persistence_pairs Python version

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3393 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5ee633545ca5754b605cdd789ca9720f5936998a

2 files changed, 46 insertions, 0 deletions

diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 0cb575d2..755cdc02 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -64,6 +64,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
         vector[int] persistent_betti_numbers(double from_value, double to_value)
         vector[pair[double,double]] intervals_in_dimension(int dimension)
         void write_output_diagram(string diagram_file_name)
+        vector[pair[vector[int], vector[int]]] persistence_pairs()
 
 # SimplexTree python interface
 cdef class SimplexTree:
@@ -486,6 +487,25 @@ cdef class SimplexTree:
                   " to be launched first.")
         return intervals_result
 
+    def persistence_pairs(self):
+        """This function returns the persistence pairs of the simplicial
+        complex.
+
+        :returns: The persistence intervals.
+        :rtype:  list of pair of list of int
+
+        :note: intervals_in_dim function requires
+            :func:`persistence()<gudhi.SimplexTree.persistence>`
+            function to be launched first.
+        """
+        cdef vector[pair[vector[int],vector[int]]] persistence_pairs_result
+        if self.pcohptr != NULL:
+            persistence_pairs_result = self.pcohptr.persistence_pairs()
+        else:
+            print("persistence_pairs function requires persistence function"
+                  " to be launched first.")
+        return persistence_pairs_result
+
     def write_persistence_diagram(self, persistence_file=''):
         """This function writes the persistence intervals of the simplicial
         complex in a user given file name.
diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h
index 55028fd0..e8889444 100644
--- a/src/cython/include/Persistent_cohomology_interface.h
+++ b/src/cython/include/Persistent_cohomology_interface.h
@@ -85,6 +85,32 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
     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();
+
+    std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs;
+    persistence_pairs.reserve(pairs.size());
+    for (auto pair : pairs) {
+      std::vector<int> birth;
+      if (get<0>(pair) != stptr_->null_simplex()) {
+        for (auto vertex : stptr_->simplex_vertex_range(get<0>(pair))) {
+          birth.push_back(vertex);
+        }
+      }
+
+      std::vector<int> death;
+      if (get<1>(pair) != stptr_->null_simplex()) {
+        for (auto vertex : stptr_->simplex_vertex_range(get<1>(pair))) {
+          death.push_back(vertex);
+        }
+      }
+
+      persistence_pairs.push_back(std::make_pair(birth,death));
+    }
+    return persistence_pairs;
+  }
+
  private:
   // A copy
   FilteredComplex* stptr_;