added wrapper functions

4 files changed, 132 insertions, 2 deletions

diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index cbeda014..5562e8a7 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -31,6 +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[int] betti_numbers()
         vector[int] persistent_betti_numbers(double from_value, double to_value)
         vector[pair[double,double]] intervals_in_dimension(int dimension)
@@ -85,7 +86,7 @@ cdef class CubicalComplex:
         elif ((dimensions is None) and (top_dimensional_cells is None)
             and (perseus_file != '')):
             if os.path.isfile(perseus_file):
-                self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file.encode('utf-8'))
+                self.thisptr = new Bitmap_cubical_complex_base_interface(str.encode(perseus_file))
             else:
                 print("file " + perseus_file + " not found.")
         else:
@@ -145,6 +146,32 @@ 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):
+        """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 top-dimensional cells.
+        :rtype:  list of pairs(dimension, pair(index of positive top-dimensional cell, index of negative top-dimensional cell))
+        """
+        if self.pcohptr != NULL:
+            del self.pcohptr
+        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)
+        return persistence_result
+
     def betti_numbers(self):
         """This function returns the Betti numbers of the complex.
 
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 1066d44b..9e52a8aa 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -48,6 +48,7 @@ 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 b18627c4..8cc58f8f 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -412,6 +412,32 @@ 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.
 
@@ -508,7 +534,7 @@ cdef class SimplexTree:
         """
         if self.pcohptr != NULL:
             if persistence_file != '':
-                self.pcohptr.write_output_diagram(persistence_file.encode('utf-8'))
+                self.pcohptr.write_output_diagram(str.encode(persistence_file))
             else:
                 print("persistence_file must be specified")
         else:
diff --git a/src/python/include/Persistent_cohomology_interface.h b/src/python/include/Persistent_cohomology_interface.h
index 8c79e6f3..774eb56a 100644
--- a/src/python/include/Persistent_cohomology_interface.h
+++ b/src/python/include/Persistent_cohomology_interface.h
@@ -73,6 +73,82 @@ 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) {
+
+    // 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); }
+    // Sort these simplex handles and compute the ordering function
+    // This function allows to go directly from the simplex handle to the position of the corresponding top-dimensional cell in the input data 
+    std::map<int, int> order; std::sort(max_splx.begin(), max_splx.end()); for (int i = 0; i < max_splx.size(); i++)  order.insert(std::make_pair(max_splx[i], i));
+
+    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, int>, std::pair<double, int>>>> persistence;
+    for (auto pair : persistent_pairs) {
+
+      int splx0, splx1;
+
+      double f0 = stptr_->filtration(get<0>(pair));
+      // Recursively get the top-dimensional cells / cofaces associated to the persistence generator
+      std::vector<int> faces0; top_dimensional_cofaces(faces0, stptr_->key(get<0>(pair)));
+      // Find the top-dimensional cell / coface with the same filtration value
+      int cf; for (int i = 0; i < faces0.size(); i++){ if (stptr_->filtration(faces0[i]) == f0){cf = i; break;}}
+      // Retrieve the index of the corresponding top-dimensional cell in the input data
+      splx0 = order[faces0[cf]];
+
+      if (isfinite(stptr_->filtration(get<1>(pair)))){
+      double f1 = stptr_->filtration(get<1>(pair));
+      // Recursively get the top-dimensional cells / cofaces associated to the persistence generator
+      std::vector<int> faces1; top_dimensional_cofaces(faces1, stptr_->key(get<1>(pair)));
+      // Find the top-dimensional cell / coface with the same filtration value
+      int cf; for (int i = 0; i < faces0.size(); i++){ if (stptr_->filtration(faces0[i]) == f0){cf = i; break;}}
+      // Retrieve the index of the corresponding top-dimensional cell in the input data
+      splx1 = order[faces1[cf]];
+      }
+
+      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;
+  }
+
   std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs() {
     auto pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
       persistent_cohomology::Field_Zp>::get_persistent_pairs();