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Fixed CopyInputSpecs to use positional inputs (added tests) #1131

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Merged
merged 3 commits into from
Jul 7, 2015
Merged

Fixed CopyInputSpecs to use positional inputs (added tests) #1131

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168f948
changed out_file to positional input and added new tests
blakedewey Jul 7, 2015
8c4b425
Updated CHANGES
blakedewey Jul 7, 2015
a27c624
updated test for Copy
blakedewey Jul 7, 2015
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1 change: 1 addition & 0 deletions CHANGES
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@ Next release
* FIX: Add QA output for TSNR to resting workflow (https://github.com/nipy/nipype/pull/1088)
* FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (https://github.com/nipy/nipype/pull/1096)
* ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (https://github.com/nipy/nipype/pull/1128)
* FIX: Fixed AFNI Copy interface to use positional inputs as required (https://github.com/nipy/nipype/pull/1131)

Release 0.10.0 (October 10, 2014)
============
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27 changes: 21 additions & 6 deletions nipype/interfaces/afni/preprocess.py
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Expand Up @@ -676,7 +676,7 @@ class CopyInputSpec(AFNICommandInputSpec):
exists=True,
copyfile=False)
out_file = File(name_template="%s_copy", desc='output image file name',
argstr='-prefix %s', name_source="in_file")
argstr='%s', position=-1, name_source="in_file")


class Copy(AFNICommand):
Expand All @@ -690,11 +690,26 @@ class Copy(AFNICommand):
========

>>> from nipype.interfaces import afni as afni
>>> copy = afni.Copy()
>>> copy.inputs.in_file = 'functional.nii'
>>> copy.inputs.out_file = 'new_func.nii'
>>> res = copy.run() # doctest: +SKIP

>>> copy3d = afni.Copy()
>>> copy3d.inputs.in_file = 'functional.nii'
>>> copy3d.cmdline
'3dcopy functional.nii functional_copy'

>>> from copy import deepcopy
>>> copy3d_2 = deepcopy(copy3d)
>>> copy3d_2.inputs.outputtype = 'NIFTI'
>>> copy3d_2.cmdline
'3dcopy functional.nii functional_copy.nii'

>>> copy3d_3 = deepcopy(copy3d)
>>> copy3d_3.inputs.outputtype = 'NIFTI_GZ'
>>> copy3d_3.cmdline
'3dcopy functional.nii functional_copy.nii.gz'

>>> copy3d_4 = deepcopy(copy3d)
>>> copy3d_4.inputs.out_file = 'new_func.nii'
>>> copy3d_4.cmdline
'3dcopy functional.nii new_func.nii'
"""

_cmd = '3dcopy'
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3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_Copy.py
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Expand Up @@ -16,9 +16,10 @@ def test_Copy_inputs():
mandatory=True,
position=-2,
),
out_file=dict(argstr='-prefix %s',
out_file=dict(argstr='%s',
name_source='in_file',
name_template='%s_copy',
position=-1,
),
outputtype=dict(),
terminal_output=dict(nohash=True,
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