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josephmjejosephmje
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add test
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‎nipype/interfaces/fsl/tests/test_auto_Eddy.py‎

Lines changed: 211 additions & 40 deletions
Original file line numberDiff line numberDiff line change
@@ -4,39 +4,204 @@
44

55
def test_Eddy_inputs():
66
input_map = dict(
7-
args=dict(argstr="%s",),
8-
cnr_maps=dict(argstr="--cnr_maps", min_ver="5.0.10",),
9-
dont_peas=dict(argstr="--dont_peas",),
10-
dont_sep_offs_move=dict(argstr="--dont_sep_offs_move",),
11-
environ=dict(nohash=True, usedefault=True,),
12-
fep=dict(argstr="--fep",),
13-
field=dict(argstr="--field=%s",),
14-
field_mat=dict(argstr="--field_mat=%s", extensions=None,),
15-
flm=dict(argstr="--flm=%s",),
16-
fudge_factor=dict(argstr="--ff=%s", usedefault=True,),
17-
fwhm=dict(argstr="--fwhm=%s",),
18-
in_acqp=dict(argstr="--acqp=%s", extensions=None, mandatory=True,),
19-
in_bval=dict(argstr="--bvals=%s", extensions=None, mandatory=True,),
20-
in_bvec=dict(argstr="--bvecs=%s", extensions=None, mandatory=True,),
21-
in_file=dict(argstr="--imain=%s", extensions=None, mandatory=True,),
22-
in_index=dict(argstr="--index=%s", extensions=None, mandatory=True,),
23-
in_mask=dict(argstr="--mask=%s", extensions=None, mandatory=True,),
7+
args=dict(argstr='%s', ),
8+
cnr_maps=dict(
9+
argstr='--cnr_maps',
10+
min_ver='5.0.10',
11+
),
12+
dont_peas=dict(argstr='--dont_peas', ),
13+
dont_sep_offs_move=dict(argstr='--dont_sep_offs_move', ),
14+
environ=dict(
15+
nohash=True,
16+
usedefault=True,
17+
),
18+
estimate_move_by_susceptibility=dict(
19+
argstr='--estimate_move_by_susceptibility',
20+
min_ver='6.0.1',
21+
),
22+
fep=dict(argstr='--fep', ),
23+
field=dict(
24+
argstr='--field=%s',
25+
extensions=None,
26+
),
27+
field_mat=dict(
28+
argstr='--field_mat=%s',
29+
extensions=None,
30+
),
31+
flm=dict(
32+
argstr='--flm=%s',
33+
usedefault=True,
34+
),
35+
fudge_factor=dict(
36+
argstr='--ff=%s',
37+
usedefault=True,
38+
),
39+
fwhm=dict(
40+
argstr='--fwhm=%s',
41+
usedefault=True,
42+
),
43+
in_acqp=dict(
44+
argstr='--acqp=%s',
45+
extensions=None,
46+
mandatory=True,
47+
),
48+
in_bval=dict(
49+
argstr='--bvals=%s',
50+
extensions=None,
51+
mandatory=True,
52+
),
53+
in_bvec=dict(
54+
argstr='--bvecs=%s',
55+
extensions=None,
56+
mandatory=True,
57+
),
58+
in_file=dict(
59+
argstr='--imain=%s',
60+
extensions=None,
61+
mandatory=True,
62+
),
63+
in_index=dict(
64+
argstr='--index=%s',
65+
extensions=None,
66+
mandatory=True,
67+
),
68+
in_mask=dict(
69+
argstr='--mask=%s',
70+
extensions=None,
71+
mandatory=True,
72+
),
2473
in_topup_fieldcoef=dict(
25-
argstr="--topup=%s", extensions=None, requires=["in_topup_movpar"],
26-
),
27-
in_topup_movpar=dict(extensions=None, requires=["in_topup_fieldcoef"],),
28-
interp=dict(argstr="--interp=%s",),
29-
is_shelled=dict(argstr="--data_is_shelled",),
30-
method=dict(argstr="--resamp=%s",),
31-
niter=dict(argstr="--niter=%s", usedefault=True,),
32-
num_threads=dict(nohash=True, usedefault=True,),
33-
nvoxhp=dict(argstr="--nvoxhp=%s", usedefault=True,),
34-
out_base=dict(argstr="--out=%s", usedefault=True,),
74+
argstr='--topup=%s',
75+
extensions=None,
76+
requires=['in_topup_movpar'],
77+
),
78+
in_topup_movpar=dict(
79+
extensions=None,
80+
requires=['in_topup_fieldcoef'],
81+
),
82+
initrand=dict(
83+
argstr='--initrand',
84+
min_ver='5.0.10',
85+
),
86+
interp=dict(
87+
argstr='--interp=%s',
88+
usedefault=True,
89+
),
90+
is_shelled=dict(argstr='--data_is_shelled', ),
91+
json=dict(
92+
argstr='--json=%s',
93+
min_ver='6.0.1',
94+
requires=['mporder'],
95+
xor=['slspec'],
96+
),
97+
mb=dict(
98+
argstr='--mb=%s',
99+
min_ver='5.0.10',
100+
),
101+
mb_offs=dict(
102+
argstr='--mb_offs=%s',
103+
min_ver='5.0.10',
104+
requires=['mb'],
105+
),
106+
mbs_ksp=dict(
107+
argstr='--mbs_ksp=%smm',
108+
min_ver='6.0.1',
109+
requires=['estimate_move_by_susceptibility'],
110+
),
111+
mbs_lambda=dict(
112+
argstr='--mbs_lambda=%s',
113+
min_ver='6.0.1',
114+
requires=['estimate_move_by_susceptibility'],
115+
),
116+
mbs_niter=dict(
117+
argstr='--mbs_niter=%s',
118+
min_ver='6.0.1',
119+
requires=['estimate_move_by_susceptibility'],
120+
),
121+
method=dict(
122+
argstr='--resamp=%s',
123+
usedefault=True,
124+
),
125+
mporder=dict(
126+
argstr='--mporder=%s',
127+
min_ver='5.0.11',
128+
),
129+
niter=dict(
130+
argstr='--niter=%s',
131+
usedefault=True,
132+
),
133+
num_threads=dict(
134+
nohash=True,
135+
usedefault=True,
136+
),
137+
nvoxhp=dict(
138+
argstr='--nvoxhp=%s',
139+
usedefault=True,
140+
),
141+
out_base=dict(
142+
argstr='--out=%s',
143+
usedefault=True,
144+
),
145+
outlier_nstd=dict(
146+
argstr='--ol_nstd',
147+
min_ver='5.0.10',
148+
requires=['repol'],
149+
),
150+
outlier_nvox=dict(
151+
argstr='--ol_nvox',
152+
min_ver='5.0.10',
153+
requires=['repol'],
154+
),
155+
outlier_pos=dict(
156+
argstr='--ol_pos',
157+
min_ver='5.0.10',
158+
requires=['repol'],
159+
),
160+
outlier_sqr=dict(
161+
argstr='--ol_sqr',
162+
min_ver='5.0.10',
163+
requires=['repol'],
164+
),
165+
outlier_type=dict(
166+
argstr='--ol_type',
167+
min_ver='5.0.10',
168+
requires=['repol'],
169+
),
35170
output_type=dict(),
36-
repol=dict(argstr="--repol",),
37-
residuals=dict(argstr="--residuals", min_ver="5.0.10",),
38-
session=dict(argstr="--session=%s", extensions=None,),
39-
slm=dict(argstr="--slm=%s",),
171+
repol=dict(argstr='--repol', ),
172+
residuals=dict(
173+
argstr='--residuals',
174+
min_ver='5.0.10',
175+
),
176+
s2v_interp=dict(
177+
argstr='--s2v_interp=%s',
178+
min_ver='5.0.11',
179+
requires=['mporder'],
180+
),
181+
s2v_lambda=dict(
182+
agstr='--s2v_lambda',
183+
min_ver='5.0.11',
184+
requires=['mporder'],
185+
),
186+
s2v_niter=dict(
187+
argstr='--s2v_niter=%s',
188+
min_ver='5.0.11',
189+
requires=['mporder'],
190+
),
191+
session=dict(
192+
argstr='--session=%s',
193+
extensions=None,
194+
),
195+
slm=dict(
196+
argstr='--slm=%s',
197+
usedefault=True,
198+
),
199+
slspec=dict(
200+
argstr='--slspec=%s',
201+
min_ver='5.0.11',
202+
requires=['mporder'],
203+
xor=['json'],
204+
),
40205
use_cuda=dict(),
41206
)
42207
inputs = Eddy.input_spec()
@@ -48,15 +213,21 @@ def test_Eddy_inputs():
48213

