get rid of persistence_generators and modified name for cubical complex

4 files changed, 8 insertions, 56 deletions

diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 5562e8a7..8ea31486 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -31,7 +31,7 @@ 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, bool persistence_dim_max)
         vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
-        vector[pair[int, pair[pair[double, int], pair[double, int]]]] get_persistence_cubical_generators(int homology_coeff_field, double min_persistence)
+        vector[pair[int, pair[pair[double, int], pair[double, int]]]] get_cofaces_of_cubical_persistence_pairs(int homology_coeff_field, double min_persistence)
         vector[int] betti_numbers()
         vector[int] persistent_betti_numbers(double from_value, double to_value)
         vector[pair[double,double]] intervals_in_dimension(int dimension)
@@ -146,7 +146,7 @@ cdef class CubicalComplex:
             persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
         return persistence_result
 
-    def persistence_generators(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False):
+    def cofaces_of_cubical_persistence_pairs(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False):
         """This function returns the persistence of the simplicial complex.
 
         :param homology_coeff_field: The homology coefficient field. Must be a
@@ -161,7 +161,7 @@ cdef class CubicalComplex:
             maximal dimension in the complex is computed. If false, it is
             ignored. Default is false.
         :type persistence_dim_max: bool
-        :returns: The persistence of the simplicial complex, together with the corresponding generators, i.e., the positive and negative top-dimensional cells.
+        :returns: The persistence of the simplicial complex, together with the cofaces of the corresponding generators, i.e., the top-dimensional cells/cofaces of the positive and negative simplices.
         :rtype:  list of pairs(dimension, pair(index of positive top-dimensional cell, index of negative top-dimensional cell))
         """
         if self.pcohptr != NULL:
@@ -169,7 +169,7 @@ cdef class CubicalComplex:
         self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr, True)
         cdef vector[pair[int, pair[pair[double, int], pair[double, int]]]] persistence_result
         if self.pcohptr != NULL:
-            persistence_result = self.pcohptr.get_persistence_cubical_generators(homology_coeff_field, min_persistence)
+            persistence_result = self.pcohptr.get_cofaces_of_cubical_persistence_pairs(homology_coeff_field, min_persistence)
         return persistence_result
 
     def betti_numbers(self):
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 9e52a8aa..1066d44b 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -48,7 +48,6 @@ 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>>":
         Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max)
         vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
-        vector[pair[int, pair[pair[double, vector[int]], pair[double, vector[int]]]]] get_persistence_generators(int homology_coeff_field, double min_persistence)
         vector[int] betti_numbers()
         vector[int] persistent_betti_numbers(double from_value, double to_value)
         vector[pair[double,double]] intervals_in_dimension(int dimension)
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 8cc58f8f..85d25492 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -412,32 +412,6 @@ cdef class SimplexTree:
             persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
         return persistence_result
 
-    def persistence_generators(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False):
-        """This function returns the persistence of the simplicial complex.
-
-        :param homology_coeff_field: The homology coefficient field. Must be a
-            prime number. Default value is 11.
-        :type homology_coeff_field: int.
-        :param min_persistence: The minimum persistence value to take into
-            account (strictly greater than min_persistence). Default value is
-            0.0.
-            Sets min_persistence to -1.0 to see all values.
-        :type min_persistence: float.
-        :param persistence_dim_max: If true, the persistent homology for the
-            maximal dimension in the complex is computed. If false, it is
-            ignored. Default is false.
-        :type persistence_dim_max: bool
-        :returns: The persistence of the simplicial complex, together with the corresponding generators, i.e., the positive and negative simplices.
-        :rtype:  list of pairs(dimension, pair(positive_simplex, negative_simplex))
-        """
-        if self.pcohptr != NULL:
-            del self.pcohptr
-        self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), persistence_dim_max)
-        cdef vector[pair[int, pair[pair[double, vector[int]], pair[double, vector[int]]]]] persistence_result
-        if self.pcohptr != NULL:
-            persistence_result = self.pcohptr.get_persistence_generators(homology_coeff_field, min_persistence)
-        return persistence_result
-
     def betti_numbers(self):
         """This function returns the Betti numbers of the simplicial complex.
 
diff --git a/src/python/include/Persistent_cohomology_interface.h b/src/python/include/Persistent_cohomology_interface.h
index 0ad14477..1a1e716e 100644
--- a/src/python/include/Persistent_cohomology_interface.h
+++ b/src/python/include/Persistent_cohomology_interface.h
@@ -73,36 +73,15 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
     return persistence;
   }
 
-  std::vector<std::pair<int, std::pair<std::pair<double, std::vector<int>>, std::pair<double,std::vector<int>>>>> get_persistence_generators(int homology_coeff_field,
-                                                                                                                                             double min_persistence) {
-    persistent_cohomology::Persistent_cohomology<FilteredComplex,
-      persistent_cohomology::Field_Zp>::init_coefficients(homology_coeff_field);
-    persistent_cohomology::Persistent_cohomology<FilteredComplex,
-      persistent_cohomology::Field_Zp>::compute_persistent_cohomology(min_persistence);
-
-    // Custom sort and output persistence
-    cmp_intervals_by_dim_then_length cmp(stptr_);
-    auto persistent_pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
-      persistent_cohomology::Field_Zp>::get_persistent_pairs();
-    std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
-
-    std::vector<std::pair<int, std::pair<std::pair<double, std::vector<int>>, std::pair<double,std::vector<int>>>>> persistence;
-    for (auto pair : persistent_pairs) {
-      std::vector<int> splx0, splx1;
-      for (auto vertex : stptr_->simplex_vertex_range(get<0>(pair))){splx0.push_back(vertex);}
-      if (isfinite(stptr_->filtration(get<1>(pair)))){ for (auto vertex : stptr_->simplex_vertex_range(get<1>(pair))){splx1.push_back(vertex);}}
-      persistence.push_back(std::make_pair(stptr_->dimension(get<0>(pair)), std::make_pair(std::make_pair(stptr_->filtration(get<0>(pair)), splx0), std::make_pair(stptr_->filtration(get<1>(pair)), splx1))));
-    }
-    return persistence;
-  }
-
   void top_dimensional_cofaces(std::vector<int> & cofaces, int splx){
     if (stptr_->dimension(stptr_->simplex(splx)) == stptr_->dimension()){cofaces.push_back(stptr_->simplex(splx));}
     else{  for (auto v : stptr_->coboundary_simplex_range(stptr_->simplex(splx))){top_dimensional_cofaces(cofaces, stptr_->key(v));}  }
   }
 
-  std::vector<std::pair<int, std::pair<std::pair<double, int>, std::pair<double, int>>>> get_persistence_cubical_generators(int homology_coeff_field,
-                                                                                                                            double min_persistence) {
+  std::vector<std::pair<int, std::pair<std::pair<double, int>, std::pair<double, int>>>> get_cofaces_of_cubical_persistence_pairs(int homology_coeff_field,
+                                                                                                                                  double min_persistence) {
+
+    // Warning: this function is meant to be used with CubicalComplex only!!
 
     // Gather all top-dimensional cells and store their simplex handles
     std::vector<int> max_splx; for (auto splx : stptr_->filtration_simplex_range()){ if (stptr_->dimension(splx) == stptr_->dimension())  max_splx.push_back(splx); }