Add Cubical complex interfaces

Warning on compilation


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1232 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 56022f52ab6a8ddcc466a36b7c4fb09615df9c7a

5 files changed, 181 insertions, 0 deletions

diff --git a/src/cython/Makefile b/src/cython/Makefile
index fd7e16e6..f4e524ad 100644
--- a/src/cython/Makefile
+++ b/src/cython/Makefile
@@ -12,6 +12,7 @@ example:
 	python example/mini_simplex_tree_example.py
 	python example/rips_complex_example.py
 	python example/alpha_complex_example.py
+	python example/cubical_complex_example.py
 
 clean:
 	rm -rf build/ *.o *.so *.cpp
diff --git a/src/cython/example/cubical_complex_example.py b/src/cython/example/cubical_complex_example.py
new file mode 100755
index 00000000..ec7d2f5f
--- /dev/null
+++ b/src/cython/example/cubical_complex_example.py
@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+
+import gudhi
+
+"""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 Saclay (France)
+
+   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 Saclay (France)"
+__license__ = "GPL v3"
+
+print("#####################################################################")
+print("CubicalComplex creation")
+cubical_complex = gudhi.CubicalComplex(dimensions=[3, 3],
+                                       top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9])
+
+print("persistence(homology_coeff_field=2, min_persistence=0)=")
+print(cubical_complex.persistence(homology_coeff_field=2, min_persistence=0))
+
+print("betti_numbers()=")
+print(cubical_complex.betti_numbers())
diff --git a/src/cython/gudhi.pyx b/src/cython/gudhi.pyx
index 77b1b4bc..d0e2df99 100644
--- a/src/cython/gudhi.pyx
+++ b/src/cython/gudhi.pyx
@@ -28,3 +28,4 @@ include "src/cython/simplex_tree.pyx"
 include "src/cython/mini_simplex_tree.pyx"
 include "src/cython/rips_complex.pyx"
 include "src/cython/alpha_complex.pyx"
+include "src/cython/cubical_complex.pyx"
diff --git a/src/cython/src/cpp/Cubical_complex_interface.h b/src/cython/src/cpp/Cubical_complex_interface.h
new file mode 100644
index 00000000..b817198d
--- /dev/null
+++ b/src/cython/src/cpp/Cubical_complex_interface.h
@@ -0,0 +1,54 @@
+/*    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 Saclay (France)
+ *
+ *    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 CUBICAL_COMPLEX_INTERFACE_H
+#define	CUBICAL_COMPLEX_INTERFACE_H
+
+#include <gudhi/Bitmap_cubical_complex.h>
+#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>
+
+namespace Gudhi {
+
+namespace Cubical_complex {
+
+template<typename CubicalComplexOptions = Bitmap_cubical_complex_base<double>>
+class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOptions> {
+ public:
+
+  Cubical_complex_interface(const std::vector<unsigned>& dimensions,
+                            const std::vector<double>& top_dimensional_cells)
+  : Bitmap_cubical_complex<CubicalComplexOptions>(dimensions, top_dimensional_cells) {
+  }
+
+};
+
+}  // namespace Cubical_complex
+
+}  // namespace Gudhi
+
+#endif  // CUBICAL_COMPLEX_INTERFACE_H
+
diff --git a/src/cython/src/cython/cubical_complex.pyx b/src/cython/src/cython/cubical_complex.pyx
new file mode 100644
index 00000000..d513191c
--- /dev/null
+++ b/src/cython/src/cython/cubical_complex.pyx
@@ -0,0 +1,85 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+
+"""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 Saclay (France)
+
+   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 Saclay (France)"
+__license__ = "GPL v3"
+
+cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Bitmap_cubical_complex_base_interface "Gudhi::Cubical_complex::Cubical_complex_interface<>":
+          Bitmap_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells)
+
+cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
+    cdef cppclass Cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface<>>":
+        Cubical_complex_persistence_interface(Bitmap_cubical_complex_base_interface * st)
+        vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
+        vector[int] betti_numbers()
+        vector[int] persistent_betti_numbers(double from_value, double to_value)
+
+
+# CubicalComplex python interface
+cdef class CubicalComplex:
+    cdef Bitmap_cubical_complex_base_interface * thisptr
+
+    cdef Cubical_complex_persistence_interface * pcohptr
+
+    def __cinit__(self, dimensions=None, top_dimensional_cells=None):
+        if dimensions is not None:
+            if top_dimensional_cells is not None:
+                self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+        if self.pcohptr != NULL:
+            del self.pcohptr
+
+    def persistence(self, homology_coeff_field=11, min_persistence=0):
+        if self.pcohptr != NULL:
+            del self.pcohptr
+        self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr)
+        cdef vector[pair[int, pair[double, double]]] persistence_result
+        if self.pcohptr != NULL:
+            persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
+        return persistence_result
+
+    def betti_numbers(self):
+        cdef vector[int] bn_result
+        if self.pcohptr != NULL:
+            bn_result = self.pcohptr.betti_numbers()
+        else:
+            print("betti_numbers function requires persistence function"
+                  " to be launched first.")
+        return bn_result
+
+    def persistent_betti_numbers(self, from_value, to_value):
+        cdef vector[int] pbn_result
+        if self.pcohptr != NULL:
+            pbn_result = self.pcohptr.persistent_betti_numbers(<double>from_value, <double>to_value)
+        else:
+            print("persistent_betti_numbers function requires persistence function"
+                  " to be launched first.")
+        return pbn_result