Add ConvertWarp interface

Author: oesteban

nipype/interfaces/fsl/__init__.py

@@ -16,7 +16,7 @@
  ImageStats, FilterRegressor, Overlay, Slicer,
  PlotTimeSeries, PlotMotionParams, ConvertXFM,
  SwapDimensions, PowerSpectrum, Reorient2Std,
- Complex, InvWarp, WarpUtils)
+ Complex, InvWarp, WarpUtils, ConvertWarp)
 
 from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp,
  SigLoss, EddyCorrect)

nipype/interfaces/fsl/preprocess.py

@@ -678,17 +678,17 @@ def _list_outputs(self):
  '_variance.ext', cwd=cwd)
  outputs['std_img'] = self._gen_fname(outputs['out_file'] +
  '_sigma.ext', cwd=cwd)
- 
+
  # The mean image created if -stats option is specified ('meanvol')
- # is missing the top and bottom slices. Therefore we only expose the 
- # mean image created by -meanvol option ('mean_reg') which isn't 
+ # is missing the top and bottom slices. Therefore we only expose the
+ # mean image created by -meanvol option ('mean_reg') which isn't
  # corrupted.
  # Note that the same problem holds for the std and variance image.
- 
+
  if isdefined(self.inputs.mean_vol) and self.inputs.mean_vol:
  outputs['mean_img'] = self._gen_fname(outputs['out_file'] +
  '_mean_reg.ext', cwd=cwd)
- 
+
  if isdefined(self.inputs.save_mats) and self.inputs.save_mats:
  _, filename = os.path.split(outputs['out_file'])
  matpathname = os.path.join(cwd, filename + '.mat')

nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py

@@ -0,0 +1,71 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.fsl.utils import ConvertWarp
+
+def test_ConvertWarp_inputs():
+ input_map = dict(abswarp=dict(argstr='--abs',
+ xor=['relwarp'],
+ ),
+ args=dict(argstr='%s',
+ ),
+ cons_jacobian=dict(argstr='--constrainj',
+ ),
+ environ=dict(nohash=True,
+ usedefault=True,
+ ),
+ ignore_exception=dict(nohash=True,
+ usedefault=True,
+ ),
+ jacobian_max=dict(argstr='--jmax=%f',
+ ),
+ jacobian_min=dict(argstr='--jmin=%f',
+ ),
+ out_abswarp=dict(argstr='--absout',
+ xor=['out_relwarp'],
+ ),
+ out_file=dict(argstr='--out=%s',
+ genfile=True,
+ hash_files=False,
+ ),
+ out_relwarp=dict(argstr='--relout',
+ xor=['out_abswarp'],
+ ),
+ output_type=dict(),
+ postmat=dict(argstr='--postmat=%s',
+ ),
+ premat=dict(argstr='--premat=%s',
+ ),
+ reference=dict(argstr='--ref=%s',
+ mandatory=True,
+ ),
+ relwarp=dict(argstr='--rel',
+ xor=['abswarp'],
+ ),
+ shift_direction=dict(argstr='--shiftdir=%s',
+ requires=['shift_in_file'],
+ ),
+ shift_in_file=dict(argstr='--shiftmap=%s',
+ ),
+ terminal_output=dict(mandatory=True,
+ nohash=True,
+ ),
+ warp1=dict(argstr='--warp1=%s',
+ ),
+ warp2=dict(argstr='--warp2=%s',
+ ),
+ )
+ inputs = ConvertWarp.input_spec()
+
+ for key, metadata in input_map.items():
+ for metakey, value in metadata.items():
+ yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_ConvertWarp_outputs():
+ output_map = dict(out_file=dict(),
+ )
+ outputs = ConvertWarp.output_spec()
+
+ for key, metadata in output_map.items():
+ for metakey, value in metadata.items():
+ yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/fsl/utils.py

@@ -1578,3 +1578,122 @@ def _gen_filename(self, name):
  return self._list_outputs()[name]
 
