diff options
Diffstat (limited to 'src/python/test/test_alpha_complex.py')
| -rwxr-xr-x | src/python/test/test_alpha_complex.py | 83 |
1 files changed, 64 insertions, 19 deletions
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py index 943ad2c4..a4ee260b 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 @@ -25,17 +25,16 @@ __license__ = "MIT" def _empty_alpha(precision): - alpha_complex = AlphaComplex(points=[[0, 0]], precision = precision) + alpha_complex = gd.AlphaComplex(points=[[0, 0]], precision = precision) assert alpha_complex.__is_defined() == True def test_empty_alpha(): - _empty_alpha('fast') - _empty_alpha('safe') - _empty_alpha('exact') + for precision in ['fast', 'safe', 'exact']: + _empty_alpha(precision) def _infinite_alpha(precision): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] - alpha_complex = AlphaComplex(points=point_list, precision = precision) + alpha_complex = gd.AlphaComplex(points=point_list, precision = precision) assert alpha_complex.__is_defined() == True simplex_tree = alpha_complex.create_simplex_tree() @@ -84,13 +83,12 @@ def _infinite_alpha(precision): assert False def test_infinite_alpha(): - _infinite_alpha('fast') - _infinite_alpha('safe') - _infinite_alpha('exact') + for precision in ['fast', 'safe', 'exact']: + _infinite_alpha(precision) def _filtered_alpha(precision): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] - filtered_alpha = AlphaComplex(points=point_list, precision = precision) + filtered_alpha = gd.AlphaComplex(points=point_list, precision = precision) simplex_tree = filtered_alpha.create_simplex_tree(max_alpha_square=0.25) @@ -128,9 +126,8 @@ def _filtered_alpha(precision): assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)] def test_filtered_alpha(): - _filtered_alpha('fast') - _filtered_alpha('safe') - _filtered_alpha('exact') + for precision in ['fast', 'safe', 'exact']: + _filtered_alpha(precision) def _safe_alpha_persistence_comparison(precision): #generate periodic signal @@ -144,10 +141,10 @@ def _safe_alpha_persistence_comparison(precision): embedding2 = [[signal[i], delayed[i]] for i in range(len(time))] #build alpha complex and simplex tree - alpha_complex1 = AlphaComplex(points=embedding1, precision = precision) + alpha_complex1 = gd.AlphaComplex(points=embedding1, precision = precision) simplex_tree1 = alpha_complex1.create_simplex_tree() - alpha_complex2 = AlphaComplex(points=embedding2, precision = precision) + alpha_complex2 = gd.AlphaComplex(points=embedding2, precision = precision) simplex_tree2 = alpha_complex2.create_simplex_tree() diag1 = simplex_tree1.persistence() @@ -165,7 +162,7 @@ def test_safe_alpha_persistence_comparison(): def _delaunay_complex(precision): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] - filtered_alpha = AlphaComplex(points=point_list, precision = precision) + filtered_alpha = gd.AlphaComplex(points=point_list, precision = precision) simplex_tree = filtered_alpha.create_simplex_tree(default_filtration_value = True) @@ -197,6 +194,54 @@ def _delaunay_complex(precision): assert math.isnan(filtered_value[1]) def test_delaunay_complex(): - _delaunay_complex('fast') - _delaunay_complex('safe') - _delaunay_complex('exact') + for precision in ['fast', 'safe', 'exact']: + _delaunay_complex(precision) + +def _3d_points_on_a_plane(precision, default_filtration_value): + alpha = gd.AlphaComplex(off_file=gd.__root_source_dir__ + '/data/points/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(): + 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) |