fix conflict

2 files changed, 55 insertions, 23 deletions

diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 7aa16926..ae32eb82 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -21,6 +21,22 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
     cdef cppclass Simplex_tree_options_full_featured:
         pass
 
+    cdef cppclass Simplex_tree_simplex_handle "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Simplex_handle":
+        pass
+
+    cdef cppclass Simplex_tree_simplices_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Complex_simplex_iterator":
+        Simplex_tree_simplices_iterator()
+        Simplex_tree_simplex_handle& operator*()
+        Simplex_tree_simplices_iterator operator++()
+        bint operator!=(Simplex_tree_simplices_iterator)
+
+    cdef cppclass Simplex_tree_skeleton_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Skeleton_simplex_iterator":
+        Simplex_tree_skeleton_iterator()
+        Simplex_tree_simplex_handle& operator*()
+        Simplex_tree_skeleton_iterator operator++()
+        bint operator!=(Simplex_tree_skeleton_iterator)
+
+
     cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>":
         Simplex_tree()
         double simplex_filtration(vector[int] simplex)
@@ -34,8 +50,6 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         bool find_simplex(vector[int] simplex)
         bool insert_simplex_and_subfaces(vector[int] simplex,
                                          double filtration)
-        vector[pair[vector[int], double]] get_filtration()
-        vector[pair[vector[int], double]] get_skeleton(int dimension)
         vector[pair[vector[int], double]] get_star(vector[int] simplex)
         vector[pair[vector[int], double]] get_cofaces(vector[int] simplex,
                                                           int dimension)
@@ -45,6 +59,14 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         bool make_filtration_non_decreasing()
         void extend_filtration()
         vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]])
+        # Iterators over Simplex tree
+        pair[vector[int], double] get_simplex_and_filtration(Simplex_tree_simplex_handle f_simplex)
+        Simplex_tree_simplices_iterator get_simplices_iterator_begin()
+        Simplex_tree_simplices_iterator get_simplices_iterator_end()
+        vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_begin()
+        vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_end()
+        Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension)
+        Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension)
 
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
     cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index e429e28a..733ecb97 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -7,6 +7,7 @@
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython.operator import dereference, preincrement
 from libc.stdint cimport intptr_t
 from numpy import array as np_array
 cimport simplex_tree
@@ -207,22 +208,34 @@ cdef class SimplexTree:
         return self.get_ptr().insert_simplex_and_subfaces(csimplex,
                                                         <double>filtration)
 
-    def get_filtration(self):
-        """This function returns a list of all simplices with their given
+    def get_simplices(self):
+        """This function returns a generator with simplices and their given
         filtration values.
 
+        :returns:  The simplices.
+        :rtype:  generator with tuples(simplex, filtration)
+        """
+        cdef Simplex_tree_simplices_iterator it = self.get_ptr().get_simplices_iterator_begin()
+        cdef Simplex_tree_simplices_iterator end = self.get_ptr().get_simplices_iterator_end()
+        cdef Simplex_tree_simplex_handle sh = dereference(it)
+
+        while it != end:
+            yield self.get_ptr().get_simplex_and_filtration(dereference(it))
+            preincrement(it)
+
+    def get_filtration(self):
+        """This function returns a generator with simplices and their given
+        filtration values sorted by increasing filtration values.
+
         :returns:  The simplices sorted by increasing filtration values.
-        :rtype:  list of tuples(simplex, filtration)
+        :rtype:  generator with tuples(simplex, filtration)
         """
-        cdef vector[pair[vector[int], double]] filtration \
-            = self.get_ptr().get_filtration()
-        ct = []
-        for filtered_complex in filtration:
-            v = []
-            for vertex in filtered_complex.first:
-                v.append(vertex)
-            ct.append((v, filtered_complex.second))
-        return ct
+        cdef vector[Simplex_tree_simplex_handle].const_iterator it = self.get_ptr().get_filtration_iterator_begin()
+        cdef vector[Simplex_tree_simplex_handle].const_iterator end = self.get_ptr().get_filtration_iterator_end()
+
+        while it != end:
+            yield self.get_ptr().get_simplex_and_filtration(dereference(it))
+            preincrement(it)
 
     def get_skeleton(self, dimension):
         """This function returns the (simplices of the) skeleton of a maximum
@@ -233,15 +246,12 @@ cdef class SimplexTree:
         :returns:  The (simplices of the) skeleton of a maximum dimension.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[pair[vector[int], double]] skeleton \
-            = self.get_ptr().get_skeleton(<int>dimension)
-        ct = []
-        for filtered_simplex in skeleton:
-            v = []
-            for vertex in filtered_simplex.first:
-                v.append(vertex)
-            ct.append((v, filtered_simplex.second))
-        return ct
+        cdef Simplex_tree_skeleton_iterator it = self.get_ptr().get_skeleton_iterator_begin(dimension)
+        cdef Simplex_tree_skeleton_iterator end = self.get_ptr().get_skeleton_iterator_end(dimension)
+
+        while it != end:
+            yield self.get_ptr().get_simplex_and_filtration(dereference(it))
+            preincrement(it)
 
     def get_star(self, simplex):
         """This function returns the star of a given N-simplex.