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WIP: antsRegistrationSyNQuick.sh wrapper #1392

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83e0aa9
wip: added wrapper for antsRegistrationSyNQuick.sh
Mar 3, 2016
26aa5d5
removed wrongly commited file
Mar 3, 2016
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86 changes: 86 additions & 0 deletions nipype/interfaces/ants/registration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -975,3 +975,89 @@ def _list_outputs(self):
if len(self.inputs.save_state):
outputs['save_state'] = os.path.abspath(self.inputs.save_state)
return outputs





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too many empty spaces (only 2 necessary)

class RegistrationSynQuickInputSpec(ANTSCommandInputSpec):
dimension = traits.Enum(3, 2, argstr='-d %d',
usedefault=True, desc='image dimension (2 or 3)')
fixed_image = InputMultiPath(File(exists=True), mandatory=True, argstr='-f %s',
desc='Fixed image or source image or reference image')
moving_image = InputMultiPath(File(exists=True), mandatory=True, argstr='-m %s',
desc='Moving image or target image')
output_prefix = traits.Str("transform", usedefault=True, argstr='-o %s',
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Please use Str from nipype base. (add from ..base import Str on the top, and then use Str instead of traits.Str here).

desc="A prefix that is prepended to all output files")

# todo ANTSCommandInputSpec already has this, but I can't figure out how to set it without defining it again
num_threads = traits.Int(default_value=1, desc='Number of threads (default = 1)', argstr='-n %d')
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I'm not 100% sure, but I think you can do traits.Int(1, desc ... here.


transform_type = traits.Enum('s', 't', 'r', 'a', 'sr', 'b', 'br', argstr='-t %s',
desc='transform type\n\
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please use block strings:

transform_type = traits.Enum('s', 't', 'r', 'a', 'sr', 'b', 'br', argstr='-t %s',
                             usedefault=True, desc="""\
transform type -
t:  translation
r:  rigid
a: rigid + affine
s:  rigid + affine + deformable syn (default)
sr: rigid + deformable syn
b:  rigid + affine + deformable b-spline syn
br: rigid + deformable b-spline syn""")

t: translation\
r: rigid \n\
a: rigid + affine\n\
s: rigid + affine + deformable syn (default)\
sr: rigid + deformable syn\
b: rigid + affine + deformable b-spline syn\n\
br: rigid + deformable b-spline syn',
usedefault=True)

use_histogram_matching = traits.Bool(default=False, argstr='-j %s',
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traits.Bool(False, argstr ...)

additionally: you may remove the _format_arg for this input setting argstr='-j %d'

desc='use histogram matching')
histogram_bins = traits.Int(default_value=32, argstr='-r %d',
desc='histogram bins for mutual information in SyN stage \
(default = 32)')
spline_distance = traits.Int(default_value=26, argstr='-s %d',
desc='spline distance for deformable B-spline SyN transform \
(default = 26)')
precision_type = traits.Enum('double', 'float', argstr='-p %s',
desc='precision type (default = double)', usedefault=True)


class RegistrationSynQuickOutputSpec(TraitedSpec):
warped_image = File(exists=True, desc="Warped image")
inverse_warped_image = File(exists=True, desc="Inverse warped image")
out_matrix = File(exists=True, desc='Affine matrix')
forward_warp_field = File(exists=True, desc='Forward warp field')
inverse_warp_field = File(exists=True, desc='Inverse warp field')


class RegistrationSynQuick(ANTSCommand):
"""
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missing brief summary

Examples
--------

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missing doctest

"""
# todo examples

_cmd = 'antsRegistrationSynQuick.sh'
input_spec = RegistrationSynQuickInputSpec
output_spec = RegistrationSynQuickOutputSpec

def _format_arg(self, name, spec, value):
if name == 'use_histogram_matching':
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please use argstr='-j %d' and remove this

if isdefined(self.inputs.use_histogram_matching):
return spec.argstr % {False: '0', True: '1'}[value]

elif name == 'precision_type':
if isdefined(self.inputs.precision_type):
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this is always True since this trait has usedefault=True

return spec.argstr % {'float': 'f', 'double': 'd'}[value]
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                return spec.argstr % value[0]

return super(RegistrationSynQuick, self)._format_arg(name, spec, value)

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['warped_image'] = os.path.abspath(self.inputs.output_prefix + 'Warped.nii.gz')
outputs['inverse_warped_image'] = os.path.abspath(
self.inputs.output_prefix + 'InverseWarped.nii.gz')
outputs['out_matrix'] = os.path.abspath(self.inputs.output_prefix + '0GenericAffine.mat')

# todo in the case of linear transformation-only there won't be fields. is there a more elegant way to specify that?
if self.inputs.transform_type not in ('t', 'r', 'a'):
outputs['forward_warp_field'] = os.path.abspath(
self.inputs.output_prefix + '1Warp.nii.gz')
outputs['inverse_warp_field'] = os.path.abspath(
self.inputs.output_prefix + '1InverseWarp.nii.gz')
return outputs