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

1 files changed, 70 insertions, 0 deletions

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