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bpinsard
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autopep8
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‎nipype/interfaces/afni/preprocess.py

Lines changed: 53 additions & 53 deletions
Original file line numberDiff line numberDiff line change
@@ -724,9 +724,9 @@ class FourierInputSpec(AFNICommandInputSpec):
724724
position=0,
725725
mandatory=True)
726726
highpass = traits.Float(desc='highpass',
727-
argstr='-highpass %f',
728-
position=1,
729-
mandatory=True)
727+
argstr='-highpass %f',
728+
position=1,
729+
mandatory=True)
730730

731731

732732
class Fourier(AFNICommand):
@@ -815,8 +815,8 @@ class BandpassInputSpec(AFNICommandInputSpec):
815815
argstr='-nfft %d',
816816
desc="set the FFT length [must be a legal value]")
817817
normalize = traits.Bool(
818-
argstr='-norm',
819-
desc="""Make all output time series have L2 norm = 1
818+
argstr='-norm',
819+
desc="""Make all output time series have L2 norm = 1
820820
++ i.e., sum of squares = 1""")
821821
automask = traits.Bool(
822822
argstr='-automask',
@@ -866,14 +866,14 @@ class Bandpass(AFNICommand):
866866

867867
class ZCutUpInputSpec(AFNICommandInputSpec):
868868
in_file = File(desc='input file to 3dZcutup',
869-
argstr='%s',
870-
position=-1,
871-
mandatory=True,
872-
exists=True)
869+
argstr='%s',
870+
position=-1,
871+
mandatory=True,
872+
exists=True)
873873
out_file = File("%s_zcupup", desc='output image file name',
874-
argstr='-prefix %s', name_source="in_file", usedefault=True)
874+
argstr='-prefix %s', name_source="in_file", usedefault=True)
875875
keep = traits.Str(desc='slice range to keep in output',
876-
argstr='-keep %s')
876+
argstr='-keep %s')
877877

878878

879879
class ZCutUp(AFNICommand):
@@ -901,10 +901,10 @@ class ZCutUp(AFNICommand):
901901

902902
class AllineateInputSpec(AFNICommandInputSpec):
903903
in_file = File(desc='input file to 3dAllineate',
904-
argstr='-source %s',
905-
position=-1,
906-
mandatory=True,
907-
exists=True)
904+
argstr='-source %s',
905+
position=-1,
906+
mandatory=True,
907+
exists=True)
908908
reference = File(
909909
exists=True,
910910
argstr='-base %s',
@@ -930,8 +930,8 @@ class AllineateInputSpec(AFNICommandInputSpec):
930930
argstr='-1Dmatrix_save %s',
931931
desc='Save the transformation matrix for each volume.')
932932
in_matrix = File(desc='matrix to align input file',
933-
argstr='-1Dmatrix_apply %s',
934-
position=-3)
933+
argstr='-1Dmatrix_apply %s',
934+
position=-3)
935935

936936
_cost_funcs = [
937937
'leastsq', 'ls',
@@ -1075,11 +1075,11 @@ class AllineateInputSpec(AFNICommandInputSpec):
10751075

10761076
# Non-linear experimental
10771077
_nwarp_types = ['bilinear',
1078-
'cubic', 'quintic', 'heptic', 'nonic',
1079-
'poly3', 'poly5', 'poly7', 'poly9'] # same non-hellenistic
1078+
'cubic', 'quintic', 'heptic', 'nonic',
1079+
'poly3', 'poly5', 'poly7', 'poly9'] # same non-hellenistic
10801080
nwarp = traits.Enum(
10811081
*_nwarp_types, argstr='-nwarp %s',
1082-
desc='Experimental nonlinear warping: bilinear or legendre poly.')
1082+
desc='Experimental nonlinear warping: bilinear or legendre poly.')
10831083
_dirs = ['X', 'Y', 'Z', 'I', 'J', 'K']
10841084
nwarp_fixmot = traits.List(
10851085
traits.Enum(*_dirs),
@@ -1128,7 +1128,7 @@ def _list_outputs(self):
11281128
outputs = self.output_spec().get()
11291129
if not isdefined(self.inputs.out_file):
11301130
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
1131-
suffix=self.inputs.suffix)
1131+
suffix=self.inputs.suffix)
11321132
else:
11331133
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
11341134
return outputs
@@ -1140,19 +1140,19 @@ def _gen_filename(self, name):
11401140

