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FIX: PEP8 - E241 multiple spaces after ',' - 2nd clean up
1 parent 1df2021 commit 42b2ae4

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+540
-558
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22 files changed

+540
-558
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‎examples/dmri_preprocessing.py

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -155,14 +155,14 @@
155155
wf = pe.Workflow(name="dMRI_Preprocessing")
156156
wf.base_dir = os.path.abspath('preprocessing_dmri_tutorial')
157157
wf.connect([
158-
(infosource, datasource, [('subject_id', 'subject_id')]),
159-
(datasource, prep, [('dwi', 'inputnode.in_file'),
160-
('dwi_rev', 'inputnode.alt_file'),
161-
('bvals', 'inputnode.in_bval'),
162-
('bvecs', 'inputnode.in_bvec')]),
163-
(prep, bias, [('outputnode.out_file', 'inputnode.in_file'),
164-
('outputnode.out_mask', 'inputnode.in_mask')]),
165-
(datasource, bias, [('bvals', 'inputnode.in_bval')])
158+
(infosource, datasource, [('subject_id', 'subject_id')]),
159+
(datasource, prep, [('dwi', 'inputnode.in_file'),
160+
('dwi_rev', 'inputnode.alt_file'),
161+
('bvals', 'inputnode.in_bval'),
162+
('bvecs', 'inputnode.in_bvec')]),
163+
(prep, bias, [('outputnode.out_file', 'inputnode.in_file'),
164+
('outputnode.out_mask', 'inputnode.in_mask')]),
165+
(datasource, bias, [('bvals', 'inputnode.in_bval')])
166166
])
167167

168168

‎examples/fmri_fsl.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -367,7 +367,7 @@ def getinormscale(medianvals):
367367
Use :class:`nipype.algorithms.modelgen.SpecifyModel` to generate design information.
368368
"""
369369

370-
modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec")
370+
modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec")
371371

372372
"""
373373
Use :class:`nipype.interfaces.fsl.Level1Design` to generate a run specific fsf

‎examples/fmri_fsl_reuse.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -65,7 +65,7 @@
6565
iterfield=['realigned_files', 'realignment_parameters', 'mask_file'],
6666
name="art")
6767

68-
modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec")
68+
modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec")
6969

7070
level1_workflow.connect([(preproc, art, [('outputspec.motion_parameters',
7171
'realignment_parameters'),

‎examples/test_spm.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -37,7 +37,7 @@
3737
workflow3d.connect([(split, stc, [("out_files", "in_files")]),
3838
(stc, realign_estimate, [('timecorrected_files', 'in_files')]),
3939
(realign_estimate, realign_write, [('modified_in_files', 'in_files')]),
40-
(stc, realign_estwrite, [('timecorrected_files', 'in_files')]),
40+
(stc, realign_estwrite, [('timecorrected_files', 'in_files')]),
4141
(realign_write, smooth, [('realigned_files', 'in_files')])])
4242

4343
workflow3d.run()
@@ -71,7 +71,7 @@
7171
workflow4d.connect([(gunzip, stc, [("out_file", "in_files")]),
7272
(stc, realign_estimate, [('timecorrected_files', 'in_files')]),
7373
(realign_estimate, realign_write, [('modified_in_files', 'in_files')]),
74-
(stc, realign_estwrite, [('timecorrected_files', 'in_files')]),
74+
(stc, realign_estwrite, [('timecorrected_files', 'in_files')]),
7575
(realign_write, smooth, [('realigned_files', 'in_files')])])
7676

7777
workflow4d.run()

‎nipype/algorithms/icc.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -46,7 +46,7 @@ def _run_interface(self, runtime):
4646

4747
for x in range(icc.shape[0]):
4848
Y = all_data[x, :, :]
49-
icc[x], subject_var[x], session_var[x], session_F[x], _, _ = ICC_rep_anova(Y)
49+
icc[x], subject_var[x], session_var[x], session_F[x], _, _ = ICC_rep_anova(Y)
5050

