix rips complex with the new interface

Remove mini simplex tree
Fix persistent cohomology doc - only simplex tree used
Remove useless type definition in Cython C++ interfaces


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2003 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fff43192b00df1c70d59109a6c14932013992ff1

7 files changed, 82 insertions, 47 deletions

diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h
index 81761c77..9f308ae9 100644
--- a/src/cython/include/Alpha_complex_interface.h
+++ b/src/cython/include/Alpha_complex_interface.h
@@ -29,9 +29,9 @@
 
 #include "Simplex_tree_interface.h"
 
-#include <vector>
-#include <utility>  // std::pair
 #include <iostream>
+#include <vector>
+#include <string>
 
 namespace Gudhi {
 
@@ -40,11 +40,6 @@ namespace alpha_complex {
 class Alpha_complex_interface {
   using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
   using Point_d = Dynamic_kernel::Point_d;
-  typedef typename Simplex_tree<>::Simplex_handle Simplex_handle;
-  typedef typename std::pair<Simplex_handle, bool> Insertion_result;
-  using Simplex = std::vector<Vertex_handle>;
-  using Filtered_complex = std::pair<Simplex, Filtration_value>;
-  using Complex_tree = std::vector<Filtered_complex>;
 
   typedef typename Simplex_tree<>::Simplex_key Simplex_key;
 
diff --git a/src/cython/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h
index 5d17ff6b..4c53523b 100644
--- a/src/cython/include/Cubical_complex_interface.h
+++ b/src/cython/include/Cubical_complex_interface.h
@@ -27,9 +27,9 @@
 #include <gudhi/Bitmap_cubical_complex_base.h>
 #include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h>
 
-#include <vector>
-#include <utility>  // std::pair
 #include <iostream>
+#include <vector>
+#include <string>
 
 namespace Gudhi {
 
diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
new file mode 100644
index 00000000..7e897b1d
--- /dev/null
+++ b/src/cython/include/Rips_complex_interface.h
@@ -0,0 +1,70 @@
+/*    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) 2016 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 RIPS_COMPLEX_INTERFACE_H
+#define	RIPS_COMPLEX_INTERFACE_H
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Rips_complex.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/distance_functions.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <iostream>
+#include <vector>
+#include <utility>  // std::pair
+#include <string>
+
+namespace Gudhi {
+
+namespace rips_complex {
+
+class Rips_complex_interface {
+  using Point_d = std::vector<double>;
+
+ public:
+  Rips_complex_interface(std::vector<std::vector<double>>&points, double threshold) {
+    rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(points, threshold,
+                                                                                 Euclidean_distance());
+  }
+
+  Rips_complex_interface(std::string off_file_name, double threshold, bool from_file = true) {
+    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
+    rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(off_reader.get_point_cloud(),
+                                                                                 threshold, Euclidean_distance());
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) {
+    rips_complex_->create_complex(*simplex_tree, dim_max);
+    simplex_tree->initialize_filtration();
+  }
+
+ private:
+  Rips_complex<Simplex_tree_interface<>::Filtration_value>* rips_complex_;
+};
+
+}  // namespace rips_complex
+
+}  // namespace Gudhi
+
+#endif  // RIPS_COMPLEX_INTERFACE_H
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index 8e9dd966..19e02ca4 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -30,15 +30,17 @@
 
 #include "Persistent_cohomology_interface.h"
 
+#include <iostream>
 #include <vector>
 #include <utility>  // std::pair
-#include <iostream>
 
 namespace Gudhi {
 
 template<typename SimplexTreeOptions = Simplex_tree_options_full_featured>
 class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
  public:
+  typedef typename Simplex_tree<SimplexTreeOptions>::Filtration_value Filtration_value;
+  typedef typename Simplex_tree<SimplexTreeOptions>::Vertex_handle Vertex_handle;
   typedef typename Simplex_tree<SimplexTreeOptions>::Simplex_handle Simplex_handle;
   typedef typename std::pair<Simplex_handle, bool> Insertion_result;
   using Simplex = std::vector<Vertex_handle>;
@@ -115,42 +117,12 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     return coface_tree;
   }
 
