def test_cubical_cofaces_of_persistence_pairs_when_pd_has_no_paired_birth_and_death(
):
cubCpx = CubicalComplex(dimensions=[1, 2],
top_dimensional_cells=[0.0, 1.0])
Diag = cubCpx.persistence(homology_coeff_field=2, min_persistence=0)
pairs = cubCpx.cofaces_of_persistence_pairs()
assert pairs[0] == []
assert np.array_equal(pairs[1][0], np.array([0]))
def test_cubical_generators():
cub = CubicalComplex(top_dimensional_cells = [[0, 0, 0], [0, 1, 0], [0, 0, 0]])
cub.persistence()
g = cub.cofaces_of_persistence_pairs()
assert len(g[0]) == 2
assert len(g[1]) == 1
assert np.array_equal(g[0][0], np.empty(shape=[0,2]))
assert np.array_equal(g[0][1], np.array([[7, 4]]))
assert np.array_equal(g[1][0], np.array([8]))
def user_case_simple_constructor(cub):
assert cub.__is_defined() == True
assert cub.__is_persistence_defined() == False
assert cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))]
assert cub.__is_persistence_defined() == True
other_cub = CubicalComplex(
dimensions=[3, 3],
top_dimensional_cells=[1000.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
)
assert other_cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))]
def test_simple_constructor_from_numpy_array():
cub = CubicalComplex(
top_dimensional_cells=np.array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]])
)
simple_constructor(cub)
def test_user_case_simple_constructor_from_numpy_array():
cub = CubicalComplex(
top_dimensional_cells=np.array([[float("inf"), 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 0.0]])
)
user_case_simple_constructor(cub)
def simple_constructor(cub):
cub = CubicalComplex(dimensions=[3, 3],
top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9])
assert cub.__is_defined() == True
assert cub.__is_persistence_defined() == False
assert cub.persistence() == [(0, (1.0, float("inf")))]
assert cub.__is_persistence_defined() == True
assert cub.betti_numbers() == [1, 0, 0]
assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0]
def test_user_case_simple_constructor_from_top_cells():
cub = CubicalComplex(
dimensions=[3, 3],
top_dimensional_cells=[
float("inf"), 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0
],
)
user_case_simple_constructor(cub)
def compute_cubical(data, hdim, finite_persistence = True):
# compute filtration
filtration_values = data.flatten()
st = CubicalComplex(dimensions = data.shape,
top_dimensional_cells = filtration_values)
st.compute_persistence()
# compute pd from filtration
dgm = st.persistence_intervals_in_dimension(hdim)
if finite_persistence:
dgm = drop_inf_features(dgm)
return dgm
def test_dimension_file_constructor():
# Create test file
test_file = open("CubicalOneSphere.txt", "w")
test_file.write("2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n")
test_file.close()
cub = CubicalComplex(perseus_file="CubicalOneSphere.txt")
assert cub.__is_defined() == True
assert cub.__is_persistence_defined() == False
assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float("inf")))]
assert cub.__is_persistence_defined() == True
assert cub.betti_numbers() == [1, 0, 0]
assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0]
def test_cubical_persistence_intervals_in_dimension():
cub = CubicalComplex(
dimensions=[3, 3],
top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9],
)
cub.compute_persistence()
H0 = cub.persistence_intervals_in_dimension(0)
assert np.array_equal(H0, np.array([[1., float("inf")]]))
assert cub.persistence_intervals_in_dimension(1).shape == (0, 2)
def test_simple_constructor_from_top_cells():
cub = CubicalComplex(
dimensions=[3, 3],
top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9],
)
simple_constructor(cub)
def test_dimension_or_perseus_file_constructor():
# Create test file
test_file = open("CubicalOneSphere.txt", "w")
test_file.write("2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n")
test_file.close()
# CubicalComplex can be constructed from dimensions and
# top_dimensional_cells OR from a Perseus-style file name.
cub = CubicalComplex(
dimensions=[3, 3],
top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9],
perseus_file="CubicalOneSphere.txt",
)
assert cub.__is_defined() == False
assert cub.__is_persistence_defined() == False
cub = CubicalComplex(
top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9],
perseus_file="CubicalOneSphere.txt",
)
assert cub.__is_defined() == False
assert cub.__is_persistence_defined() == False
cub = CubicalComplex(dimensions=[3, 3],
perseus_file="CubicalOneSphere.txt")
assert cub.__is_defined() == False
assert cub.__is_persistence_defined() == False
def test_non_existing_perseus_file_constructor():
# Try to open a non existing file
cub = CubicalComplex(perseus_file="pouetpouettralala.toubiloubabdou")
assert cub.__is_defined() == False
assert cub.__is_persistence_defined() == False
def test_empty_constructor():
# Try to create an empty CubicalComplex
cub = CubicalComplex()
assert cub.__is_defined() == False
assert cub.__is_persistence_defined() == False
def test_connected_sublevel_sets():
array_cells = np.array([[3, 3], [2, 2], [4, 4]])
linear_cells = [3, 3, 2, 2, 4, 4]
dimensions = [2, 3]
periodic_dimensions = [False, False]
# with a numpy array version
cub = CubicalComplex(top_dimensional_cells=array_cells)
assert cub.persistence() == [(0, (2.0, float("inf")))]
assert cub.betti_numbers() == [1, 0, 0]
# with vector of dimensions
cub = CubicalComplex(dimensions=dimensions,
top_dimensional_cells=linear_cells)
assert cub.persistence() == [(0, (2.0, float("inf")))]
assert cub.betti_numbers() == [1, 0, 0]
# periodic with a numpy array version
cub = PeriodicCubicalComplex(top_dimensional_cells=array_cells,
periodic_dimensions=periodic_dimensions)
assert cub.persistence() == [(0, (2.0, float("inf")))]
assert cub.betti_numbers() == [1, 0, 0]
# periodic with vector of dimensions
cub = PeriodicCubicalComplex(dimensions=dimensions,
top_dimensional_cells=linear_cells,
periodic_dimensions=periodic_dimensions)
assert cub.persistence() == [(0, (2.0, float("inf")))]
assert cub.betti_numbers() == [1, 0, 0]
def test_non_existing_perseus_file_constructor():
# Try to open a non existing file
with pytest.raises(FileNotFoundError):
cub = CubicalComplex(perseus_file="pouetpouettralala.toubiloubabdou")
