diff options
Diffstat (limited to 'cython/test')
| -rwxr-xr-x | cython/test/test_alpha_complex.py | 86 | ||||
| -rwxr-xr-x | cython/test/test_bottleneck_distance.py | 35 | ||||
| -rwxr-xr-x | cython/test/test_cover_complex.py | 92 | ||||
| -rwxr-xr-x | cython/test/test_cubical_complex.py | 97 | ||||
| -rwxr-xr-x | cython/test/test_euclidean_witness_complex.py | 71 | ||||
| -rwxr-xr-x | cython/test/test_reader_utils.py | 88 | ||||
| -rwxr-xr-x | cython/test/test_rips_complex.py | 111 | ||||
| -rwxr-xr-x | cython/test/test_simplex_tree.py | 207 | ||||
| -rwxr-xr-x | cython/test/test_subsampling.py | 133 | ||||
| -rwxr-xr-x | cython/test/test_tangential_complex.py | 52 | ||||
| -rwxr-xr-x | cython/test/test_witness_complex.py | 62 |
11 files changed, 0 insertions, 1034 deletions
diff --git a/cython/test/test_alpha_complex.py b/cython/test/test_alpha_complex.py deleted file mode 100755 index e97f2530..00000000 --- a/cython/test/test_alpha_complex.py +++ /dev/null @@ -1,86 +0,0 @@ -from gudhi import AlphaComplex, SimplexTree - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2016 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - - -def test_empty_alpha(): - 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) - assert alpha_complex.__is_defined() == True - - simplex_tree = alpha_complex.create_simplex_tree() - assert simplex_tree.__is_persistence_defined() == False - - 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 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) - assert point_list[3] == alpha_complex.get_point(3) - 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) - - simplex_tree = filtered_alpha.create_simplex_tree(max_alpha_square=0.25) - - assert simplex_tree.num_simplices() == 8 - assert simplex_tree.num_vertices() == 4 - - assert point_list[0] == filtered_alpha.get_point(0) - assert point_list[1] == filtered_alpha.get_point(1) - assert point_list[2] == filtered_alpha.get_point(2) - assert point_list[3] == filtered_alpha.get_point(3) - 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)] diff --git a/cython/test/test_bottleneck_distance.py b/cython/test/test_bottleneck_distance.py deleted file mode 100755 index 4eb5848f..00000000 --- a/cython/test/test_bottleneck_distance.py +++ /dev/null @@ -1,35 +0,0 @@ -import gudhi - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2016 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - - -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')]] - - assert(gudhi.bottleneck_distance(diag1, diag2, 0.1) == 0.8081763781405569) - assert(gudhi.bottleneck_distance(diag1, diag2) == 0.75) diff --git a/cython/test/test_cover_complex.py b/cython/test/test_cover_complex.py deleted file mode 100755 index 58935264..00000000 --- a/cython/test/test_cover_complex.py +++ /dev/null @@ -1,92 +0,0 @@ -from gudhi import CoverComplex - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2018 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2018 Inria" -__license__ = "GPL v3" - - -def test_empty_constructor(): - # Try to create an empty CoverComplex - 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) - -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.close() - 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.close() - -def test_nerve(): - nerve = CoverComplex() - 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.find_simplices() - stree = nerve.create_simplex_tree() - - 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_color_from_coordinate() - 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) - -def test_voronoi_graph_induced_complex(): - gic = CoverComplex() - 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_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) diff --git a/cython/test/test_cubical_complex.py b/cython/test/test_cubical_complex.py deleted file mode 100755 index 92e591e9..00000000 --- a/cython/test/test_cubical_complex.py +++ /dev/null @@ -1,97 +0,0 @@ -from gudhi import CubicalComplex - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2016 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - - -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_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_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_dimension_simple_constructor(): - 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(): - cub = CubicalComplex(dimensions=[3, 3], - top_dimensional_cells = [float('inf'), 0.,0.,0.,1.,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.__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')))] - -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] diff --git a/cython/test/test_euclidean_witness_complex.py b/cython/test/test_euclidean_witness_complex.py deleted file mode 100755 index 2f77210a..00000000 --- a/cython/test/test_euclidean_witness_complex.py +++ /dev/null @@ -1,71 +0,0 @@ -import gudhi - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2016 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - - -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]] - landmarks = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0]] - 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)] - -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]] - 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) - - assert landmarks[0] == euclidean_strong_witness_complex.get_point(0) - assert landmarks[1] == euclidean_strong_witness_complex.get_point(1) - assert landmarks[2] == euclidean_strong_witness_complex.get_point(2) - - 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)] - diff --git a/cython/test/test_reader_utils.py b/cython/test/test_reader_utils.py deleted file mode 100755 index b240c84f..00000000 --- a/cython/test/test_reader_utils.py +++ /dev/null @@ -1,88 +0,0 @@ -import gudhi - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2017 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 Inria" -__license__ = "GPL v3" - - -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') - 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.close() - 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.close() - 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') - assert persistence == [] - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='pouetpouettralala.toubiloubabdou', only_this_dim=1) - assert 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.close() - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers') - assert 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) - assert persistence == [] - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=1) - assert 