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")