remove bad named *_tree() functions

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2300 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 512403fe0838fb2691e0af94c55772bff942b740

14 files changed, 57 insertions, 66 deletions

diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index d26a1a93..9d40a8b5 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -46,8 +46,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         bint find_simplex(vector[int] simplex)
         bint insert_simplex_and_subfaces(vector[int] simplex,
                                          double filtration)
-        vector[pair[vector[int], double]] get_filtered_tree()
-        vector[pair[vector[int], double]] get_skeleton_tree(int dimension)
+        vector[pair[vector[int], double]] get_filtration()
+        vector[pair[vector[int], double]] get_skeleton(int dimension)
         vector[pair[vector[int], double]] get_star(vector[int] simplex)
         vector[pair[vector[int], double]] get_cofaces(vector[int] simplex,
                                                           int dimension)
@@ -102,14 +102,6 @@ cdef class SimplexTree:
          """
         return self.pcohptr != NULL
 
-    def get_filtration(self):
-        """This function returns the main simplicial complex filtration value.
-
-        :returns:  The simplicial complex filtration value.
-        :rtype:  float
-        """
-        return self.thisptr.filtration()
-
     def filtration(self, simplex):
         """This function returns the simplicial complex filtration value for a
         given N-simplex.
@@ -136,7 +128,7 @@ cdef class SimplexTree:
         .. note::
 
             This function must be launched before persistence, betti_numbers,
-            persistent_betti_numbers or get_filtered_tree after inserting or
+            persistent_betti_numbers or get_filtration after inserting or
             removing simplices.
         """
         self.thisptr.initialize_filtration()
@@ -214,36 +206,36 @@ cdef class SimplexTree:
         return self.thisptr.insert_simplex_and_subfaces(complex,
                                                         <double>filtration)
 
-    def get_filtered_tree(self):
-        """This function returns the tree sorted by increasing filtration
-        values.
+    def get_filtration(self):
+        """This function returns a list of all simplices with their given
+        filtration values.
 
-        :returns:  The tree sorted by increasing filtration values.
+        :returns:  The simplices sorted by increasing filtration values.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[pair[vector[int], double]] filtered_tree \
-            = self.thisptr.get_filtered_tree()
+        cdef vector[pair[vector[int], double]] filtration \
+            = self.thisptr.get_filtration()
         ct = []
-        for filtered_complex in filtered_tree:
+        for filtered_complex in filtration:
             v = []
             for vertex in filtered_complex.first:
                 v.append(vertex)
             ct.append((v, filtered_complex.second))
         return ct
 
-    def get_skeleton_tree(self, dimension):
-        """This function returns the tree skeleton of a maximum given
-        dimension.
+    def get_skeleton(self, dimension):
+        """This function returns the (simplices of the) skeleton of a maximum
+        given dimension.
 
         :param dimension: The skeleton dimension value.
         :type dimension: int.
-        :returns:  The skeleton tree of a maximum dimension.
+        :returns:  The (simplices of the) skeleton of a maximum dimension.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[pair[vector[int], double]] sk_tree \
-            = self.thisptr.get_skeleton_tree(<int>dimension)
+        cdef vector[pair[vector[int], double]] skeletons \
+            = self.thisptr.get_skeleton(<int>dimension)
         ct = []
-        for filtered_complex in sk_tree:
+        for filtered_complex in skeletons:
             v = []
             for vertex in filtered_complex.first:
                 v.append(vertex)
@@ -255,7 +247,7 @@ cdef class SimplexTree:
 
