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TEST: Run make specs
1 parent 14653a4 commit 0ecb22a

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lines changed

‎nipype/algorithms/tests/test_auto_CompCor.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..confounds import CompCor
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def test_CompCor_inputs():
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input_map = dict(components_file=dict(usedefault=True,
7+
),
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header=dict(),
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ignore_exception=dict(nohash=True,
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usedefault=True,
11+
),
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mask_file=dict(),
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num_components=dict(usedefault=True,
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),
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realigned_file=dict(mandatory=True,
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),
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regress_poly_degree=dict(usedefault=True,
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),
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use_regress_poly=dict(usedefault=True,
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),
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)
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inputs = CompCor.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_CompCor_outputs():
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output_map = dict(components_file=dict(),
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)
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outputs = CompCor.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value

‎nipype/algorithms/tests/test_auto_ErrorMap.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..metrics import ErrorMap
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def test_ErrorMap_inputs():
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input_map = dict(ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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in_ref=dict(mandatory=True,
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),
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in_tst=dict(mandatory=True,
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),
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mask=dict(),
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metric=dict(mandatory=True,
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usedefault=True,
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),
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out_map=dict(),
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)
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inputs = ErrorMap.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_ErrorMap_outputs():
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output_map = dict(distance=dict(),
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out_map=dict(),
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)
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outputs = ErrorMap.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value

‎nipype/algorithms/tests/test_auto_Overlap.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..misc import Overlap
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def test_Overlap_inputs():
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input_map = dict(bg_overlap=dict(mandatory=True,
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usedefault=True,
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),
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ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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mask_volume=dict(),
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out_file=dict(usedefault=True,
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),
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vol_units=dict(mandatory=True,
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usedefault=True,
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),
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volume1=dict(mandatory=True,
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),
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volume2=dict(mandatory=True,
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),
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weighting=dict(usedefault=True,
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),
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)
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inputs = Overlap.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_Overlap_outputs():
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output_map = dict(dice=dict(),
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diff_file=dict(),
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jaccard=dict(),
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labels=dict(),
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roi_di=dict(),
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roi_ji=dict(),
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roi_voldiff=dict(),
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volume_difference=dict(),
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)
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outputs = Overlap.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value

‎nipype/algorithms/tests/test_auto_TSNR.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..misc import TSNR
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def test_TSNR_inputs():
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input_map = dict(detrended_file=dict(hash_files=False,
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usedefault=True,
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),
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ignore_exception=dict(nohash=True,
10+
usedefault=True,
11+
),
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in_file=dict(mandatory=True,
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),
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mean_file=dict(hash_files=False,
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usedefault=True,
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),
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regress_poly=dict(),
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stddev_file=dict(hash_files=False,
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usedefault=True,
20+
),
21+
tsnr_file=dict(hash_files=False,
22+
usedefault=True,
23+
),
24+
)
25+
inputs = TSNR.input_spec()
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27+
for key, metadata in list(input_map.items()):
28+
for metakey, value in list(metadata.items()):
29+
assert getattr(inputs.traits()[key], metakey) == value
30+
31+
32+
def test_TSNR_outputs():
33+
output_map = dict(detrended_file=dict(),
34+
mean_file=dict(),
35+
stddev_file=dict(),
36+
tsnr_file=dict(),
37+
)
38+
outputs = TSNR.output_spec()
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40+
for key, metadata in list(output_map.items()):
41+
for metakey, value in list(metadata.items()):
42+
assert getattr(outputs.traits()[key], metakey) == value

‎nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py

+16
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@@ -55,7 +55,23 @@ def test_antsBrainExtraction_inputs():
5555

