diff options
Diffstat (limited to 'src/cython/test')
| -rwxr-xr-x | src/cython/test/test_alpha_complex.py | 58 | ||||
| -rwxr-xr-x | src/cython/test/test_bottleneck_distance.py | 8 | ||||
| -rwxr-xr-x | src/cython/test/test_cover_complex.py | 59 | ||||
| -rwxr-xr-x | src/cython/test/test_cubical_complex.py | 59 | ||||
| -rwxr-xr-x | src/cython/test/test_euclidean_witness_complex.py | 68 | ||||
| -rwxr-xr-x | src/cython/test/test_reader_utils.py | 105 | ||||
| -rwxr-xr-x | src/cython/test/test_rips_complex.py | 92 | ||||
| -rwxr-xr-x | src/cython/test/test_simplex_tree.py | 133 | ||||
| -rwxr-xr-x | src/cython/test/test_subsampling.py | 140 | ||||
| -rwxr-xr-x | src/cython/test/test_tangential_complex.py | 16 | ||||
| -rwxr-xr-x | src/cython/test/test_witness_complex.py | 40 |
11 files changed, 524 insertions, 254 deletions
diff --git a/src/cython/test/test_alpha_complex.py b/src/cython/test/test_alpha_complex.py index a573115a..24f8bf53 100755 --- a/src/cython/test/test_alpha_complex.py +++ b/src/cython/test/test_alpha_complex.py @@ -16,9 +16,10 @@ __license__ = "MIT" def test_empty_alpha(): - alpha_complex = AlphaComplex(points=[[0,0]]) + alpha_complex = AlphaComplex(points=[[0, 0]]) assert alpha_complex.__is_defined() == True + def test_infinite_alpha(): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] alpha_complex = AlphaComplex(points=point_list) @@ -29,18 +30,28 @@ def test_infinite_alpha(): assert simplex_tree.num_simplices() == 11 assert simplex_tree.num_vertices() == 4 - - assert simplex_tree.get_filtration() == \ - [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0), - ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25), - ([2, 3], 0.25), ([1, 2], 0.5), ([0, 1, 2], 0.5), - ([1, 2, 3], 0.5)] - assert simplex_tree.get_star([0]) == \ - [([0], 0.0), ([0, 1], 0.25), ([0, 1, 2], 0.5), - ([0, 2], 0.25)] - assert simplex_tree.get_cofaces([0], 1) == \ - [([0, 1], 0.25), ([0, 2], 0.25)] - + + assert simplex_tree.get_filtration() == [ + ([0], 0.0), + ([1], 0.0), + ([2], 0.0), + ([3], 0.0), + ([0, 1], 0.25), + ([0, 2], 0.25), + ([1, 3], 0.25), + ([2, 3], 0.25), + ([1, 2], 0.5), + ([0, 1, 2], 0.5), + ([1, 2, 3], 0.5), + ] + assert simplex_tree.get_star([0]) == [ + ([0], 0.0), + ([0, 1], 0.25), + ([0, 1, 2], 0.5), + ([0, 2], 0.25), + ] + assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)] + assert point_list[0] == alpha_complex.get_point(0) assert point_list[1] == alpha_complex.get_point(1) assert point_list[2] == alpha_complex.get_point(2) @@ -48,6 +59,7 @@ def test_infinite_alpha(): assert alpha_complex.get_point(4) == [] assert alpha_complex.get_point(125) == [] + def test_filtered_alpha(): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] filtered_alpha = AlphaComplex(points=point_list) @@ -64,11 +76,15 @@ def test_filtered_alpha(): assert filtered_alpha.get_point(4) == [] assert filtered_alpha.get_point(125) == [] - assert simplex_tree.get_filtration() == \ - [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0), - ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25), - ([2, 3], 0.25)] - assert simplex_tree.get_star([0]) == \ - [([0], 0.0), ([0, 1], 0.25), ([0, 2], 0.25)] - assert simplex_tree.get_cofaces([0], 1) == \ - [([0, 1], 0.25), ([0, 2], 0.25)] + assert simplex_tree.get_filtration() == [ + ([0], 0.0), + ([1], 0.0), + ([2], 0.0), + ([3], 0.0), + ([0, 1], 0.25), + ([0, 2], 0.25), + ([1, 3], 0.25), + ([2, 3], 0.25), + ] + assert simplex_tree.get_star([0]) == [([0], 0.0), ([0, 1], 0.25), ([0, 2], 0.25)] + assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)] diff --git a/src/cython/test/test_bottleneck_distance.py b/src/cython/test/test_bottleneck_distance.py index 409fba9c..f5f019b9 100755 --- a/src/cython/test/test_bottleneck_distance.py +++ b/src/cython/test/test_bottleneck_distance.py @@ -16,8 +16,8 @@ __license__ = "MIT" def test_basic_bottleneck(): - diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]] - diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]] + diag1 = [[2.7, 3.7], [9.6, 14.0], [34.2, 34.974], [3.0, float("Inf")]] + diag2 = [[2.8, 4.45], [9.5, 14.1], [3.2, float("Inf")]] - assert(gudhi.bottleneck_distance(diag1, diag2, 0.1) == 0.8081763781405569) - assert(gudhi.bottleneck_distance(diag1, diag2) == 0.75) + assert gudhi.bottleneck_distance(diag1, diag2, 0.1) == 0.8081763781405569 + assert gudhi.bottleneck_distance(diag1, diag2) == 0.75 diff --git a/src/cython/test/test_cover_complex.py b/src/cython/test/test_cover_complex.py index 1eb4ed37..8cd12272 100755 --- a/src/cython/test/test_cover_complex.py +++ b/src/cython/test/test_cover_complex.py @@ -20,61 +20,66 @@ def test_empty_constructor(): cover = CoverComplex() assert cover.