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authorVincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com>2020-11-02 11:21:23 +0100
committerGitHub <noreply@github.com>2020-11-02 11:21:23 +0100
commit5900b2d802a7387f7fd4a87b5251dcbe6931371c (patch)
tree44fde353aa1e7c41e680c153182af0933b489487
parent6b995c03793096459a333c907b606770113b96d7 (diff)
parentaf5af2df409576035f2e31564f4048278d4f0f19 (diff)
Merge pull request #362 from VincentRouvreau/python_stree_boundaries
A fix proposal for boudaries of a simplex python version
-rw-r--r--src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h6
-rw-r--r--src/python/gudhi/simplex_tree.pxd7
-rw-r--r--src/python/gudhi/simplex_tree.pyx14
-rw-r--r--src/python/include/Simplex_tree_interface.h10
-rwxr-xr-xsrc/python/test/test_simplex_tree.py19
5 files changed, 56 insertions, 0 deletions
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
index 9007b6bd..ee64a277 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
@@ -85,6 +85,12 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
typedef typename SimplexTree::Vertex_handle Vertex_handle;
typedef typename SimplexTree::Siblings Siblings;
+ // For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is overwritten.
+ Simplex_tree_boundary_simplex_iterator()
+ : sib_(nullptr),
+ st_(nullptr) {
+ }
+
// any end() iterator
explicit Simplex_tree_boundary_simplex_iterator(SimplexTree * st)
: last_(st->null_vertex()),
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 3b494ba3..3c4cbed3 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -36,6 +36,12 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
Simplex_tree_skeleton_iterator operator++() nogil
bint operator!=(Simplex_tree_skeleton_iterator) nogil
+ cdef cppclass Simplex_tree_boundary_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Boundary_simplex_iterator":
+ Simplex_tree_boundary_iterator() nogil
+ Simplex_tree_simplex_handle& operator*() nogil
+ Simplex_tree_boundary_iterator operator++() nogil
+ bint operator!=(Simplex_tree_boundary_iterator) nogil
+
cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>":
Simplex_tree() nogil
@@ -67,6 +73,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_end() nogil
Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension) nogil
Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension) nogil
+ pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] get_boundary_iterators(vector[int] simplex) nogil except +
cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 910711a9..c671da56 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -285,6 +285,20 @@ cdef class SimplexTree:
ct.append((v, filtered_simplex.second))
return ct
+ def get_boundaries(self, simplex):
+ """This function returns a generator with the boundaries of a given N-simplex.
+
+ :param simplex: The N-simplex, represented by a list of vertex.
+ :type simplex: list of int.
+ :returns: The (simplices of the) boundary of a simplex
+ :rtype: generator with tuples(simplex, filtration)
+ """
+ cdef pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] it = self.get_ptr().get_boundary_iterators(simplex)
+
+ while it.first != it.second:
+ yield self.get_ptr().get_simplex_and_filtration(dereference(it.first))
+ preincrement(it.first)
+
def remove_maximal_simplex(self, simplex):
"""This function removes a given maximal N-simplex from the simplicial
complex.
diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index e288a8cf..baff3850 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -39,6 +39,7 @@ 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 Boundary_simplex_iterator = typename Base::Boundary_simplex_iterator;
public:
@@ -219,6 +220,15 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
// this specific case works because the range is just a pair of iterators - won't work if range was a vector
return Base::skeleton_simplex_range(dimension).end();
}
+
+ std::pair<Boundary_simplex_iterator, Boundary_simplex_iterator> get_boundary_iterators(const Simplex& simplex) {
+ auto bd_sh = Base::find(simplex);
+ if (bd_sh == Base::null_simplex())
+ throw std::runtime_error("simplex not found - cannot find boundaries");
+ // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+ auto boundary_srange = Base::boundary_simplex_range(bd_sh);
+ return std::make_pair(boundary_srange.begin(), boundary_srange.end());
+ }
};
} // namespace Gudhi
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index ac2b59c7..3b23fa0b 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -380,3 +380,22 @@ def test_reset_filtration():
assert st.filtration(simplex[0]) >= 2.
else:
assert st.filtration(simplex[0]) == 0.
+
+def test_boundaries_iterator():
+ st = SimplexTree()
+
+ assert st.insert([0, 1, 2, 3], filtration=1.0) == True
+ assert st.insert([1, 2, 3, 4], filtration=2.0) == True
+
+ assert list(st.get_boundaries([1, 2, 3])) == [([1, 2], 1.0), ([1, 3], 1.0), ([2, 3], 1.0)]
+ assert list(st.get_boundaries([2, 3, 4])) == [([2, 3], 1.0), ([2, 4], 2.0), ([3, 4], 2.0)]
+ assert list(st.get_boundaries([2])) == []
+
+ with pytest.raises(RuntimeError):
+ list(st.get_boundaries([]))
+
+ with pytest.raises(RuntimeError):
+ list(st.get_boundaries([0, 4])) # (0, 4) does not exist
+
+ with pytest.raises(RuntimeError):
+ list(st.get_boundaries([6])) # (6) does not exist