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[ENH] Add "profiling" outputs to ants.Registration #1985

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Merged
merged 8 commits into from
Oct 13, 2017
Merged

[ENH] Add "profiling" outputs to ants.Registration #1985

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12f9073
[ENH] Add "profiling" outputs to ants.Registration
oesteban May 1, 2017
44a71bb
set False as default value for profiling
oesteban May 1, 2017
e746d94
initialize class properties (avoids test errors if profiling is True)
oesteban May 1, 2017
031e0c3
fix doctests, update outputs hash in base
oesteban May 2, 2017
d7dc606
Merge remote-tracking branch 'upstream/master' into enh/antsRegistrat…
oesteban Oct 11, 2017
b372a14
address @chrisfilo's comments
oesteban Oct 11, 2017
e7fe893
fix tests
oesteban Oct 11, 2017
6909149
update CHANGES [skip ci]
oesteban Oct 13, 2017
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1 change: 1 addition & 0 deletions CHANGES
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
Upcoming release
================

* ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985)
* ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
* ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/2209, prev #1398)
* ENH: Centralize virtual/physical $DISPLAYs (https://github.com/nipy/nipype/pull/#2203)
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33 changes: 33 additions & 0 deletions nipype/interfaces/ants/registration.py
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Expand Up @@ -416,6 +416,8 @@ 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')
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Is there a difference between this elapsed_time and duration stored in every CommandLineInterface runtime? If you need this as an output it might be better to enable this for all interfaces.

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Elapsed time is calculated by ANTs so it refers exclusively to the registration process. The duration of the runtime object adds the (little) overhead of nipype. In general, they will be equivalent, but this could be a good handle to catch problems.

Additionally, my plan would be to add the elapsed_time per registration stage at some point. Then, it will make sense to be consistent with ANTs calculations.



class Registration(ANTSCommand):
Expand Down Expand Up @@ -535,10 +537,12 @@ class Registration(ANTSCommand):
>>> outputs = reg4._list_outputs()
>>> pprint.pprint(outputs) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE +ALLOW_UNICODE
{'composite_transform': '.../nipype/testing/data/output_Composite.h5',
'elapsed_time': <undefined>,
'forward_invert_flags': [],
'forward_transforms': [],
'inverse_composite_transform': '.../nipype/testing/data/output_InverseComposite.h5',
'inverse_warped_image': <undefined>,
'metric_value': <undefined>,
'reverse_invert_flags': [],
'reverse_transforms': [],
'save_state': '.../nipype/testing/data/trans.mat',
Expand All @@ -560,11 +564,13 @@ class Registration(ANTSCommand):
>>> outputs = reg4b._list_outputs()
>>> pprint.pprint(outputs) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE +ALLOW_UNICODE
{'composite_transform': <undefined>,
'elapsed_time': <undefined>,
'forward_invert_flags': [False, False],
'forward_transforms': ['.../nipype/testing/data/output_0GenericAffine.mat',
'.../nipype/testing/data/output_1Warp.nii.gz'],
'inverse_composite_transform': <undefined>,
'inverse_warped_image': <undefined>,
'metric_value': <undefined>,
'reverse_invert_flags': [True, False],
'reverse_transforms': ['.../nipype/testing/data/output_0GenericAffine.mat', \
'.../nipype/testing/data/output_1InverseWarp.nii.gz'],
Expand Down Expand Up @@ -683,6 +689,29 @@ class Registration(ANTSCommand):
_quantilesDone = False
_linear_transform_names = ['Rigid', 'Affine', 'Translation', 'CompositeAffine', 'Similarity']

def __init__(self, **inputs):
super(Registration, self).__init__(**inputs)
self._elapsed_time = None
self._metric_value = None

def _run_interface(self, runtime, correct_return_codes=(0,)):
runtime = super(Registration, self)._run_interface(runtime)

# Parse some profiling info
output = runtime.stdout or runtime.merged
if output:
lines = output.split('\n')
for l in lines[::-1]:
# This should be the last line
if l.strip().startswith('Total elapsed time:'):
self._elapsed_time = float(l.strip().replace(
'Total elapsed time: ', ''))
elif 'DIAGNOSTIC' in l:
self._metric_value = float(l.split(',')[2])
break

return runtime

def _format_metric(self, index):
"""
Format the antsRegistration -m metric argument(s).
Expand Down Expand Up @@ -1033,6 +1062,10 @@ 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._metric_value:
outputs['metric_value'] = self._metric_value
if self._elapsed_time:
outputs['elapsed_time'] = self._elapsed_time
return outputs


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2 changes: 2 additions & 0 deletions nipype/interfaces/ants/tests/test_auto_Registration.py
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Expand Up @@ -137,10 +137,12 @@ 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(),
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