Streamline initialize_filtration

15 files changed, 13 insertions, 75 deletions

diff --git a/src/python/doc/simplex_tree_ref.rst b/src/python/doc/simplex_tree_ref.rst
index 9eb8c199..46b2c1e5 100644
--- a/src/python/doc/simplex_tree_ref.rst
+++ b/src/python/doc/simplex_tree_ref.rst
@@ -8,7 +8,6 @@ Simplex tree reference manual
 
 .. autoclass:: gudhi.SimplexTree
    :members:
-   :undoc-members:
    :show-inheritance:
 
    .. automethod:: gudhi.SimplexTree.__init__
diff --git a/src/python/example/alpha_complex_from_points_example.py b/src/python/example/alpha_complex_from_points_example.py
index 73faf17c..465632eb 100755
--- a/src/python/example/alpha_complex_from_points_example.py
+++ b/src/python/example/alpha_complex_from_points_example.py
@@ -46,9 +46,6 @@ if simplex_tree.find([4]):
 else:
     print("[4] Not found...")
 
-# Some insertions, simplex_tree needs to initialize filtrations
-simplex_tree.initialize_filtration()
-
 print("dimension=", simplex_tree.dimension())
 print("filtrations=")
 for simplex_with_filtration in simplex_tree.get_filtration():
diff --git a/src/python/example/simplex_tree_example.py b/src/python/example/simplex_tree_example.py
index 34833899..c4635dc5 100755
--- a/src/python/example/simplex_tree_example.py
+++ b/src/python/example/simplex_tree_example.py
@@ -42,7 +42,6 @@ print("simplices=")
 for simplex_with_filtration in st.get_simplices():
     print("(%s, %.2f)" % tuple(simplex_with_filtration))
 
-st.initialize_filtration()
 print("filtration=")
 for simplex_with_filtration in st.get_filtration():
     print("(%s, %.2f)" % tuple(simplex_with_filtration))
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 595f22bb..7e3bba2b 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -48,8 +48,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         int dimension()
         int upper_bound_dimension()
         bool find_simplex(vector[int] simplex)
-        bool insert_simplex_and_subfaces(vector[int] simplex,
-                                         double filtration)
+        bool insert(vector[int] simplex, double filtration)
         vector[pair[vector[int], double]] get_star(vector[int] simplex)
         vector[pair[vector[int], double]] get_cofaces(vector[int] simplex,
                                                           int dimension)
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index cc3753e1..a709980f 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -90,7 +90,7 @@ cdef class SimplexTree:
             (with more :meth:`assign_filtration` or
             :meth:`make_filtration_non_decreasing` for instance) before calling
             any function that relies on the filtration property, like
-            :meth:`initialize_filtration`.
+            :meth:`persistence`.
         """
         self.get_ptr().assign_simplex_filtration(simplex, filtration)
 
@@ -98,16 +98,7 @@ cdef class SimplexTree:
         """This function initializes and sorts the simplicial complex
         filtration vector.
 
-        .. note::
-
-            This function must be launched before
-            :func:`persistence()<gudhi.SimplexTree.persistence>`,
-            :func:`betti_numbers()<gudhi.SimplexTree.betti_numbers>`,
-            :func:`persistent_betti_numbers()<gudhi.SimplexTree.persistent_betti_numbers>`,
-            or :func:`get_filtration()<gudhi.SimplexTree.get_filtration>`
-            after :func:`inserting<gudhi.SimplexTree.insert>` or
-            :func:`removing<gudhi.SimplexTree.remove_maximal_simplex>`
-            simplices.
+        .. deprecated:: 3.2.0
         """
         self.get_ptr().initialize_filtration()
 
@@ -182,10 +173,7 @@ cdef class SimplexTree:
         :returns:  true if the simplex was found, false otherwise.
         :rtype:  bool
         """
-        cdef vector[int] csimplex
-        for i in simplex:
-            csimplex.push_back(i)
-        return self.get_ptr().find_simplex(csimplex)
+        return self.get_ptr().find_simplex(simplex)
 
     def insert(self, simplex, filtration=0.0):
         """This function inserts the given N-simplex and its subfaces with the
@@ -202,11 +190,7 @@ cdef class SimplexTree:
             otherwise (whatever its original filtration value).
         :rtype:  bool
         """
-        cdef vector[int] csimplex
-        for i in simplex:
-            csimplex.push_back(i)
-        return self.get_ptr().insert_simplex_and_subfaces(csimplex,
-                                                        <double>filtration)
+        return self.get_ptr().insert(simplex, <double>filtration)
 
     def get_simplices(self):
         """This function returns a generator with simplices and their given
@@ -308,11 +292,6 @@ cdef class SimplexTree:
 
