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fix: renamed mask_file to mask_files #1984

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fix: renamed mask_file to mask_files #1984

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8949299
fix: renamed mask_file to mask_files
mgxd Apr 30, 2017
2f76fbb
fix: add clarity to log message
mgxd Apr 30, 2017
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14 changes: 5 additions & 9 deletions nipype/algorithms/confounds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -302,9 +302,6 @@ def _list_outputs(self):
class CompCorInputSpec(BaseInterfaceInputSpec):
realigned_file = File(exists=True, mandatory=True,
desc='already realigned brain image (4D)')
mask_file = InputMultiPath(File(exists=True, deprecated='0.13',
new_name='mask_files',
desc='One or more mask files that determines ROI (3D)'))
mask_files = InputMultiPath(File(exists=True,
desc='One or more mask files that determines ROI (3D)'))
merge_method = traits.Enum('union', 'intersect', 'none', xor=['mask_index'],
Expand Down Expand Up @@ -342,7 +339,7 @@ class CompCor(BaseInterface):
>>> ccinterface.inputs.num_components = 1
>>> ccinterface.inputs.use_regress_poly = True
>>> ccinterface.inputs.regress_poly_degree = 2

"""
input_spec = CompCorInputSpec
output_spec = CompCorOutputSpec
Expand All @@ -366,7 +363,7 @@ def _run_interface(self, runtime, tCompCor_mask=False):
mmap=NUMPY_MMAP).get_data()
components = None

if isdefined(self.inputs.mask_files) or isdefined(self.inputs.mask_file):
if isdefined(self.inputs.mask_files):
if (not isdefined(self.inputs.mask_index) and
not isdefined(self.inputs.merge_method)):
self.inputs.mask_index = 0
Expand Down Expand Up @@ -509,7 +506,7 @@ class TCompCor(CompCor):
>>> ccinterface.inputs.use_regress_poly = True
>>> ccinterface.inputs.regress_poly_degree = 2
>>> ccinterface.inputs.percentile_threshold = .03

"""

input_spec = TCompCorInputSpec
Expand Down Expand Up @@ -588,7 +585,7 @@ def _run_interface(self, runtime):
mask_file = os.path.abspath('mask.nii')
nb.Nifti1Image(mask_data, aff).to_filename(mask_file)
IFLOG.debug('tCompcor computed and saved mask of shape {} to '
'mask_file {}'.format(mask.shape, mask_file))
'mask file {}'.format(mask.shape, mask_file))
_out_masks.append(mask_file)
self._set_header('tCompCor')

Expand All @@ -604,7 +601,7 @@ def _run_interface(self, runtime):
mask_file = os.path.abspath('mask.nii')
nb.Nifti1Image(mask_data, aff).to_filename(mask_file)
IFLOG.debug('tCompcor computed and saved mask of shape {} to '
'mask_file {}'.format(mask.shape, mask_file))
'mask file {}'.format(mask.shape, mask_file))
_out_masks.append(mask_file)
self._set_header('tCompCor')

Expand Down Expand Up @@ -927,4 +924,3 @@ def regress_poly(degree, data, remove_mean=True, axis=-1):

# Back to original shape
return regressed_data.reshape(datashape)