5151
nim = nb.load(self.inputs.subjects_sessions[0][0])
5252
new_data = np.zeros(nim.get_shape())

‎nipype/algorithms/metrics.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -443,7 +443,7 @@ def _run_interface(self, runtime):
443443

444444
weights = weights / np.sum(weights)
445445

446-
setattr(self, '_jaccard', np.sum(weights * self._jaccards))
446+
setattr(self, '_jaccard', np.sum(weights * self._jaccards))
447447
setattr(self, '_dice', np.sum(weights * self._dices))
448448

449449
diff = np.zeros(diff_im[0].shape)

‎nipype/external/provcopy.py

Lines changed: 19 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -90,25 +90,25 @@
9090
)
9191

9292
PROV_N_MAP = {
93-
PROV_REC_ENTITY: u'entity',
94-
PROV_REC_ACTIVITY: u'activity',
95-
PROV_REC_GENERATION: u'wasGeneratedBy',
96-
PROV_REC_USAGE: u'used',
97-
PROV_REC_COMMUNICATION: u'wasInformedBy',
98-
PROV_REC_START: u'wasStartedBy',
99-
PROV_REC_END: u'wasEndedBy',
100-
PROV_REC_INVALIDATION: u'wasInvalidatedBy',
101-
PROV_REC_DERIVATION: u'wasDerivedFrom',
102-
PROV_REC_AGENT: u'agent',
103-
PROV_REC_ATTRIBUTION: u'wasAttributedTo',
104-
PROV_REC_ASSOCIATION: u'wasAssociatedWith',
105-
PROV_REC_DELEGATION: u'actedOnBehalfOf',
106-
PROV_REC_INFLUENCE: u'wasInfluencedBy',
107-
PROV_REC_ALTERNATE: u'alternateOf',
108-
PROV_REC_SPECIALIZATION: u'specializationOf',
109-
PROV_REC_MENTION: u'mentionOf',
110-
PROV_REC_MEMBERSHIP: u'hadMember',
111-
PROV_REC_BUNDLE: u'bundle',
93+
PROV_REC_ENTITY: u'entity',
94+
PROV_REC_ACTIVITY: u'activity',
95+
PROV_REC_GENERATION: u'wasGeneratedBy',
96+
PROV_REC_USAGE: u'used',
97+
PROV_REC_COMMUNICATION: u'wasInformedBy',
98+
PROV_REC_START: u'wasStartedBy',
99+
PROV_REC_END: u'wasEndedBy',
100+
PROV_REC_INVALIDATION: u'wasInvalidatedBy',
101+
PROV_REC_DERIVATION: u'wasDerivedFrom',
102+
PROV_REC_AGENT: u'agent',
103+
PROV_REC_ATTRIBUTION: u'wasAttributedTo',
104+
PROV_REC_ASSOCIATION: u'wasAssociatedWith',
105+
PROV_REC_DELEGATION: u'actedOnBehalfOf',
106+
PROV_REC_INFLUENCE: u'wasInfluencedBy',
107+
PROV_REC_ALTERNATE: u'alternateOf',
108+
PROV_REC_SPECIALIZATION: u'specializationOf',
109+
PROV_REC_MENTION: u'mentionOf',
110+
PROV_REC_MEMBERSHIP: u'hadMember',
111+
PROV_REC_BUNDLE: u'bundle',
112112
}
113113

114114
# # Identifiers for PROV's attributes

‎nipype/interfaces/afni/preprocess.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1095,7 +1095,7 @@ class AllineateInputSpec(AFNICommandInputSpec):
10951095
# Non-linear experimental
10961096
_nwarp_types = ['bilinear',
10971097
'cubic', 'quintic', 'heptic', 'nonic',
1098-
'poly3', 'poly5', 'poly7', 'poly9'] # same non-hellenistic
1098+
'poly3', 'poly5', 'poly7', 'poly9'] # same non-hellenistic
10991099
nwarp = traits.Enum(
11001100
*_nwarp_types, argstr='-nwarp %s',
11011101
desc='Experimental nonlinear warping: bilinear or legendre poly.')

