From 6ed2a97421a223b4ebe31b91f48d779c2209f470 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 16 Mar 2020 13:38:18 +0100 Subject: Add get_simplices method - contrary to get_filtration method, sort is not performed --- src/python/example/simplex_tree_example.py | 4 ++++ src/python/gudhi/simplex_tree.pxd | 8 ++++++++ src/python/gudhi/simplex_tree.pyx | 17 ++++++++++++++++- src/python/include/Simplex_tree_interface.h | 11 +++++++++++ src/python/test/test_simplex_tree.py | 12 ++++++++++++ 5 files changed, 51 insertions(+), 1 deletion(-) (limited to 'src/python') diff --git a/src/python/example/simplex_tree_example.py b/src/python/example/simplex_tree_example.py index 7f20c389..34833899 100755 --- a/src/python/example/simplex_tree_example.py +++ b/src/python/example/simplex_tree_example.py @@ -38,6 +38,10 @@ else: print("dimension=", st.dimension()) +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(): diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 66c173a6..82f155de 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -24,6 +24,12 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_simplex_handle "Gudhi::Simplex_tree_interface::Simplex_handle": pass + cdef cppclass Simplex_tree_simplices_iterator "Gudhi::Simplex_tree_interface::Complex_simplex_iterator": + Simplex_tree_simplices_iterator() + Simplex_tree_simplex_handle& operator*() + Simplex_tree_simplices_iterator operator++() + bint operator!=(Simplex_tree_simplices_iterator) + cdef cppclass Simplex_tree_skeleton_iterator "Gudhi::Simplex_tree_interface::Skeleton_simplex_iterator": Simplex_tree_skeleton_iterator() Simplex_tree_simplex_handle& operator*() @@ -53,6 +59,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": bool make_filtration_non_decreasing() # 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() + Simplex_tree_simplices_iterator get_simplices_iterator_end() vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_begin() vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_end() Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension) diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index efac2d80..c01cc905 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -208,10 +208,25 @@ cdef class SimplexTree: return self.get_ptr().insert_simplex_and_subfaces(csimplex, filtration) - def get_filtration(self): + def get_simplices(self): """This function returns a generator with simplices and their given filtration values. + :returns: The simplices. + :rtype: generator with tuples(simplex, filtration) + """ + cdef Simplex_tree_simplices_iterator it = self.get_ptr().get_simplices_iterator_begin() + cdef Simplex_tree_simplices_iterator end = self.get_ptr().get_simplices_iterator_end() + cdef Simplex_tree_simplex_handle sh = dereference(it) + + while it != end: + yield self.get_ptr().get_simplex_and_filtration(dereference(it)) + preincrement(it) + + def get_filtration(self): + """This function returns a generator with simplices and their given + filtration values sorted by increasing filtration values. + :returns: The simplices sorted by increasing filtration values. :rtype: generator with tuples(simplex, filtration) """ diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index 66ce5afd..4a7062d6 100644 --- a/src/python/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h @@ -36,6 +36,7 @@ class Simplex_tree_interface : public Simplex_tree { using Simplex_and_filtration = std::pair; using Filtered_simplices = std::vector; using Skeleton_simplex_iterator = typename Base::Skeleton_simplex_iterator; + using Complex_simplex_iterator = typename Base::Complex_simplex_iterator; public: bool find_simplex(const Simplex& vh) { @@ -122,6 +123,16 @@ class Simplex_tree_interface : public Simplex_tree { } // Iterator over the simplex tree + Complex_simplex_iterator get_simplices_iterator_begin() { + // this specific case works because the range is just a pair of iterators - won't work if range was a vector + return Base::complex_simplex_range().begin(); + } + + Complex_simplex_iterator get_simplices_iterator_end() { + // this specific case works because the range is just a pair of iterators - won't work if range was a vector + return Base::complex_simplex_range().end(); + } + typename std::vector::const_iterator get_filtration_iterator_begin() { // Base::initialize_filtration(); already performed in filtration_simplex_range // this specific case works because the range is just a pair of iterators - won't work if range was a vector diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 04b26e92..f7848379 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -249,3 +249,15 @@ def test_make_filtration_non_decreasing(): assert st.filtration([3, 4, 5]) == 2.0 assert st.filtration([3, 4]) == 2.0 assert st.filtration([4, 5]) == 2.0 + +def test_simplices_iterator(): + st = SimplexTree() + + assert st.insert([0, 1, 2], filtration=4.0) == True + assert st.insert([2, 3, 4], filtration=2.0) == True + + for simplex in st.get_simplices(): + print("simplex is: ", simplex[0]) + assert st.find(simplex[0]) == True + print("filtration is: ", simplex[1]) + assert st.filtration(simplex[0]) == simplex[1] -- cgit v1.2.3