1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
|
# coding: utf-8
# /*##########################################################################
# Copyright (C) 2016 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ############################################################################*/
"""Tests of the marchingcubes module"""
from __future__ import division
__authors__ = ["T. Vincent"]
__license__ = "MIT"
__date__ = "05/12/2016"
import unittest
import numpy
from silx.test.utils import ParametricTestCase
from silx.math import marchingcubes
class TestMarchingCubes(ParametricTestCase):
"""Tests of marching cubes"""
def assertAllClose(self, array1, array2, msg=None,
rtol=1e-05, atol=1e-08):
"""Assert that the 2 numpy.ndarrays are almost equal.
:param str msg: Message to provide when assert fails
:param float rtol: Relative tolerance, see :func:`numpy.allclose`
:param float atol: Absolute tolerance, see :func:`numpy.allclose`
"""
if not numpy.allclose(array1, array2, rtol, atol):
raise self.failureException(msg)
def test_cube(self):
"""Unit tests with a single cube"""
# No isosurface
cube_zero = numpy.zeros((2, 2, 2), dtype=numpy.float32)
result = marchingcubes.MarchingCubes(cube_zero, 1.)
self.assertEqual(result.shape, cube_zero.shape)
self.assertEqual(result.isolevel, 1.)
self.assertEqual(result.invert_normals, True)
vertices, normals, indices = result
self.assertEqual(len(vertices), 0)
self.assertEqual(len(normals), 0)
self.assertEqual(len(indices), 0)
# Cube array dimensions: shape = (dim 0, dim 1, dim2)
#
# dim 0 (Z)
# ^
# |
# 4 +------+ 5
# /| /|
# / | / |
# 6 +------+ 7|
# | | | |
# |0 +---|--+ 1 -> dim 2 (X)
# | / | /
# |/ |/
# 2 +------+ 3
# /
# dim 1 (Y)
# isosurface perpendicular to dim 0 (Z)
cube = numpy.array(
(((0., 0.), (0., 0.)),
((1., 1.), (1., 1.))), dtype=numpy.float32)
level = 0.5
vertices, normals, indices = marchingcubes.MarchingCubes(
cube, level, invert_normals=False)
self.assertAllClose(vertices[:, 0], level)
self.assertAllClose(normals, (1., 0., 0.))
self.assertEqual(len(indices), 2)
# isosurface perpendicular to dim 1 (Y)
cube = numpy.array(
(((0., 0.), (1., 1.)),
((0., 0.), (1., 1.))), dtype=numpy.float32)
level = 0.2
vertices, normals, indices = marchingcubes.MarchingCubes(cube, level)
self.assertAllClose(vertices[:, 1], level)
self.assertAllClose(normals, (0., -1., 0.))
self.assertEqual(len(indices), 2)
# isosurface perpendicular to dim 2 (X)
cube = numpy.array(
(((0., 1.), (0., 1.)),
((0., 1.), (0., 1.))), dtype=numpy.float32)
level = 0.9
vertices, normals, indices = marchingcubes.MarchingCubes(
cube, level, invert_normals=False)
self.assertAllClose(vertices[:, 2], level)
self.assertAllClose(normals, (0., 0., 1.))
self.assertEqual(len(indices), 2)
# isosurface normal in dim1, dim 0 (Y, Z) plane
cube = numpy.array(
(((0., 0.), (0., 0.)),
((0., 0.), (1., 1.))), dtype=numpy.float32)
level = 0.5
vertices, normals, indices = marchingcubes.MarchingCubes(cube, level)
self.assertAllClose(normals[:, 2], 0.)
self.assertEqual(len(indices), 2)
def test_sampling(self):
"""Test different sampling, comparing to reference without sampling"""
isolevel = 0.5
size = 9
chessboard = numpy.zeros((size, size, size), dtype=numpy.float32)
chessboard.reshape(-1)[::2] = 1 # OK as long as dimensions are odd
ref_result = marchingcubes.MarchingCubes(chessboard, isolevel)
samplings = [
(2, 1, 1),
(1, 2, 1),
(1, 1, 2),
(2, 2, 2),
(3, 3, 3),
(1, 3, 1),
(1, 1, 3),
]
for sampling in samplings:
with self.subTest(sampling=sampling):
sampling = numpy.array(sampling)
data = 1e6 * numpy.ones(
sampling * size, dtype=numpy.float32)
# Copy ref chessboard in data according to sampling
data[::sampling[0], ::sampling[1], ::sampling[2]] = chessboard
result = marchingcubes.MarchingCubes(data, isolevel,
sampling=sampling)
# Compare vertices normalized with shape
self.assertAllClose(
ref_result.get_vertices() / ref_result.shape,
result.get_vertices() / result.shape,
atol=0., rtol=0.)
# Compare normals
# This comparison only works for normals aligned with axes
# otherwise non uniform sampling would make different normals
self.assertAllClose(ref_result.get_normals(),
result.get_normals(),
atol=0., rtol=0.)
self.assertAllClose(ref_result.get_indices(),
result.get_indices(),
atol=0., rtol=0.)
test_cases = (TestMarchingCubes,)
def suite():
test_suite = unittest.TestSuite()
for test_class in test_cases:
test_suite.addTests(
unittest.defaultTestLoader.loadTestsFromTestCase(test_class))
return test_suite
if __name__ == '__main__':
unittest.main(defaultTest="suite")
|
