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kesshijordankesshijordan
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changed relative imports to absolute, fixed docstring tests
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‎nipype/interfaces/dtitk/registration.py

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from nipype.interfaces.base import TraitedSpec, CommandLineInputSpec, \
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traits, isdefined
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from nipype.utils.filemanip import fname_presuffix
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import os
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from base import CommandLineDtitk
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class RigidInputSpec(CommandLineInputSpec):
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fixed_file = traits.Str(desc="fixed diffusion tensor image",
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exists=True, mandatory=True,
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position=0, argstr="%s")
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moving_file = traits.Str(desc="diffusion tensor image path", exists=True,
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mandatory=True, position=1, argstr="%s")
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similarity_metric = traits.Enum('EDS', 'GDS', 'DDS', 'NMI', exists=True,
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mandatory=True, position=2, argstr="%s",
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desc="similarity metric")
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class RigidOutputSpec(TraitedSpec):
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out_file = traits.File(exists=True)
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out_file_xfm = traits.File(exists=True)
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class RigidTask(CommandLineDtitk):
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"""
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Performs rigid registration between two tensor volumes
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Example
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-------
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>>> import nipype.interfaces.dtitk as dtitk
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>>> node = dtitk.RigidTask()
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>>> node.inputs.fixed_file = 'diffusion.nii'
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>>> node.inputs.moving_file = 'diffusion.nii'
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>>> node.inputs.similarity_metric = 'EDS'
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>>> node.run()
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"""
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input_spec = RigidInputSpec
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output_spec = RigidOutputSpec
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_cmd = 'dti_rigid_sn'
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['out_file_xfm'] = self.inputs.in_file.replace('.nii.gz', '.aff')
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outputs['out_file'] = self.inputs.in_file.replace('.nii.gz',
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'_aff.nii.gz')
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return outputs
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class AffineInputSpec(CommandLineInputSpec):
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in_fixed_tensor = traits.Str(desc="fixed diffusion tensor image",
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exists=True, mandatory=False, position=0,
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argstr="%s")
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in_moving_txt = traits.Str(
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desc="moving list of diffusion tensor image paths", exists=True,
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mandatory=False, position=1, argstr="%s")
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in_similarity_metric = traits.Enum('EDS', 'GDS', 'DDS', 'NMI', exists=True,
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mandatory=False, position=3, argstr="%s",
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desc = "similarity metric")
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in_usetrans_flag = traits.Enum('--useTrans', '', exists=True,
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mandatory=False, position=4, argstr="%s",
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desc="initialize using rigid transform??")
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class AffineOutputSpec(TraitedSpec):
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out_file = traits.File(exists=True)
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out_file_xfm = traits.File(exists=True)
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class AffineTask(CommandLineDtitk):
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"""
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Performs affine registration between two tensor volumes
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Example
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-------
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>>> import nipype.interfaces.dtitk as dtitk
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>>> node = dtitk.AffineTask()
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>>> node.inputs.in_fixed_tensor = 'diffusion.nii'
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>>> node.inputs.in_moving_txt = 'dirs.txt'
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>>> node.inputs.in_similarity_metric = 'EDS'
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>>> node.run()
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"""
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input_spec = AffineInputSpec
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output_spec = AffineOutputSpec
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_cmd = 'dti_affine_sn'
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['out_file_xfm'] = self.inputs.in_fixed_tensor.replace('.nii.gz',
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'.aff')
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outputs['out_file'] = self.inputs.in_fixed_tensor.replace('.nii.gz',
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'_aff.nii.gz')
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return outputs
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class DiffeoInputSpec(CommandLineInputSpec):
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in_fixed_tensor = traits.Str(desc="fixed diffusion tensor image",
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exists=True, mandatory=False, position=0,
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argstr="%s")
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in_moving_txt = traits.Str(desc="moving list of diffusion tensor image "
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"paths", exists=True, mandatory=False,
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position=1, argstr="%s")
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in_mask = traits.Str(desc="mask", exists=True, mandatory=False, position=2,
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argstr="%s")
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in_numbers = traits.Str(desc='#iters ftol', exists=True, mandatory=False,
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position=3, argstr="%s")
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class DiffeoOutputSpec(TraitedSpec):
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out_file = traits.File(exists=True)