__is_defined() == True + def test_non_existing_file_read(): # Try to open a non existing file cover = CoverComplex() - assert (cover.read_point_cloud('pouetpouettralala.toubiloubabdou') == False) + assert cover.read_point_cloud("pouetpouettralala.toubiloubabdou") == False + def test_files_creation(): # Create test file - cloud_file = open('cloud', 'w') - cloud_file.write('nOFF\n3\n3 0 0\n0 0 0\n2 1 0\n4 0 0') + cloud_file = open("cloud", "w") + cloud_file.write("nOFF\n3\n3 0 0\n0 0 0\n2 1 0\n4 0 0") cloud_file.close() - cover_file = open('cover', 'w') - cover_file.write('1\n2\n3') + cover_file = open("cover", "w") + cover_file.write("1\n2\n3") cover_file.close() - graph_file = open('graph', 'w') - graph_file.write('0 1\n0 2\n1 2') + graph_file = open("graph", "w") + graph_file.write("0 1\n0 2\n1 2") graph_file.close() + def test_nerve(): nerve = CoverComplex() - nerve.set_type('Nerve') - assert (nerve.read_point_cloud('cloud') == True) + nerve.set_type("Nerve") + assert nerve.read_point_cloud("cloud") == True nerve.set_color_from_coordinate() - nerve.set_graph_from_file('graph') - nerve.set_cover_from_file('cover') + nerve.set_graph_from_file("graph") + nerve.set_cover_from_file("cover") nerve.find_simplices() stree = nerve.create_simplex_tree() - assert (stree.num_vertices() == 3) - assert ((stree.num_simplices() - stree.num_vertices()) == 0) - assert (stree.dimension() == 0) + assert stree.num_vertices() == 3 + assert (stree.num_simplices() - stree.num_vertices()) == 0 + assert stree.dimension() == 0 + def test_graph_induced_complex(): gic = CoverComplex() - gic.set_type('GIC') - assert (gic.read_point_cloud('cloud') == True) + gic.set_type("GIC") + assert gic.read_point_cloud("cloud") == True gic.set_color_from_coordinate() - gic.set_graph_from_file('graph') - gic.set_cover_from_file('cover') + gic.set_graph_from_file("graph") + gic.set_cover_from_file("cover") gic.find_simplices() stree = gic.create_simplex_tree() - assert (stree.num_vertices() == 3) - assert ((stree.num_simplices() - stree.num_vertices()) == 4) - assert (stree.dimension() == 2) + assert stree.num_vertices() == 3 + assert (stree.num_simplices() - stree.num_vertices()) == 4 + assert stree.dimension() == 2 + def test_voronoi_graph_induced_complex(): gic = CoverComplex() - gic.set_type('GIC') - assert (gic.read_point_cloud('cloud') == True) + gic.set_type("GIC") + assert gic.read_point_cloud("cloud") == True gic.set_color_from_coordinate() - gic.set_graph_from_file('graph') + gic.set_graph_from_file("graph") gic.set_cover_from_Voronoi(2) gic.find_simplices() stree = gic.create_simplex_tree() - assert (stree.num_vertices() == 2) - assert ((stree.num_simplices() - stree.num_vertices()) == 1) - assert (stree.dimension() == 1) + assert stree.num_vertices() == 2 + assert (stree.num_simplices() - stree.num_vertices()) == 1 + assert stree.dimension() == 1 diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py index 6dc7fdfc..68f54fbe 100755 --- a/src/cython/test/test_cubical_complex.py +++ b/src/cython/test/test_cubical_complex.py @@ -21,65 +21,78 @@ def test_empty_constructor(): 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') + cub = CubicalComplex(perseus_file="pouetpouettralala.toubiloubabdou") assert cub.__is_defined() == False assert cub.__is_persistence_defined() == False + 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 = 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') + 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') + 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') + cub = CubicalComplex(dimensions=[3, 3], perseus_file="CubicalOneSphere.txt") assert cub.__is_defined() == False assert cub.__is_persistence_defined() == False + def test_dimension_simple_constructor(): - cub = CubicalComplex(dimensions=[3, 3], - top_dimensional_cells = [1,2,3,4,5,6,7,8,9]) + 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.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(): - cub = CubicalComplex(dimensions=[3, 3], - top_dimensional_cells = [float('inf'), 0.,0.,0.,1.,0.,0.,0.,0.]) + 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], + ) 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.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.,1.,0.,0.,0.,0.]) - assert other_cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float('inf')))] + 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_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 = 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') + 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.