|
1
|
|
|
import unittest |
|
2
|
|
|
from mock import Mock, patch |
|
3
|
|
|
|
|
4
|
|
|
|
|
5
|
|
|
class MnefunTests(unittest.TestCase): |
|
6
|
|
|
|
|
7
|
|
|
def setUp(self): |
|
8
|
|
|
self.listener = Mock() |
|
9
|
|
|
self.libs = Mock() |
|
10
|
|
|
self.dependencies = Mock() |
|
11
|
|
|
self.dependencies.getListener.return_value = self.listener |
|
12
|
|
|
self.dependencies.getLibraries.return_value = self.libs |
|
13
|
|
|
|
|
14
|
|
|
@unittest.skip("Needs to be fixed for new mnefun support code.") |
|
15
|
|
|
def test_Discovers_fetched_raw_files(self): |
|
16
|
|
|
import niprov.mnefunsupport |
|
17
|
|
|
class MockParams(object): |
|
18
|
|
|
pass |
|
19
|
|
|
params = MockParams() |
|
20
|
|
|
params.work_dir = '/root' |
|
21
|
|
|
params.subjects = ['johndoe','janedoe'] |
|
22
|
|
|
params.raw_dir = 'rawdir' |
|
23
|
|
|
def fetch_raw_files(): |
|
24
|
|
|
pass |
|
25
|
|
|
with patch('niprov.mnefunsupport.discover') as discover: |
|
26
|
|
|
niprov.mnefunsupport.handler('Pulling raw files from acquisition machine', |
|
27
|
|
|
fetch_raw_files, None, params, dependencies=self.dependencies) |
|
28
|
|
|
discover.assert_any_call('/root/johndoe/rawdir') |
|
29
|
|
|
discover.assert_any_call('/root/janedoe/rawdir') |
|
30
|
|
|
self.listener.mnefunEventReceived.assert_called_with('fetch_raw_files') |
|
31
|
|
|
|
|
32
|
|
View Code Duplication |
@unittest.skip("Needs to be fixed for new mnefun support code.") |
|
|
|
|
|
|
33
|
|
|
def test_Logs_sss_operation(self): |
|
34
|
|
|
import niprov.mnefunsupport |
|
35
|
|
|
class MockParams(object): |
|
36
|
|
|
pass |
|
37
|
|
|
params = MockParams() |
|
38
|
|
|
params.subjects = ['s1','s2'] |
|
39
|
|
|
fnames = {'raw':{'s1':['subj 1 raw file 1','subj 1 raw file 2'], |
|
40
|
|
|
's2':['subj 2 raw file 1','subj 2 raw file 2']}, |
|
41
|
|
|
'sss': {'s1':['subj 1 sss file 1','subj 1 sss file 2'], |
|
42
|
|
|
's2':['subj 2 sss file 1','subj 2 sss file 2']}} |
|
43
|
|
|
self.libs.mnefun.get_raw_fnames.side_effect = lambda p, s, t: fnames[t][s] |
|
44
|
|
|
def fetch_sss_files(): |
|
45
|
|
|
pass |
|
46
|
|
|
with patch('niprov.mnefunsupport.log') as log: |
|
47
|
|
|
niprov.mnefunsupport.handler('Pulling SSS files from remote workstation', |
|
48
|
|
|
fetch_sss_files, None, params, dependencies=self.dependencies) |
|
49
|
|
|
log.assert_any_call(fnames['sss']['s1'][0], |
|
50
|
|
|
'Signal Space Separation', |
|
51
|
|
|
fnames['raw']['s1'][0], provenance = {'mnefun':{}}) |
|
52
|
|
|
log.assert_any_call(fnames['sss']['s2'][1], |
|
53
|
|
|
'Signal Space Separation', |
|
54
|
|
|
fnames['raw']['s2'][1], provenance = {'mnefun':{}}) |
|
55
|
|
|
|
|
56
|
|
View Code Duplication |
@unittest.skip("Needs to be fixed for new mnefun support code.") |
|
|
|
|
|
|
57
|
|
|
def test_Logs_ssp_operation(self): |
|
58
|
|
|
import niprov.mnefunsupport |
|
59
|
|
|
class MockParams(object): |
|
60
|
|
|
pass |
|
61
|
|
|
params = MockParams() |
|
62
|
|
|
params.subjects = ['s1','s2'] |
|
63
|
|
|
fnames = {'pca':{'s1':['subj 1 pca file 1','subj 1 pca file 2'], |
|
64
|
|
|
's2':['subj 2 pca file 1','subj 2 pca file 2']}, |
|
65
|
|
|
'sss': {'s1':['subj 1 sss file 1','subj 1 sss file 2'], |
|
66
|
|
|
's2':['subj 2 sss file 1','subj 2 sss file 2']}} |
|
67
|
|
|
self.libs.mnefun.get_raw_fnames.side_effect = lambda p, s, t: fnames[t][s] |
|
68
|
|
|
def apply_preprocessing_combined(): |
|
69
|
|
|
pass |
|
70
|
|
|
with patch('niprov.mnefunsupport.log') as log: |
|
71
|
|
|
niprov.mnefunsupport.handler('Apply SSP vectors and filtering.', |
|
72
|
|
|
apply_preprocessing_combined, None, params, |
