diff options
Diffstat (limited to 'src/python/test/test_alpha_complex.py')
| -rwxr-xr-x | src/python/test/test_alpha_complex.py | 133 |
1 files changed, 123 insertions, 10 deletions
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py index 77121302..814f8289 100755 --- a/src/python/test/test_alpha_complex.py +++ b/src/python/test/test_alpha_complex.py @@ -8,7 +8,7 @@ - YYYY/MM Author: Description of the modification """ -from gudhi import AlphaComplex, SimplexTree +import gudhi as gd import math import numpy as np import pytest @@ -24,14 +24,17 @@ __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" -def test_empty_alpha(): - alpha_complex = AlphaComplex(points=[[0, 0]]) +def _empty_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) -def test_infinite_alpha(): +def _infinite_alpha(precision): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] - alpha_complex = AlphaComplex(points=point_list) + alpha_complex = gd.AlphaComplex(points=point_list, precision = precision) assert alpha_complex.__is_defined() == True simplex_tree = alpha_complex.create_simplex_tree() @@ -79,10 +82,13 @@ def test_infinite_alpha(): else: assert False +def test_infinite_alpha(): + for precision in ['fast', 'safe', 'exact']: + _infinite_alpha(precision) -def test_filtered_alpha(): +def _filtered_alpha(precision): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] - filtered_alpha = AlphaComplex(points=point_list) + filtered_alpha = gd.AlphaComplex(points=point_list, precision = precision) simplex_tree = filtered_alpha.create_simplex_tree(max_alpha_square=0.25) @@ -119,7 +125,11 @@ def test_filtered_alpha(): 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)] -def test_safe_alpha_persistence_comparison(): +def test_filtered_alpha(): + for precision in ['fast', 'safe', 'exact']: + _filtered_alpha(precision) + +def _safe_alpha_persistence_comparison(precision): #generate periodic signal time = np.arange(0, 10, 1) signal = [math.sin(x) for x in time] @@ -131,10 +141,10 @@ def test_safe_alpha_persistence_comparison(): embedding2 = [[signal[i], delayed[i]] for i in range(len(time))] #build alpha complex and simplex tree - alpha_complex1 = AlphaComplex(points=embedding1) + alpha_complex1 = gd.AlphaComplex(points=embedding1, precision = precision) simplex_tree1 = alpha_complex1.create_simplex_tree() - alpha_complex2 = AlphaComplex(points=embedding2) + alpha_complex2 = gd.AlphaComplex(points=embedding2, precision = precision) simplex_tree2 = alpha_complex2.create_simplex_tree() diag1 = simplex_tree1.persistence() @@ -143,3 +153,106 @@ def test_safe_alpha_persistence_comparison(): for (first_p, second_p) in zip_longest(diag1, diag2): assert first_p[0] == pytest.approx(second_p[0]) assert first_p[1] == pytest.approx(second_p[1]) + + +def test_safe_alpha_persistence_comparison(): + # Won't work for 'fast' version + _safe_alpha_persistence_comparison('safe') + _safe_alpha_persistence_comparison('exact') + +def _delaunay_complex(precision): + point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] + filtered_alpha = gd.AlphaComplex(points=point_list, precision = precision) + + simplex_tree = filtered_alpha.create_simplex_tree(default_filtration_value = True) + + assert simplex_tree.num_simplices() == 11 + 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) + try: + filtered_alpha.get_point(4) == [] + except IndexError: + pass + else: + assert False + try: + filtered_alpha.get_point(125) == [] + except IndexError: + pass + else: + assert False + + for filtered_value in simplex_tree.get_filtration(): + assert math.isnan(filtered_value[1]) + for filtered_value in simplex_tree.get_star([0]): + assert math.isnan(filtered_value[1]) + for filtered_value in simplex_tree.get_cofaces([0], 1): + assert math.isnan(filtered_value[1]) + +def test_delaunay_complex(): + for precision in ['fast', 'safe', 'exact']: + _delaunay_complex(precision) + +def _3d_points_on_a_plane(precision, default_filtration_value): + alpha = gd.AlphaComplex(off_file='alphacomplexdoc.off', precision = precision) + + simplex_tree = alpha.create_simplex_tree(default_filtration_value = default_filtration_value) + assert simplex_tree.dimension() == 2 + assert simplex_tree.num_vertices() == 7 + 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) + st_alpha = alpha.create_simplex_tree(default_filtration_value = False) + # New AlphaComplex for get_point to work + delaunay = gd.AlphaComplex(points=points, precision = precision) + st_delaunay = delaunay.create_simplex_tree(default_filtration_value = True) + + delaunay_tetra = [] + for sk in st_delaunay.get_skeleton(4): + if len(sk[0]) == 4: + tetra = [delaunay.get_point(sk[0][0]), + delaunay.get_point(sk[0][1]), + delaunay.get_point(sk[0][2]), + delaunay.get_point(sk[0][3]) ] + delaunay_tetra.append(sorted(tetra, key=lambda tup: tup[0])) + + alpha_tetra = [] + for sk in st_alpha.get_skeleton(4): + if len(sk[0]) == 4: + tetra = [alpha.get_point(sk[0][0]), + alpha.get_point(sk[0][1]), + alpha.get_point(sk[0][2]), + alpha.get_point(sk[0][3]) ] + alpha_tetra.append(sorted(tetra, key=lambda tup: tup[0])) + + # Check the tetrahedrons from one list are in the second one + assert len(alpha_tetra) == len(delaunay_tetra) + for tetra_from_del in delaunay_tetra: + assert tetra_from_del in alpha_tetra + +def test_3d_tetrahedrons(): + for precision in ['fast', 'safe', 'exact']: + _3d_tetrahedrons(precision) |