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
-        :returns:  The star tree of a simplex.
+        :returns:  The (simplices of the) star of a simplex.
         :rtype:  list of tuples(simplex, filtration)
         """
         cdef vector[int] complex
@@ -280,7 +272,7 @@ cdef class SimplexTree:
         :param codimension: The codimension. If codimension = 0, all cofaces
             are returned (equivalent of get_star function)
         :type codimension: int.
-        :returns:  The coface tree of a simplex.
+        :returns:  The (simplices of the) cofaces of a simplex
         :rtype:  list of tuples(simplex, filtration)
         """
         cdef vector[int] complex
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
index 68e53a77..2356944d 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -30,7 +30,7 @@ This example builds the Delaunay triangulation from the given points, and initia
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 The output is:
@@ -164,7 +164,7 @@ Then, it is asked to display information about the alpha complex:
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 the program output is:
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index 027c3bf7..c89409a0 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -60,7 +60,7 @@ Finally, it is asked to display information about the simplicial complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 When launching (Rips maximal distance between 2 points is 12.0, is expanded
@@ -107,7 +107,7 @@ Finally, it is asked to display information about the Rips complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 the program output is:
@@ -162,7 +162,7 @@ Finally, it is asked to display information about the simplicial complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 When launching (Rips maximal distance between 2 points is 12.0, is expanded
@@ -209,7 +209,7 @@ Finally, it is asked to display information about the Rips complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 the program output is:
diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst
index c4e4c1b5..b2efca8b 100644
--- a/src/cython/doc/simplex_tree_user.rst
+++ b/src/cython/doc/simplex_tree_user.rst
@@ -45,8 +45,8 @@ Example
    print(result_str)
    result_str = 'num_simplices=' + repr(st.num_simplices())
    print(result_str)
-   print("skeleton_tree(2) =")
-   for sk_value in st.get_skeleton_tree(2):
+   print("skeleton(2) =")
+   for sk_value in st.get_skeleton(2):
        print(sk_value)
 
 
@@ -59,7 +59,7 @@ The output is:
     [0, 1] found
     num_vertices=3
     num_simplices=7
-    skeleton_tree(2) =
+    skeleton(2) =
     ([0, 1, 2], 4.0)
     ([0, 1], 0.0)
     ([0, 2], 4.0)
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index 6a7e6e41..24f68f85 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -133,7 +133,7 @@ This example builds the Tangential complex of point set read in an OFF file.
         ' - ' + repr(st.num_simplices()) + ' simplices - ' + \
         repr(st.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in st.get_filtered_tree():
+    for filtered_value in st.get_filtration():
         print(filtered_value)
 
 The output is:
diff --git a/src/cython/example/alpha_complex_from_points_example.py b/src/cython/example/alpha_complex_from_points_example.py
index 688edb65..7d6278ce 100755
--- a/src/cython/example/alpha_complex_from_points_example.py
+++ b/src/cython/example/alpha_complex_from_points_example.py
@@ -59,7 +59,7 @@ else:
     print("[4] Not found...")
 
 print("dimension=", simplex_tree.dimension())
-print("filtered_tree=", simplex_tree.get_filtered_tree())
+print("filtrations=", simplex_tree.get_filtration())
 print("star([0])=", simplex_tree.get_star([0]))
 print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1))
 
diff --git a/src/cython/example/rips_complex_from_points_example.py b/src/cython/example/rips_complex_from_points_example.py
index 9b7fc79d..5d411b1a 100755
--- a/src/cython/example/rips_complex_from_points_example.py
+++ b/src/cython/example/rips_complex_from_points_example.py
@@ -35,6 +35,6 @@ rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]],
 
 simplex_tree = rips.create_simplex_tree(max_dimension=1)
 
-print("filtered_tree=", simplex_tree.get_filtered_tree())
+print("filtrations=", simplex_tree.get_filtration())
 print("star([0])=", simplex_tree.get_star([0]))
 print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1))
diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py
index bf5f17a2..3af20fcf 100755
--- a/src/cython/example/simplex_tree_example.py
+++ b/src/cython/example/simplex_tree_example.py
@@ -61,6 +61,6 @@ print("filtration[4, 2]=", st.filtration([4, 2]))
 print("num_simplices=", st.num_simplices())
 print("num_vertices=", st.num_vertices())
 
-print("skeleton_tree[2]=", st.get_skeleton_tree(2))
-print("skeleton_tree[1]=", st.get_skeleton_tree(1))
-print("skeleton_tree[0]=", st.get_skeleton_tree(0))
+print("skeleton[2]=", st.get_skeleton(2))
+print("skeleton[1]=", st.get_skeleton(1))
+print("skeleton[0]=", st.get_skeleton(0))
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index 6bdf7830..45ce1916 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -90,29 +90,29 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     Base::initialize_filtration();
   }
 
