def test_simplex_tree_deep_copy():
st = SimplexTree()
st.insert([1, 2, 3], 0.)
# compute persistence only on the original
st.compute_persistence()
st_copy = st.copy()
assert st_copy == st
st_filt_list = list(st.get_filtration())
# check persistence is not copied
assert st.__is_persistence_defined() == True
assert st_copy.__is_persistence_defined() == False
# remove something in the copy and check the copy is included in the original
st_copy.remove_maximal_simplex([1, 2, 3])
a_filt_list = list(st_copy.get_filtration())
assert len(a_filt_list) < len(st_filt_list)
for a_splx in a_filt_list:
assert a_splx in st_filt_list
# test double free
del st
del st_copy
def create_simplex_from_graph(G):
st = SimplexTree()
node_values = nx.get_node_attributes(G, "intensity")
print("node intensities", node_values)
for clique in nx.enumerate_all_cliques(G):
clique_value = node_values[clique[0]]
for n in clique:
# take max values
if clique_value < node_values[n]:
clique_value = node_values[n]
st.insert(clique, clique_value)
return st
def test_equality_operator():
st1 = SimplexTree()
st2 = SimplexTree()
assert st1 == st2
st1.insert([1, 2, 3], 4.)
assert st1 != st2
st2.insert([1, 2, 3], 4.)
assert st1 == st2
def tograph2(cplx: gd.SimplexTree):
graph = nx.Graph()
simplices = cplx.get_filtration()
for (simplex, filtration) in simplices:
if len(simplex) == 2:
#print("hei")
#print(simplex)
graph.add_nodes_from(simplex)
graph.add_edge(simplex[0], simplex[1])
return graph
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
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]
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 toGraph(cplx: gd.SimplexTree, capDict: dict, vertexName: dict):
# Initializes output graph
graph = nx.Graph()
# Gets list of simplices
simplices = cplx.get_filtration()
# Adds 1 simplices with labels from the dictionary
for (simplex, filtration) in simplices:
if len(simplex) == 1:
graph.add_node(str(vertexName[simplex[0]]))
# Adds 2-simplices to graph
for (simplex, filtration) in simplices:
if len(simplex) == 2:
graph.add_edge(str(vertexName[simplex[0]]),
str(vertexName[simplex[1]]),
capacity=capDict[tuple(simplex)])
return graph
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_simplex_tree_constructor_exception():
with pytest.raises(TypeError):
st = SimplexTree(
other="Construction from a string shall raise an exception")
def test_collapse_edges():
st = SimplexTree()
assert st.insert([0, 1], filtration=1.0) == True
assert st.insert([1, 2], filtration=1.0) == True
assert st.insert([2, 3], filtration=1.0) == True
assert st.insert([0, 3], filtration=1.0) == True
assert st.insert([0, 2], filtration=2.0) == True
assert st.insert([1, 3], filtration=2.0) == True
assert st.num_simplices() == 10
st.collapse_edges()
assert st.num_simplices() == 9
assert st.find([1, 3]) == False
for simplex in st.get_skeleton(0):
assert simplex[1] == 1.
def test_persistence_intervals_in_dimension():
# Here is our triangulation of a 2-torus - taken from https://dioscuri-tda.org/Paris_TDA_Tutorial_2021.html
# 0-----3-----4-----0
# | \ | \ | \ | \ |
# | \ | \ | \| \ |
# 1-----8-----7-----1
# | \ | \ | \ | \ |
# | \ | \ | \ | \ |
# 2-----5-----6-----2
# | \ | \ | \ | \ |
# | \ | \ | \ | \ |
# 0-----3-----4-----0
st = SimplexTree()
st.insert([0, 1, 8])
st.insert([0, 3, 8])
st.insert([3, 7, 8])
st.insert([3, 4, 7])
st.insert([1, 4, 7])
st.insert([0, 1, 4])
st.insert([1, 2, 5])
st.insert([1, 5, 8])
st.insert([5, 6, 8])
st.insert([6, 7, 8])
st.insert([2, 6, 7])
st.insert([1, 2, 7])
st.insert([0, 2, 3])
st.insert([2, 3, 5])
st.insert([3, 4, 5])
st.insert([4, 5, 6])
st.insert([0, 4, 6])
st.insert([0, 2, 6])
st.compute_persistence(persistence_dim_max=True)
H0 = st.persistence_intervals_in_dimension(0)
assert np.array_equal(H0, np.array([[0., float("inf")]]))
H1 = st.persistence_intervals_in_dimension(1)
assert np.array_equal(H1, np.array([[0., float("inf")], [0.,
float("inf")]]))
H2 = st.persistence_intervals_in_dimension(2)
assert np.array_equal(H2, np.array([[0., float("inf")]]))
# Test empty case
assert st.persistence_intervals_in_dimension(3).shape == (0, 2)
def test_reset_filtration():
st = SimplexTree()
assert st.insert([0, 1, 2], 3.) == True
assert st.insert([0, 3], 2.) == True
assert st.insert([3, 4, 5], 3.) == True
assert st.insert([0, 1, 6, 7], 4.) == True
# Guaranteed by construction
for simplex in st.get_simplices():
assert st.filtration(simplex[0]) >= 2.