         .. note::
 
-            Be aware that removing is shifting data in a flat_map
-            (:func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>` to be done).
-
-        .. note::
-
             The dimension of the simplicial complex may be lower after calling
             remove_maximal_simplex than it was before. However,
             :func:`upper_bound_dimension()<gudhi.SimplexTree.upper_bound_dimension>`
@@ -334,16 +313,6 @@ cdef class SimplexTree:
 
         .. note::
 
-            Some simplex tree functions require the filtration to be valid.
-            prune_above_filtration function is not launching
-            :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>`
-            but returns the filtration modification
-            information. If the complex has changed , please call
-            :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>`
-            to recompute it.
-
-        .. note::
-
             Note that the dimension of the simplicial complex may be lower
             after calling
             :func:`prune_above_filtration()<gudhi.SimplexTree.prune_above_filtration>`
@@ -382,17 +351,6 @@ cdef class SimplexTree:
         :returns: True if any filtration value was modified,
             False if the filtration was already non-decreasing.
         :rtype: bool
-
-
-        .. note::
-
-            Some simplex tree functions require the filtration to be valid.
-            make_filtration_non_decreasing function is not launching
-            :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>`
-            but returns the filtration modification
-            information. If the complex has changed , please call
-            :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>`
-            to recompute it.
         """
         return self.get_ptr().make_filtration_non_decreasing()
 
diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h
index 8614eee3..40de88f3 100644
--- a/src/python/include/Alpha_complex_interface.h
+++ b/src/python/include/Alpha_complex_interface.h
@@ -58,7 +58,6 @@ class Alpha_complex_interface {
 
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square) {
     alpha_complex_->create_complex(*simplex_tree, max_alpha_square);
-    simplex_tree->initialize_filtration();
   }
 
  private:
diff --git a/src/python/include/Euclidean_strong_witness_complex_interface.h b/src/python/include/Euclidean_strong_witness_complex_interface.h
index c1c72737..f94c51ef 100644
--- a/src/python/include/Euclidean_strong_witness_complex_interface.h
+++ b/src/python/include/Euclidean_strong_witness_complex_interface.h
@@ -50,12 +50,10 @@ class Euclidean_strong_witness_complex_interface {
   void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square,
                            std::size_t limit_dimension) {
     witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension);
-    simplex_tree->initialize_filtration();
   }
 
   void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square) {
     witness_complex_->create_complex(*simplex_tree, max_alpha_square);
-    simplex_tree->initialize_filtration();
   }
 
   std::vector<double> get_point(unsigned vh) {
diff --git a/src/python/include/Euclidean_witness_complex_interface.h b/src/python/include/Euclidean_witness_complex_interface.h
index 5d7dbdc2..4411ae79 100644
--- a/src/python/include/Euclidean_witness_complex_interface.h
+++ b/src/python/include/Euclidean_witness_complex_interface.h
@@ -49,12 +49,10 @@ class Euclidean_witness_complex_interface {
 
   void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square, std::size_t limit_dimension) {
     witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension);
-    simplex_tree->initialize_filtration();
   }
 
   void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square) {
     witness_complex_->create_complex(*simplex_tree, max_alpha_square);
-    simplex_tree->initialize_filtration();
   }
 
   std::vector<double> get_point(unsigned vh) {
diff --git a/src/python/include/Nerve_gic_interface.h b/src/python/include/Nerve_gic_interface.h
index 5e7f8ae6..ab14c318 100644
--- a/src/python/include/Nerve_gic_interface.h
+++ b/src/python/include/Nerve_gic_interface.h
@@ -29,7 +29,6 @@ class Nerve_gic_interface : public Cover_complex<std::vector<double>> {
  public:
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree) {
     create_complex(*simplex_tree);
-    simplex_tree->initialize_filtration();
   }
   void set_cover_from_Euclidean_Voronoi(int m) {
     set_cover_from_Voronoi(Gudhi::Euclidean_distance(), m);
diff --git a/src/python/include/Rips_complex_interface.h b/src/python/include/Rips_complex_interface.h
index a66b0e5b..d98b0226 100644
--- a/src/python/include/Rips_complex_interface.h
+++ b/src/python/include/Rips_complex_interface.h
@@ -53,7 +53,6 @@ class Rips_complex_interface {
       rips_complex_->create_complex(*simplex_tree, dim_max);
     else
       sparse_rips_complex_->create_complex(*simplex_tree, dim_max);
-    simplex_tree->initialize_filtration();
   }
 
  private:
diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index 1a18aed6..5b456baa 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -43,16 +43,19 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
 