|
73
|
|
|
dependencies=self.dependencies) |
|
74
|
|
|
log.assert_any_call(fnames['pca']['s1'][0], |
|
75
|
|
|
'Signal Space Projection', |
|
76
|
|
|
fnames['sss']['s1'][0], provenance = {'mnefun':{}}) |
|
77
|
|
|
log.assert_any_call(fnames['pca']['s2'][1], |
|
78
|
|
|
'Signal Space Projection', |
|
79
|
|
|
fnames['sss']['s2'][1], provenance = {'mnefun':{}}) |
|
80
|
|
|
|
|
81
|
|
|
@unittest.skip("Needs to be fixed for new mnefun support code.") |
|
82
|
|
|
def test_Logs_epoch_operation(self): |
|
83
|
|
|
import niprov.mnefunsupport |
|
84
|
|
|
class MockParams(object): |
|
85
|
|
|
pass |
|
86
|
|
|
params = MockParams() |
|
87
|
|
|
params.subjects = ['s1','s2'] |
|
88
|
|
|
params.analyses = ['a'] |
|
89
|
|
|
fnames = {'pca':{'s1':['subj 1 pca file 1','subj 1 pca file 2'], |
|
90
|
|
|
's2':['subj 2 pca file 1','subj 2 pca file 2']}} |
|
91
|
|
|
epochfnames = {'s1':['s1 evt 1','s1 evt 2','s1 evt 3'], |
|
92
|
|
|
's2':['s2 evt 1','s2 evt 2','s2 evt 3']} |
|
93
|
|
|
self.libs.mnefun.get_raw_fnames.side_effect = \ |
|
94
|
|
|
lambda p, s, t: fnames[t][s] |
|
95
|
|
|
self.libs.mnefun._paths.get_epochs_evokeds_fnames.side_effect = \ |
|
96
|
|
|
lambda p, s, a: epochfnames[s] |
|
97
|
|
|
def save_epochs(): |
|
98
|
|
|
pass |
|
99
|
|
|
with patch('niprov.mnefunsupport.log') as log: |
|
100
|
|
|
niprov.mnefunsupport.handler('Doing epoch EQ/DQ', |
|
101
|
|
|
save_epochs, None, params, dependencies=self.dependencies) |
|
102
|
|
|
log.assert_any_call(epochfnames['s1'][0], #any event file |
|
103
|
|
|
'Epoching', |
|
104
|
|
|
fnames['pca']['s1'], provenance = {'mnefun':{}}) #all raw files for subj |
|
105
|
|
|
log.assert_any_call(epochfnames['s2'][1], #any event file |
|
106
|
|
|
'Epoching', |
|
107
|
|
|
fnames['pca']['s2'], provenance = {'mnefun':{}}) #all raw files for subj |
|
108
|
|
|
|
|
109
|
|
|
@unittest.skip("Needs to be fixed for new mnefun support code.") |
|
110
|
|
|
def test_Log_seeded_with_params_based_custom_provenance(self): |
|
111
|
|
|
import niprov.mnefunsupport |
|
112
|
|
|
class MockParams(object): |
|
113
|
|
|
pass |
|
114
|
|
|
params = MockParams() |
|
115
|
|
|
params.tmin = -0.2 |
|
116
|
|
|
params.quat_tol = 5e-2 |
|
117
|
|
|
params.subjects = ['s1','s2'] |
|
118
|
|
|
fnames = {'raw':{'s1':['subj 1 raw file 1','subj 1 raw file 2'], |
|
119
|
|
|
's2':['subj 2 raw file 1','subj 2 raw file 2']}, |
|
120
|
|
|
'sss': {'s1':['subj 1 sss file 1','subj 1 sss file 2'], |
|
121
|
|
|
's2':['subj 2 sss file 1','subj 2 sss file 2']}} |
|
122
|
|
|
self.libs.mnefun.get_raw_fnames.side_effect = lambda p, s, t: fnames[t][s] |
|
123
|
|
|
def fetch_sss_files(): |
|
124
|
|
|
pass |
|
125
|
|
|
with patch('niprov.mnefunsupport.log') as log: |
|
126
|
|
|
niprov.mnefunsupport.handler('Pulling SSS files from remote workstation', |
|
127
|
|
|
fetch_sss_files, None, params, dependencies=self.dependencies) |
|
128
|
|
|
log.assert_called_with(fnames['sss']['s2'][1], |
|
129
|
|
|
'Signal Space Separation', |
|
130
|
|
|
fnames['raw']['s2'][1], |
|
131
|
|
|
provenance={'mnefun':{ |
|
132
|
|
|
'tmin':-0.2, |
|
133
|
|
|
'quat_tol':5e-2}}) |
|
134
|
|
|
|
|
135
|
|
|
|
|
136
|
|
|
# write_epochs : bool |
|
137
|
|
|
# Write epochs to disk. |
|
138
|
|
|
# gen_covs : bool |
|
139
|
|
|
# Generate covariances. |
|
140
|
|
|
# gen_fwd : bool |
|
141
|
|
|
# Generate forward solutions. |
|
142
|
|
|
# get_inv : bool |
|
143
|
|
|
# Generate inverses. |
|
144
|
|
|
# gen_report : bool |
|
145
|
|
|
# Generate HTML reports. |
|
146
|
|
|
|
|
147
|
|
|
|
ilogue /
niprov
Loading history...