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out_file_xfm = traits.File(exists=True)
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class DiffeoTask(CommandLineDtitk):
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"""
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Performs diffeomorphic registration between two tensor volumes
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Example
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-------
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>>> import nipype.interfaces.dtitk as dtitk
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>>> node = dtitk.DiffeoTask()
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>>> node.inputs.in_fixed_tensor = 'diffusion.nii'
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>>> node.inputs.in_moving_txt = 'dirs.txt'
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>>> node.inputs.in_mask = 'mask.nii'
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>>> node.inputs.in_numbers = '6 0.002'
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>>> node.run()
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"""
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input_spec = DiffeoInputSpec
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output_spec = DiffeoOutputSpec
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_cmd = 'dti_diffeomorphic_sn'
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['out_file_xfm'] = self.inputs.in_fixed_tensor.replace(
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'.nii.gz','_aff_diffeo.df.nii.gz')
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outputs['out_file'] = self.inputs.in_fixed_tensor.replace(
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'.nii.gz', '_aff_diffeo.nii.gz')
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return outputs
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class ComposeXfmInputSpec(CommandLineInputSpec):
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in_df = traits.Str(desc='diffeomorphic file.df.nii.gz', exists=True,
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mandatory=False, position=1, argstr="-df %s")
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in_aff = traits.Str(desc='affine file.aff', exists=True, mandatory=False,
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position=0, argstr="-aff %s")
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out_path = traits.Str(desc='output_path', exists=True, mandatory=False,
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position=2, argstr="-out %s", name_source="in_df",
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name_template="%s_comboaff.nii.gz")
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class ComposeXfmOutputSpec(TraitedSpec):
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out_file = traits.File(desc='cheese', exists=True)
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class ComposeXfmTask(CommandLineDtitk):
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"""
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Combines diffeomorphic and affine transforms
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Example
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-------
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>>> import nipype.interfaces.dtitk as dtitk
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>>> node = dtitk.ComposeXfmTask()
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>>> node.inputs.in_df = 'ants_Warp.nii.gz'
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>>> node.inputs.in_aff= 'ants_Affine.txt'
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>>> node.run()
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"""
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input_spec = ComposeXfmInputSpec
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output_spec = ComposeXfmOutputSpec
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_cmd = 'dfRightComposeAffine'
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['out_file'] = self.inputs.in_df.replace('.df.nii.gz',
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'_combo.df.nii.gz')
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return outputs
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class diffeoSymTensor3DVolInputSpec(CommandLineInputSpec):
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in_tensor = traits.Str(desc='moving tensor', exists=True, mandatory=False,
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position=0, argstr="-in %s")
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in_xfm = traits.Str(desc='transform to apply', exists=True, mandatory=False,
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position=1, argstr="-trans %s")
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in_target = traits.Str(desc='', exists=True, mandatory=False, position=2,
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argstr="-target %s")
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out_path = traits.Str(desc='', exists=True, mandatory=False, position=3,
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argstr="-out %s", name_source="in_tensor",
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name_template="%s_diffeoxfmd.nii.gz")
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class diffeoSymTensor3DVolOutputSpec(TraitedSpec):
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out_file = traits.File(desc='cheese', exists=True)
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class diffeoSymTensor3DVolTask(CommandLineDtitk):
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"""
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Applies diffeomorphic transform to a tensor volume
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Example
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-------
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>>> import nipype.interfaces.dtitk as dtitk
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>>> node = dtitk.diffeoSymTensor3DVolTask()
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>>> node.inputs.in_tensor = 'diffusion.nii'
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>>> node.inputs.in_xfm = 'ants_Warp.nii.gz'
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>>> node.run()
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"""
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input_spec = diffeoSymTensor3DVolInputSpec
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output_spec = diffeoSymTensor3DVolOutputSpec
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_cmd = 'deformationSymTensor3DVolume'
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['out_file'] = self.inputs.out_path
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return outputs
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class affSymTensor3DVolInputSpec(CommandLineInputSpec):
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in_tensor = traits.Str(desc='moving tensor', exists=True, mandatory=False,
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position=0, argstr="-in %s")
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in_xfm = traits.Str(desc='transform to apply', exists=True, mandatory=False,
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position=1, argstr="-trans %s")
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in_target = traits.Str(desc='', exists=True, mandatory=False, position=2,
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argstr="-target %s")
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out_path = traits.Str(desc='', exists=True, mandatory=False, position=3,
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argstr="-out %s", name_source="in_tensor",
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name_template="%s_affxfmd.nii.gz")