49214
def test_Eddy_outputs():
50215
output_map = dict(
51-
out_cnr_maps=dict(extensions=None,),
52-
out_corrected=dict(extensions=None,),
53-
out_movement_rms=dict(extensions=None,),
54-
out_outlier_report=dict(extensions=None,),
55-
out_parameter=dict(extensions=None,),
56-
out_residuals=dict(extensions=None,),
57-
out_restricted_movement_rms=dict(extensions=None,),
58-
out_rotated_bvecs=dict(extensions=None,),
59-
out_shell_alignment_parameters=dict(extensions=None,),
216+
out_cnr_maps=dict(extensions=None, ),
217+
out_corrected=dict(extensions=None, ),
218+
out_movement_over_time=dict(extensions=None, ),
219+
out_movement_rms=dict(extensions=None, ),
220+
out_outlier_free=dict(extensions=None, ),
221+
out_outlier_map=dict(extensions=None, ),
222+
out_outlier_n_sqr_stdev_map=dict(extensions=None, ),
223+
out_outlier_n_stdev_map=dict(extensions=None, ),
224+
out_outlier_report=dict(extensions=None, ),
225+
out_parameter=dict(extensions=None, ),
226+
out_residuals=dict(extensions=None, ),
227+
out_restricted_movement_rms=dict(extensions=None, ),
228+
out_rotated_bvecs=dict(extensions=None, ),
229+
out_shell_alignment_parameters=dict(extensions=None, ),
230+
out_shell_pe_translation_parameters=dict(extensions=None, ),
60231
)
61232
outputs = Eddy.output_spec()
62233

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