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] diff --git a/src/cython/test/test_euclidean_witness_complex.py b/src/cython/test/test_euclidean_witness_complex.py index c8510b1e..f5eae5fa 100755 --- a/src/cython/test/test_euclidean_witness_complex.py +++ b/src/cython/test/test_euclidean_witness_complex.py @@ -19,31 +19,60 @@ def test_empty_euclidean_witness_complex(): euclidean_witness = gudhi.EuclideanWitnessComplex() assert euclidean_witness.__is_defined() == False + def test_witness_complex(): - point_cloud = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0], [9.0, 6.0], - [0.0, 14.0], [2.0, 19.0], [9.0, 17.0]] + point_cloud = [ + [1.0, 1.0], + [7.0, 0.0], + [4.0, 6.0], + [9.0, 6.0], + [0.0, 14.0], + [2.0, 19.0], + [9.0, 17.0], + ] landmarks = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0]] - euclidean_witness_complex = gudhi.EuclideanWitnessComplex(landmarks=landmarks, witnesses = point_cloud) + euclidean_witness_complex = gudhi.EuclideanWitnessComplex( + landmarks=landmarks, witnesses=point_cloud + ) simplex_tree = euclidean_witness_complex.create_simplex_tree(max_alpha_square=4.1) assert landmarks[0] == euclidean_witness_complex.get_point(0) assert landmarks[1] == euclidean_witness_complex.get_point(1) assert landmarks[2] == euclidean_witness_complex.get_point(2) - assert simplex_tree.get_filtration() == [([0], 0.0), ([1], 0.0), - ([0, 1], 0.0), ([2], 0.0), ([0, 2], 0.0), ([1, 2], 0.0), - ([0, 1, 2], 0.0)] + assert simplex_tree.get_filtration() == [ + ([0], 0.0), + ([1], 0.0), + ([0, 1], 0.0), + ([2], 0.0), + ([0, 2], 0.0), + ([1, 2], 0.0), + ([0, 1, 2], 0.0), + ] + def test_empty_euclidean_strong_witness_complex(): euclidean_strong_witness = gudhi.EuclideanStrongWitnessComplex() assert euclidean_strong_witness.__is_defined() == False + def test_strong_witness_complex(): - point_cloud = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0], [9.0, 6.0], - [0.0, 14.0], [2.0, 19.0], [9.0, 17.0]] + point_cloud = [ + [1.0, 1.0], + [7.0, 0.0], + [4.0, 6.0], + [9.0, 6.0], + [0.0, 14.0], + [2.0, 19.0], + [9.0, 17.0], + ] landmarks = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0]] - euclidean_strong_witness_complex = gudhi.EuclideanStrongWitnessComplex(landmarks=landmarks, witnesses = point_cloud) - simplex_tree = euclidean_strong_witness_complex.create_simplex_tree(max_alpha_square=14.9) + euclidean_strong_witness_complex = gudhi.EuclideanStrongWitnessComplex( + landmarks=landmarks, witnesses=point_cloud + ) + simplex_tree = euclidean_strong_witness_complex.create_simplex_tree( + max_alpha_square=14.9 + ) assert landmarks[0] == euclidean_strong_witness_complex.get_point(0) assert landmarks[1] == euclidean_strong_witness_complex.get_point(1) @@ -51,9 +80,16 @@ def test_strong_witness_complex(): assert simplex_tree.get_filtration() == [([0], 0.0), ([1], 0.0), ([2], 0.0)] - simplex_tree = euclidean_strong_witness_complex.create_simplex_tree(max_alpha_square=100.0) - - assert simplex_tree.get_filtration() == [([0], 0.0), ([1], 0.0), - ([2], 0.0), ([1, 2], 15.0), ([0, 2], 34.0), ([0, 1], 37.0), - ([0, 1, 2], 37.0)] - + simplex_tree = euclidean_strong_witness_complex.create_simplex_tree( + max_alpha_square=100.0 + ) + + assert simplex_tree.get_filtration() == [ + ([0], 0.0), + ([1], 0.0), + ([2], 0.0), + ([1, 2], 15.0), + ([0, 2], 34.0), + ([0, 1], 37.0), + ([0, 1, 2], 37.0), + ] diff --git a/src/cython/test/test_reader_utils.py b/src/cython/test/test_reader_utils.py index 4b87adf2..4c7b32c2 100755 --- a/src/cython/test/test_reader_utils.py +++ b/src/cython/test/test_reader_utils.py @@ -18,60 +18,109 @@ __license__ = "MIT" def test_non_existing_csv_file(): # Try to open a non existing file - matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file='pouetpouettralala.toubiloubabdou') + matrix = gudhi.read_lower_triangular_matrix_from_csv_file( + csv_file="pouetpouettralala.toubiloubabdou" + ) assert matrix == [] + def test_full_square_distance_matrix_csv_file(): # Create test file - test_file = open('full_square_distance_matrix.csv', 'w') - test_file.write('0;1;2;3;\n1;0;4;5;\n2;4;0;6;\n3;5;6;0;') + test_file = open("full_square_distance_matrix.csv", "w") + test_file.write("0;1;2;3;\n1;0;4;5;\n2;4;0;6;\n3;5;6;0;") test_file.close() - matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file="full_square_distance_matrix.csv") + matrix = gudhi.read_lower_triangular_matrix_from_csv_file( + csv_file="full_square_distance_matrix.csv" + ) assert matrix == [[], [1.0], [2.0, 4.0], [3.0, 5.0, 6.0]] + def test_lower_triangular_distance_matrix_csv_file(): # Create test file - test_file = open('lower_triangular_distance_matrix.csv', 'w') - test_file.write('\n1,\n2,3,\n4,5,6,\n7,8,9,10,') + test_file = open("lower_triangular_distance_matrix.csv", "w") + test_file.write("\n1,\n2,3,\n4,5,6,\n7,8,9,10,") test_file.close() - matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file="lower_triangular_distance_matrix.csv", separator=",") + matrix = gudhi.read_lower_triangular_matrix_from_csv_file( + csv_file="lower_triangular_distance_matrix.csv", separator="," + ) assert matrix == [[], [1.0], [2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0, 10.0]] + def test_non_existing_persistence_file(): # Try to open a non existing file - persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='pouetpouettralala.toubiloubabdou') + persistence = gudhi.read_persistence_intervals_grouped_by_dimension( + persistence_file="pouetpouettralala.toubiloubabdou" + ) assert persistence == [] - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='pouetpouettralala.toubiloubabdou', only_this_dim=1) + persistence = gudhi.read_persistence_intervals_in_dimension( + persistence_file="pouetpouettralala.toubiloubabdou", only_this_dim=1 + ) np.testing.assert_array_equal(persistence, []) + def test_read_persistence_intervals_without_dimension(): # Create test file - test_file = open('persistence_intervals_without_dimension.pers', 'w') - test_file.write('# Simple persistence diagram without dimension\n2.7 3.7\n9.6 14.\n34.2 34.974\n3. inf') + test_file = open("persistence_intervals_without_dimension.pers", "w") + test_file.write( + "# Simple persistence diagram without dimension\n2.7 3.7\n9.6 14.\n34.2 34.974\n3. inf" + ) test_file.close() - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers') - np.testing.assert_array_equal(persistence, [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]) - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=0) + persistence = gudhi.read_persistence_intervals_in_dimension( + persistence_file="persistence_intervals_without_dimension.pers" + ) + np.testing.assert_array_equal( + persistence, [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float("Inf"))] + ) + persistence = gudhi.read_persistence_intervals_in_dimension( + persistence_file="persistence_intervals_without_dimension.pers", only_this_dim=0 + ) np.testing.assert_array_equal(persistence, []) - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=1) + persistence = gudhi.read_persistence_intervals_in_dimension( + persistence_file="persistence_intervals_without_dimension.pers", only_this_dim=1 + ) np.testing.assert_array_equal(persistence, []) - persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_without_dimension.pers') - assert persistence == {-1: [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float('Inf'))]} + persistence = gudhi.read_persistence_intervals_grouped_by_dimension( + persistence_file="persistence_intervals_without_dimension.pers" + ) + assert persistence == { + -1: [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float("Inf"))] + } + def test_read_persistence_intervals_with_dimension(): # Create test file - test_file = open('persistence_intervals_with_dimension.pers', 'w') - test_file.write('# Simple persistence diagram with dimension\n0 2.7 3.7\n1 9.6 14.\n3 34.2 34.974\n1 3. inf') + test_file = open("persistence_intervals_with_dimension.pers", "w") + test_file.write( + "# Simple persistence diagram with dimension\n0 2.7 3.7\n1 9.6 14.\n3 34.2 34.974\n1 3. inf" + ) test_file.close() - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers') - np.testing.assert_array_equal(persistence, [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]) - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=0) + persistence = gudhi.read_persistence_intervals_in_dimension( + persistence_file="persistence_intervals_with_dimension.pers" + ) + np.testing.assert_array_equal( + persistence, [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float("Inf"))] + ) + persistence = gudhi.read_persistence_intervals_in_dimension( + persistence_file="persistence_intervals_with_dimension.pers", only_this_dim=0 + ) np.testing.assert_array_equal(persistence, [(2.7, 3.7)]) - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=1) - np.testing.assert_array_equal(persistence, [(9.6, 14.), (3., float('Inf'))]) - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=2) + persistence = gudhi.read_persistence_intervals_in_dimension( + persistence_file="persistence_intervals_with_dimension.pers", only_this_dim=1 + ) + np.testing.assert_array_equal(persistence, [(9.6, 14.0), (3.0, float("Inf"))]) + persistence = gudhi.read_persistence_intervals_in_dimension( + persistence_file="persistence_intervals_with_dimension.pers", only_this_dim=2 + ) np.testing.assert_array_equal(persistence, []) - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=3) + persistence = gudhi.read_persistence_intervals_in_dimension( + persistence_file="persistence_intervals_with_dimension.pers", only_this_dim=3 + ) np.testing.assert_array_equal(persistence, [(34.2, 34.974)]) - persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_with_dimension.pers') - assert persistence == {0: [(2.7, 3.7)], 1: [(9.6, 14.0), (3.0, float('Inf'))], 3: [(34.2, 34.974)]} + persistence = gudhi.read_persistence_intervals_grouped_by_dimension( + persistence_file="persistence_intervals_with_dimension.pers" + ) + assert persistence == { + 0: [(2.7, 3.7)], + 1: [(9.6, 14.0), (3.0, float("Inf"))], + 3: [(34.2, 34.974)], + } diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py index 975b447a..d55ae22f 100755 --- a/src/cython/test/test_rips_complex.py +++ b/src/cython/test/test_rips_complex.py @@ -19,6 +19,7 @@ __license__ = "MIT" def test_empty_rips(): rips_complex = RipsComplex() + def test_rips_from_points(): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] rips_complex = RipsComplex(points=point_list, max_edge_length=42) @@ -31,17 +32,30 @@ def test_rips_from_points(): assert simplex_tree.num_simplices() == 10 assert simplex_tree.num_vertices() == 4 - assert simplex_tree.get_filtration() == \ - [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0), - ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0), - ([2, 3], 1.0), ([1, 2], 1.4142135623730951), - ([0, 3], 1.4142135623730951)] - assert simplex_tree.get_star([0]) == \ - [([0], 0.0), ([0, 1], 1.0), ([0, 2], 1.0), - ([0, 3], 1.4142135623730951)] - assert simplex_tree.get_cofaces([0], 1) == \ - [([0, 1], 1.0), ([0, 2], 1.0), - ([0, 3], 1.4142135623730951)] + assert simplex_tree.get_filtration() == [ + ([0], 0.0), + ([1], 0.0), + ([2], 0.0), + ([3], 0.0), + ([0, 1], 1.0), + ([0, 2], 1.0), + ([1, 3], 1.0), + ([2, 3], 1.0), + ([1, 2], 1.4142135623730951), + ([0, 3], 1.4142135623730951), + ] + assert simplex_tree.get_star([0]) == [ + ([0], 0.0), + ([0, 1], 1.0), + ([0, 2], 1.0), + ([0, 3], 1.4142135623730951), + ] + assert simplex_tree.get_cofaces([0], 1) == [ + ([0, 1], 1.0), + ([0, 2], 1.0), + ([0, 3], 1.4142135623730951), + ] + def test_filtered_rips_from_points(): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] @@ -55,10 +69,10 @@ def test_filtered_rips_from_points(): assert simplex_tree.num_simplices() == 8 assert simplex_tree.num_vertices() == 4 + def test_sparse_filtered_rips_from_points(): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] - filtered_rips = RipsComplex(points=point_list, max_edge_length=1.0, - sparse=.001) + filtered_rips = RipsComplex(points=point_list, max_edge_length=1.0, sparse=0.001) simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1) @@ -68,13 +82,10 @@ def test_sparse_filtered_rips_from_points(): assert simplex_tree.num_simplices() == 8 assert simplex_tree.num_vertices() == 4 + def test_rips_from_distance_matrix(): - distance_matrix = [[0], - [1, 0], - [1, sqrt(2), 0], - [sqrt(2), 1, 1, 0]] - rips_complex = RipsComplex(distance_matrix=distance_matrix, - max_edge_length=42) + distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]] + rips_complex = RipsComplex(distance_matrix=distance_matrix, max_edge_length=42) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) @@ -84,25 +95,34 @@ def test_rips_from_distance_matrix(): assert simplex_tree.num_simplices() == 10 assert simplex_tree.num_vertices() == 4 - assert simplex_tree.get_filtration() == \ - [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0), - ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0), - ([2, 3], 1.0), ([1, 2], 1.4142135623730951), - ([0, 3], 1.4142135623730951)] - assert simplex_tree.get_star([0]) == \ - [([0], 0.0), ([0, 1], 1.0), ([0, 2], 1.0), - ([0, 3], 1.4142135623730951)] - assert simplex_tree.get_cofaces([0], 1) == \ - [([0, 1], 1.0), ([0, 2], 1.0), - ([0, 3], 1.4142135623730951)] + assert simplex_tree.get_filtration() == [ + ([0], 0.0), + ([1], 0.0), + ([2], 0.0), + ([3], 0.0), + ([0, 1], 1.0), + ([0, 2], 1.0), + ([1, 3], 1.0), + ([2, 3], 1.0), + ([1, 2], 1.4142135623730951), + ([0, 3], 1.4142135623730951), + ] + assert simplex_tree.get_star([0]) == [ + ([0], 0.0), + ([0, 1], 1.0), + ([0, 2], 1.0), + ([0, 3], 1.4142135623730951), + ] + assert simplex_tree.get_cofaces([0], 1) == [ + ([0, 1], 1.0), + ([0, 2], 1.0), + ([0, 3], 1.4142135623730951), + ] + def test_filtered_rips_from_distance_matrix(): - distance_matrix = [[0], - [1, 0], - [1, sqrt(2), 0], - [sqrt(2), 1, 1, 0]] - filtered_rips = RipsComplex(distance_matrix=distance_matrix, - max_edge_length=1.0) + distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]] + filtered_rips = RipsComplex(distance_matrix=distance_matrix, max_edge_length=1.0) simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1) diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py