Add Windows and CGAL_HEADER_ONLY cythonization support

Add OFF reader interfaces (required by Euclidean witness complex)
Add Euclidean_witness_complex



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2186 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4d780f05c3409bea47a81e4377dbaf509b9e718c

4 files changed, 157 insertions, 2 deletions

diff --git a/src/cython/include/Euclidean_witness_complex_interface.h b/src/cython/include/Euclidean_witness_complex_interface.h
new file mode 100644
index 00000000..f79d93ab
--- /dev/null
+++ b/src/cython/include/Euclidean_witness_complex_interface.h
@@ -0,0 +1,113 @@
+/*    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 EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H
+#define	EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Euclidean_witness_complex.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <CGAL/Epick_d.h>
+
+#include <vector>
+#include <utility>  // std::pair
+#include <iostream>
+#include <cstddef>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+
+class Euclidean_witness_complex_interface {
+  using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+  using Point_d = Dynamic_kernel::Point_d;
+
+  typedef typename Simplex_tree<>::Simplex_key Simplex_key;
+
+ public:
+  Euclidean_witness_complex_interface(std::vector<std::vector<double>>&landmarks, std::vector<std::vector<double>>&witnesses)
+    : landmarks_(landmarks.begin(), landmarks.end()),
+      witnesses_(witnesses.begin(), witnesses.end()),
+      witness_complex_(landmarks_, witnesses_) {
+  }
+  Euclidean_witness_complex_interface(std::vector<Point_d>&landmarks, std::vector<Point_d>&witnesses)
+    : landmarks_(landmarks.begin(), landmarks.end()),
+      witnesses_(witnesses.begin(), witnesses.end()),
+      witness_complex_(landmarks_, witnesses_) {
+  }
+
+  void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square, std::size_t limit_dimension) {
+    witness_complex_.create_complex(*simplex_tree, max_alpha_square, limit_dimension);
+    simplex_tree->initialize_filtration();
+  }
+
+  void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square) {
+    witness_complex_.create_complex(*simplex_tree, max_alpha_square);
+    simplex_tree->initialize_filtration();
+  }
+
+ private:
+  std::vector<Point_d> landmarks_;
+  std::vector<Point_d> witnesses_;
+  Euclidean_witness_complex<Dynamic_kernel> witness_complex_;
+};
+
+/*template<typename Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>>
+class Euclidean_witness_complex_interface : public Euclidean_witness_complex<Kernel> {
+//class Euclidean_witness_complex_interface {
+  using Point_d = Kernel::Point_d;
+
+ public:
+  Euclidean_witness_complex_interface(const std::vector<std::vector<double>>& landmarks, const std::vector<std::vector<double>>& witnesses) {
+    : landmarks_(std::begin(landmarks), std::end(landmarks)),
+      witnesses_(std::begin(witnesses), std::end(witnesses)),
+      Gudhi::witness_complex::Euclidean_witness_complex<Kernel>(landmarks_, witnesses_) {
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double  max_alpha_square,
+                           std::size_t limit_dimension) {
+    create_complex(*simplex_tree, max_alpha_square, limit_dimension);
+    simplex_tree->initialize_filtration();
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree,
+                           double  max_alpha_square) {
+    create_complex(*simplex_tree, max_alpha_square);
+    simplex_tree->initialize_filtration();
+  }
+
+ private:
+//  Euclidean_witness_complex<Kernel>* witness_complex_;
+  std::vector<Point_d> landmarks_;
+  std::vector<Point_d> witnesses_;
+
+};*/
+
+}  // namespace witness_complex
+
+} // namespace Gudhi
+
+#endif  // EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H
+
diff --git a/src/cython/include/Off_reader_interface.h b/src/cython/include/Off_reader_interface.h
new file mode 100644
index 00000000..257331f8
--- /dev/null
+++ b/src/cython/include/Off_reader_interface.h
@@ -0,0 +1,42 @@
+/*    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 OFF_READER_INTERFACE_H
+#define	OFF_READER_INTERFACE_H
+
+#include <gudhi/Points_off_io.h>
+
+#include <iostream>
+#include <vector>
+#include <string>
+
+namespace Gudhi {
+
+std::vector<std::vector<double>> read_points_from_OFF_file(std::string& off_file) {
+  Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file);
+  return off_reader.get_point_cloud();
+}
+
+}  // namespace Gudhi
+
+#endif  // OFF_READER_INTERFACE_H
+
diff --git a/src/cython/include/Strong_witness_complex_interface.h b/src/cython/include/Strong_witness_complex_interface.h
index e59e58ea..5081ec2d 100644
--- a/src/cython/include/Strong_witness_complex_interface.h
+++ b/src/cython/include/Strong_witness_complex_interface.h
@@ -54,7 +54,7 @@ class Strong_witness_complex_interface {
 
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree,
                            double  max_alpha_square) {
-    witness_complex_->create_complex(*simplex_tree, max_alpha_square, std::numeric_limits<std::size_t>::max());
+    witness_complex_->create_complex(*simplex_tree, max_alpha_square);
     simplex_tree->initialize_filtration();
   }
 
diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h
index 38661cb6..3761b43d 100644
--- a/src/cython/include/Witness_complex_interface.h
+++ b/src/cython/include/Witness_complex_interface.h
@@ -54,7 +54,7 @@ class Witness_complex_interface {
 
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree,
                            double  max_alpha_square) {
-    witness_complex_->create_complex(*simplex_tree, max_alpha_square, std::numeric_limits<std::size_t>::max());
+    witness_complex_->create_complex(*simplex_tree, max_alpha_square);
     simplex_tree->initialize_filtration();
   }