added files for cythonization of kernels

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/kernels@3263 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5bc7aadf2696ea2f94384a163451237016a7effb

3 files changed, 97 insertions, 0 deletions

diff --git a/src/cython/cython/kernels.pyx b/src/cython/cython/kernels.pyx
new file mode 100644
index 00000000..220fc6ce
--- /dev/null
+++ b/src/cython/cython/kernels.pyx
@@ -0,0 +1,47 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+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):       Mathieu Carriere
+
+   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/>.
+"""
+
+__author__ = "Mathieu Carriere"
+__copyright__ = "Copyright (C) 2018 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Kernels_interface.h" namespace "Gudhi::persistence_diagram":
+    double sw(vector[pair[double, double]], vector[pair[double, double]], double, int)
+
+def sliced_wasserstein(diagram_1, diagram_2, sigma = 1, N = 100):
+    """
+
+    :param diagram_1: The first diagram.
+    :type diagram_1: vector[pair[double, double]]
+    :param diagram_2: The second diagram.
+    :type diagram_2: vector[pair[double, double]]
+    :param sigma: bandwidth of Gaussian
+    :param N: number of directions
+
+    :returns: the sliced wasserstein kernel.
+    """
+    return sw(diagram_1, diagram_2, sigma, N)
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index a8dd9f80..7f42968d 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -36,6 +36,7 @@ include '@CMAKE_CURRENT_SOURCE_DIR@/cython/persistence_graphical_tools.py'
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/reader_utils.pyx'
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/witness_complex.pyx'
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/strong_witness_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/kernels.pyx'
 @GUDHI_CYTHON_ALPHA_COMPLEX@
 @GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX@
 @GUDHI_CYTHON_SUBSAMPLING@
diff --git a/src/cython/include/Kernels_interface.h b/src/cython/include/Kernels_interface.h
new file mode 100644
index 00000000..9eb610b0
--- /dev/null
+++ b/src/cython/include/Kernels_interface.h
@@ -0,0 +1,49 @@
+/*    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):       Mathieu Carriere
+ *
+ *    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_KERNELS_INTERFACE_H_
+#define INCLUDE_KERNELS_INTERFACE_H_
+
+#include <gudhi/Sliced_Wasserstein.h>
+
+#include <iostream>
+#include <vector>
+#include <utility>  // for std::pair
+
+namespace Gudhi {
+
+namespace persistence_diagram {
+
+  double sw(const std::vector<std::pair<double, double>>& diag1,
+            const std::vector<std::pair<double, double>>& diag2,
+            double sigma, int N) {
+    Gudhi::Persistence_representations::Sliced_Wasserstein sw1(diag1, sigma, N);
+    Gudhi::Persistence_representations::Sliced_Wasserstein sw2(diag2, sigma, N);
+    return sw1.compute_scalar_product(sw2);
+  }
+
+}  // namespace persistence_diagram
+
+}  // namespace Gudhi
+
+
+#endif  // INCLUDE_KERNELS_INTERFACE_H_