index 5c903d93..8d8971c1 100755 --- a/src/cython/test/test_simplex_tree.py +++ b/src/cython/test/test_simplex_tree.py @@ -39,7 +39,7 @@ def test_insertion(): assert st.find([0]) == True assert st.find([1]) == True assert st.find([2]) == True - assert st.find([3]) == False + assert st.find([3]) == False assert st.find([0, 3]) == False assert st.find([1, 3]) == False assert st.find([2, 3]) == False @@ -55,21 +55,36 @@ def test_insertion(): assert st.filtration([1]) == 0.0 # skeleton test - assert 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 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 st.get_skeleton(0) == \ - [([0], 0.0), ([1], 0.0), ([2], 4.0)] + assert 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 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 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 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.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 @@ -78,7 +93,10 @@ def test_insertion(): assert st.find([2]) == True st.initialize_filtration() - assert st.persistence(persistence_dim_max = True) == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))] + 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] @@ -88,6 +106,7 @@ def test_insertion(): assert st.persistent_betti_numbers(4.0, 10000.0) == [1, 1] assert st.persistent_betti_numbers(9999.0, 10000.0) == [1, 1] + def test_expansion(): st = SimplexTree() assert st.__is_defined() == True @@ -107,21 +126,56 @@ def test_expansion(): assert st.num_vertices() == 7 assert st.num_simplices() == 17 - assert 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)] + assert 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 st.initialize_filtration() - assert 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)] + assert 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), + ] + def test_automatic_dimension(): st = SimplexTree() @@ -129,8 +183,8 @@ def test_automatic_dimension(): 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.) == True + 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 @@ -150,6 +204,7 @@ def test_automatic_dimension(): assert st.dimension() == 1 assert st.upper_bound_dimension() == 1 + def test_make_filtration_non_decreasing(): st = SimplexTree() assert st.__is_defined() == True @@ -171,25 +226,25 @@ def test_make_filtration_non_decreasing(): # 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); + 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); + 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. - assert st.filtration([0,1,6]) == 1. - assert st.filtration([0,1]) == 1. - assert st.filtration([0]) == 1. - assert st.filtration([1]) == 1. - assert st.filtration([3,4,5]) == 2. - assert st.filtration([3,4]) == 2. - assert st.filtration([4,5]) == 2. + 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 diff --git a/src/cython/test/test_subsampling.py b/src/cython/test/test_subsampling.py index f7a97539..c816e203 100755 --- a/src/cython/test/test_subsampling.py +++ b/src/cython/test/test_subsampling.py @@ -28,45 +28,72 @@ def test_write_off_file_for_tests(): file.write("9.0 17.0\n") file.close() + def test_simple_choose_n_farthest_points_with_a_starting_point(): - point_set = [[0,1], [0,0], [1,0], [1,1]] + point_set = [[0, 1], [0, 0], [1, 0], [1, 1]] i = 0 for point in point_set: # The iteration starts with the given starting point - sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 1, starting_point = i) + sub_set = gudhi.choose_n_farthest_points( + points=point_set, nb_points=1, starting_point=i + ) assert sub_set[0] == point_set[i] i = i + 1 # The iteration finds then the farthest - sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 1) + sub_set = gudhi.choose_n_farthest_points( + points=point_set, nb_points=2, starting_point=1 + ) assert sub_set[1] == point_set[3] - sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 3) + sub_set = gudhi.choose_n_farthest_points( + points=point_set, nb_points=2, starting_point=3 + ) assert sub_set[1] == point_set[1] - sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 0) + sub_set = gudhi.choose_n_farthest_points( + points=point_set, nb_points=2, starting_point=0 + ) assert sub_set[1] == point_set[2] - sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 2) + sub_set = gudhi.choose_n_farthest_points( + points=point_set, nb_points=2, starting_point=2 + ) assert sub_set[1] == point_set[0] # Test the limits - assert gudhi.choose_n_farthest_points(points = [], nb_points = 0, starting_point = 0) == [] - assert gudhi.choose_n_farthest_points(points = [], nb_points = 1, starting_point = 0) == [] - assert gudhi.choose_n_farthest_points(points = [], nb_points = 0, starting_point = 1) == [] - assert gudhi.choose_n_farthest_points(points = [], nb_points = 1, starting_point = 1) == [] + assert ( + gudhi.choose_n_farthest_points(points=[], nb_points=0, starting_point=0) == [] + ) + assert ( + gudhi.choose_n_farthest_points(points=[], nb_points=1, starting_point=0) == [] + ) + assert ( + gudhi.choose_n_farthest_points(points=[], nb_points=0, starting_point=1) == [] + ) + assert ( + gudhi.choose_n_farthest_points(points=[], nb_points=1, starting_point=1) == [] + ) # From off file test - for i in range (0, 7): - assert len(gudhi.choose_n_farthest_points(off_file = 'subsample.off', nb_points = i, starting_point = i)) == i + for i in range(0, 7): + assert ( + len( + gudhi.choose_n_farthest_points( + off_file="subsample.off", nb_points=i, starting_point=i + ) + ) + == i + ) + def test_simple_choose_n_farthest_points_randomed(): - point_set = [[0,1], [0,0], [1,0], [1,1]] + point_set = [[0, 1], [0, 0], [1, 0], [1, 1]] # Test the limits - assert gudhi.choose_n_farthest_points(points = [], nb_points = 0) == [] - assert gudhi.choose_n_farthest_points(points = [], nb_points = 1) == [] - assert gudhi.choose_n_farthest_points(points = point_set, nb_points = 0) == [] + assert gudhi.choose_n_farthest_points(points=[], nb_points=0) == [] + assert gudhi.choose_n_farthest_points(points=[], nb_points=1) == [] + assert gudhi.choose_n_farthest_points(points=point_set, nb_points=0) == [] # Go furter than point set on purpose - for iter in range(1,10): - sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = iter) + for iter in range(1, 10): + sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=iter) for sub in sub_set: found = False for point in point_set: @@ -76,19 +103,23 @@ def test_simple_choose_n_farthest_points_randomed(): assert found == True # From off file test - for i in range (0, 7): - assert len(gudhi.choose_n_farthest_points(off_file = 'subsample.off', nb_points = i)) == i + for i in range(0, 7): + assert ( + len(gudhi.choose_n_farthest_points(off_file="subsample.off", nb_points=i)) + == i + ) + def test_simple_pick_n_random_points(): - point_set = [[0,1], [0,0], [1,0], [1,1]] + point_set = [[0, 1], [0, 0], [1, 0], [1, 1]] # Test the limits - assert gudhi.pick_n_random_points(points = [], nb_points = 0) == [] - assert gudhi.pick_n_random_points(points = [], nb_points = 1) == [] - assert gudhi.pick_n_random_points(points = point_set, nb_points = 0) == [] + assert gudhi.pick_n_random_points(points=[], nb_points=0) == [] + assert gudhi.pick_n_random_points(points=[], nb_points=1) == [] + assert gudhi.pick_n_random_points(points=point_set, nb_points=0) == [] # Go furter than point set on purpose - for iter in range(1,10): - sub_set = gudhi.pick_n_random_points(points = point_set, nb_points = iter) + for iter in range(1, 10): + sub_set = gudhi.pick_n_random_points(points=point_set, nb_points=iter) print(5) for sub in sub_set: found = False @@ -99,23 +130,50 @@ def test_simple_pick_n_random_points(): assert found == True # From off file test - for i in range (0, 7): - assert len(gudhi.pick_n_random_points(off_file = 'subsample.off', nb_points = i)) == i + for i in range(0, 7): + assert ( + len(gudhi.pick_n_random_points(off_file="subsample.off", nb_points=i)) == i + ) + def test_simple_sparsify_points(): - point_set = [[0,1], [0,0], [1,0], [1,1]] + point_set = [[0, 1], [0, 0], [1, 0], [1, 1]] # Test the limits # assert gudhi.sparsify_point_set(points = [], min_squared_dist = 0.0) == [] # assert gudhi.sparsify_point_set(points = [], min_squared_dist = 10.0) == [] - assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 0.0) == point_set - assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 1.0) == point_set - assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 2.0) == [[0,1], [1,0]] - assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 2.01) == [[0,1]] - - assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 0.0)) == 7 - assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 30.0)) == 5 - assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 40.0)) == 4 - assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 90.0)) == 3 - assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 100.0)) == 2 - assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 325.0)) == 2 - assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 325.01)) == 1 + assert gudhi.sparsify_point_set(points=point_set, min_squared_dist=0.0) == point_set + assert gudhi.sparsify_point_set(points=point_set, min_squared_dist=1.0) == point_set + assert gudhi.sparsify_point_set(points=point_set, min_squared_dist=2.0) == [ + [0, 1], + [1, 0], + ] + assert