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[ENH] Add copy_header option to N4BiasFieldCorrection #2034

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Merged
merged 4 commits into from
May 26, 2017
Merged

[ENH] Add copy_header option to N4BiasFieldCorrection #2034

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c1548a6
[ENH] Add copy_header option to N4BiasFieldCorrection
oesteban May 18, 2017
98af18e
@effigies suggestions
oesteban May 19, 2017
d973105
RF: Factor _copy_header, update bias image
effigies May 19, 2017
720809b
Merge pull request #4 from effigies/enh/N4-header
oesteban May 19, 2017
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24 changes: 24 additions & 0 deletions nipype/interfaces/ants/segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -259,6 +259,9 @@ class N4BiasFieldCorrectionInputSpec(ANTSCommandInputSpec):
' to file.'), xor=['bias_image'])
bias_image = File(desc='Filename for the estimated bias.',
hash_files=False)
copy_header = traits.Bool(False, mandatory=True, usedefault=True,
desc='copy headers of the original image into the '
'output (corrected) file')


class N4BiasFieldCorrectionOutputSpec(TraitedSpec):
Expand Down Expand Up @@ -384,6 +387,27 @@ def _list_outputs(self):
self._gen_filename('bias_image'))
return outputs

def _run_interface(self, runtime, correct_return_codes=(0,)):
runtime = super(N4BiasFieldCorrection, self)._run_interface(
runtime, correct_return_codes)

if self.inputs.copy_header and runtime.returncode in correct_return_codes:
self._copy_header(self._gen_filename('output_image'))
if self.inputs.save_bias or isdefined(self.inputs.bias_image):
self._copy_header(self._gen_filename('bias_image'))

return runtime

def _copy_header(self, fname):
"""Copy header from input image to an output image"""
import nibabel as nb
in_img = nb.load(self.inputs.input_image)
out_img = nb.load(fname, mmap=False)
new_img = out_img.__class__(out_img.get_data(), in_img.affine,
in_img.header)
new_img.set_data_dtype(out_img.get_data_dtype())
new_img.to_filename(fname)


class CorticalThicknessInputSpec(ANTSCommandInputSpec):
dimension = traits.Enum(3, 2, argstr='-d %d', usedefault=True,
Expand Down
3 changes: 3 additions & 0 deletions nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py
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Expand Up @@ -14,6 +14,9 @@ def test_N4BiasFieldCorrection_inputs():
),
convergence_threshold=dict(requires=['n_iterations'],
),
copy_header=dict(mandatory=True,
usedefault=True,
),
dimension=dict(argstr='-d %d',
usedefault=True,
),
Expand Down