5656
def test_antsBrainExtraction_outputs():
5757
output_map = dict(BrainExtractionBrain=dict(),
58+
BrainExtractionCSF=dict(),
59+
BrainExtractionGM=dict(),
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BrainExtractionInitialAffine=dict(),
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BrainExtractionInitialAffineFixed=dict(),
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BrainExtractionInitialAffineMoving=dict(),
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BrainExtractionLaplacian=dict(),
5864
BrainExtractionMask=dict(),
65+
BrainExtractionPrior0GenericAffine=dict(),
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BrainExtractionPrior1InverseWarp=dict(),
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BrainExtractionPrior1Warp=dict(),
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BrainExtractionPriorWarped=dict(),
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BrainExtractionSegmentation=dict(),
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BrainExtractionTemplateLaplacian=dict(),
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BrainExtractionTmp=dict(),
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BrainExtractionWM=dict(),
73+
N4Corrected0=dict(),
74+
N4Truncated0=dict(),
5975
)
6076
outputs = antsBrainExtraction.output_spec()
6177

‎nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py

+2
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@@ -26,6 +26,8 @@ def test_ReconAll_inputs():
2626
),
2727
openmp=dict(argstr='-openmp %d',
2828
),
29+
parallel=dict(argstr='-parallel',
30+
),
2931
subject_id=dict(argstr='-subjid %s',
3032
usedefault=True,
3133
),

‎nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py

+163
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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..preprocess import ApplyXFM
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def test_ApplyXFM_inputs():
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input_map = dict(angle_rep=dict(argstr='-anglerep %s',
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),
8+
apply_isoxfm=dict(argstr='-applyisoxfm %f',
9+
xor=[u'apply_xfm'],
10+
),
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apply_xfm=dict(argstr='-applyxfm',
12+
requires=[u'in_matrix_file'],
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usedefault=True,
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),
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args=dict(argstr='%s',
16+
),
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bbrslope=dict(argstr='-bbrslope %f',
18+
min_ver='5.0.0',
19+
),
20+
bbrtype=dict(argstr='-bbrtype %s',
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min_ver='5.0.0',
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),
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bgvalue=dict(argstr='-setbackground %f',
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),
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bins=dict(argstr='-bins %d',
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),
27+
coarse_search=dict(argstr='-coarsesearch %d',
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units='degrees',
29+
),
30+
cost=dict(argstr='-cost %s',
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),
32+
cost_func=dict(argstr='-searchcost %s',
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),
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datatype=dict(argstr='-datatype %s',
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),
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display_init=dict(argstr='-displayinit',
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),
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dof=dict(argstr='-dof %d',
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),
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echospacing=dict(argstr='-echospacing %f',
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min_ver='5.0.0',
42+
),
43+
environ=dict(nohash=True,
44+
usedefault=True,
45+
),
46+
fieldmap=dict(argstr='-fieldmap %s',
47+
min_ver='5.0.0',
48+
),
49+
fieldmapmask=dict(argstr='-fieldmapmask %s',
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min_ver='5.0.0',
51+
),
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fine_search=dict(argstr='-finesearch %d',
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units='degrees',
54+
),
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force_scaling=dict(argstr='-forcescaling',
56+
),
57+
ignore_exception=dict(nohash=True,
58+
usedefault=True,
59+
),
60+
in_file=dict(argstr='-in %s',
61+
mandatory=True,
62+
position=0,
63+
),
64+
in_matrix_file=dict(argstr='-init %s',
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),
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in_weight=dict(argstr='-inweight %s',
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),
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interp=dict(argstr='-interp %s',
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),
70+
min_sampling=dict(argstr='-minsampling %f',
71+
units='mm',
72+
),
73+
no_clamp=dict(argstr='-noclamp',
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),
75+
no_resample=dict(argstr='-noresample',
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),
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no_resample_blur=dict(argstr='-noresampblur',
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),
79+
no_search=dict(argstr='-nosearch',
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),
81+
out_file=dict(argstr='-out %s',
82+
hash_files=False,
83+
name_source=[u'in_file'],
84+
name_template='%s_flirt',
85+
position=2,
86+
),
87+
out_log=dict(keep_extension=True,
88+
name_source=[u'in_file'],
89+
name_template='%s_flirt.log',
90+
requires=[u'save_log'],
91+
),
92+
out_matrix_file=dict(argstr='-omat %s',
93+
hash_files=False,
94+
keep_extension=True,
95+
name_source=[u'in_file'],
96+
name_template='%s_flirt.mat',
97+
position=3,
98+
),
99+
output_type=dict(),
100+
padding_size=dict(argstr='-paddingsize %d',
101+
units='voxels',
102+
),
103+
pedir=dict(argstr='-pedir %d',
104+
min_ver='5.0.0',
105+
),
106+
ref_weight=dict(argstr='-refweight %s',
107+
),
108+
reference=dict(argstr='-ref %s',
109+
mandatory=True,
110+
position=1,
111+
),
112+
rigid2D=dict(argstr='-2D',
113+
),
114+
save_log=dict(),
115+
schedule=dict(argstr='-schedule %s',
116+
),
117+
searchr_x=dict(argstr='-searchrx %s',
118+
units='degrees',
119+
),
120+
searchr_y=dict(argstr='-searchry %s',
121+
units='degrees',
122+
),
123+
searchr_z=dict(argstr='-searchrz %s',
124+
units='degrees',
125+
),
126+
sinc_width=dict(argstr='-sincwidth %d',
127+
units='voxels',
128+
),
129+
sinc_window=dict(argstr='-sincwindow %s',
130+
),
131+
terminal_output=dict(nohash=True,
132+
),
133+
uses_qform=dict(argstr='-usesqform',
134+
),
135+
verbose=dict(argstr='-verbose %d',
136+
),
137+
wm_seg=dict(argstr='-wmseg %s',
138+
min_ver='5.0.0',
139+
),
140+
wmcoords=dict(argstr='-wmcoords %s',
141+
min_ver='5.0.0',
142+
),
143+
wmnorms=dict(argstr='-wmnorms %s',
144+
min_ver='5.0.0',
145+
),
146+
)
147+
inputs = ApplyXFM.input_spec()
148+
149+
for key, metadata in list(input_map.items()):
150+
for metakey, value in list(metadata.items()):
151+
assert getattr(inputs.traits()[key], metakey) == value
152+
153+
154+
def test_ApplyXFM_outputs():
155+
output_map = dict(out_file=dict(),
156+
out_log=dict(),
157+
out_matrix_file=dict(),
158+
)
159+
outputs = ApplyXFM.output_spec()
160+
161+
for key, metadata in list(output_map.items()):
162+
for metakey, value in list(metadata.items()):
163+
assert getattr(outputs.traits()[key], metakey) == value