-  void graph_expansion(std::vector<std::vector<double>>&points, int max_dimension, double max_edge_length) {
-    Graph_t prox_graph = compute_proximity_graph(points, max_edge_length, euclidean_distance<std::vector<double>>);
-    Simplex_tree<SimplexTreeOptions>::insert_graph(prox_graph);
-    Simplex_tree<SimplexTreeOptions>::expansion(max_dimension);
-    Simplex_tree<SimplexTreeOptions>::initialize_filtration();
-  }
-
-  void graph_expansion(std::string& off_file_name, int max_dimension, double max_edge_length, bool from_file=true) {
-    Gudhi::Points_off_reader<std::vector <double>> off_reader(off_file_name);
-    // Check the read operation was correct
-    if (!off_reader.is_valid()) {
-      std::cerr << "Unable to read file " << off_file_name << std::endl;
-    } else {
-      std::vector<std::vector <double>> points = off_reader.get_point_cloud();
-      Graph_t prox_graph = compute_proximity_graph(points, max_edge_length,
-                                                   euclidean_distance<std::vector<double>>);
-      Simplex_tree<SimplexTreeOptions>::insert_graph(prox_graph);
-      Simplex_tree<SimplexTreeOptions>::expansion(max_dimension);
-      Simplex_tree<SimplexTreeOptions>::initialize_filtration();
-    }
-  }
-
   void create_persistence(Gudhi::Persistent_cohomology_interface<Simplex_tree<SimplexTreeOptions>>* pcoh) {
     pcoh = new Gudhi::Persistent_cohomology_interface<Simplex_tree<SimplexTreeOptions>>(*this);
   }
 
 };
 
-struct Simplex_tree_options_mini : Simplex_tree_options_full_featured {
-  // Not doing persistence, so we don't need those
-  static const bool store_key = true;
-  static const bool store_filtration = false;
-  // I have few vertices
-  typedef short Vertex_handle;
-};
-
 } // namespace Gudhi
 
 #endif  // SIMPLEX_TREE_INTERFACE_H
diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h
index 9340cd86..fb047441 100644
--- a/src/cython/include/Subsampling_interface.h
+++ b/src/cython/include/Subsampling_interface.h
@@ -29,8 +29,9 @@
 #include <gudhi/Points_off_io.h>
 #include <CGAL/Epick_d.h>
 
-#include <vector>
 #include <iostream>
+#include <vector>
+#include <string>
 
 namespace Gudhi {
 
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 9da32757..7c774c73 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -41,11 +41,6 @@ namespace tangential_complex {
 class Tangential_complex_interface {
   using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
   using Point_d = Dynamic_kernel::Point_d;
-  typedef typename Simplex_tree<>::Simplex_handle Simplex_handle;
-  typedef typename std::pair<Simplex_handle, bool> Insertion_result;
-  using Simplex = std::vector<Vertex_handle>;
-  using Filtered_complex = std::pair<Simplex, Filtration_value>;
-  using Complex_tree = std::vector<Filtered_complex>;
   using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>;
 
  public:
diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h
index ab99adf5..a753bc1d 100644
--- a/src/cython/include/Witness_complex_interface.h
+++ b/src/cython/include/Witness_complex_interface.h
@@ -40,6 +40,8 @@ namespace witness_complex {
 
 class Witness_complex_interface {
   typedef typename Simplex_tree<>::Simplex_handle Simplex_handle;
+  typedef typename Simplex_tree<>::Filtration_value Filtration_value;
+  typedef typename Simplex_tree<>::Vertex_handle Vertex_handle;
   typedef typename std::pair<Simplex_handle, bool> Insertion_result;
   using Simplex = std::vector<Vertex_handle>;
   using Filtered_complex = std::pair<Simplex, Filtration_value>;
@@ -51,7 +53,7 @@ class Witness_complex_interface {
     std::vector<std::vector< int > > knn;
     std::vector<std::vector<double>> landmarks;
     Gudhi::subsampling::pick_n_random_points(points, number_of_landmarks, std::back_inserter(landmarks));
-    Gudhi::witness_complex::construct_closest_landmark_table(points, landmarks, knn);
+    Gudhi::witness_complex::construct_closest_landmark_table<Filtration_value>(points, landmarks, knn);
 
     Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, points[0].size(), simplex_tree_);
   }