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[FIX] fix afni.allineate interface #2502

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Merged
merged 7 commits into from
Apr 24, 2018
Merged

[FIX] fix afni.allineate interface #2502

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234893e
fix afni.allineate interface
vanandrew Mar 20, 2018
34f67b4
FIX: Do not generate filenames in violation of xor
effigies Apr 23, 2018
ef25d15
RF: Use name_source for Allineate.inputs.out_file
effigies Apr 23, 2018
32cd9b8
FIX: Undo defined check, simplify abspath call
effigies Apr 23, 2018
4179f5c
ENH: Simplify nwarp_fixmot, nwarp_fixdep
effigies Apr 23, 2018
78f68ae
Merge pull request #1 from effigies/fix_afni_allineate
vanandrew Apr 23, 2018
cda56e9
make specs
effigies Apr 23, 2018
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38 changes: 16 additions & 22 deletions nipype/interfaces/afni/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -218,7 +218,9 @@ class AllineateInputSpec(AFNICommandInputSpec):
out_file = File(
desc='output file from 3dAllineate',
argstr='-prefix %s',
genfile=True,
name_template='%s_allineate',
name_source='in_file',
hash_files=False,
xor=['allcostx'])
out_param_file = File(
argstr='-1Dparam_save %s',
Expand Down Expand Up @@ -424,11 +426,11 @@ class AllineateInputSpec(AFNICommandInputSpec):
_dirs = ['X', 'Y', 'Z', 'I', 'J', 'K']
nwarp_fixmot = traits.List(
traits.Enum(*_dirs),
argstr='-nwarp_fixmot%s',
argstr='-nwarp_fixmot%s...',
desc='To fix motion along directions.')
nwarp_fixdep = traits.List(
traits.Enum(*_dirs),
argstr='-nwarp_fixdep%s',
argstr='-nwarp_fixdep%s...',
desc='To fix non-linear warp dependency along directions.')
verbose = traits.Bool(
argstr='-verb', desc='Print out verbose progress reports.')
Expand Down Expand Up @@ -465,31 +467,29 @@ class Allineate(AFNICommand):
'3dAllineate -source functional.nii -prefix functional_allineate.nii -1Dmatrix_apply cmatrix.mat'
>>> res = allineate.run() # doctest: +SKIP

>>> from nipype.interfaces import afni
>>> allineate = afni.Allineate()
>>> allineate.inputs.in_file = 'functional.nii'
>>> allineate.inputs.reference = 'structural.nii'
>>> allineate.inputs.allcostx = 'out.allcostX.txt'
>>> allineate.cmdline
'3dAllineate -source functional.nii -base structural.nii -allcostx |& tee out.allcostX.txt'
>>> res = allineate.run() # doctest: +SKIP

>>> allineate = afni.Allineate()
>>> allineate.inputs.in_file = 'functional.nii'
>>> allineate.inputs.reference = 'structural.nii'
>>> allineate.inputs.nwarp_fixmot = ['X', 'Y']
>>> allineate.cmdline
'3dAllineate -source functional.nii -nwarp_fixmotX -nwarp_fixmotY -prefix functional_allineate -base structural.nii'
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A question: Is -prefix functional_allineate the correct default, or should it be functional_allineate.nii?
If it should have the extension, we should add keep_extension=True to the out_file trait spec.

@tsalo @salma1601 You might also be good people to chime in here.

>>> res = allineate.run() # doctest: +SKIP
"""

_cmd = '3dAllineate'
input_spec = AllineateInputSpec
output_spec = AllineateOutputSpec

def _format_arg(self, name, trait_spec, value):
if name == 'nwarp_fixmot' or name == 'nwarp_fixdep':
arg = ' '.join([trait_spec.argstr % v for v in value])
return arg
return super(Allineate, self)._format_arg(name, trait_spec, value)

def _list_outputs(self):
outputs = self.output_spec().get()

if self.inputs.out_file:
outputs['out_file'] = op.abspath(self.inputs.out_file)
outputs = super(Allineate, self)._list_outputs()

if self.inputs.out_weight_file:
outputs['out_weight_file'] = op.abspath(
Expand All @@ -512,16 +512,10 @@ def _list_outputs(self):
outputs['out_param_file'] = op.abspath(
self.inputs.out_param_file)

if isdefined(self.inputs.allcostx):
outputs['allcostX'] = os.path.abspath(
os.path.join(os.getcwd(), self.inputs.allcostx))
if self.inputs.allcostx:
outputs['allcostX'] = os.path.abspath(self.inputs.allcostx)
return outputs

def _gen_filename(self, name):
if name == 'out_file':
return self._list_outputs()[name]
return None


class AutoTcorrelateInputSpec(AFNICommandInputSpec):
in_file = File(
Expand Down
8 changes: 5 additions & 3 deletions nipype/interfaces/afni/tests/test_auto_Allineate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,12 +61,14 @@ def test_Allineate_inputs():
usedefault=True,
),
nwarp=dict(argstr='-nwarp %s', ),
nwarp_fixdep=dict(argstr='-nwarp_fixdep%s', ),
nwarp_fixmot=dict(argstr='-nwarp_fixmot%s', ),
nwarp_fixdep=dict(argstr='-nwarp_fixdep%s...', ),
nwarp_fixmot=dict(argstr='-nwarp_fixmot%s...', ),
one_pass=dict(argstr='-onepass', ),
out_file=dict(
argstr='-prefix %s',
genfile=True,
hash_files=False,
name_source='in_file',
name_template='%s_allineate',
xor=['allcostx'],
),
out_matrix=dict(
Expand Down
6 changes: 6 additions & 0 deletions nipype/interfaces/base/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1072,6 +1072,12 @@ def _filename_from_source(self, name, chain=None):
if not isdefined(retval) or "%s" in retval:
if not trait_spec.name_source:
return retval

# Do not generate filename when excluded by other inputs
if trait_spec.xor and any(isdefined(getattr(self.inputs, field))
for field in trait_spec.xor):
return retval
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@satra @oesteban Does this constitute a full fix of #2506?

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@effigies - this is a good addition, but i'm not sure this addresses #2506, which does not have any xor. isn't it the case in #2506 that out_file should be populated if in_files is defined and set to some default otherwise?

i think this PR is fine, just not sure if it addresses #2506.

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Ah, right. I had it kind of backwards, but a similar fix to this should resolve #2506. I'll merge and propose a quick PR for that one.


if isdefined(retval) and "%s" in retval:
name_template = retval
else:
Expand Down