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_cubical_complex.py | 86 | ||||
| -rwxr-xr-x | cython/test/test_euclidean_witness_complex.py | 71 | ||||
| -rwxr-xr-x | cython/test/test_rips_complex.py | 111 | ||||
| -rwxr-xr-x | cython/test/test_simplex_tree.py | 132 | ||||
| -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 |
9 files changed, 768 insertions, 0 deletions
diff --git a/cython/test/test_alpha_complex.py b/cython/test/test_alpha_complex.py new file mode 100755 index 00000000..2c76d9d7 --- /dev/null +++ b/cython/test/test_alpha_complex.py @@ -0,0 +1,86 @@ +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 new file mode 100755 index 00000000..3d982d34 --- /dev/null +++ b/cython/test/test_bottleneck_distance.py @@ -0,0 +1,35 @@ +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_cubical_complex.py b/cython/test/test_cubical_complex.py new file mode 100755 index 00000000..2e281ee4 --- /dev/null +++ b/cython/test/test_cubical_complex.py @@ -0,0 +1,86 @@ +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_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() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))] + assert cub.__is_persistence_defined() == True + assert cub.betti_numbers() == [1, 0] + assert cub.persistent_betti_numbers(0, 1000) == [0, 0] + +def test_dimension_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, 1.8446744073709552e+19))] + 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 new file mode 100755 index 00000000..737f1ef4 --- /dev/null +++ b/cython/test/test_euclidean_witness_complex.py @@ -0,0 +1,71 @@ +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_rips_complex.py b/cython/test/test_rips_complex.py new file mode 100755 index 00000000..c7d2ead4 --- /dev/null +++ b/cython/test/test_rips_complex.py @@ -0,0 +1,111 @@ +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 new file mode 100755 index 00000000..3ae537e3 --- /dev/null +++ b/cython/test/test_simplex_tree.py @@ -0,0 +1,132 @@ +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.insert([0, 1, 2], filtration=4.0) == True + # FIXME: Remove this line + st.set_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.set_filtration(5.0) + 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() == [(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)] diff --git a/cython/test/test_subsampling.py b/cython/test/test_subsampling.py new file mode 100755 index 00000000..2caf4ddb --- /dev/null +++ b/cython/test/test_subsampling.py @@ -0,0 +1,133 @@ +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 new file mode 100755 index 00000000..8aa4023c --- /dev/null +++ b/cython/test/test_tangential_complex.py @@ -0,0 +1,52 @@ +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(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 new file mode 100755 index 00000000..7d1fb6be --- /dev/null +++ b/cython/test/test_witness_complex.py @@ -0,0 +1,62 @@ +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 |