diff options
Diffstat (limited to 'src/python/test')
| -rwxr-xr-x | src/python/test/test_alpha_complex.py | 87 | ||||
| -rwxr-xr-x | src/python/test/test_reader_utils.py | 33 |
2 files changed, 89 insertions, 31 deletions
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py index 814f8289..e0f2b5df 100755 --- a/src/python/test/test_alpha_complex.py +++ b/src/python/test/test_alpha_complex.py @@ -12,6 +12,8 @@ import gudhi as gd import math import numpy as np import pytest +import warnings + try: # python3 from itertools import zip_longest @@ -25,12 +27,17 @@ __license__ = "MIT" def _empty_alpha(precision): + alpha_complex = gd.AlphaComplex(precision = precision) + assert alpha_complex.__is_defined() == True + +def _one_2d_point_alpha(precision): alpha_complex = gd.AlphaComplex(points=[[0, 0]], precision = precision) assert alpha_complex.__is_defined() == True def test_empty_alpha(): for precision in ['fast', 'safe', 'exact']: _empty_alpha(precision) + _one_2d_point_alpha(precision) def _infinite_alpha(precision): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] @@ -198,7 +205,13 @@ def test_delaunay_complex(): _delaunay_complex(precision) def _3d_points_on_a_plane(precision, default_filtration_value): - alpha = gd.AlphaComplex(off_file='alphacomplexdoc.off', precision = precision) + alpha = gd.AlphaComplex(points = [[1.0, 1.0 , 0.0], + [7.0, 0.0 , 0.0], + [4.0, 6.0 , 0.0], + [9.0, 6.0 , 0.0], + [0.0, 14.0, 0.0], + [2.0, 19.0, 0.0], + [9.0, 17.0, 0.0]], precision = precision) simplex_tree = alpha.create_simplex_tree(default_filtration_value = default_filtration_value) assert simplex_tree.dimension() == 2 @@ -206,28 +219,16 @@ def _3d_points_on_a_plane(precision, default_filtration_value): assert simplex_tree.num_simplices() == 25 def test_3d_points_on_a_plane(): - off_file = open("alphacomplexdoc.off", "w") - off_file.write("OFF \n" \ - "7 0 0 \n" \ - "1.0 1.0 0.0\n" \ - "7.0 0.0 0.0\n" \ - "4.0 6.0 0.0\n" \ - "9.0 6.0 0.0\n" \ - "0.0 14.0 0.0\n" \ - "2.0 19.0 0.0\n" \ - "9.0 17.0 0.0\n" ) - off_file.close() - for default_filtration_value in [True, False]: for precision in ['fast', 'safe', 'exact']: _3d_points_on_a_plane(precision, default_filtration_value) def _3d_tetrahedrons(precision): points = 10*np.random.rand(10, 3) - alpha = gd.AlphaComplex(points=points, precision = precision) + alpha = gd.AlphaComplex(points = points, precision = precision) st_alpha = alpha.create_simplex_tree(default_filtration_value = False) # New AlphaComplex for get_point to work - delaunay = gd.AlphaComplex(points=points, precision = precision) + delaunay = gd.AlphaComplex(points = points, precision = precision) st_delaunay = delaunay.create_simplex_tree(default_filtration_value = True) delaunay_tetra = [] @@ -256,3 +257,59 @@ def _3d_tetrahedrons(precision): def test_3d_tetrahedrons(): for precision in ['fast', 'safe', 'exact']: _3d_tetrahedrons(precision) + +def test_off_file_deprecation_warning(): + off_file = open("alphacomplexdoc.off", "w") + off_file.write("OFF \n" \ + "7 0 0 \n" \ + "1.0 1.0 0.0\n" \ + "7.0 0.0 0.0\n" \ + "4.0 6.0 0.0\n" \ + "9.0 6.0 0.0\n" \ + "0.0 14.0 0.0\n" \ + "2.0 19.0 0.0\n" \ + "9.0 17.0 0.0\n" ) + off_file.close() + + with pytest.warns(DeprecationWarning): + alpha = gd.AlphaComplex(off_file="alphacomplexdoc.off") + +def test_non_existing_off_file(): + with pytest.raises(FileNotFoundError): + alpha = gd.AlphaComplex(off_file="pouetpouettralala.toubiloubabdou") + +def test_inconsistency_points_and_weights(): + points = [[1.0, 1.0 , 0.0], + [7.0, 0.0 , 0.0], + [4.0, 6.0 , 0.0], + [9.0, 6.0 , 0.0], + [0.0, 14.0, 0.0], + [2.0, 19.0, 0.0], + [9.0, 17.0, 0.0]] + with