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""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
Author(s): Vincent Rouvreau
Copyright (C) 2021 Inria
Modification(s):
- YYYY/MM Author: Description of the modification
"""
from gudhi import AlphaComplex3D
import pytest
try:
# python3
from itertools import zip_longest
except ImportError:
# python2
from itertools import izip_longest as zip_longest
def _empty_alpha(precision):
alpha_complex = AlphaComplex3D(precision = precision)
assert alpha_complex.__is_defined() == True
def _one_3d_point_alpha(precision):
alpha_complex = AlphaComplex3D(points=[[0, 0, 0]], precision = precision)
assert alpha_complex.__is_defined() == True
def test_empty_alpha():
for precision in ['fast', 'safe', 'exact']:
_empty_alpha(precision)
_one_3d_point_alpha(precision)
def _infinite_alpha(precision):
point_list = [[0, 0, 0], [1, 0, 0], [0, 1, 0], [1, 1, 0], [0, 0, 1], [1, 0, 1], [0, 1, 1], [1, 1, 1]]
alpha_complex = AlphaComplex3D(points=point_list, precision = precision)
assert alpha_complex.__is_defined() == True
stree = alpha_complex.create_simplex_tree()
assert stree.__is_persistence_defined() == False
assert stree.num_simplices() == 51
assert stree.num_vertices() == len(point_list)
for filtration in stree.get_filtration():
if len(filtration[0]) == 1:
assert filtration[1] == 0.
if len(filtration[0]) == 4:
assert filtration[1] == 0.75
for idx in range(len(point_list)):
pt_idx = point_list.index(alpha_complex.get_point(idx))
assert pt_idx >= 0
assert pt_idx < len(point_list)
with pytest.raises(IndexError):
alpha_complex.get_point(len(point_list))
def test_infinite_alpha():
for precision in ['fast', 'safe', 'exact']:
_infinite_alpha(precision)
def _filtered_alpha(precision):
point_list = [[0, 0, 0], [1, 0, 0], [0, 1, 0], [1, 1, 0], [0, 0, 1], [1, 0, 1], [0, 1, 1], [1, 1, 1]]
filtered_alpha = AlphaComplex3D(points=point_list, precision = precision)
stree = filtered_alpha.create_simplex_tree(max_alpha_square=0.25)
assert stree.num_simplices() == 20
assert stree.num_vertices() == len(point_list)
for filtration in stree.get_filtration():
if len(filtration[0]) == 1:
assert filtration[1] == 0.
elif len(filtration[0]) == 2:
assert filtration[1] == 0.25
else:
assert False
for idx in range(len(point_list)):
pt_idx = point_list.index(filtered_alpha.get_point(idx))
assert pt_idx >= 0
assert pt_idx < len(point_list)
with pytest.raises(IndexError):
filtered_alpha.get_point(len(point_list))
def test_filtered_alpha():
for precision in ['fast', 'safe', 'exact']:
_filtered_alpha(precision)
def _3d_points_on_a_plane(precision):
alpha = AlphaComplex3D(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)
with pytest.raises(ValueError):
stree = alpha.create_simplex_tree()
def test_3d_points_on_a_plane():
for precision in ['fast', 'safe', 'exact']:
_3d_points_on_a_plane(precision)
def test_inconsistency_points_and_weights():
points = [[1.0, 1.0 , 1.0],
[7.0, 0.0 , 2.0],
[4.0, 6.0 , 0.0],
[9.0, 6.0 , 1.0],
[0.0, 14.0, 2.0],
[2.0, 19.0, 0.0],
[9.0, 17.0, 1.0]]
with pytest.raises(ValueError):
# 7 points, 8 weights, on purpose
alpha = AlphaComplex3D(points = points,
weights = [1., 2., 3., 4., 5., 6., 7., 8.])
with pytest.raises(ValueError):
# 7 points, 6 weights, on purpose
alpha = AlphaComplex3D(points = points,
weights = [1., 2., 3., 4., 5., 6.])
def _weighted_doc_example(precision):
pts = [[ 1., -1., -1.],
[-1., 1., -1.],
[-1., -1., 1.],
[ 1., 1., 1.],
[ 2., 2., 2.]]
wgts = [4., 4., 4., 4., 1.]
alpha = AlphaComplex3D(points = pts, weights = wgts, precision = precision)
stree = alpha.create_simplex_tree()
# Needs to retrieve points as points are shuffled
get_idx = lambda idx: pts.index(alpha.get_point(idx))
indices = [get_idx(x) for x in range(len(pts))]
assert stree.filtration([indices[x] for x in [0, 1, 2, 3]]) == pytest.approx(-1.)
assert stree.filtration([indices[x] for x in [0, 1, 3, 4]]) == pytest.approx(95.)
assert stree.filtration([indices[x] for x in [0, 2, 3, 4]]) == pytest.approx(95.)
assert stree.filtration([indices[x] for x in [1, 2, 3, 4]]) == pytest.approx(95.)
def test_weighted_doc_example():
for precision in ['fast', 'safe', 'exact']:
_weighted_doc_example(precision)
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