/
test_align.py
157 lines (121 loc) · 6.19 KB
/
test_align.py
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
import numpy.testing as npt
import nibabel as nib
from nibabel.tmpdirs import TemporaryDirectory
from dipy.data import get_data
from dipy.workflows.align import ResliceFlow
import os.path
from os.path import join as pjoin
import shutil
from dipy.align.tests.test_parzenhist import setup_random_transform
from dipy.align.transforms import (Transform,
regtransforms)
from dipy.io.image import save_nifti
from glob import glob
from dipy.workflows.align import ImageRegistrationFlow
def test_reslice():
with TemporaryDirectory() as out_dir:
data_path, _, _ = get_data('small_25')
vol_img = nib.load(data_path)
volume = vol_img.get_data()
reslice_flow = ResliceFlow()
reslice_flow.run(data_path, [1.5, 1.5, 1.5], out_dir=out_dir)
out_path = reslice_flow.last_generated_outputs['out_resliced']
out_img = nib.load(out_path)
resliced = out_img.get_data()
npt.assert_equal(resliced.shape[0] > volume.shape[0], True)
npt.assert_equal(resliced.shape[1] > volume.shape[1], True)
npt.assert_equal(resliced.shape[2] > volume.shape[2], True)
npt.assert_equal(resliced.shape[-1], volume.shape[-1])
def test_image_registration():
with TemporaryDirectory() as temp_out_dir:
static, moving, static_g2w, moving_g2w, sm, mm, m = \
setup_random_transform(transform=regtransforms[('AFFINE', 3)],
rfactor=0.1)
save_nifti(pjoin(temp_out_dir, 'b0.nii.gz'), data=static,
affine=static_g2w)
save_nifti(pjoin(temp_out_dir, 't1.nii.gz'), data=moving,
affine=moving_g2w)
static_image_file = pjoin(temp_out_dir, 'b0.nii.gz')
moving_image_file = pjoin(temp_out_dir, 't1.nii.gz')
image_registeration_flow = ImageRegistrationFlow()
def read_distance(qual_fname):
temp_val = 0
with open(pjoin(temp_out_dir, qual_fname), 'r') as f:
for line in f:
pass
temp_val = line
return float(temp_val)
def test_com():
out_moved = pjoin(temp_out_dir, "com_moved.nii.gz")
out_affine = pjoin(temp_out_dir, "com_affine.txt")
image_registeration_flow.run(static_image_file,
moving_image_file,
transform='com',
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine)
npt.assert_equal(os.path.exists(out_moved), True)
npt.assert_equal(os.path.exists(out_affine), True)
def test_translation():
out_moved = pjoin(temp_out_dir, "trans_moved.nii.gz")
out_affine = pjoin(temp_out_dir, "trans_affine.txt")
image_registeration_flow.run(static_image_file,
moving_image_file,
transform='trans',
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine,
save_metric=True,
level_iters=[100, 10, 1],
out_quality='trans_q.txt')
dist = read_distance('trans_q.txt')
npt.assert_equal('%.2f' % dist, '%.2f' % -0.3953547764454917)
npt.assert_equal(os.path.exists(out_moved), True)
npt.assert_equal(os.path.exists(out_affine), True)
def test_rigid():
out_moved = pjoin(temp_out_dir, "rigid_moved.nii.gz")
out_affine = pjoin(temp_out_dir, "rigid_affine.txt")
image_registeration_flow.run(static_image_file,
moving_image_file,
transform='rigid',
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine,
save_metric=True,
level_iters=[100, 10, 1],
out_quality='rigid_q.txt')
dist = read_distance('rigid_q.txt')
npt.assert_equal('%.2f' % dist, '%.2f' % -0.6900534794005155)
npt.assert_equal(os.path.exists(out_moved), True)
npt.assert_equal(os.path.exists(out_affine), True)
def test_affine():
out_moved = pjoin(temp_out_dir, "affine_moved.nii.gz")
out_affine = pjoin(temp_out_dir, "affine_affine.txt")
image_registeration_flow.run(static_image_file,
moving_image_file,
transform='affine',
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine,
save_metric=True,
level_iters=[100, 10, 1],
out_quality='affine_q.txt')
dist = read_distance('affine_q.txt')
npt.assert_equal('%.2f' % dist, '%.2f' % -0.7670650775914811)
npt.assert_equal(os.path.exists(out_moved), True)
npt.assert_equal(os.path.exists(out_affine), True)
# Creating the erroneous behavior
def test_err():
npt.assert_raises(ValueError, image_registeration_flow.run,
static_image_file,
moving_image_file,
transform='notransform')
npt.assert_raises(ValueError, image_registeration_flow.run,
static_image_file,
moving_image_file,
metric='wrong_metric')
test_com()
test_translation()
test_rigid()
test_affine()
test_err()