pytest.raises(ValueError): + # 7 points, 8 weights, on purpose + alpha = gd.AlphaComplex(points = points, + weights = [1., 2., 3., 4., 5., 6., 7., 8.]) + + with pytest.raises(ValueError): + # 7 points, 6 weights, on purpose + alpha = gd.AlphaComplex(points = points, + weights = [1., 2., 3., 4., 5., 6.]) + +def _doc_example(precision): + stree_from_values = gd.AlphaComplex(points=[[ 1., -1., -1.], + [-1., 1., -1.], + [-1., -1., 1.], + [ 1., 1., 1.], + [ 2., 2., 2.]], + weights = [4., 4., 4., 4., 1.], + precision = precision).create_simplex_tree() + + assert stree_from_values.filtration([0, 1, 2, 3]) == pytest.approx(-1.) + assert stree_from_values.filtration([0, 1, 3, 4]) == pytest.approx(95.) + assert stree_from_values.filtration([0, 2, 3, 4]) == pytest.approx(95.) + assert stree_from_values.filtration([1, 2, 3, 4]) == pytest.approx(95.) + +def test_doc_example(): + for precision in ['fast', 'safe', 'exact']: + _doc_example(precision) diff --git a/src/python/test/test_reader_utils.py b/src/python/test/test_reader_utils.py index 90da6651..4fc7c00f 100755 --- a/src/python/test/test_reader_utils.py +++ b/src/python/test/test_reader_utils.py @@ -8,8 +8,9 @@ - YYYY/MM Author: Description of the modification """ -import gudhi +import gudhi as gd import numpy as np +from pytest import raises __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2017 Inria" @@ -18,7 +19,7 @@ __license__ = "MIT" def test_non_existing_csv_file(): # Try to open a non existing file - matrix = gudhi.read_lower_triangular_matrix_from_csv_file( + matrix = gd.read_lower_triangular_matrix_from_csv_file( csv_file="pouetpouettralala.toubiloubabdou" ) assert matrix == [] @@ -29,7 +30,7 @@ def test_full_square_distance_matrix_csv_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( + matrix = gd.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]] @@ -40,7 +41,7 @@ def test_lower_triangular_distance_matrix_csv_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( + matrix = gd.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]] @@ -48,11 +49,11 @@ def test_lower_triangular_distance_matrix_csv_file(): def test_non_existing_persistence_file(): # Try to open a non existing file - persistence = gudhi.read_persistence_intervals_grouped_by_dimension( + persistence = gd.read_persistence_intervals_grouped_by_dimension( persistence_file="pouetpouettralala.toubiloubabdou" ) assert persistence == [] - persistence = gudhi.read_persistence_intervals_in_dimension( + persistence = gd.read_persistence_intervals_in_dimension( persistence_file="pouetpouettralala.toubiloubabdou", only_this_dim=1 ) np.testing.assert_array_equal(persistence, []) @@ -65,21 +66,21 @@ def test_read_persistence_intervals_without_dimension(): "# 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 = gd.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 = gd.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 = gd.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 = gd.read_persistence_intervals_grouped_by_dimension( persistence_file="persistence_intervals_without_dimension.pers" ) assert persistence == { @@ -94,29 +95,29 @@ def test_read_persistence_intervals_with_dimension(): "# 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 = gd.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 = gd.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 = gd.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 = gd.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 = gd.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 = gd.read_persistence_intervals_grouped_by_dimension( persistence_file="persistence_intervals_with_dimension.pers" ) assert persistence == { |