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[FIX] modified afni's cat_matvec to accept empty string opposed to opkey #2943

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Merged
merged 4 commits into from
Sep 18, 2019
Merged

[FIX] modified afni's cat_matvec to accept empty string opposed to opkey #2943

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ab4e15a
modified afni's cat_matvec to accept empty string opposed to opkey
ostanley Jun 10, 2019
67b10fb
made required PR changes to logic and spacing
ostanley Sep 17, 2019
88a59ac
Merge branch 'master' of https://github.com/nipy/nipype
ostanley Sep 17, 2019
845463d
added style change
ostanley Sep 17, 2019
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10 changes: 7 additions & 3 deletions nipype/interfaces/afni/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -617,11 +617,15 @@ class CatMatvec(AFNICommand):

def _format_arg(self, name, spec, value):
if name == 'in_file':
return spec.argstr % (' '.join([i[0] + ' -' + i[1]
for i in value]))
xfm_args=''
for v in value:
if len(v[1])>0:
xfm_args += ' ' + v[0] + ' -' + v[1] + ' '
else:
xfm_args += ' ' + v[0] + ' '
return spec.argstr % (xfm_args)
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I think it would be clearer to continue writing this as a comprehension, using the x if y else z idiom, but we can use more verbose variable names to make the logic clearer. I also think it would be useful to include a comment:

# Concatenate a series of filenames, with optional opkeys
return ' '.join('%s -%s' % (mfile, opkey) if opkey else mfile
                for mfile, opkey in value)

I dropped the initial spec.argstr %, just because spec.argstr is "%s", so there's no real point, but you could keep it if you wanted.

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I agree this is more elegant, I changed it and confirmed it passed my test for formatting.

return super(CatMatvec, self)._format_arg(name, spec, value)


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Can you re-add this? Python style guidelines suggest 2 lines between classes.

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Done

class CenterMassInputSpec(CommandLineInputSpec):
in_file = File(
desc='input file to 3dCM',
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