11411141
class MaskaveInputSpec(AFNICommandInputSpec):
11421142
in_file = File(desc='input file to 3dmaskave',
1143-
argstr='%s',
1144-
position=-2,
1145-
mandatory=True,
1146-
exists=True)
1143+
argstr='%s',
1144+
position=-2,
1145+
mandatory=True,
1146+
exists=True)
11471147
out_file = File("%s_maskave.1D", desc='output image file name',
1148-
argstr="> %s", name_source="in_file", usedefault=True, position=-1)
1148+
argstr="> %s", name_source="in_file", usedefault=True, position=-1)
11491149
mask = File(desc='matrix to align input file',
1150-
argstr='-mask %s',
1151-
position=1,
1152-
exists=True)
1150+
argstr='-mask %s',
1151+
position=1,
1152+
exists=True)
11531153
quiet = traits.Bool(desc='matrix to align input file',
1154-
argstr='-quiet',
1155-
position=2)
1154+
argstr='-quiet',
1155+
position=2)
11561156

11571157

11581158
class Maskave(AFNICommand):
@@ -1183,12 +1183,12 @@ class Maskave(AFNICommand):
11831183

11841184
class SkullStripInputSpec(AFNICommandInputSpec):
11851185
in_file = File(desc='input file to 3dSkullStrip',
1186-
argstr='-input %s',
1187-
position=1,
1188-
mandatory=True,
1189-
exists=True)
1186+
argstr='-input %s',
1187+
position=1,
1188+
mandatory=True,
1189+
exists=True)
11901190
out_file = File("%s_skullstrip", desc='output image file name',
1191-
argstr='-prefix %s', name_source="in_file", usedefault=True)
1191+
argstr='-prefix %s', name_source="in_file", usedefault=True)
11921192

11931193

11941194
class SkullStrip(AFNICommand):
@@ -1221,7 +1221,7 @@ class TCatInputSpec(AFNICommandInputSpec):
12211221
position=-1,
12221222
mandatory=True)
12231223
out_file = File("%s_tcat", desc='output image file name',
1224-
argstr='-prefix %s', name_source="in_file", usedefault=True)
1224+
argstr='-prefix %s', name_source="in_file", usedefault=True)
12251225
rlt = traits.Str(desc='options', argstr='-rlt%s', position=1)
12261226

12271227

@@ -1251,21 +1251,21 @@ class TCat(AFNICommand):
12511251

12521252
class FimInputSpec(AFNICommandInputSpec):
12531253
in_file = File(desc='input file to 3dfim+',
1254-
argstr=' -input %s',
1255-
position=1,
1256-
mandatory=True,
1257-
exists=True)
1254+
argstr=' -input %s',
1255+
position=1,
1256+
mandatory=True,
1257+
exists=True)
12581258
out_file = File("%s_fim", desc='output image file name',
1259-
argstr='-bucket %s', name_source="in_file", usedefault=True)
1259+
argstr='-bucket %s', name_source="in_file", usedefault=True)
12601260
ideal_file = File(desc='ideal time series file name',
1261-
argstr='-ideal_file %s',
1262-
position=2,
1263-
mandatory=True,
1264-
exists=True)
1261+
argstr='-ideal_file %s',
1262+
position=2,
1263+
mandatory=True,
1264+
exists=True)
12651265
fim_thr = traits.Float(desc='fim internal mask threshold value',
1266-
argstr='-fim_thr %f', position=3)
1266+
argstr='-fim_thr %f', position=3)
12671267
out = traits.Str(desc='Flag to output the specified parameter',
1268-
argstr='-out %s', position=4)
1268+
argstr='-out %s', position=4)
12691269

12701270

12711271
class Fim(AFNICommand):
@@ -1297,12 +1297,12 @@ class Fim(AFNICommand):
12971297

12981298
class TCorrelateInputSpec(AFNIBaseCommandInputSpec):
12991299
xset = File(desc='input xset',
1300-
argstr=' %s',
1301-
position=-2,
1302-
mandatory=True,
1303-
exists=True)
1300+
argstr=' %s',
1301+
position=-2,
1302+
mandatory=True,
1303+
exists=True)
13041304
yset = File(desc='input yset',
1305-
argstr=' %s',
1305+
argstr=' %s',
13061306
position=-1,
13071307
mandatory=True,
13081308
exists=True)

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