  return None
+
+
+
+
+class ConvertWarpInputSpec(FSLCommandInputSpec):
+ reference = File(exists=True, argstr='--ref=%s', mandatory=True,
+ desc=('Name of a file in target space of the full transform.'))
+
+ out_file = File(genfile=True, hash_files=False, argstr='--out=%s',
+ desc=('Name of output file, containing warps that are the combination of all '
+ 'those given as arguments. The format of this will be a field-file (rather '
+ 'than spline coefficients) with any affine components included.'))
+
+ premat = File(exists=True, argstr='--premat=%s',
+ desc='filename for pre-transform (affine matrix)')
+
+ warp1 = File(exists=True, argstr='--warp1=%s',
+ desc=('Name of file containing warp-fields/coefficients. This could e.g. be a '
+ 'fnirt-transform from a subjects structural scan to an average of a group '
+ 'of subjects.'))
+
+ warp2 = File(exists=True, argstr='--warp2=%s',
+ desc=('Name of file containing warp-fields/coefficients. This could e.g. be a '
+ 'fnirt-transform from the average of a group of subjects to some standard '
+ 'space (e.g. MNI152).'))
+
+ postmat = File(exists=True, argstr='--postmat=%s',
+ desc=('Name of file containing an affine transform. It could e.g. be an affine '
+ 'transform that maps the MNI152-space into a better approximation to the '
+ 'Talairach-space (if indeed there is one).'))
+
+ shift_in_file = File(exists=True, argstr='--shiftmap=%s',
+ desc=('Name of file containing a "shiftmap", a non-linear transform with '
+ 'displacements only in one direction. This would typically be a '
+ 'fieldmap that has been pre-processed using fugue that maps a '
+ 'subjects functional (EPI) data onto an undistorted space (i.e. a space '
+ 'that corresponds to his/her true anatomy).'))
+
+ shift_direction = traits.Enum('-y','y','x','-x','z','-z',
+ argstr="--shiftdir=%s", requires=['shift_in_file'],
+ desc=('Indicates the direction that the distortions from '
+ '--shiftmap goes. It depends on the direction and '
+ 'polarity of the phase-encoding in the EPI sequence.'))
+
+ cons_jacobian = traits.Bool(False, argstr='--constrainj',
+ desc=('Constrain the Jacobian of the warpfield to lie within specified '
+ 'min/max limits.'))
+
+ jacobian_min = traits.Float(argstr='--jmin=%f',
+ desc=('Minimum acceptable Jacobian value for '
+ 'constraint (default 0.01)'))
+ jacobian_max = traits.Float(argstr='--jmax=%f',
+ desc=('Maximum acceptable Jacobian value for '
+ 'constraint (default 100.0)'))
+
+ abswarp = traits.Bool(argstr='--abs', xor=['relwarp'],
+ desc=('If set it indicates that the warps in --warp1 and --warp2 should be '
+ 'interpreted as absolute. I.e. the values in --warp1/2 are the '
+ 'coordinates in the next space, rather than displacements. This flag '
+ 'is ignored if --warp1/2 was created by fnirt, which always creates '
+ 'relative displacements.'))
+
+ relwarp = traits.Bool(argstr='--rel', xor=['abswarp'],
+ desc=('If set it indicates that the warps in --warp1/2 should be interpreted '
+ 'as relative. I.e. the values in --warp1/2 are displacements from the '
+ 'coordinates in the next space.'))
+
+ out_abswarp = traits.Bool(argstr='--absout', xor=['out_relwarp'],
+ desc=('If set it indicates that the warps in --out should be relative, i.e. '
+ 'the vaulues in --out are displacements from the coordinates in --ref.'))
+
+ out_relwarp = traits.Bool(argstr='--relout', xor=['out_abswarp'],
+ desc=('If set it indicates that the warps in --out should be relative, i.e. '
+ 'the vaulues in --out are displacements from the coordinates in --ref.'))
+
+
+class ConvertWarpOutputSpec(TraitedSpec):
+ out_file = File(exists=True,
+ desc=('Name of output file, containing the warp as field or coefficients.'))
+
+
+class ConvertWarp(FSLCommand):
+ """Use FSL `convertwarp <http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fnirt/warp_utils.html>`_
+ for combining multiple transforms into one.
+
+
+ Examples::
+
+ >>> from nipype.interfaces.fsl import ConvertWarp
+ >>> warputils = ConvertWarp()
+ >>> warputils.inputs.warp1 = "warpfield.nii"
+ >>> warputils.inputs.reference = "T1.nii"
+ >>> warputils.inputs.relwarp = True
+ >>> warputils.cmdline # doctest: +ELLIPSIS
+ 'convertwarp --out=.../T1_concatwarps.nii.gz --ref=T1.nii --rel --warp1=warpfield.nii'
+ >>> res = invwarp.run() # doctest: +SKIP
+ """
+
+ input_spec = ConvertWarpInputSpec
+ output_spec = ConvertWarpOutputSpec
+
+ _cmd = 'convertwarp'
+
+ def _list_outputs(self):
+ outputs = self.output_spec().get()
+ outputs['out_file'] = self.inputs.out_file
+
+ if not isdefined(outputs['out_file']):
+ outputs['out_file'] = self._gen_fname(self.inputs.reference,
+ suffix='_concatwarps')
+
+ outputs['out_file'] = os.path.abspath(outputs['out_file'])
+ return outputs
+
+ def _gen_filename(self, name):
+ if name == 'out_file':
+ return self._list_outputs()[name]
+
+ return None