|
1
|
|
|
import os |
|
2
|
|
|
|
|
3
|
|
|
import pytest |
|
4
|
|
|
|
|
5
|
|
|
from deepreg.vis import main, string_to_list |
|
6
|
|
|
|
|
7
|
|
|
|
|
8
|
|
|
def test_string_to_list(): |
|
9
|
|
|
string = "abc, 123, def, 456" |
|
10
|
|
|
got = string_to_list(string) |
|
11
|
|
|
expected = ["abc", "123", "def", "456"] |
|
12
|
|
|
assert got == expected |
|
13
|
|
|
|
|
14
|
|
|
|
|
15
|
|
|
class TestMain: |
|
16
|
|
|
img_paths = "./data/test/nifti/unit_test/moving_image.nii.gz" |
|
17
|
|
|
ddf_path = "./data/test/nifti/unit_test/ddf.nii.gz" |
|
18
|
|
|
|
|
19
|
|
|
def test_mode0(self): |
|
20
|
|
|
# test mode 0 and check output |
|
21
|
|
|
out_path = "logs/moving_image.gif" |
|
22
|
|
|
main( |
|
23
|
|
|
args=[ |
|
24
|
|
|
"--mode", |
|
25
|
|
|
0, |
|
26
|
|
|
"--image-paths", |
|
27
|
|
|
self.img_paths, |
|
28
|
|
|
"--save-path", |
|
29
|
|
|
"logs", |
|
30
|
|
|
"--interval", |
|
31
|
|
|
"50", |
|
32
|
|
|
] |
|
33
|
|
|
) |
|
34
|
|
|
assert os.path.exists(out_path) |
|
35
|
|
|
os.remove(out_path) |
|
36
|
|
|
|
|
37
|
|
|
def test_mode1_output(self): |
|
38
|
|
|
# test mode 1 and check output |
|
39
|
|
|
out_path_1 = "logs/moving_image_slice_1.gif" |
|
40
|
|
|
out_path_2 = "logs/moving_image_slice_2.gif" |
|
41
|
|
|
out_path_3 = "logs/moving_image_slice_3.gif" |
|
42
|
|
|
main( |
|
43
|
|
|
args=[ |
|
44
|
|
|
"--mode", |
|
45
|
|
|
"1", |
|
46
|
|
|
"--image-paths", |
|
47
|
|
|
self.img_paths, |
|
48
|
|
|
"--save-path", |
|
49
|
|
|
"logs", |
|
50
|
|
|
"--interval", |
|
51
|
|
|
"50", |
|
52
|
|
|
"--num-interval", |
|
53
|
|
|
"100", |
|
54
|
|
|
"--slice-inds", |
|
55
|
|
|
"1,2,3", |
|
56
|
|
|
"--ddf-path", |
|
57
|
|
|
self.ddf_path, |
|
58
|
|
|
] |
|
59
|
|
|
) |
|
60
|
|
|
assert os.path.exists(out_path_1) |
|
61
|
|
|
assert os.path.exists(out_path_2) |
|
62
|
|
|
assert os.path.exists(out_path_3) |
|
63
|
|
|
os.remove(out_path_1) |
|
64
|
|
|
os.remove(out_path_2) |
|
65
|
|
|
os.remove(out_path_3) |
|
66
|
|
|
|
|
67
|
|
|
def test_mode1_no_slidce_inds(self): |
|
68
|
|
|
# test mode 1 and check output when no slice_inds |
|
69
|
|
|
out_path_partial = "moving_image_slice" |
|
70
|
|
|
main( |
|
71
|
|
|
args=[ |
|
72
|
|
|
"--mode", |
|
73
|
|
|
"1", |
|
74
|
|
|
"--image-paths", |
|
75
|
|
|
self.img_paths, |
|
76
|
|
|
"--save-path", |
|
77
|
|
|
"logs", |
|
78
|
|
|
"--interval", |
|
79
|
|
|
"50", |
|
80
|
|
|
"--num-interval", |
|
81
|
|
|
"100", |
|
82
|
|
|
"--ddf-path", |
|
83
|
|
|
self.ddf_path, |
|
84
|
|
|
] |
|
85
|
|
|
) |
|
86
|
|
|
assert any([out_path_partial in file for file in os.listdir("logs")]) |
|
87
|
|
|
|
|
88
|
|
|
def test_mode1_err(self): |
|
89
|
|
|
# test mode 1 and check if exception is caught |
|
90
|
|
|
with pytest.raises(Exception) as err_info: |
|
91
|
|
|
main( |
|
92
|
|
|
args=[ |
|
93
|
|
|
"--mode", |
|
94
|
|
|
"1", |
|
95
|
|
|
"--image-paths", |
|
96
|
|
|
self.img_paths, |
|
97
|
|
|
"--save-path", |
|
98
|
|
|
"logs", |
|
99
|
|
|
"--interval", |
|
100
|
|
|
"50", |
|
101
|
|
|
"--num-interval", |
|
102
|
|
|
"100", |
|
103
|
|
|
"--slice-inds", |
|
104
|
|
|
"1,2,3", |
|
105
|
|
|
] |
|
106
|
|
|
) |
|
107
|
|
|
assert "--ddf-path is required when using --mode 1" in str(err_info.value) |
|
108
|
|
|
|
|
109
|
|
|
@pytest.mark.parametrize( |
|
110
|
|
|
"extra_args", |
|
111
|
|
|
[ |
|
112
|
|
|
[ |
|
113
|
|
|
"--slice-inds", |
