def test_simplex_tree_deep_copy_constructor():
st = SimplexTree()
st.insert([1, 2, 3], 0.)
# compute persistence only on the original
st.compute_persistence()
st_copy = SimplexTree(st)
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 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 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 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 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),
]