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Aug 5, 2015
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ENH: Add ants JointFusion() node with testing #1160

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29 changes: 17 additions & 12 deletions nipype/interfaces/ants/segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -574,6 +574,7 @@ def _list_outputs(self):
'brainvols.csv')
return outputs


class JointFusionInputSpec(ANTSCommandInputSpec):
dimension = traits.Enum(3, 2, 4, argstr='%d', position=0, usedefault=True, mandatory=True,
desc='image dimension (2, 3, or 4)')
Expand All @@ -588,21 +589,23 @@ class JointFusionInputSpec(ANTSCommandInputSpec):
patch_radius = traits.ListInt(minlen=3, maxlen=3, argstr='-rp %s', desc='Patch radius for similarity measures, scalar or vector. Default: 2x2x2')
search_radius = traits.ListInt(minlen=3, maxlen=3, argstr='-rs %s', desc='Local search radius. Default: 3x3x3')
exclusion_region = File(exists=True, argstr='-x %s', desc='Specify an exclusion region for the given label.')
output_posteriors_name_template = traits.Str('POSTERIOR_%02d.nii.gz', argstr='-p %s',
desc="Save the posterior maps (probability that each voxel belongs to each " +\
"label) as images. The number of images saved equals the number of labels. " +\
"The filename pattern must be in C printf format, e.g. posterior%04d.nii.gz")
output_voting_weights_name_template = traits.Str('WEIGHTED_%04d.nii.gz', argstr='-w %s', desc="Save the voting weights as " +\
"images. The number of images saved equals the number of atlases. The " +\
"filename pattern must be in C printf format, e.g. weight%04d.nii.gz")
# TODO: These are almost never needed except for debugging
# output_posteriors_name_template = traits.Str('POSTERIOR_%02d.nii.gz', argstr='-p %s',
# desc="Save the posterior maps (probability that each voxel belongs to each " +\
# "label) as images. The number of images saved equals the number of labels. " +\
# "The filename pattern must be in C printf format, e.g. posterior%04d.nii.gz")
# output_voting_weights_name_template = traits.Str('WEIGHTED_%04d.nii.gz', argstr='-w %s', desc="Save the voting weights as " +\
# "images. The number of images saved equals the number of atlases. The " +\
# "filename pattern must be in C printf format, e.g. weight%04d.nii.gz")
atlas_group_id = traits.ListInt(argstr='-gp %d...', desc='Assign a group ID for each atlas')
atlas_group_weights = traits.ListInt(argstr='-gpw %d...', desc='Assign the voting weights to each atlas group')


class JointFusionOutputSpec(TraitedSpec):
output_label_image = File(exists=True)
# TODO: optional outputs - output_posteriors, output_voting_weights

# TODO: These are almost never needed except for debugging,
# so delay complicated implementation until a need arises
# optional outputs - output_posteriors, output_voting_weights

class JointFusion(ANTSCommand):
"""
Expand All @@ -616,22 +619,24 @@ class JointFusion(ANTSCommand):
>>> at.inputs.method = 'Joint[0.1,2]'
>>> at.inputs.output_label_image ='fusion_labelimage_output.nii'
>>> at.inputs.warped_intensity_images = ['im1.nii',
... 'im2.nii']
... 'im2.nii',
... 'im3.nii']
>>> at.inputs.warped_label_images = ['segmentation0.nii.gz',
... 'segmentation1.nii.gz',
... 'segmentation1.nii.gz']
>>> at.inputs.target_image = 'T1.nii'
>>> at.inputs.patch_radius = [3,2,1]
>>> at.inputs.search_radius = [1,2,3]
>>> at.cmdline
'jointfusion 3 1 -m Joint[0.1,2] -rp 3x2x1 -rs 1x2x3 -tg T1.nii -g im1.nii -g im2.nii -l segmentation0.nii.gz -l segmentation1.nii.gz fusion_labelimage_output.nii'
'jointfusion 3 1 -m Joint[0.1,2] -rp 3x2x1 -rs 1x2x3 -tg T1.nii -g im1.nii -g im2.nii -g im3.nii -l segmentation0.nii.gz -l segmentation1.nii.gz -l segmentation1.nii.gz fusion_labelimage_output.nii'

Alternately, you can specify the voting method and parameters more 'Pythonically':

>>> at.inputs.method = 'Joint'
>>> at.inputs.alpha = 0.5
>>> at.inputs.beta = 1
>>> at.cmdline
'jointfusion 3 1 -m Joint[0.5,1] -rp 3x2x1 -rs 1x2x3 -tg T1.nii -g im1.nii -g im2.nii -l segmentation0.nii.gz -l segmentation1.nii.gz fusion_labelimage_output.nii'
'jointfusion 3 1 -m Joint[0.5,1] -rp 3x2x1 -rs 1x2x3 -tg T1.nii -g im1.nii -g im2.nii -g im3.nii -l segmentation0.nii.gz -l segmentation1.nii.gz -l segmentation1.nii.gz fusion_labelimage_output.nii'
"""
input_spec = JointFusionInputSpec
output_spec = JointFusionOutputSpec
Expand Down