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copy files to avoid concurrency issues in mris_expand #1938

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41822ea
copy files to avoid concurency issues
chrisgorgo Apr 5, 2017
fe3998a
fix tests
chrisgorgo Apr 5, 2017
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8 changes: 4 additions & 4 deletions nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ def test_MRIsExpand_inputs():
usedefault=True,
),
in_file=dict(argstr='%s',
copyfile=False,
copyfile=True,
mandatory=True,
position=-3,
),
Expand All @@ -32,11 +32,11 @@ def test_MRIsExpand_inputs():
usedefault=True,
),
pial=dict(argstr='-pial %s',
copyfile=False,
copyfile=True,
),
smooth_averages=dict(argstr='-A %d',
),
sphere=dict(copyfile=False,
sphere=dict(copyfile=True,
usedefault=True,
),
spring=dict(argstr='-S %g',
Expand All @@ -47,7 +47,7 @@ def test_MRIsExpand_inputs():
thickness=dict(argstr='-thickness',
),
thickness_name=dict(argstr='-thickness_name %s',
copyfile=False,
copyfile=True,
),
write_iterations=dict(argstr='-W %d',
),
Expand Down
8 changes: 4 additions & 4 deletions nipype/interfaces/freesurfer/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2912,7 +2912,7 @@ class MRIsExpandInputSpec(FSTraitedSpec):
# Input spec derived from
# https://github.com/freesurfer/freesurfer/blob/102e053/mris_expand/mris_expand.c
in_file = File(
exists=True, mandatory=True, argstr='%s', position=-3, copyfile=False,
exists=True, mandatory=True, argstr='%s', position=-3, copyfile=True,
desc='Surface to expand')
distance = traits.Float(
mandatory=True, argstr='%g', position=-2,
Expand All @@ -2926,7 +2926,7 @@ class MRIsExpandInputSpec(FSTraitedSpec):
argstr='-thickness',
desc='Expand by fraction of cortical thickness, not mm')
thickness_name = traits.Str(
argstr="-thickness_name %s", copyfile=False,
argstr="-thickness_name %s", copyfile=True,
desc=('Name of thickness file (implicit: "thickness")\n'
'If no path, uses directory of `in_file`\n'
'If no path AND missing "lh." or "rh.", derive from `in_file`'))
Expand All @@ -2936,12 +2936,12 @@ class MRIsExpandInputSpec(FSTraitedSpec):
desc=('Tuple of (n_averages, min_averages) parameters '
'(implicit: (16, 0))'))
pial = traits.Str(
argstr='-pial %s', copyfile=False,
argstr='-pial %s', copyfile=True,
desc=('Name of pial file (implicit: "pial")\n'
'If no path, uses directory of `in_file`\n'
'If no path AND missing "lh." or "rh.", derive from `in_file`'))
sphere = traits.Str(
'sphere', copyfile=False, usedefault=True,
'sphere', copyfile=True, usedefault=True,
desc='WARNING: Do not change this trait')
spring = traits.Float(argstr='-S %g', desc="Spring term (implicit: 0.05)")
dt = traits.Float(argstr='-T %g', desc='dt (implicit: 0.25)')
Expand Down