[ENH] Add "profiling" outputs to ants.Registration

Adds a `profiling` flag that enables parsing of the standard output
from ANTS. This first version only reads two values: the total elapsed
time and the final value of the metric.

Author: oesteban

nipype/interfaces/ants/registration.py

@@ -379,6 +379,8 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
         low=0.0, high=1.0, value=0.0, argstr='%s', usedefault=True, desc="The Lower quantile to clip image ranges")
 
     verbose = traits.Bool(argstr='-v', default=False)
+    profiling = traits.Bool(True, usedefault=True,
+                            desc='generate profiling output fields')
 
 
 class RegistrationOutputSpec(TraitedSpec):
@@ -395,6 +397,8 @@ class RegistrationOutputSpec(TraitedSpec):
     warped_image = File(desc="Outputs warped image")
     inverse_warped_image = File(desc="Outputs the inverse of the warped image")
     save_state = File(desc="The saved registration state to be restored")
+    metric_value = traits.Float(desc='the final value of metric')
+    elapsed_time = traits.Float(desc='the total elapsed time as reported by ANTs')
 
 
 class Registration(ANTSCommand):
@@ -648,6 +652,24 @@ class Registration(ANTSCommand):
     _quantilesDone = False
     _linear_transform_names = ['Rigid', 'Affine', 'Translation', 'CompositeAffine', 'Similarity']
 
+    def _run_interface(self, runtime, correct_return_codes=(0,)):
+        runtime = super(Registration, self)._run_interface(runtime)
+
+        # Parse some profiling info
+        if self.inputs.profiling:
+            lines = runtime.stdout.split('\n')
+            for l in lines[::-1]:
+                # This should be the last line
+                if l.strip().startswith('Total elapsed time:'):
+                    setattr(self, '_elapsed_time', float(
+                        l.strip().replace('Total elapsed time: ', '')))
+                elif 'DIAGNOSTIC' in l:
+                    setattr(self, '_metric_value', float(
+                        l.split(',')[2]))
+                    break
+
+        return runtime
+
     def _format_metric(self, index):
         """
         Format the antsRegistration -m metric argument(s).
@@ -981,4 +1003,7 @@ def _list_outputs(self):
             outputs['inverse_warped_image'] = os.path.abspath(inv_out_filename)
         if len(self.inputs.save_state):
             outputs['save_state'] = os.path.abspath(self.inputs.save_state)
+        if self.inputs.profiling:
+            outputs['metric_value'] = getattr(self, '_metric_value')
+            outputs['elapsed_time'] = getattr(self, '_elapsed_time')
         return outputs

nipype/interfaces/ants/tests/test_auto_Registration.py

@@ -72,6 +72,8 @@ def test_Registration_inputs():
     ),
     output_warped_image=dict(hash_files=False,
     ),
+    profiling=dict(usedefault=True,
+    ),
     radius_bins_item_trait=dict(),
     radius_bins_stage_trait=dict(),
     radius_or_number_of_bins=dict(requires=['metric_weight'],
@@ -125,10 +127,12 @@ def test_Registration_inputs():
 
 def test_Registration_outputs():
     output_map = dict(composite_transform=dict(),
+    elapsed_time=dict(),
     forward_invert_flags=dict(),
     forward_transforms=dict(),
     inverse_composite_transform=dict(),
     inverse_warped_image=dict(),
+    metric_value=dict(),
     reverse_invert_flags=dict(),
     reverse_transforms=dict(),
     save_state=dict(),