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class affSymTensor3DVolOutputSpec(TraitedSpec):
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out_file = traits.File(desc='cheese', exists=True)
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class affSymTensor3DVolTask(CommandLineDtitk):
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"""
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Applies affine transform to a tensor volume
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Example
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-------
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>>> import nipype.interfaces.dtitk as dtitk
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>>> node = dtitk.affSymTensor3DVolTask()
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>>> node.inputs.in_tensor = 'diffusion.nii'
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>>> node.inputs.in_xfm = 'ants_Affine.txt'
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>>> node.run()
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"""
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input_spec = affSymTensor3DVolInputSpec
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output_spec = affSymTensor3DVolOutputSpec
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_cmd = 'affineSymTensor3DVolume'
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['out_file'] = os.path.abspath(self.inputs.out_path)
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return outputs
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class affScalarVolInputSpec(CommandLineInputSpec):
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in_volume = traits.Str(desc='moving volume', exists=True, mandatory=False,
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position=0, argstr="-in %s")
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in_xfm = traits.Str(desc='transform to apply', exists=True, mandatory=False,
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position=1, argstr="-trans %s")
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in_target = traits.Str(desc='', position=2, argstr="-target %s")
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out_path = traits.Str(desc='', mandatory=False, position=3,
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argstr="-out %s", name_source="in_volume",
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name_template="%s_affxfmd.nii.gz")
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class affScalarVolOutputSpec(TraitedSpec):
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out_file = traits.File(desc='moved volume', exists=True)
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class affScalarVolTask(CommandLineDtitk):
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"""
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Applies affine transform to a scalar volume
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Example
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-------
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>>> import nipype.interfaces.dtitk as dtitk
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>>> node = dtitk.affScalarVolTask()
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>>> node.inputs.in_volume = 'fa.nii.gz'
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>>> node.inputs.in_xfm = 'ants_Affine.txt'
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>>> node.run()
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"""
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input_spec = affScalarVolInputSpec
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output_spec = affScalarVolOutputSpec
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_cmd = 'affineScalarVolume'
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['out_file'] = os.path.abspath(self.inputs.out_path)
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return outputs
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class diffeoScalarVolInputSpec(CommandLineInputSpec):
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in_volume = traits.Str(desc='moving volume', exists=True, mandatory=False,
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position=0, argstr="-in %s")
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in_xfm = traits.Str(desc='transform to apply', exists=True, mandatory=False,
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position=2, argstr="-trans %s")
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in_target = traits.Str(desc='', exists=True, mandatory=False, position=3,
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argstr="-target %s")
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out_path = traits.Str(desc='', position=1, argstr="-out %s",
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name_source="in_volume",
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name_template="%s_diffeoxfmd.nii.gz")
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in_vsize = traits.Str(desc='', exists=True, mandatory=False, position=4,
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argstr="-vsize %s")
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in_flip = traits.Str(desc='', exists=True, mandatory=False, position=5,
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argstr="-flip %s")
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in_type = traits.Str(desc='', exists=True, mandatory=False, position=6,
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argstr="-type %s")
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in_interp = traits.Str(desc='0 trilin, 1 NN', exists=True, mandatory=False,
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position=7, argstr="-interp %s")
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class diffeoScalarVolOutputSpec(TraitedSpec):
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out_file = traits.File(desc='moved volume', exists=True)
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class diffeoScalarVolTask(CommandLineDtitk):
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"""
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Applies diffeomorphic transform to a scalar volume
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Example
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-------
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>>> import nipype.interfaces.dtitk as dtitk
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>>> node = dtitk.diffeoScalarVolTask()
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>>> node.inputs.in_tensor = 'fa.nii.gz'
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>>> node.inputs.in_xfm = 'ants_Warp.nii.gz'
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>>> node.run()
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"""
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input_spec = diffeoScalarVolInputSpec
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output_spec = diffeoScalarVolOutputSpec
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_cmd = 'deformationScalarVolume'
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def _list_outputs(self):
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outputs = self.output_spec().get()
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if not isdefined(self.inputs.out_path):
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self.inputs.out_path = fname_presuffix(self.inputs.in_volume,
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suffix="_diffeoxfmd",
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newpath=os.path.abspath("."))
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outputs['out_file'] = os.path.abspath(self.inputs.out_path)
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return outputs

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