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[FIX] Make ignore_exception a class attribute #2414

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Merged
merged 3 commits into from
Jan 28, 2018
Merged

[FIX] Make ignore_exception a class attribute #2414

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87ef62f
make ignore_exception a class attribute
oesteban Jan 27, 2018
23b6c94
Merge remote-tracking branch 'upstream/master' into fix/master
oesteban Jan 27, 2018
5cc98f5
redo changes
oesteban Jan 27, 2018
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8 changes: 4 additions & 4 deletions doc/users/saving_workflows.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -66,34 +66,34 @@ This will create a file "outputtestsave.py" with the following content:
inode = Node(IdentityInterface(fields=['a'], mandatory_inputs=True), name="inode")
# Node: testsave.testfunc
testfunc = Node(Function(input_names=['a'], output_names=['output']), name="testfunc")
testfunc.interface.ignore_exception = False
def testfunc_1(in1):
"""dummy func
"""
out = in1 + 'foo' + "out1"
return out

testfunc.inputs.function_str = getsource(testfunc_1)
testfunc.inputs.ignore_exception = False
testfunc.inputs.in1 = '-sub'
testsave.connect(inode, "a", testfunc, "in1")
# Node: testsave.bet2
bet2 = MapNode(BET(), iterfield=['infile'], name="bet2")
bet2.interface.ignore_exception = False
bet2.iterables = ('frac', [0.4, 0.5])
bet2.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
bet2.inputs.ignore_exception = False
bet2.inputs.output_type = 'NIFTI_GZ'
bet2.terminal_output = 'stream'
# Node: testsave.bet
bet = Node(BET(), name="bet")
bet.interface.ignore_exception = False
bet.iterables = ('frac', [0.3, 0.4])
bet.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
bet.inputs.ignore_exception = False
bet.inputs.output_type = 'NIFTI_GZ'
bet.terminal_output = 'stream'
# Node: testsave.maths
maths = Node(ImageMaths(), name="maths")
maths.interface.ignore_exception = False
maths.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
maths.inputs.ignore_exception = False
maths.inputs.output_type = 'NIFTI_GZ'
maths.terminal_output = 'stream'
testsave.connect(bet2, ('mask_file', func), maths, "in_file2")
Expand Down
7 changes: 4 additions & 3 deletions nipype/interfaces/base/core.py
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Expand Up @@ -170,12 +170,14 @@ class BaseInterface(Interface):
references_ = []
resource_monitor = True # Enabled for this interface IFF enabled in the config

def __init__(self, from_file=None, resource_monitor=None, **inputs):
def __init__(self, from_file=None, resource_monitor=None,
ignore_exception=False, **inputs):
if not self.input_spec:
raise Exception(
'No input_spec in class: %s' % self.__class__.__name__)

self.inputs = self.input_spec(**inputs)
self.ignore_exception = ignore_exception

if resource_monitor is not None:
self.resource_monitor = resource_monitor
Expand Down Expand Up @@ -470,7 +472,6 @@ def run(self, cwd=None, **inputs):
os.chdir(cwd) # Change to the interface wd

enable_rm = config.resource_monitor and self.resource_monitor
force_raise = not getattr(self.inputs, 'ignore_exception', False)
self.inputs.trait_set(**inputs)
self._check_mandatory_inputs()
self._check_version_requirements(self.inputs)
Expand Down Expand Up @@ -530,7 +531,7 @@ def run(self, cwd=None, **inputs):
runtime.traceback_args = ('\n'.join(
['%s' % arg for arg in exc_args]), )

if force_raise:
if not self.ignore_exception:
raise
finally:
# This needs to be done always
Expand Down
4 changes: 2 additions & 2 deletions nipype/workflows/smri/ants/ANTSBuildTemplate.py
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Expand Up @@ -183,7 +183,7 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''):
output_names=['out']),
run_without_submitting=True,
name='MakeTransformsLists')
MakeTransformsLists.inputs.ignore_exception = True
MakeTransformsLists.interface.ignore_exception = True
TemplateBuildSingleIterationWF.connect(
BeginANTS, 'warp_transform', MakeTransformsLists, 'warpTransformList')
TemplateBuildSingleIterationWF.connect(BeginANTS, 'affine_transform',
Expand Down Expand Up @@ -263,7 +263,7 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''):
output_names=['TransformListWithGradientWarps']),
run_without_submitting=True,
name='MakeTransformListWithGradientWarps')
ApplyInvAverageAndFourTimesGradientStepWarpImage.inputs.ignore_exception = True
ApplyInvAverageAndFourTimesGradientStepWarpImage.interface.ignore_exception = True

TemplateBuildSingleIterationWF.connect(
AvgAffineTransform, 'affine_transform',
Expand Down
2 changes: 1 addition & 1 deletion nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py
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Expand Up @@ -360,7 +360,7 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''):
output_names=['TransformListWithGradientWarps']),
run_without_submitting=True,
name='99_MakeTransformListWithGradientWarps')
ApplyInvAverageAndFourTimesGradientStepWarpImage.inputs.ignore_exception = True
ApplyInvAverageAndFourTimesGradientStepWarpImage.interface.ignore_exception = True

TemplateBuildSingleIterationWF.connect(
AvgAffineTransform, 'affine_transform',
Expand Down