new fixes

4 files changed, 29 insertions, 35 deletions

diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index b6284af4..595f22bb 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -58,7 +58,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         bool prune_above_filtration(double filtration)
         bool make_filtration_non_decreasing()
         void compute_extended_filtration()
-        vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]] dgm)
+        vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]] dgm, double min_persistence)
         # 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()
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 5b850462..bcb1578d 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -411,7 +411,7 @@ cdef class SimplexTree:
         .. note::
 
             Note that this code creates an extra vertex internally, so you should make sure that
-            the Simplex_tree does not contain a vertex with the largest Vertex_handle. 
+            the Simplex_tree does not contain a vertex with the largest possible value (i.e., 4294967295). 
         """
         return self.get_ptr().compute_extended_filtration()
 
@@ -422,18 +422,16 @@ cdef class SimplexTree:
         :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
+        :param min_persistence: The minimum persistence value (i.e., the absolute value of the difference between the persistence diagram point coordinates) 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.
-        :returns: A vector of four persistence diagrams. The first one is Ordinary, the second one is Relative, the third one is Extended+ and the fourth one is Extended-. See section 2.2 in https://link.springer.com/article/10.1007/s10208-017-9370-z for a description of these subtypes.
+        :returns: A list of four persistence diagrams in the format described in :func:`persistence()<gudhi.SimplexTree.persistence>`. The first one is Ordinary, the second one is Relative, the third one is Extended+ and the fourth one is Extended-. See section 2.2 in https://link.springer.com/article/10.1007/s10208-017-9370-z for a description of these subtypes.
 
         .. note::
 
-            This function should be called only if :func:`extend_filtration()<gudhi.SimplexTree.extend_filtration>`,
-            :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>`, 
-            and (optionally) :func:`persistence()<gudhi.SimplexTree.persistence>` have been called first!
+            This function should be called only if :func:`extend_filtration()<gudhi.SimplexTree.extend_filtration>` has been called first!
 
         .. note::
 
@@ -442,14 +440,11 @@ cdef class SimplexTree:
             performed on these values during the computation of extended persistence.
         """
         cdef vector[pair[int, pair[double, double]]] persistence_result
-        if self.pcohptr == NULL:
-            self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), False)
-            if self.pcohptr != NULL:
-                self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
         if self.pcohptr != NULL:
-            pairs = self.pcohptr.persistence_pairs()
-            persistence_result = [(len(splx1)-1, [self.filtration(splx1), self.filtration(splx2)]) for [splx1, splx2] in pairs]
-        return self.get_ptr().compute_extended_persistence_subdiagrams(persistence_result)
+            del self.pcohptr
+        self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), False)
+        persistence_result = self.pcohptr.get_persistence(homology_coeff_field, -1.)
+        return self.get_ptr().compute_extended_persistence_subdiagrams(persistence_result, min_persistence)
 
 
     def persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False):
diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index a6b1a06e..1a18aed6 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -38,7 +38,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   using Skeleton_simplex_iterator = typename Base::Skeleton_simplex_iterator;
   using Complex_simplex_iterator = typename Base::Complex_simplex_iterator;
   using Extended_filtration_data = typename Base::Extended_filtration_data;
-  using Extended_simplex_type = typename Base::Extended_simplex_type;
 
  public:
 
@@ -124,31 +123,34 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
 
   void compute_extended_filtration() {
     this->efd = this->extend_filtration();
+    this->initialize_filtration();
     return;
   }
 
-  std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> compute_extended_persistence_subdiagrams(const std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>& dgm){
+  std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> compute_extended_persistence_subdiagrams(const std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>& dgm, Filtration_value min_persistence){
     std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> new_dgm(4);
     for (unsigned int i = 0; i < dgm.size(); i++){
       std::pair<Filtration_value, Extended_simplex_type> px = this->decode_extended_filtration(dgm[i].second.first, this->efd);
       std::pair<Filtration_value, Extended_simplex_type> py = this->decode_extended_filtration(dgm[i].second.second, this->efd);
       std::pair<int, std::pair<Filtration_value, Filtration_value>> pd_point = std::make_pair(dgm[i].first, std::make_pair(px.first, py.first));
-      //Ordinary
-      if (px.second == Base::UP && py.second == Base::UP){
-        new_dgm[0].push_back(pd_point);
-      }
-      // Relative
-      else if (px.second == Base::DOWN && py.second == Base::DOWN){
-        new_dgm[1].push_back(pd_point);
-      }
-      else{
-        // Extended+
-        if (px.first < py.first){
-          new_dgm[2].push_back(pd_point);
+      if(std::abs(px.first - py.first) > min_persistence){
+        //Ordinary
+        if (px.second == Extended_simplex_type::UP && py.second == Extended_simplex_type::UP){
+          new_dgm[0].push_back(pd_point);
+        }
+        // Relative
+        else if (px.second == Extended_simplex_type::DOWN && py.second == Extended_simplex_type::DOWN){
+          new_dgm[1].push_back(pd_point);
         }
-        //Extended-
         else{
-          new_dgm[3].push_back(pd_point);
+          // Extended+
+          if (px.first < py.first){
+            new_dgm[2].push_back(pd_point);
+          }
+          //Extended-
+          else{
+            new_dgm[3].push_back(pd_point);
+          }
         }
       }
     }
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 20f6aabf..70b26e97 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -291,10 +291,8 @@ def test_extend_filtration():
         ([5], 6.0)
     ]
         
-
     st.extend_filtration()
-    st.initialize_filtration()
-                                                                                                                      
+    
     assert list(st.get_filtration()) == [                                                                                                                         
         ([6], -3.0), 
         ([0], -2.0), 
@@ -323,7 +321,7 @@ def test_extend_filtration():
         ([0, 3, 6], 2.0)
     ]
 
-    dgms = st.extended_persistence()
+    dgms = st.extended_persistence(min_persistence=-1.)
 
     assert dgms[0][0][1][0] == pytest.approx(2.)
     assert dgms[0][0][1][1] == pytest.approx(3.)
@@ -334,7 +332,6 @@ def test_extend_filtration():
     assert dgms[3][0][1][0] == pytest.approx(6.)
     assert dgms[3][0][1][1] == pytest.approx(1.) 
 
-
 def test_simplices_iterator():
     st = SimplexTree()