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'))]} - -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.close() - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers') - assert 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) - assert persistence == [(2.7, 3.7)] - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=1) - assert 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) - assert persistence == [] - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=3) - assert 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)]} diff --git a/cython/test/test_rips_complex.py b/cython/test/test_rips_complex.py deleted file mode 100755 index c37b5400..00000000 --- a/cython/test/test_rips_complex.py +++ /dev/null @@ -1,111 +0,0 @@ -from gudhi import RipsComplex -from math import sqrt - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2016 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - - -def test_empty_rips(): - rips_complex = RipsComplex() - assert rips_complex.__is_defined() == True - -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) - - simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) - - assert simplex_tree.__is_defined() == True - assert simplex_tree.__is_persistence_defined() == False - - 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)] - -def test_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) - - simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1) - - assert simplex_tree.__is_defined() == True - assert simplex_tree.__is_persistence_defined() == False - - 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) - - simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) - - assert simplex_tree.__is_defined() == True - assert simplex_tree.__is_persistence_defined() == False - - 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)] - -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) - - simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1) - - assert simplex_tree.__is_defined() == True - assert simplex_tree.__is_persistence_defined() == False - - assert simplex_tree.num_simplices() == 8 - assert simplex_tree.num_vertices() == 4 diff --git a/cython/test/test_simplex_tree.py b/cython/test/test_simplex_tree.py deleted file mode 100755 index cb701c9a..00000000 --- a/cython/test/test_simplex_tree.py +++ /dev/null @@ -1,207 +0,0 @@ -from gudhi import SimplexTree - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2016 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - - -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 - st.initialize_filtration() - 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 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.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 - - st.initialize_filtration() - 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_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 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)] - -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.) == 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_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. - 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. diff --git a/cython/test/test_subsampling.py b/cython/test/test_subsampling.py deleted file mode 100755 index 96906a6f..00000000 --- a/cython/test/test_subsampling.py +++ /dev/null @@ -1,133 +0,0 @@ -import gudhi - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2016 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - - -def test_write_off_file_for_tests(): - file = open("subsample.off", "w") - file.write("nOFF\n") - file.write("2 7 0 0\n") - file.write("1.0 1.0\n") - file.write("7.0 0.0\n") - file.write("4.0 6.0\n") - file.write("9.0 6.0\n") - file.write("0.0 14.0\n") - file.write("2.0 19.0\n") - 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]] - 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) - 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) - assert sub_set[1] == point_set[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) - assert sub_set[1] == point_set[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) == [] - - # 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 - -def test_simple_choose_n_farthest_points_randomed(): - 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) == [] - - # 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 sub in sub_set: - found = False - for point in point_set: - if point == sub: - found = True - # Check each sub set point is existing in the point set - 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 - -def test_simple_pick_n_random_points(): - 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) == [] - - # 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) - print(5) - for sub in sub_set: - found = False - for point in point_set: - if point == sub: - found = True - # Check each sub set point is existing in the point set - 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 - -def test_simple_sparsify_points(): - 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 diff --git a/cython/test/test_tangential_complex.py b/cython/test/test_tangential_complex.py deleted file mode 100755 index 5385a0d3..00000000 --- a/cython/test/test_tangential_complex.py +++ /dev/null @@ -1,52 +0,0 @@ -from gudhi import TangentialComplex, SimplexTree - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2016 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - - -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) - assert tc.__is_defined() == True - assert tc.num_vertices() == 4 - - st = tc.create_simplex_tree() - assert st.__is_defined() == True - assert st.__is_persistence_defined() == False - - 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_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) - assert point_list[3] == tc.get_point(3) - assert tc.get_point(4) == [] - assert tc.get_point(125) == [] diff --git a/cython/test/test_witness_complex.py b/cython/test/test_witness_complex.py deleted file mode 100755 index bcbc521b..00000000 --- a/cython/test/test_witness_complex.py +++ /dev/null @@ -1,62 +0,0 @@ -from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2016 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - - -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]]] - - 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) - 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) - 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) - assert simplex_tree.num_vertices() == 5 - assert simplex_tree.num_simplices() == 25 |