def make_gudhi_simplex_tree(points,
edges,
max_simplex_dim=2,
metric=chebyshev):
"""Returns the `gudhi.SimplexTree()` object containing
all simplices up to dimension `max_sim_dim`
Parameters
----------
points: list of list of floats
"""
sim_tree = SimplexTree()
vertices = list(range(len(points)))
for v in vertices:
sim_tree.insert(simplex=[v], filtration=0.0)
for e in edges:
p, q = points[e[0]], points[e[1]]
sim_tree.insert(simplex=e, filtration=metric(p, q))
sim_tree.expansion(max_simplex_dim)
return sim_tree
def create_simplex_tree(self, max_dimension):
"""
Args:
max_dimension (int): graph expansion until this given dimension.
"""
dist = self.distance_matrix
F = self.weights
num_pts = len(dist)
st = SimplexTree()
for i in range(num_pts):
if 2 * F[i] <= self.max_filtration:
st.insert([i], 2 * F[i])
for i in range(num_pts):
for j in range(i):
value = max(2 * F[i], 2 * F[j], dist[i][j] + F[i] + F[j])
# max is needed when F is not 1-Lipschitz
if value <= self.max_filtration:
st.insert([i, j], filtration=value)
st.expansion(max_dimension)
return st
def test_expansion():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# insert test
assert st.insert([3, 2], 0.1) == True
assert st.insert([2, 0], 0.2) == True
assert st.insert([1, 0], 0.3) == True
assert st.insert([3, 1], 0.4) == True
assert st.insert([2, 1], 0.5) == True
assert st.insert([6, 5], 0.6) == True
assert st.insert([4, 2], 0.7) == True
assert st.insert([3, 0], 0.8) == True
assert st.insert([6, 4], 0.9) == True
assert st.insert([6, 3], 1.0) == True
assert st.num_vertices() == 7
assert st.num_simplices() == 17
assert list(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),
]
st.expansion(3)
assert st.num_vertices() == 7
assert st.num_simplices() == 22
assert list(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),
([0, 2, 3], 0.8),
([0, 1, 2, 3], 0.8),
([4, 6], 0.9),
([3, 6], 1.0),
]