gudhi.sparsify_point_set(points=point_set, min_squared_dist=2.01) == [[0, 1]] + + assert ( + len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=0.0)) + == 7 + ) + assert ( + len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=30.0)) + == 5 + ) + assert ( + len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=40.0)) + == 4 + ) + assert ( + len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=90.0)) + == 3 + ) + assert ( + len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=100.0)) + == 2 + ) + assert ( + len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=325.0)) + == 2 + ) + assert ( + len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=325.01)) + == 1 + ) diff --git a/src/cython/test/test_tangential_complex.py b/src/cython/test/test_tangential_complex.py index aa3820d1..0f828d8e 100755 --- a/src/cython/test/test_tangential_complex.py +++ b/src/cython/test/test_tangential_complex.py @@ -17,7 +17,7 @@ __license__ = "MIT" def test_tangential(): point_list = [[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]] - tc = TangentialComplex(intrisic_dim = 1, points=point_list) + tc = TangentialComplex(intrisic_dim=1, points=point_list) assert tc.__is_defined() == True assert tc.num_vertices() == 4 assert tc.num_simplices() == 0 @@ -36,11 +36,17 @@ def test_tangential(): assert st.num_simplices() == 6 assert st.num_vertices() == 4 - - assert st.get_filtration() == \ - [([0], 0.0), ([1], 0.0), ([2], 0.0), ([0, 2], 0.0), ([3], 0.0), ([1, 3], 0.0)] + + assert st.get_filtration() == [ + ([0], 0.0), + ([1], 0.0), + ([2], 0.0), + ([0, 2], 0.0), + ([3], 0.0), + ([1, 3], 0.0), + ] assert st.get_cofaces([0], 1) == [([0, 2], 0.0)] - + assert point_list[0] == tc.get_point(0) assert point_list[1] == tc.get_point(1) assert point_list[2] == tc.get_point(2) diff --git a/src/cython/test/test_witness_complex.py b/src/cython/test/test_witness_complex.py index 70511107..36ced635 100755 --- a/src/cython/test/test_witness_complex.py +++ b/src/cython/test/test_witness_complex.py @@ -19,32 +19,44 @@ def test_empty_witness_complex(): witness = WitnessComplex() assert witness.__is_defined() == False + def test_witness_complex(): - nearest_landmark_table = [[[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]], - [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]], - [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]], - [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]], - [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]]] + nearest_landmark_table = [ + [[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]], + [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]], + [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]], + [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]], + [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]], + ] witness_complex = WitnessComplex(nearest_landmark_table=nearest_landmark_table) simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=4.1) assert simplex_tree.num_vertices() == 5 assert simplex_tree.num_simplices() == 31 - simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=4.1, limit_dimension=2) + simplex_tree = witness_complex.create_simplex_tree( + max_alpha_square=4.1, limit_dimension=2 + ) assert simplex_tree.num_vertices() == 5 assert simplex_tree.num_simplices() == 25 -def test_strong_witness_complex(): - nearest_landmark_table = [[[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]], - [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]], - [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]], - [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]], - [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]]] - strong_witness_complex = StrongWitnessComplex(nearest_landmark_table=nearest_landmark_table) +def test_strong_witness_complex(): + nearest_landmark_table = [ + [[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]], + [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]], + [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]], + [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]], + [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]], + ] + + strong_witness_complex = StrongWitnessComplex( + nearest_landmark_table=nearest_landmark_table + ) simplex_tree = strong_witness_complex.create_simplex_tree(max_alpha_square=4.1) assert simplex_tree.num_vertices() == 5 assert simplex_tree.num_simplices() == 31 - simplex_tree = strong_witness_complex.create_simplex_tree(max_alpha_square=4.1, limit_dimension=2) + simplex_tree = strong_witness_complex.create_simplex_tree( + max_alpha_square=4.1, limit_dimension=2 + ) assert simplex_tree.num_vertices() == 5 assert simplex_tree.num_simplices() == 25 |