# dimension until 5 even if simplex tree is of dimension 3 to test the limits
for dimension in range(5, -1, -1):
st.reset_filtration(0., dimension)
for simplex in st.get_skeleton(3):
print(simplex)
if len(simplex[0]) < (dimension) + 1:
assert st.filtration(simplex[0]) >= 2.
else:
assert st.filtration(simplex[0]) == 0.
def test_collapse_edges():
st = SimplexTree()
assert st.insert([0, 1], filtration=1.0) == True
assert st.insert([1, 2], filtration=1.0) == True
assert st.insert([2, 3], filtration=1.0) == True
assert st.insert([0, 3], filtration=1.0) == True
assert st.insert([0, 2], filtration=2.0) == True
assert st.insert([1, 3], filtration=2.0) == True
assert st.num_simplices() == 10
if __GUDHI_USE_EIGEN3:
st.collapse_edges()
assert st.num_simplices() == 9
assert st.find([1, 3]) == False
for simplex in st.get_skeleton(0):
assert simplex[1] == 1.
else:
# If no Eigen3, collapse_edges throws an exception
with pytest.raises(RuntimeError):
st.collapse_edges()
def test_extend_filtration():
# Inserted simplex:
# 5 4
# o o
# / \ /
# o o
# /2\ /3
# o o
# 1 0
st = SimplexTree()
st.insert([0, 2])
st.insert([1, 2])
st.insert([0, 3])
st.insert([2, 5])
st.insert([3, 4])
st.insert([3, 5])
st.assign_filtration([0], 1.)
st.assign_filtration([1], 2.)
st.assign_filtration([2], 3.)
st.assign_filtration([3], 4.)
st.assign_filtration([4], 5.)
st.assign_filtration([5], 6.)
assert list(st.get_filtration()) == [([0, 2], 0.0), ([1, 2], 0.0),
([0, 3], 0.0), ([3, 4], 0.0),
([2, 5], 0.0), ([3, 5], 0.0),
([0], 1.0), ([1], 2.0), ([2], 3.0),
([3], 4.0), ([4], 5.0), ([5], 6.0)]
st.extend_filtration()
assert list(st.get_filtration()) == [([6], -3.0), ([0], -2.0), ([1], -1.8),
([2], -1.6), ([0, 2], -1.6),
([1, 2], -1.6), ([3], -1.4),
([0, 3], -1.4), ([4], -1.2),
([3, 4], -1.2), ([5], -1.0),
([2, 5], -1.0), ([3, 5], -1.0),
([5, 6], 1.0), ([4, 6], 1.2),
([3, 6], 1.4), ([3, 4, 6], 1.4),
([3, 5, 6], 1.4), ([2, 6], 1.6),
([2, 5, 6], 1.6), ([1, 6], 1.8),
([1, 2, 6], 1.8), ([0, 6], 2.0),
([0, 2, 6], 2.0), ([0, 3, 6], 2.0)]
dgms = st.extended_persistence(min_persistence=-1.)
assert dgms[0][0][1][0] == pytest.approx(2.)
assert dgms[0][0][1][1] == pytest.approx(3.)
assert dgms[1][0][1][0] == pytest.approx(5.)
assert dgms[1][0][1][1] == pytest.approx(4.)
