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enh: trait for imaging files + implementation in SPM preproc #1949

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Merged
merged 11 commits into from
May 3, 2017
Merged

enh: trait for imaging files + implementation in SPM preproc #1949

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32ea82d
fix: catch compressed files for spm realign
mgxd Apr 11, 2017
a2c3f28
Merge branch 'fix/realign' of github.com:mgxd/nipype into fix/realign
mgxd Apr 18, 2017
fdd7e8b
enh: new traits applied to spm
mgxd Apr 19, 2017
0de0026
Merge branch 'master' of git://github.com/nipy/nipype into fix/realign
mgxd Apr 19, 2017
3ec370c
wip: check against image format
mgxd Apr 25, 2017
519e96c
Merge branch 'master' of git://github.com/nipy/nipype into fix/realign
mgxd Apr 25, 2017
e6626af
enh: imagetype base for spm, new image formats, allow_compression
mgxd Apr 26, 2017
a2f434f
fix: trailing parenthesis
mgxd Apr 26, 2017
7100768
fix: clarity allow_compression
mgxd Apr 26, 2017
d879587
Merge branch 'master' of git://github.com/nipy/nipype into fix/realign
mgxd May 1, 2017
bf564f7
enh: preliminary testing + altered auto tests
mgxd May 1, 2017
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1 change: 1 addition & 0 deletions nipype/interfaces/afni/tests/test_auto_Autobox.py
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Expand Up @@ -20,6 +20,7 @@ def test_Autobox_inputs():
),
out_file=dict(argstr='-prefix %s',
name_source='in_file',
name_template='%s_autobox',
),
outputtype=dict(),
padding=dict(argstr='-npad %d',
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9 changes: 9 additions & 0 deletions nipype/interfaces/spm/preprocess.py
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Expand Up @@ -217,6 +217,15 @@ def _parse_inputs(self):
"""validate spm realign options if set to None ignore
"""
einputs = super(Realign, self)._parse_inputs()
is_gz = lambda x: x.endswith('.gz')
if isdefined(self.inputs.in_files):
if isinstance(self.inputs.in_files, list):
for imgf in self.inputs.in_files:
if is_gz(imgf):
raise TypeError('Input files must be uncompressed')
else:
if is_gz(self.inputs.in_files):
raise TypeError('Input files must be uncompressed')
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Not sure if there's a better approach in general, but the test can be made much more concise:

if isdefined(self.inputs.in_files) and any(imgf.endswith('.gz')
                                           for imgf in filename_to_list(self.inputs.in_files)):
    raise TypeError('Input files must be uncompressed')

return [{'%s' % (self.inputs.jobtype): einputs[0]}]

def _list_outputs(self):
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2 changes: 2 additions & 0 deletions nipype/interfaces/utility/tests/test_auto_Merge.py
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Expand Up @@ -11,6 +11,8 @@ def test_Merge_inputs():
),
no_flatten=dict(usedefault=True,
),
ravel_inputs=dict(usedefault=True,
),
)
inputs = Merge.input_spec()

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