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FIX: topup out_base and params #750

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Merged
merged 4 commits into from
Dec 19, 2013
Merged

FIX: topup out_base and params #750

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7230ef0
FIX: topup out file and params
Dec 16, 2013
4531e6c
Merge branch 'master' into tst/martin
satra Dec 19, 2013
75f1520
fix: fixed autotest for applytopup
satra Dec 19, 2013
a3ac6c2
Merge pull request #1 from satra/tst/martin
Dec 19, 2013
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12 changes: 8 additions & 4 deletions nipype/interfaces/fsl/epi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,9 @@ def _parse_inputs( self, skip=None ):
skip = []

if not isdefined(self.inputs.out_base ):
self.inputs.out_base = os.path.abspath( './nipypetu' )
self.inputs.out_base = './nipypetu'

self.inputs.out_base = os.path.abspath(self.inputs.out_base)

if isdefined( self.inputs.encoding_file ):
skip.append( 'encoding_direction' )
Expand Down Expand Up @@ -238,8 +240,8 @@ class ApplyTOPUPInputSpec( FSLCommandInputSpec ):
in_topup = File( mandatory=True, desc='basename of field/movements (from topup)', argstr='--topup=%s' )

out_base = File( desc='basename for output (warped) image', argstr='--out=%s' )
method = traits.Enum( ('jac','lsr'), argstr='-m=%s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
interp = traits.Enum( ('trilinear','spline'), argstr='-n=%s', desc='interpolation method' )
method = traits.Enum( ('jac','lsr'), argstr='--method=%s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
interp = traits.Enum( ('trilinear','spline'), argstr='--interp=%s', desc='interpolation method' )
datatype = traits.Enum( ('char', 'short', 'int', 'float', 'double' ), argstr='-d=%s', desc='force output data type' )


Expand Down Expand Up @@ -289,7 +291,9 @@ def _parse_inputs( self, skip=None ):
skip = []

if not isdefined(self.inputs.out_base ):
self.inputs.out_base = os.path.abspath( './nipypeatu' )
self.inputs.out_base = './nipypeatu'

self.inputs.out_base = os.path.abspath(self.inputs.out_base)
return super(ApplyTOPUP, self)._parse_inputs(skip=skip)


Expand Down
4 changes: 2 additions & 2 deletions nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ def test_ApplyTOPUP_inputs():
),
args=dict(argstr='%s',
),
interp=dict(argstr='-n=%s',
interp=dict(argstr='--interp=%s',
),
in_files=dict(mandatory=True,
argstr='%s',
Expand All @@ -32,7 +32,7 @@ def test_ApplyTOPUP_inputs():
out_base=dict(argstr='--out=%s',
),
output_type=dict(),
method=dict(argstr='-m=%s',
method=dict(argstr='--method=%s',
),
)
inputs = ApplyTOPUP.input_spec()
Expand Down