Add Subsampling cpp interface and cython

Remove deref cyton import


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1809 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2dc0469d2401e0c99e879c064a0f608c8ba78ed6

6 files changed, 106 insertions, 3 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 2746cab9..c2026682 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -49,8 +49,16 @@ if(PYTHON_PATH AND CYTHON_PATH)
     file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
     
     if (CGAL_FOUND)
+      if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+          # If CGAL_VERSION >= 4.8.1, include subsampling
+          # CGAL things are done in CGAL_VERSION >= 4.8.0
+          set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
+      else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+        # Remove alpha complex unitary tests
+        file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
+      endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
       if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-        # If CGAL_VERSION >= 4.8.0, include alpha complex
+        # If CGAL_VERSION >= 4.8.0, include alpha and tangential complex
         set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ")
         set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
         # GMP and GMPXX are not required, but if present, CGAL will link with them.
diff --git a/src/cython/cython/alpha_complex.pyx b/src/cython/cython/alpha_complex.pyx
index 93f9b87e..56cf925c 100644
--- a/src/cython/cython/alpha_complex.pyx
+++ b/src/cython/cython/alpha_complex.pyx
@@ -3,7 +3,6 @@ from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp.string cimport string
 from libcpp cimport bool
-from cython.operator cimport dereference as deref
 import os
 
 """This file is part of the Gudhi Library. The Gudhi library
diff --git a/src/cython/cython/subsampling.pyx b/src/cython/cython/subsampling.pyx
new file mode 100644
index 00000000..e59e0c6a
--- /dev/null
+++ b/src/cython/cython/subsampling.pyx
@@ -0,0 +1,37 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.string cimport string
+from libcpp cimport bool
+import os
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Subsampling_interface.h" namespace "Gudhi::subsampling":
+    vector[vector[double]] subsampling_n_farthest_points(vector[vector[double]] points, unsigned nb_points)
+
+def choose_n_farthest_points(points, nb_points):
+    subsampling_n_farthest_points(points, nb_points)
diff --git a/src/cython/cython/tangential_complex.pyx b/src/cython/cython/tangential_complex.pyx
index 5a7ebd1a..c0260577 100644
--- a/src/cython/cython/tangential_complex.pyx
+++ b/src/cython/cython/tangential_complex.pyx
@@ -3,7 +3,6 @@ from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp.string cimport string
 from libcpp cimport bool
-from cython.operator cimport dereference as deref
 import os
 
 """This file is part of the Gudhi Library. The Gudhi library
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index 09d765b6..60f4c30b 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -32,4 +32,5 @@ include "cython/periodic_cubical_complex.pyx"
 include "cython/persistence_graphical_tools.py"
 include "cython/witness_complex.pyx"
 @GUDHI_CYTHON_ALPHA_COMPLEX@
+@GUDHI_CYTHON_SUBSAMPLING@
 @GUDHI_CYTHON_TANGENTIAL_COMPLEX@
diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h
new file mode 100644
index 00000000..bd37a015
--- /dev/null
+++ b/src/cython/include/Subsampling_interface.h
@@ -0,0 +1,59 @@
+/*    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 SUBSAMPLING_INTERFACE_H
+#define	SUBSAMPLING_INTERFACE_H
+
+#include <gudhi/choose_n_farthest_points.h>
+#include <gudhi/Points_off_io.h>
+#include <CGAL/Epick_d.h>
+
+#include <vector>
+#include <iostream>
+
+namespace Gudhi {
+
+namespace subsampling {
+
+using Subsampling_dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+using Subsampling_point_d = Subsampling_dynamic_kernel::Point_d;
+using Subsampling_ft = Subsampling_dynamic_kernel::FT;
+
+std::vector<std::vector<double>> subsampling_n_farthest_points(std::vector<std::vector<double>>& points, unsigned nb_points) {
+  std::vector<Subsampling_point_d> input, output;
+  for (auto point : points)
+      input.push_back(Subsampling_point_d(point.size(), point.begin(), point.end()));
+  std::vector<std::vector<double>> landmarks;
+  Subsampling_dynamic_kernel k;
+  choose_n_farthest_points(k, points, nb_points, std::back_inserter(landmarks));
+  std::cout << "output " << landmarks.size() << std::endl;
+
+
+  return landmarks;
+}
+
+}  // namespace subsampling
+
+}  // namespace Gudhi
+
+#endif  // SUBSAMPLING_INTERFACE_H
+