From 202bf9722358355c12e85c0718da567ce9d9a6ae Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Sat, 1 Apr 2017 09:36:35 +0000 Subject: 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 --- src/cython/cython/simplex_tree.pyx | 46 +++++++++------------- src/cython/doc/alpha_complex_user.rst | 4 +- src/cython/doc/rips_complex_user.rst | 8 ++-- src/cython/doc/simplex_tree_user.rst | 6 +-- src/cython/doc/tangential_complex_user.rst | 2 +- .../example/alpha_complex_from_points_example.py | 2 +- .../example/rips_complex_from_points_example.py | 2 +- src/cython/example/simplex_tree_example.py | 6 +-- src/cython/include/Simplex_tree_interface.h | 16 ++++---- src/cython/test/test_alpha_complex.py | 4 +- src/cython/test/test_euclidean_witness_complex.py | 6 +-- src/cython/test/test_rips_complex.py | 4 +- src/cython/test/test_simplex_tree.py | 15 ++++--- src/cython/test/test_tangential_complex.py | 2 +- 14 files changed, 57 insertions(+), 66 deletions(-) (limited to 'src/cython') 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, 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(dimension) + cdef vector[pair[vector[int], double]] skeletons \ + = self.thisptr.get_skeleton(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 { 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)] -- cgit v1.2.3