FSL slice #2585
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FSL slice #2585
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effigies
reviewed
May 18, 2018
nipype/interfaces/fsl/utils.py
Outdated
| @@ -262,6 +262,70 @@ def _format_arg(self, name, trait_spec, value): | |||
| return super(Smooth, self)._format_arg(name, trait_spec, value) | |||
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| class SliceInputSpec(FSLCommandInputSpec): | |||
| in_file = File(exists=True, argstr="%s", position=0, mandatory=True, | |||
| desc="input filename") | |||
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Since this places outputs in the same directory as in_file (unless out_base_name is defined), you should add copyfile=False to this trait.
nipype/interfaces/fsl/utils.py
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| outbase = in_base + '_slice*' | ||
| outputs['out_files'] = sorted(glob(os.path.join(out_dir, | ||
| outbase + ext))) |
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This doesn't account for if out_base_name is an absolute path. You can simplify this a bit, too, using fname_presuffix:
suffix = '_slice_*' + ext
if isdefined(self.inputs.out_base_name):
fname_template = os.abspath(self.inputs.out_base_name + suffix)
else:
fname_template = fname_presuffix(self.inputs.in_file, suffix=suffix, use_ext=False)
outputs['out_file'] = sorted(glob(fname_template))
Codecov Report
@@ Coverage Diff @@
## master #2585 +/- ##
==========================================
- Coverage 67.55% 67.55% -0.01%
==========================================
Files 335 335
Lines 42589 42611 +22
Branches 5269 5271 +2
==========================================
+ Hits 28772 28784 +12
- Misses 13144 13154 +10
Partials 673 673
Continue to review full report at Codecov.
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effigies
approved these changes
May 21, 2018
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added interface for
fslslice