Strong witness cythonization

Biblio for doc simplification


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2184 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c191c6b79bb14f799d6cd08ac59a6b007a7874dc

13 files changed, 196 insertions, 27 deletions

diff --git a/src/cython/cython/strong_witness_complex.pyx b/src/cython/cython/strong_witness_complex.pyx
new file mode 100644
index 00000000..5febffbb
--- /dev/null
+++ b/src/cython/cython/strong_witness_complex.pyx
@@ -0,0 +1,81 @@
+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
+
+   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 "Strong_witness_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Strong_witness_complex_interface "Gudhi::witness_complex::Strong_witness_complex_interface":
+        Strong_witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square,
+            unsigned limit_dimension)
+
+# StrongWitnessComplex python interface
+cdef class StrongWitnessComplex:
+    """StrongWitnessComplex is a simplicial complex constructed from ...
+
+    """
+
+    cdef Strong_witness_complex_interface * thisptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, nearest_landmark_table=None):
+        """StrongWitnessComplex constructor.
+
+        :param nearest_landmark_table: A list of nearest landmark.
+        :type nearest_landmark_table: list of list of pair of unsigned and double
+        """
+
+    # The real cython constructor
+    def __cinit__(self, nearest_landmark_table=None):
+        if nearest_landmark_table is not None:
+            self.thisptr = new Strong_witness_complex_interface(nearest_landmark_table)
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+
+    def __is_defined(self):
+        """Returns true if StrongWitnessComplex pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def create_simplex_tree(self, max_alpha_square, limit_dimension = -1):
+        """
+        :param max_alpha_square: The maximum alpha square threshold the
+            simplices shall not exceed. Default is set to infinity.
+        :type max_alpha_square: float
+        :returns: A simplex tree created from the Delaunay Triangulation.
+        :rtype: SimplexTree
+        """
+        simplex_tree = SimplexTree()
+        if limit_dimension is not -1:
+            self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square, limit_dimension)
+        else:
+            self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square)
+        return simplex_tree
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
index f1c57248..68e53a77 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -196,4 +196,10 @@ the program output is:
    ([2, 3, 6], 36.5)
    ([2, 4, 6], 37.24489795918368)
 
-.. :include: how_to_cite_cgal.rst
+==============
+CGAL citations
+==============
+
+.. bibliography:: how_to_cite_cgal.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/biblio.rst b/src/cython/doc/biblio.rst
deleted file mode 100644
index 3995e9c0..00000000
--- a/src/cython/doc/biblio.rst
+++ /dev/null
@@ -1,6 +0,0 @@
-Bibliography
-************
-
-.. bibliography:: bibliography.bib
-   :filter: docnames
-   :style: unsrt
diff --git a/src/cython/doc/cgal_citation.rst b/src/cython/doc/cgal_citation.rst
deleted file mode 100644
index bbc4ef9e..00000000
--- a/src/cython/doc/cgal_citation.rst
+++ /dev/null
@@ -1,8 +0,0 @@
-==============
-CGAL citations
-==============
-
-..
-    bibliography:: how_to_cite_cgal.bib
-        :filter: docnames
-        :style: unsrt
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 002a648b..692acdd9 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -153,4 +153,9 @@ Examples.
 
 End user programs are available in cython/example/ folder.
 
-.. include:: biblio.rst
+Bibliography
+************
+
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/how_to_cite_cgal.rst b/src/cython/doc/how_to_cite_cgal.rst
deleted file mode 100644
index 192e0562..00000000
--- a/src/cython/doc/how_to_cite_cgal.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-==============
-CGAL citations
-==============
-
-.. bibliography:: how_to_cite_cgal.bib
-   :filter: docnames
-   :style: unsrt
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
index d0165588..fca63d65 100644
--- a/src/cython/doc/index.rst
+++ b/src/cython/doc/index.rst
@@ -79,4 +79,9 @@ Persistence graphical tools
 
 .. include:: persistence_graphical_tools_sum.rst
 
-.. include:: biblio.rst
+Bibliography
+************
+
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst
index a68e9bdd..69be3b86 100644
--- a/src/cython/doc/persistent_cohomology_user.rst
+++ b/src/cython/doc/persistent_cohomology_user.rst
@@ -107,4 +107,9 @@ We provide several example files: run these examples with -h for details on thei
     * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>`
     * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
 
-.. include:: biblio.rst
+Bibliography
+************
+
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index 6c3debb4..6a7e6e41 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -187,4 +187,9 @@ The output is:
     Tangential contains 4 vertices.
     Inconsistencies has been fixed.
 
-.. include:: biblio.rst
+Bibliography
+************
+
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst
index 071d8ef5..72b8d839 100644
--- a/src/cython/doc/witness_complex_user.rst
+++ b/src/cython/doc/witness_complex_user.rst
@@ -81,5 +81,9 @@ Example2: Computing persistence using strong relaxed witness complex
 
 Here is an example of constructing a strong witness complex filtration and computing persistence on it:
 
-.. include:: biblio.rst
+Bibliography
+************
 
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index 2d743d4d..60bf0cd7 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -30,6 +30,7 @@ include "cython/cubical_complex.pyx"
 include "cython/periodic_cubical_complex.pyx"
 include "cython/persistence_graphical_tools.py"
 include "cython/witness_complex.pyx"
+include "cython/strong_witness_complex.pyx"
 @GUDHI_CYTHON_ALPHA_COMPLEX@
 @GUDHI_CYTHON_SUBSAMPLING@
 @GUDHI_CYTHON_TANGENTIAL_COMPLEX@
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index 19e02ca4..4f3096c0 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -59,6 +59,13 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     return (result.second);
   }
 
+  // Do not interface this function, only used in strong witness interface for complex creation
+  bool insert_simplex_and_subfaces(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
+    Insertion_result result = Simplex_tree<SimplexTreeOptions>::insert_simplex_and_subfaces(complex, filtration);
+    Simplex_tree<SimplexTreeOptions>::initialize_filtration();
+    return (result.second);
+  }
+
   Filtration_value simplex_filtration(const Simplex& complex) {
     return Simplex_tree<SimplexTreeOptions>::filtration(Simplex_tree<SimplexTreeOptions>::find(complex));
   }
diff --git a/src/cython/include/Strong_witness_complex_interface.h b/src/cython/include/Strong_witness_complex_interface.h
new file mode 100644
index 00000000..e59e58ea
--- /dev/null
+++ b/src/cython/include/Strong_witness_complex_interface.h
@@ -0,0 +1,71 @@
+/*    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 STRONG_WITNESS_COMPLEX_INTERFACE_H
+#define	STRONG_WITNESS_COMPLEX_INTERFACE_H
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Strong_witness_complex.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <vector>
+#include <utility>  // std::pair
+#include <iostream>
+#include <cstddef>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+class Strong_witness_complex_interface {
+  using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>;
+  using Nearest_landmark_table = std::vector<Nearest_landmark_range>;
+
+ public:
+  Strong_witness_complex_interface(Nearest_landmark_table& nlt) {
+    witness_complex_ = new Strong_witness_complex<Nearest_landmark_table>(nlt);
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* 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(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());
+    simplex_tree->initialize_filtration();
+  }
+
+ private:
+  Strong_witness_complex<Nearest_landmark_table>* witness_complex_;
+
+};
+
+}  // namespace witness_complex
+
+} // namespace Gudhi
+
+#endif  // STRONG_WITNESS_COMPLEX_INTERFACE_H
+