-  Complex get_filtered_tree() {
+  Complex get_filtration() {
     Base::initialize_filtration();
-    Complex filtered_tree;
+    Complex filtrations;
     for (auto f_simplex : Base::filtration_simplex_range()) {
       Simplex simplex;
       for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
         simplex.insert(simplex.begin(), vertex);
       }
-      filtered_tree.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
+      filtrations.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
     }
-    return filtered_tree;
+    return filtrations;
   }
 
-  Complex get_skeleton_tree(int dimension) {
-    Complex skeleton_tree;
+  Complex get_skeleton(int dimension) {
+    Complex skeletons;
     for (auto f_simplex : Base::skeleton_simplex_range(dimension)) {
       Simplex simplex;
       for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
         simplex.insert(simplex.begin(), vertex);
       }
-      skeleton_tree.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
+      skeletons.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
     }
-    return skeleton_tree;
+    return skeletons;
   }
 
   Complex get_star(const Simplex& simplex) {
diff --git a/src/cython/test/test_alpha_complex.py b/src/cython/test/test_alpha_complex.py
index 2625d529..2c76d9d7 100755
--- a/src/cython/test/test_alpha_complex.py
+++ b/src/cython/test/test_alpha_complex.py
@@ -42,7 +42,7 @@ def test_infinite_alpha():
     assert simplex_tree.num_simplices() == 11
     assert simplex_tree.num_vertices() == 4
  
-    assert simplex_tree.get_filtered_tree() == \
+    assert simplex_tree.get_filtration() == \
            [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
             ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25),
             ([2, 3], 0.25), ([1, 2], 0.5), ([0, 1, 2], 0.5),
@@ -76,7 +76,7 @@ def test_filtered_alpha():
     assert filtered_alpha.get_point(4) == []
     assert filtered_alpha.get_point(125) == []
 
-    assert simplex_tree.get_filtered_tree() == \
+    assert simplex_tree.get_filtration() == \
            [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
             ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25),
             ([2, 3], 0.25)]
diff --git a/src/cython/test/test_euclidean_witness_complex.py b/src/cython/test/test_euclidean_witness_complex.py
index 0947cc09..737f1ef4 100755
--- a/src/cython/test/test_euclidean_witness_complex.py
+++ b/src/cython/test/test_euclidean_witness_complex.py
@@ -42,7 +42,7 @@ def test_witness_complex():
     assert landmarks[1] == euclidean_witness_complex.get_point(1)
     assert landmarks[2] == euclidean_witness_complex.get_point(2)
 
-    assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0),
+    assert simplex_tree.get_filtration() == [([0], 0.0), ([1], 0.0),
         ([0, 1], 0.0), ([2], 0.0), ([0, 2], 0.0), ([1, 2], 0.0),
         ([0, 1, 2], 0.0)]
 
@@ -61,11 +61,11 @@ def test_strong_witness_complex():
     assert landmarks[1] == euclidean_strong_witness_complex.get_point(1)
     assert landmarks[2] == euclidean_strong_witness_complex.get_point(2)
 
-    assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0), ([2], 0.0)]
+    assert simplex_tree.get_filtration() == [([0], 0.0), ([1], 0.0), ([2], 0.0)]
 
     simplex_tree = euclidean_strong_witness_complex.create_simplex_tree(max_alpha_square=100.0)
 
-    assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0),
+    assert simplex_tree.get_filtration() == [([0], 0.0), ([1], 0.0),
     ([2], 0.0), ([1, 2], 15.0), ([0, 2], 34.0), ([0, 1], 37.0),
     ([0, 1, 2], 37.0)]
 
diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py
index 286a645b..c7d2ead4 100755
--- a/src/cython/test/test_rips_complex.py
+++ b/src/cython/test/test_rips_complex.py
@@ -44,7 +44,7 @@ def test_rips_from_points():
     assert simplex_tree.num_simplices() == 10
     assert simplex_tree.num_vertices() == 4
 