   Extended_filtration_data efd;
   
-  bool find_simplex(const Simplex& vh) {
-    return (Base::find(vh) != Base::null_simplex());
+  bool find_simplex(const Simplex& simplex) {
+    return (Base::find(simplex) != Base::null_simplex());
   }
 
-  void assign_simplex_filtration(const Simplex& vh, Filtration_value filtration) {
-    Base::assign_filtration(Base::find(vh), filtration);
+  void assign_simplex_filtration(const Simplex& simplex, Filtration_value filtration) {
+    Base::assign_filtration(Base::find(simplex), filtration);
+    Base::clear_filtration();
   }
 
   bool insert(const Simplex& simplex, Filtration_value filtration = 0) {
     Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration);
+    if (result.first != Base::null_simplex())
+      Base::clear_filtration();
     return (result.second);
   }
 
@@ -86,7 +89,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
 
   void remove_maximal_simplex(const Simplex& simplex) {
     Base::remove_maximal_simplex(Base::find(simplex));
-    Base::initialize_filtration();
+    Base::clear_filtration();
   }
 
   Simplex_and_filtration get_simplex_and_filtration(Simplex_handle f_simplex) {
@@ -123,7 +126,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
 
   void compute_extended_filtration() {
     this->efd = this->extend_filtration();
-    this->initialize_filtration();
     return;
   }
 
@@ -158,7 +160,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   }
 
   void create_persistence(Gudhi::Persistent_cohomology_interface<Base>* pcoh) {
-    Base::initialize_filtration();
     pcoh = new Gudhi::Persistent_cohomology_interface<Base>(*this);
   }
 
diff --git a/src/python/include/Strong_witness_complex_interface.h b/src/python/include/Strong_witness_complex_interface.h
index cda5b514..e9ab0c7b 100644
--- a/src/python/include/Strong_witness_complex_interface.h
+++ b/src/python/include/Strong_witness_complex_interface.h
@@ -41,13 +41,11 @@ class Strong_witness_complex_interface {
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double  max_alpha_square,
                            std::size_t limit_dimension) {
     witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension);
-    simplex_tree->initialize_filtration();
   }
 
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree,
                            double  max_alpha_square) {
     witness_complex_->create_complex(*simplex_tree, max_alpha_square);
-    simplex_tree->initialize_filtration();
   }
 
  private:
diff --git a/src/python/include/Tangential_complex_interface.h b/src/python/include/Tangential_complex_interface.h
index 698226cc..b1afce94 100644
--- a/src/python/include/Tangential_complex_interface.h
+++ b/src/python/include/Tangential_complex_interface.h
@@ -90,7 +90,6 @@ class Tangential_complex_interface {
 
   void create_simplex_tree(Simplex_tree<>* simplex_tree) {
     tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(*simplex_tree);
-    simplex_tree->initialize_filtration();
   }
 
   void set_max_squared_edge_length(double max_squared_edge_length) {
diff --git a/src/python/include/Witness_complex_interface.h b/src/python/include/Witness_complex_interface.h
index 45e14253..76947e53 100644
--- a/src/python/include/Witness_complex_interface.h
+++ b/src/python/include/Witness_complex_interface.h
@@ -41,13 +41,11 @@ class Witness_complex_interface {
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double  max_alpha_square,
                            std::size_t limit_dimension) {
     witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension);
-    simplex_tree->initialize_filtration();
   }
 
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree,
                            double  max_alpha_square) {
     witness_complex_->create_complex(*simplex_tree, max_alpha_square);
-    simplex_tree->initialize_filtration();
   }
 
  private:
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 70b26e97..2137d822 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -46,7 +46,6 @@ def test_insertion():
     assert st.find([2, 3]) == False
 
     # filtration test
-    st.initialize_filtration()
     assert st.filtration([0, 1, 2]) == 4.0
     assert st.filtration([0, 2]) == 4.0
     assert st.filtration([1, 2]) == 4.0
@@ -93,7 +92,6 @@ def test_insertion():
     assert st.find([1]) == True
     assert st.find([2]) == True
 
-    st.initialize_filtration()
     assert st.persistence(persistence_dim_max=True) == [
         (1, (4.0, float("inf"))),
         (0, (0.0, float("inf"))),
@@ -151,7 +149,6 @@ def test_expansion():
     st.expansion(3)
     assert st.num_vertices() == 7
     assert st.num_simplices() == 22
-    st.initialize_filtration()
 
     assert list(st.get_filtration()) == [
         ([2], 0.1),