enh: add threading option to Eddy

Author: satra

nipype/interfaces/fsl/epi.py

@@ -424,6 +424,8 @@ class EddyInputSpec(FSLCommandInputSpec):
                                'squares)'))
     repol = traits.Bool(False, argstr='--repol',
                         desc='Detect and replace outlier slices')
+    num_threads = traits.Int(1, usedefault=True, nohash=True,
+                             desc="Number of openmp threads to use")
 
 
 class EddyOutputSpec(TraitedSpec):
@@ -465,6 +467,25 @@ class Eddy(FSLCommand):
     input_spec = EddyInputSpec
     output_spec = EddyOutputSpec
 
+    _num_threads = 1
+
+    def __init__(self, **inputs):
+        super(Eddy, self).__init__(**inputs)
+        self.inputs.on_trait_change(self._num_threads_update, 'num_threads')
+
+        if not isdefined(self.inputs.num_threads):
+            self.inputs.num_threads = self._num_threads
+        else:
+            self._num_threads_update()
+
+    def _num_threads_update(self):
+        self._num_threads = self.inputs.num_threads
+        if not isdefined(self.inputs.num_threads):
+            if 'OMP_NUM_THREADS' in self.inputs.environ:
+                del self.inputs.environ['OMP_NUM_THREADS']
+        else:
+            self.inputs.environ['OMP_NUM_THREADS'] = self.inputs.num_threads
+
     def _format_arg(self, name, spec, value):
         if name == 'in_topup_fieldcoef':
             return spec.argstr % value.split('_fieldcoef')[0]

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -42,6 +42,9 @@ def test_Eddy_inputs():
     ),
     niter=dict(argstr='--niter=%s',
     ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
     out_base=dict(argstr='--out=%s',
     ),
     output_type=dict(),