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changing ANTS input traits, fixes #2245 #2261

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Merged
merged 5 commits into from
Nov 28, 2017
Merged

changing ANTS input traits, fixes #2245 #2261

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ec5d3b1
changing some ants inputs to mandatory
djarecka Oct 29, 2017
3196726
adding description to radius
djarecka Oct 31, 2017
a1d62ca
adding a simple example to test issue 2245
djarecka Nov 12, 2017
e214b54
unicode_literals
djarecka Nov 27, 2017
51585be
ading tmpdir; applying pep8 to my changes
djarecka Nov 27, 2017
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10 changes: 8 additions & 2 deletions nipype/interfaces/ants/registration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,8 +49,14 @@ class ANTSInputSpec(ANTSCommandInputSpec):
metric = traits.List(traits.Enum('CC', 'MI', 'SMI', 'PR', 'SSD',
'MSQ', 'PSE'), mandatory=True, desc='')

metric_weight = traits.List(traits.Float(), requires=['metric'], desc='')
radius = traits.List(traits.Int(), requires=['metric'], desc='')
metric_weight = traits.List(traits.Float(), value=[1.0], usedefault=True,
requires=['metric'], mandatory=True,
desc='the metric weight(s) for each stage. '
'The weights must sum to 1 per stage.')
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isn't this a pep8 warning?

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@djarecka djarecka Nov 27, 2017 •
edited
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this line doesn't give any warning, but the files indeed violates many. will edit

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I will actually review pep8 only for the first part I was changing, will review pep8 for entire file together with other updates


radius = traits.List(traits.Int(), requires=['metric'], mandatory=True,
desc='radius of the region (i.e. number of layers around a voxel point)'
' that is used for computing cross correlation')

output_transform_prefix = Str('out', usedefault=True, argstr='--output-naming %s',
mandatory=True, desc='')
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21 changes: 21 additions & 0 deletions nipype/interfaces/ants/tests/test_registration.py
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@@ -0,0 +1,21 @@
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:

from nipype.interfaces.ants import registration
import os
import pytest

def test_ants_mand():
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does the interface actually create files? if so (and I guess it would), we should include tmpdir.chdir()

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done

filepath = os.path.dirname( os.path.realpath( __file__ ) )
datadir = os.path.realpath(os.path.join(filepath, '../../../testing/data'))

ants = registration.ANTS()
ants.inputs.transformation_model= "SyN"
ants.inputs.moving_image = [os.path.join(datadir, 'resting.nii')]
ants.inputs.fixed_image = [os.path.join(datadir, 'T1.nii')]
ants.inputs.metric = [u'MI']
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can we just import unicode literals?

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done


with pytest.raises(ValueError) as er:
ants.run()
assert "ANTS requires a value for input 'radius'" in str(er.value)