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Afni qwarp output paths #2222

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Merged
merged 2 commits into from
Oct 21, 2017
Merged

Afni qwarp output paths #2222

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70970d3
fix typo and output paths in qwarp
salma1601 Oct 9, 2017
ca3e8a3
update test
salma1601 Oct 9, 2017
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32 changes: 21 additions & 11 deletions nipype/interfaces/afni/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,8 @@
import os
import os.path as op

from ...utils.filemanip import (load_json, save_json, split_filename)
from ...utils.filemanip import (load_json, save_json, split_filename,
fname_presuffix)
from ..base import (
CommandLineInputSpec, CommandLine, TraitedSpec,
traits, isdefined, File, InputMultiPath, Undefined, Str)
Expand Down Expand Up @@ -3131,7 +3132,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
'Note that the source dataset in the second run is the SAME as'
'in the first run. If you don\'t see why this is necessary,'
'then you probably need to seek help from an AFNI guru.',
argstr='-inlev %d',
argstr='-inilev %d',
xor=['duplo'])
minpatch = traits.Int(
desc='* The value of mm should be an odd integer.'
Expand Down Expand Up @@ -3462,7 +3463,7 @@ class Qwarp(AFNICommand):
>>> qwarp2.inputs.inilev = 7
>>> qwarp2.inputs.iniwarp = ['Q25_warp+tlrc.HEAD']
>>> qwarp2.cmdline # doctest: +ALLOW_UNICODE
'3dQwarp -base mni.nii -blur 0.0 2.0 -source structural.nii -inlev 7 -iniwarp Q25_warp+tlrc.HEAD -prefix Q11'
'3dQwarp -base mni.nii -blur 0.0 2.0 -source structural.nii -inilev 7 -iniwarp Q25_warp+tlrc.HEAD -prefix Q11'
>>> res2 = qwarp2.run() # doctest: +SKIP
"""
_cmd = '3dQwarp'
Expand All @@ -3475,29 +3476,38 @@ def _list_outputs(self):
if not isdefined(self.inputs.out_file):
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@oesteban oesteban Oct 9, 2017 •
edited
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All of this should not be here:

  1. The out_file input spec can only define one of name_source or genfile (currently it defines both). Since we are trying to deprecate genfile, name_source should be preferred.

  2. In theory, name_source should fix this issue.

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@oesteban - i'm leaving the afni stuff to @Shotgunosine and others to figure out. right now, because of the way afni works with various kinds of extensions, the straight up namesource can run into issues.

prefix = self._gen_fname(self.inputs.in_file, suffix='_QW')
ext = '.HEAD'
suffix ='+tlrc'
else:
prefix = self.inputs.out_file
ext_ind = max([prefix.lower().rfind('.nii.gz'),
prefix.lower().rfind('.nii.')])
if ext_ind == -1:
ext = '.HEAD'
suffix = '+tlrc'
else:
ext = prefix[ext_ind:]
suffix = ''
print(ext,"ext")
outputs['warped_source'] = os.path.abspath(self._gen_fname(prefix, suffix='+tlrc')+ext)
outputs['warped_source'] = fname_presuffix(prefix, suffix=suffix,
use_ext=False) + ext
if not self.inputs.nowarp:
outputs['source_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_WARP+tlrc')+ext)
outputs['source_warp'] = fname_presuffix(prefix,
suffix='_WARP' + suffix, use_ext=False) + ext
if self.inputs.iwarp:
outputs['base_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_WARPINV+tlrc')+ext)
outputs['base_warp'] = fname_presuffix(prefix,
suffix='_WARPINV' + suffix, use_ext=False) + ext
if isdefined(self.inputs.out_weight_file):
outputs['weights'] = os.path.abspath(self.inputs.out_weight_file)

if self.inputs.plusminus:
outputs['warped_source'] = os.path.abspath(self._gen_fname(prefix, suffix='_PLUS+tlrc')+ext)
outputs['warped_base'] = os.path.abspath(self._gen_fname(prefix, suffix='_MINUS+tlrc')+ext)
outputs['source_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_PLUS_WARP+tlrc')+ext)
outputs['base_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_MINUS_WARP+tlrc',)+ext)

outputs['warped_source'] = fname_presuffix(prefix,
suffix='_PLUS' + suffix, use_ext=False) + ext
outputs['warped_base'] = fname_presuffix(prefix,
suffix='_MINUS' + suffix, use_ext=False) + ext
outputs['source_warp'] = fname_presuffix(prefix,
suffix='_PLUS_WARP' + suffix, use_ext=False) + ext
outputs['base_warp'] = fname_presuffix(prefix,
suffix='_MINUS_WARP' + suffix, use_ext=False) + ext
return outputs

def _gen_filename(self, name):
Expand Down
2 changes: 1 addition & 1 deletion nipype/interfaces/afni/tests/test_auto_Qwarp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ def test_Qwarp_inputs():
copyfile=False,
mandatory=True,
),
inilev=dict(argstr='-inlev %d',
inilev=dict(argstr='-inilev %d',
xor=['duplo'],
),
iniwarp=dict(argstr='-iniwarp %s',
Expand Down