-    assert simplex_tree.get_filtered_tree() == \
+    assert simplex_tree.get_filtration() == \
            [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
             ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0),
             ([2, 3], 1.0), ([1, 2], 1.4142135623730951),
@@ -83,7 +83,7 @@ def test_rips_from_distance_matrix():
     assert simplex_tree.num_simplices() == 10
     assert simplex_tree.num_vertices() == 4
 
-    assert simplex_tree.get_filtered_tree() == \
+    assert simplex_tree.get_filtration() == \
            [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
             ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0),
             ([2, 3], 1.0), ([1, 2], 1.4142135623730951),
diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
index db61f84c..3ae537e3 100755
--- a/src/cython/test/test_simplex_tree.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -55,7 +55,6 @@ def test_insertion():
     # filtration test
     st.set_filtration(5.0)
     st.initialize_filtration()
-    assert st.get_filtration() == 5.0
     assert st.filtration([0, 1, 2]) == 4.0
     assert st.filtration([0, 2]) == 4.0
     assert st.filtration([1, 2]) == 4.0
@@ -64,20 +63,20 @@ def test_insertion():
     assert st.filtration([0]) == 0.0
     assert st.filtration([1]) == 0.0
 
-    # skeleton_tree test
-    assert st.get_skeleton_tree(2) == \
+    # skeleton test
+    assert st.get_skeleton(2) == \
         [([0, 1, 2], 4.0), ([0, 1], 0.0), ([0, 2], 4.0),
         ([0], 0.0), ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)]
-    assert st.get_skeleton_tree(1) == \
+    assert st.get_skeleton(1) == \
         [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0),
         ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)]
-    assert st.get_skeleton_tree(0) == \
+    assert st.get_skeleton(0) == \
         [([0], 0.0), ([1], 0.0), ([2], 4.0)]
 
     # remove_maximal_simplex test
     assert st.get_cofaces([0, 1, 2], 1) == []
     st.remove_maximal_simplex([0, 1, 2])
-    assert st.get_skeleton_tree(2) == \
+    assert st.get_skeleton(2) == \
         [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0),
         ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)]
     assert st.find([0, 1, 2]) == False
@@ -116,7 +115,7 @@ def test_expansion():
 
     assert st.num_vertices() == 7
     assert st.num_simplices() == 17
-    assert st.get_filtered_tree() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1),
+    assert st.get_filtration() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1),
     ([0], 0.2), ([0, 2], 0.2), ([1], 0.3), ([0, 1], 0.3), ([1, 3], 0.4),
     ([1, 2], 0.5), ([5], 0.6), ([6], 0.6), ([5, 6], 0.6), ([4], 0.7),
     ([2, 4], 0.7), ([0, 3], 0.8), ([4, 6], 0.9), ([3, 6], 1.0)]
@@ -126,7 +125,7 @@ def test_expansion():
     assert st.num_simplices() == 22
     st.initialize_filtration()
 
-    assert st.get_filtered_tree() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1),
+    assert st.get_filtration() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1),
     ([0], 0.2), ([0, 2], 0.2), ([1], 0.3), ([0, 1], 0.3), ([1, 3], 0.4),
     ([1, 2], 0.5), ([0, 1, 2], 0.5), ([1, 2, 3], 0.5), ([5], 0.6), ([6], 0.6),
     ([5, 6], 0.6), ([4], 0.7), ([2, 4], 0.7), ([0, 3], 0.8), ([0, 1, 3], 0.8),
diff --git a/src/cython/test/test_tangential_complex.py b/src/cython/test/test_tangential_complex.py
index c191baa4..8aa4023c 100755
--- a/src/cython/test/test_tangential_complex.py
+++ b/src/cython/test/test_tangential_complex.py
@@ -40,7 +40,7 @@ def test_tangential():
     assert st.num_simplices() == 6
     assert st.num_vertices() == 4
  
-    assert st.get_filtered_tree() == \
+    assert st.get_filtration() == \
         [([0], 0.0), ([1], 0.0), ([2], 0.0), ([0, 2], 0.0), ([3], 0.0), ([1, 3], 0.0)]
     assert st.get_cofaces([0], 1) == [([0, 2], 0.0)]