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Clark
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PEP8 compliance for epi.py (100%)
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-32
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1 file changed

+40
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‎nipype/interfaces/fsl/epi.py

Lines changed: 40 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -378,7 +378,8 @@ def _parse_inputs(self, skip=None):
378378
# If not defined, assume index are the first N entries in the
379379
# parameters file, for N input images.
380380
if not isdefined(self.inputs.in_index):
381-
self.inputs.in_index = list(range(1, len(self.inputs.in_files) + 1))
381+
self.inputs.in_index = list(
382+
range(1, len(self.inputs.in_files) + 1))
382383

383384
return super(ApplyTOPUP, self)._parse_inputs(skip=skip)
384385

@@ -491,7 +492,8 @@ def _num_threads_update(self):
491492
if 'OMP_NUM_THREADS' in self.inputs.environ:
492493
del self.inputs.environ['OMP_NUM_THREADS']
493494
else:
494-
self.inputs.environ['OMP_NUM_THREADS'] = str(self.inputs.num_threads)
495+
self.inputs.environ['OMP_NUM_THREADS'] = str(
496+
self.inputs.num_threads)
495497

496498
def _format_arg(self, name, spec, value):
497499
if name == 'in_topup_fieldcoef':
@@ -502,8 +504,10 @@ def _format_arg(self, name, spec, value):
502504

503505
def _list_outputs(self):
504506
outputs = self.output_spec().get()
505-
outputs['out_corrected'] = os.path.abspath('%s.nii.gz' % self.inputs.out_base)
506-
outputs['out_parameter'] = os.path.abspath('%s.eddy_parameters' % self.inputs.out_base)
507+
outputs['out_corrected'] = os.path.abspath(
508+
'%s.nii.gz' % self.inputs.out_base)
509+
outputs['out_parameter'] = os.path.abspath(
510+
'%s.eddy_parameters' % self.inputs.out_base)
507511
return outputs
508512

509513

@@ -575,7 +579,8 @@ class EpiRegInputSpec(FSLCommandInputSpec):
575579
position=-3, desc='wholehead T1 image')
576580
t1_brain = File(exists=True, argstr='--t1brain=%s', mandatory=True,
577581
position=-2, desc='brain extracted T1 image')
578-
out_base = traits.String("epi2struct", desc='output base name', argstr='--out=%s',
582+
out_base = traits.String("epi2struct", desc='output base name',
583+
argstr='--out=%s',
579584
position=-1, usedefault=True)
580585
fmap = File(exists=True, argstr='--fmap=%s',
581586
desc='fieldmap image (in rad/s)')
@@ -622,7 +627,8 @@ class EpiRegOutputSpec(TraitedSpec):
622627
fullwarp = File(exists=True,
623628
desc='warpfield to unwarp epi and transform into \
624629
structural space')
625-
wmseg = File(exists=True, desc='white matter segmentation used in flirt bbr')
630+
wmseg = File(exists=True,
631+
desc='white matter segmentation used in flirt bbr')
626632
wmedge = File(exists=True, desc='white matter edges for visualization')
627633

628634

@@ -661,32 +667,34 @@ def _list_outputs(self):
661667
outputs = self.output_spec().get()
662668
outputs['out_file'] = os.path.join(os.getcwd(),
663669
self.inputs.out_base + '.nii.gz')
664-
if not (isdefined(self.inputs.no_fmapreg) and self.inputs.no_fmapreg) and isdefined(self.inputs.fmap):
665-
outputs['out_1vol'] = os.path.join(os.getcwd(),
666-
self.inputs.out_base + '_1vol.nii.gz')
667-
outputs['fmap2str_mat'] = os.path.join(os.getcwd(),
668-
self.inputs.out_base + '_fieldmap2str.mat')
669-
outputs['fmap2epi_mat'] = os.path.join(os.getcwd(),
670-
self.inputs.out_base + '_fieldmaprads2epi.mat')
671-
outputs['fmap_epi'] = os.path.join(os.getcwd(),
672-
self.inputs.out_base + '_fieldmaprads2epi.nii.gz')
673-
outputs['fmap_str'] = os.path.join(os.getcwd(),
674-
self.inputs.out_base + '_fieldmaprads2str.nii.gz')
675-
outputs['fmapmag_str'] = os.path.join(os.getcwd(),
676-
self.inputs.out_base + '_fieldmap2str.nii.gz')
677-
outputs['shiftmap'] = os.path.join(os.getcwd(),
678-
self.inputs.out_base + '_fieldmaprads2epi_shift.nii.gz')
679-
outputs['fullwarp'] = os.path.join(os.getcwd(),
680-
self.inputs.out_base + '_warp.nii.gz')
681-
outputs['epi2str_inv'] = os.path.join(os.getcwd(),
682-
self.inputs.out_base + '_inv.mat')
683-
684-
outputs['epi2str_mat'] = os.path.join(os.getcwd(),
685-
self.inputs.out_base + '.mat')
686-
outputs['wmedge'] = os.path.join(os.getcwd(),
687-
self.inputs.out_base + '_fast_wmedge.nii.gz')
688-
outputs['wmseg'] = os.path.join(os.getcwd(),
689-
self.inputs.out_base + '_fast_wmseg.nii.gz')
670+
if (not (isdefined(self.inputs.no_fmapreg) and
671+
self.inputs.no_fmapreg) and isdefined(self.inputs.fmap)):
672+
outputs['out_1vol'] = os.path.join(
673+
os.getcwd(), self.inputs.out_base + '_1vol.nii.gz')
674+
outputs['fmap2str_mat'] = os.path.join(
675+
os.getcwd(), self.inputs.out_base + '_fieldmap2str.mat')
676+
outputs['fmap2epi_mat'] = os.path.join(
677+
os.getcwd(), self.inputs.out_base + '_fieldmaprads2epi.mat')
678+
outputs['fmap_epi'] = os.path.join(
679+
os.getcwd(), self.inputs.out_base + '_fieldmaprads2epi.nii.gz')
680+
outputs['fmap_str'] = os.path.join(
681+
os.getcwd(), self.inputs.out_base + '_fieldmaprads2str.nii.gz')
682+
outputs['fmapmag_str'] = os.path.join(
683+
os.getcwd(), self.inputs.out_base + '_fieldmap2str.nii.gz')
684+
outputs['shiftmap'] = os.path.join(
685+
os.getcwd(),
686+
self.inputs.out_base + '_fieldmaprads2epi_shift.nii.gz')
687+
outputs['fullwarp'] = os.path.join(
688+
os.getcwd(), self.inputs.out_base + '_warp.nii.gz')
689+
outputs['epi2str_inv'] = os.path.join(
690+
os.getcwd(), self.inputs.out_base + '_inv.mat')
691+
692+
outputs['epi2str_mat'] = os.path.join(
693+
os.getcwd(), self.inputs.out_base + '.mat')
694+
outputs['wmedge'] = os.path.join(
695+
os.getcwd(), self.inputs.out_base + '_fast_wmedge.nii.gz')
696+
outputs['wmseg'] = os.path.join(
697+
os.getcwd(), self.inputs.out_base + '_fast_wmseg.nii.gz')
690698

691699
return outputs
692700

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