|
114
|
|
|
"1,2,3", |
|
115
|
|
|
"--fname", |
|
116
|
|
|
"visualisation.png", |
|
117
|
|
|
"--col-titles", |
|
118
|
|
|
"abc", |
|
119
|
|
|
], |
|
120
|
|
|
[ |
|
121
|
|
|
"--slice-inds", |
|
122
|
|
|
"1,2,3", |
|
123
|
|
|
"--fname", |
|
124
|
|
|
"visualisation.png", |
|
125
|
|
|
], # no col_titles |
|
126
|
|
|
[ |
|
127
|
|
|
"--col-titles", |
|
128
|
|
|
"abc", |
|
129
|
|
|
], # no slice_inds and no fname |
|
130
|
|
|
], |
|
131
|
|
|
) |
|
132
|
|
|
def test_mode2_output(self, extra_args): |
|
133
|
|
|
# test mode 2 and check output |
|
134
|
|
|
common_args = [ |
|
135
|
|
|
"--mode", |
|
136
|
|
|
"2", |
|
137
|
|
|
"--image-paths", |
|
138
|
|
|
self.img_paths, |
|
139
|
|
|
"--save-path", |
|
140
|
|
|
"logs", |
|
141
|
|
|
] |
|
142
|
|
|
out_path = "logs/visualisation.png" |
|
143
|
|
|
main(args=common_args + extra_args) |
|
144
|
|
|
assert os.path.exists(out_path) |
|
145
|
|
|
os.remove(out_path) |
|
146
|
|
|
|
|
147
|
|
|
@pytest.mark.parametrize( |
|
148
|
|
|
"extra_args", |
|
149
|
|
|
[ |
|
150
|
|
|
[ |
|
151
|
|
|
"--fname", |
|
152
|
|
|
"visualisation.gif", |
|
153
|
|
|
], |
|
154
|
|
|
[], # no fname |
|
155
|
|
|
], |
|
156
|
|
|
) |
|
157
|
|
|
def test_case3(self, extra_args): |
|
158
|
|
|
# test mode 3 and check output |
|
159
|
|
|
out_path = "logs/visualisation.gif" |
|
160
|
|
|
img_paths_moded = ",".join([self.img_paths] * 6) |
|
161
|
|
|
common_args = [ |
|
162
|
|
|
"--mode", |
|
163
|
|
|
"3", |
|
164
|
|
|
"--image-paths", |
|
165
|
|
|
img_paths_moded, |
|
166
|
|
|
"--save-path", |
|
167
|
|
|
"logs", |
|
168
|
|
|
"--interval", |
|
169
|
|
|
"50", |
|
170
|
|
|
"--size", |
|
171
|
|
|
"2,3", |
|
172
|
|
|
] |
|
173
|
|
|
main( |
|
174
|
|
|
args=common_args + extra_args, |
|
175
|
|
|
) |
|
176
|
|
|
assert os.path.exists(out_path) |
|
177
|
|
|
os.remove(out_path) |
|
178
|
|
|
|
|
179
|
|
|
def test_mode3_num_image_err(self): |
|
180
|
|
|
# test mode 3 and check if exception is caught |
|
181
|
|
|
img_paths = ",".join([self.img_paths] * 6) |
|
182
|
|
|
with pytest.raises(Exception) as err_info: |
|
183
|
|
|
main( |
|
184
|
|
|
args=[ |
|
185
|
|
|
"--mode", |
|
186
|
|
|
"3", |
|
187
|
|
|
"--image-paths", |
|
188
|
|
|
img_paths, |
|
189
|
|
|
"--save-path", |
|
190
|
|
|
"logs", |
|
191
|
|
|
"--interval", |
|
192
|
|
|
"50", |
|
193
|
|
|
"--size", |
|
194
|
|
|
"2,1", |
|
195
|
|
|
"--fname", |
|
196
|
|
|
"visualisation.gif", |
|
197
|
|
|
] |
|
198
|
|
|
) |
|
199
|
|
|
assert "The number of images supplied is " in str(err_info.value) |
|
200
|
|
|
|
|
201
|
|
|
def test_mode3_shape_err(self): |
|
202
|
|
|
# test mode 3 and check if exception is caught |
|
203
|
|
|
new_img_path = "data/test/nifti/paired/test/fixed_images/case000025.nii.gz" |
|
204
|
|
|
img_paths_moded = self.img_paths + "," + new_img_path |
|
205
|
|
|
with pytest.raises(Exception) as err_info: |
|
206
|
|
|
main( |
|
207
|
|
|
args=[ |
|
208
|
|
|
"--mode", |
|
209
|
|
|
"3", |
|
210
|
|
|
"--image-paths", |
|
211
|
|
|
img_paths_moded, |
|
212
|
|
|
"--save-path", |
|
213
|
|
|
"logs", |
|
214
|
|
|
"--interval", |
|
215
|
|
|
"50", |
|
216
|
|
|
"--size", |
|
217
|
|
|
"2,1", |
|
218
|
|
|
"--fname", |
|
219
|
|
|
"visualisation.gif", |
|
220
|
|
|
] |
|
221
|
|
|
) |
|
222
|
|
|
assert "all images do not have equal shapes" in str(err_info.value) |
|
223
|
|
|
|
DeepRegNet /
DeepReg