assert dgms[2][0][1][0] == pytest.approx(1.)
assert dgms[2][0][1][1] == pytest.approx(6.)
assert dgms[3][0][1][0] == pytest.approx(6.)
assert dgms[3][0][1][1] == pytest.approx(1.)
def test_make_filtration_non_decreasing():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# Inserted simplex:
# 1
# o
# /X\
# o---o---o---o
# 2 0 3\X/4
# o
# 5
assert st.insert([2, 1, 0], filtration=2.0) == True
assert st.insert([3, 0], filtration=2.0) == True
assert st.insert([3, 4, 5], filtration=2.0) == True
assert st.make_filtration_non_decreasing() == False
# Because of non decreasing property of simplex tree, { 0 } , { 1 } and
# { 0, 1 } are going to be set from value 2.0 to 1.0
st.insert([0, 1, 6, 7], filtration=1.0)
assert st.make_filtration_non_decreasing() == False
# Modify specific values to test make_filtration_non_decreasing
st.assign_filtration([0, 1, 6, 7], 0.8)
st.assign_filtration([0, 1, 6], 0.9)
st.assign_filtration([0, 6], 0.6)
st.assign_filtration([3, 4, 5], 1.2)
st.assign_filtration([3, 4], 1.1)
st.assign_filtration([4, 5], 1.99)
assert st.make_filtration_non_decreasing() == True
assert st.filtration([0, 1, 6, 7]) == 1.0
assert st.filtration([0, 1, 6]) == 1.0
assert st.filtration([0, 1]) == 1.0
assert st.filtration([0]) == 1.0
assert st.filtration([1]) == 1.0
assert st.filtration([3, 4, 5]) == 2.0
assert st.filtration([3, 4]) == 2.0
assert st.filtration([4, 5]) == 2.0
def test_insertion():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# insert test
assert st.insert([0, 1]) == True
assert st.dimension() == 1
assert st.insert([0, 1, 2], filtration=4.0) == True
assert st.dimension() == 2
assert st.num_simplices() == 7
assert st.num_vertices() == 3
# find test
assert st.find([0, 1, 2]) == True
assert st.find([0, 1]) == True
assert st.find([0, 2]) == True
assert st.find([0]) == True
assert st.find([1]) == True
assert st.find([2]) == True
assert st.find([3]) == False
assert st.find([0, 3]) == False
assert st.find([1, 3]) == False
assert st.find([2, 3]) == False
# filtration test
assert st.filtration([0, 1, 2]) == 4.0
assert st.filtration([0, 2]) == 4.0
assert st.filtration([1, 2]) == 4.0
assert st.filtration([2]) == 4.0
assert st.filtration([0, 1]) == 0.0
assert st.filtration([0]) == 0.0
assert st.filtration([1]) == 0.0
# skeleton test
assert list(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 list(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 list(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 list(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
assert st.find([0, 1]) == True
assert st.find([0, 2]) == True
assert st.find([0]) == True
assert st.find([1]) == True
assert st.find([2]) == True
assert st.persistence(persistence_dim_max=True) == [
(1, (4.0, float("inf"))),
(0, (0.0, float("inf"))),
]
assert st.__is_persistence_defined() == True
assert st.betti_numbers() == [1, 1]
assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0]
assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0]
assert st.persistent_betti_numbers(3.9, 10000.0) == [1, 0]
assert st.persistent_betti_numbers(4.0, 10000.0) == [1, 1]
assert st.persistent_betti_numbers(9999.0, 10000.0) == [1, 1]
def test_automatic_dimension():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# insert test
assert st.insert([0, 1, 3], filtration=0.5) == True
assert st.insert([0, 1, 2], filtration=1.0) == True
assert st.num_vertices() == 4
assert st.num_simplices() == 11
assert st.dimension() == 2
assert st.upper_bound_dimension() == 2
assert st.prune_above_filtration(0.6) == True
assert st.dimension() == 2
assert st.upper_bound_dimension() == 2
st.assign_filtration([0, 1, 3], 0.7)
assert st.filtration([0, 1, 3]) == 0.7
st.remove_maximal_simplex([0, 1, 3])
assert st.upper_bound_dimension() == 2
assert st.dimension() == 1
assert st.upper_bound_dimension() == 1
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),
]