Split compute_persistence from get_persistence.

5 files changed, 30 insertions, 20 deletions

diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index d5ad1266..ce844558 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -35,7 +35,8 @@ cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
 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)
+        void compute_persistence(int homology_coeff_field, double min_persistence)
+        vector[pair[int, pair[double, double]]] get_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)
@@ -149,7 +150,8 @@ cdef class CubicalComplex:
             self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr, True)
         cdef vector[pair[int, pair[double, double]]] persistence_result
         if self.pcohptr != NULL:
-            persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
+            self.pcohptr.compute_persistence(homology_coeff_field, min_persistence)
+            persistence_result = self.pcohptr.get_persistence()
         return persistence_result
 
     def betti_numbers(self):
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index fd08b976..ff5ef3bd 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -32,7 +32,8 @@ cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
     cdef cppclass Periodic_cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface<Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>>>":
         Periodic_cubical_complex_persistence_interface(Periodic_cubical_complex_base_interface * st, bool persistence_dim_max)
-        vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
+        void compute_persistence(int homology_coeff_field, double min_persistence)
+        vector[pair[int, pair[double, double]]] get_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)
@@ -154,7 +155,8 @@ cdef class PeriodicCubicalComplex:
             self.pcohptr = new Periodic_cubical_complex_persistence_interface(self.thisptr, True)
         cdef vector[pair[int, pair[double, double]]] persistence_result
         if self.pcohptr != NULL:
-            persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
+            self.pcohptr.compute_persistence(homology_coeff_field, min_persistence)
+            persistence_result = self.pcohptr.get_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 595f22bb..44040bcb 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -71,7 +71,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
 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)
+        void compute_persistence(int homology_coeff_field, double min_persistence)
+        vector[pair[int, pair[double, double]]] get_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 cc3753e1..69e645b4 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -443,7 +443,8 @@ cdef class SimplexTree:
         if self.pcohptr != NULL:
             del self.pcohptr
         self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), False)
-        persistence_result = self.pcohptr.get_persistence(homology_coeff_field, -1.)
+        self.pcohptr.compute_persistence(homology_coeff_field, -1.)
+        persistence_result = self.pcohptr.get_persistence()
         return self.get_ptr().compute_extended_persistence_subdiagrams(persistence_result, min_persistence)
 
 
@@ -470,7 +471,8 @@ cdef class SimplexTree:
         self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), persistence_dim_max)
         cdef vector[pair[int, pair[double, double]]] persistence_result
         if self.pcohptr != NULL:
-            persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
+            self.pcohptr.compute_persistence(homology_coeff_field, min_persistence)
+            persistence_result = self.pcohptr.get_persistence()
         return persistence_result
 
     def betti_numbers(self):
diff --git a/src/python/include/Persistent_cohomology_interface.h b/src/python/include/Persistent_cohomology_interface.h
index 8c79e6f3..a29ebbee 100644
--- a/src/python/include/Persistent_cohomology_interface.h
+++ b/src/python/include/Persistent_cohomology_interface.h
@@ -23,6 +23,7 @@ template<class FilteredComplex>
 class Persistent_cohomology_interface : public
 persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp> {
  private:
+   typedef persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp> Base;
   /*
    * Compare two intervals by dimension, then by length.
    */
@@ -43,25 +44,28 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
 
  public:
   Persistent_cohomology_interface(FilteredComplex* stptr)
-      : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr),
+      : Base(*stptr),
       stptr_(stptr) { }
 
   Persistent_cohomology_interface(FilteredComplex* stptr, bool persistence_dim_max)
-      : persistent_cohomology::Persistent_cohomology<FilteredComplex,
-          persistent_cohomology::Field_Zp>(*stptr, persistence_dim_max),
+      : Base(*stptr, persistence_dim_max),
         stptr_(stptr) { }
 
-  std::vector<std::pair<int, std::pair<double, double>>> get_persistence(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);
+  void compute_persistence(int homology_coeff_field, double min_persistence) {
+    Base::init_coefficients(homology_coeff_field);
+    Base::compute_persistent_cohomology(min_persistence);
+  }
+
+  void maybe_compute_persistence(int homology_coeff_field, double min_persistence) {
+    // Currently get_persistent_pairs safely returns an empty vector before compute_persistent_cohomology
+    if(Base::get_persistent_pairs().empty())
+      compute_persistence(homology_coeff_field, min_persistence);
+  }
 
+  std::vector<std::pair<int, std::pair<double, double>>> get_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();
+    auto persistent_pairs = Base::get_persistent_pairs();
     std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
 
     std::vector<std::pair<int, std::pair<double, double>>> persistence;
@@ -74,8 +78,7 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
   }
 
   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();
+    auto pairs = Base::get_persistent_pairs();
 
     std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs;
     persistence_pairs.reserve(pairs.size());