‎nipype/interfaces/camino/__init__.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111
TrackBayesDirac, TrackDT, TrackBallStick, TrackBootstrap,
1212
TrackBedpostxDeter, TrackBedpostxProba,
1313
ComputeFractionalAnisotropy, ComputeMeanDiffusivity,
14-
ComputeTensorTrace, ComputeEigensystem, DTMetric)
14+
ComputeTensorTrace, ComputeEigensystem, DTMetric)
1515
from .calib import (SFPICOCalibData, SFLUTGen)
1616
from .odf import (QBallMX, LinRecon, SFPeaks, MESD)
1717
from .utils import ImageStats

‎nipype/interfaces/diffusion_toolkit/dti.py

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -92,18 +92,18 @@ def _list_outputs(self):
9292
output_type = self.inputs.output_type
9393

9494
outputs = self.output_spec().get()
95-
outputs['ADC'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_adc.' + output_type))
96-
outputs['B0'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_b0.' + output_type))
97-
outputs['L1'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e1.' + output_type))
98-
outputs['L2'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e2.' + output_type))
99-
outputs['L3'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e3.' + output_type))
100-
outputs['exp'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_exp.' + output_type))
101-
outputs['FA'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_fa.' + output_type))
102-
outputs['FA_color'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_fa_color.' + output_type))
103-
outputs['tensor'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_tensor.' + output_type))
104-
outputs['V1'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v1.' + output_type))
105-
outputs['V2'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v2.' + output_type))
106-
outputs['V3'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v3.' + output_type))
95+
outputs['ADC'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_adc.' + output_type))
96+
outputs['B0'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_b0.' + output_type))
97+
outputs['L1'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e1.' + output_type))
98+
outputs['L2'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e2.' + output_type))
99+
outputs['L3'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e3.' + output_type))
100+
outputs['exp'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_exp.' + output_type))
101+
outputs['FA'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_fa.' + output_type))
102+
outputs['FA_color'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_fa_color.' + output_type))
103+
outputs['tensor'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_tensor.' + output_type))
104+
outputs['V1'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v1.' + output_type))
105+
outputs['V2'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v2.' + output_type))
106+
outputs['V3'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v3.' + output_type))
107107

108108
return outputs
109109

‎nipype/interfaces/diffusion_toolkit/odf.py

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -143,12 +143,12 @@ def _list_outputs(self):
143143
output_type = self.inputs.output_type
144144

145145
outputs = self.output_spec().get()
146-
outputs['B0'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_b0.' + output_type))
147-
outputs['DWI'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_dwi.' + output_type))
148-
outputs['max'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_max.' + output_type))
149-
outputs['ODF'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_odf.' + output_type))
146+
outputs['B0'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_b0.' + output_type))
147+
outputs['DWI'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_dwi.' + output_type))
148+
outputs['max'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_max.' + output_type))
149+
outputs['ODF'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_odf.' + output_type))
150150
if isdefined(self.inputs.output_entropy):
151-
outputs['entropy'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_entropy.' + output_type))
151+
outputs['entropy'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_entropy.' + output_type))
152152

153153
return outputs
154154

‎nipype/interfaces/fsl/dti.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -552,7 +552,7 @@ class BEDPOSTX4OutputSpec(TraitedSpec):
552552
desc='a list of path/name of 3D volume with mean of distribution on phi')
553553
mean_fsamples = traits.List(File(exists=True),
554554
desc='a list of path/name of 3D volume with mean of distribution on f anisotropy')
555-
dyads = traits.List(File(exists=True), desc='a list of path/name of mean of PDD distribution in vector form')
555+
dyads = traits.List(File(exists=True), desc='a list of path/name of mean of PDD distribution in vector form')
556556

557557

558558
class BEDPOSTX4(FSLCommand):

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