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Fixing the base interface _run_interface function for NiftyRegCommand #2005

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Merged
merged 3 commits into from
May 11, 2017
Merged

Fixing the base interface _run_interface function for NiftyRegCommand #2005

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fcae4f7
Fixing the base interface _run_interface function for NiftyRegCommand…
byvernault May 10, 2017
bda7c32
Adding changes for omp_val_core and editing the tests.
byvernault May 11, 2017
4757bec
Changing NiftySegCommand to use NiftyFitCommand instead since no omp_…
byvernault May 11, 2017
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7 changes: 5 additions & 2 deletions nipype/interfaces/niftyreg/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,8 +105,11 @@ def exists(self):
def _run_interface(self, runtime):
# Update num threads estimate from OMP_NUM_THREADS env var
# Default to 1 if not set
if not isdefined(self.inputs.environ['OMP_NUM_THREADS']):
self.inputs.environ['OMP_NUM_THREADS'] = self.num_threads
omp_key = 'OMP_NUM_THREADS'
if omp_key in os.environ:
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@oesteban oesteban May 10, 2017 •
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I'd suggest this instead of the if .. else:
self.inputs.environ[omp_key] = os.getenv(omp_key, '%d' % self.num_threads)
self.inputs.environ[omp_key] = os.environ[omp_key]
else:
self.inputs.environ[omp_key] = str(self.num_threads)
return super(NiftyRegCommand, self)._run_interface(runtime)

def _format_arg(self, name, spec, value):
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