‎nipype/interfaces/fsl/tests/test_auto_Eddy.py

+7-2
Original file line numberDiff line numberDiff line change
@@ -38,9 +38,9 @@ def test_Eddy_inputs():
3838
mandatory=True,
3939
),
4040
in_topup_fieldcoef=dict(argstr='--topup=%s',
41-
requires=['in_topup_movpar'],
41+
requires=[u'in_topup_movpar'],
4242
),
43-
in_topup_movpar=dict(requires=['in_topup_fieldcoef'],
43+
in_topup_movpar=dict(requires=[u'in_topup_fieldcoef'],
4444
),
4545
is_shelled=dict(argstr='--data_is_shelled',
4646
),
@@ -72,7 +72,12 @@ def test_Eddy_inputs():
7272

7373
def test_Eddy_outputs():
7474
output_map = dict(out_corrected=dict(),
75+
out_movement_rms=dict(),
76+
out_outlier_report=dict(),
7577
out_parameter=dict(),
78+
out_restricted_movement_rms=dict(),
79+
out_rotated_bvecs=dict(),
80+
out_shell_alignment_parameters=dict(),
7681
)
7782
outputs = Eddy.output_spec()
7883

‎nipype/interfaces/fsl/tests/test_auto_FNIRT.py

+1
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@@ -47,6 +47,7 @@ def test_FNIRT_inputs():
4747
sep=',',
4848
),
4949
in_intensitymap_file=dict(argstr='--intin=%s',
50+
copyfiles=False,
5051
),
5152
inmask_file=dict(argstr='--inmask=%s',
5253
),

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