Merge pull request #2674 from mgxd/fix/cmd

MAINT: ensure interface _cmd only includes executable

Author: effigies

nipype/interfaces/afni/preprocess.py

@@ -2953,107 +2953,6 @@ def _list_outputs(self):
  return outputs
 
 
-class QwarpPlusMinusInputSpec(CommandLineInputSpec):
- source_file = File(
- desc=
- 'Source image (opposite phase encoding direction than base image).',
- argstr='-source %s',
- mandatory=True,
- exists=True,
- copyfile=False)
- base_file = File(
- desc=
- 'Base image (opposite phase encoding direction than source image).',
- argstr='-base %s',
- mandatory=True,
- exists=True,
- copyfile=False)
- pblur = traits.List(
- traits.Float(),
- desc='The fraction of the patch size that'
- 'is used for the progressive blur by providing a '
- 'value between 0 and 0.25. If you provide TWO '
- 'values, the first fraction is used for '
- 'progressively blurring the base image and the '
- 'second for the source image.',
- argstr='-pblur %s',
- minlen=1,
- maxlen=2)
- blur = traits.List(
- traits.Float(),
- desc="Gaussian blur the input images by (FWHM) voxels "
- "before doing the alignment (the output dataset "
- "will not be blurred). The default is 2.345 (for "
- "no good reason). Optionally, you can provide 2 "
- "values, and then the first one is applied to the "
- "base volume, the second to the source volume. A "
- "negative blur radius means to use 3D median "
- "filtering, rather than Gaussian blurring. This "
- "type of filtering will better preserve edges, "
- "which can be important in alignment.",
- argstr='-blur %s',
- minlen=1,
- maxlen=2)
- noweight = traits.Bool(
- desc='If you want a binary weight (the old default), use this option.'
- 'That is, each voxel in the base volume automask will be'
- 'weighted the same in the computation of the cost functional.',
- argstr='-noweight')
- minpatch = traits.Int(
- desc="Set the minimum patch size for warp searching to 'mm' voxels.",
- argstr='-minpatch %d')
- nopadWARP = traits.Bool(
- desc='If for some reason you require the warp volume to'
- 'match the base volume, then use this option to have the output'
- 'WARP dataset(s) truncated.',
- argstr='-nopadWARP')
-
-
-class QwarpPlusMinusOutputSpec(TraitedSpec):
- warped_source = File(desc='Undistorted source file.', exists=True)
- warped_base = File(desc='Undistorted base file.', exists=True)
- source_warp = File(
- desc="Field suceptibility correction warp (in 'mm') for source image.",
- exists=True)
- base_warp = File(
- desc="Field suceptibility correction warp (in 'mm') for base image.",
- exists=True)
-
-
-class QwarpPlusMinus(CommandLine):
- """A version of 3dQwarp for performing field susceptibility correction
- using two images with opposing phase encoding directions.
-
- For complete details, see the `3dQwarp Documentation.
- <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dQwarp.html>`_
-
- Examples
- ========
-
- >>> from nipype.interfaces import afni
- >>> qwarp = afni.QwarpPlusMinus()
- >>> qwarp.inputs.source_file = 'sub-01_dir-LR_epi.nii.gz'
- >>> qwarp.inputs.nopadWARP = True
- >>> qwarp.inputs.base_file = 'sub-01_dir-RL_epi.nii.gz'
- >>> qwarp.cmdline
- '3dQwarp -prefix Qwarp.nii.gz -plusminus -base sub-01_dir-RL_epi.nii.gz -nopadWARP -source sub-01_dir-LR_epi.nii.gz'
- >>> res = warp.run() # doctest: +SKIP
-
- """
- _cmd = '3dQwarp -prefix Qwarp.nii.gz -plusminus'
- input_spec = QwarpPlusMinusInputSpec
- output_spec = QwarpPlusMinusOutputSpec
-
- def _list_outputs(self):
- outputs = self.output_spec().get()
- outputs['warped_source'] = os.path.abspath("Qwarp_PLUS.nii.gz")
- outputs['warped_base'] = os.path.abspath("Qwarp_MINUS.nii.gz")
- outputs['source_warp'] = os.path.abspath("Qwarp_PLUS_WARP.nii.gz")
- outputs['base_warp'] = os.path.abspath("Qwarp_MINUS_WARP.nii.gz")
-
- return outputs
-
-
 class QwarpInputSpec(AFNICommandInputSpec):
  in_file = File(
  desc=
@@ -3722,3 +3621,54 @@ def _list_outputs(self):
  def _gen_filename(self, name):
  if name == 'out_file':
  return self._gen_fname(self.inputs.source_file, suffix='_QW')
+
+
+class QwarpPlusMinusInputSpec(QwarpInputSpec):
+ source_file = File(
+ desc='Source image (opposite phase encoding direction than base image)',
+ argstr='-source %s',
+ exists=True,
+ deprecated='1.1.2',
+ new_name='in_file',
+ copyfile=False)
+ out_file = File(
+ argstr='-prefix %s',
+ value='Qwarp.nii.gz',
+ position=0,
+ usedefault=True,
+ desc="Output file")
+ plusminus = traits.Bool(
+ True,
+ usedefault=True,
+ position=1,
+ desc='Normally, the warp displacements dis(x) are defined to match'
+ 'base(x) to source(x+dis(x)). With this option, the match'
+ 'is between base(x-dis(x)) and source(x+dis(x)) -- the two'
+ 'images \'meet in the middle\'. For more info, view Qwarp` interface',
+ argstr='-plusminus',
+ xor=['duplo', 'allsave', 'iwarp'])
+
+
+class QwarpPlusMinus(Qwarp):
+ """A version of 3dQwarp for performing field susceptibility correction
+ using two images with opposing phase encoding directions.
+
+ For complete details, see the `3dQwarp Documentation.
+ <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dQwarp.html>`_
+
+ Examples
+ ========
+
+ >>> from nipype.interfaces import afni
+ >>> qwarp = afni.QwarpPlusMinus()
+ >>> qwarp.inputs.in_file = 'sub-01_dir-LR_epi.nii.gz'
+ >>> qwarp.inputs.nopadWARP = True
+ >>> qwarp.inputs.base_file = 'sub-01_dir-RL_epi.nii.gz'
+ >>> qwarp.cmdline
+ '3dQwarp -prefix Qwarp.nii.gz -plusminus -base sub-01_dir-RL_epi.nii.gz \
+ -source sub-01_dir-LR_epi.nii.gz -nopadWARP'
+ >>> res = warp.run() # doctest: +SKIP
+
+ """
+
+ input_spec = QwarpPlusMinusInputSpec

nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py

@@ -5,25 +5,154 @@
 
 def test_QwarpPlusMinus_inputs():
  input_map = dict(
+ Qfinal=dict(argstr='-Qfinal', ),
+ Qonly=dict(argstr='-Qonly', ),
+ allineate=dict(argstr='-allineate', ),
+ allineate_opts=dict(
+ argstr='-allineate_opts %s',
+ requires=['allineate'],
+ ),
+ allsave=dict(
+ argstr='-allsave',
+ xor=['nopadWARP', 'duplo', 'plusminus'],
+ ),
  args=dict(argstr='%s', ),
+ ballopt=dict(
+ argstr='-ballopt',
+ xor=['workhard', 'boxopt'],
+ ),
  base_file=dict(
  argstr='-base %s',
  copyfile=False,
  mandatory=True,
  ),
+ baxopt=dict(
+ argstr='-boxopt',
+ xor=['workhard', 'ballopt'],
+ ),
  blur=dict(argstr='-blur %s', ),
+ duplo=dict(
+ argstr='-duplo',
+ xor=[
+ 'gridlist', 'maxlev', 'inilev', 'iniwarp', 'plusminus',
+ 'allsave'
+ ],
+ ),
+ emask=dict(
+ argstr='-emask %s',
+ copyfile=False,
+ ),
  environ=dict(
  nohash=True,
  usedefault=True,
  ),
+ expad=dict(
+ argstr='-expad %d',
+ xor=['nopadWARP'],
+ ),
+ gridlist=dict(
+ argstr='-gridlist %s',
+ copyfile=False,
+ xor=['duplo', 'plusminus'],
+ ),
+ hel=dict(
+ argstr='-hel',
+ xor=['nmi', 'mi', 'lpc', 'lpa', 'pear'],
+ ),
+ in_file=dict(
+ argstr='-source %s',
+ copyfile=False,
+ mandatory=True,
+ ),
+ inilev=dict(
+ argstr='-inilev %d',
+ xor=['duplo'],
+ ),
+ iniwarp=dict(
+ argstr='-iniwarp %s',
+ xor=['duplo'],
+ ),
+ iwarp=dict(
+ argstr='-iwarp',
+ xor=['plusminus'],
+ ),
+ lpa=dict(
+ argstr='-lpa',
+ xor=['nmi', 'mi', 'lpc', 'hel', 'pear'],
+ ),
+ lpc=dict(
+ argstr='-lpc',
+ position=-2,
+ xor=['nmi', 'mi', 'hel', 'lpa', 'pear'],
+ ),
+ maxlev=dict(
+ argstr='-maxlev %d',
+ position=-1,
+ xor=['duplo'],
+ ),
+ mi=dict(
+ argstr='-mi',
+ xor=['mi', 'hel', 'lpc', 'lpa', 'pear'],
+ ),
  minpatch=dict(argstr='-minpatch %d', ),
- nopadWARP=dict(argstr='-nopadWARP', ),
+ nmi=dict(
+ argstr='-nmi',
+ xor=['nmi', 'hel', 'lpc', 'lpa', 'pear'],
+ ),
+ noXdis=dict(argstr='-noXdis', ),
+ noYdis=dict(argstr='-noYdis', ),
+ noZdis=dict(argstr='-noZdis', ),
+ noneg=dict(argstr='-noneg', ),
+ nopad=dict(argstr='-nopad', ),
+ nopadWARP=dict(
+ argstr='-nopadWARP',
+ xor=['allsave', 'expad'],
+ ),
+ nopenalty=dict(argstr='-nopenalty', ),
+ nowarp=dict(argstr='-nowarp', ),
  noweight=dict(argstr='-noweight', ),
+ num_threads=dict(
+ nohash=True,
+ usedefault=True,
+ ),
+ out_file=dict(
+ argstr='-prefix %s',
+ position=0,
+ usedefault=True,
+ ),
+ out_weight_file=dict(argstr='-wtprefix %s', ),
+ outputtype=dict(),
+ overwrite=dict(argstr='-overwrite', ),
  pblur=dict(argstr='-pblur %s', ),
+ pear=dict(argstr='-pear', ),
+ penfac=dict(argstr='-penfac %f', ),
+ plusminus=dict(
+ argstr='-plusminus',
+ position=1,
+ usedefault=True,
+ xor=['duplo', 'allsave', 'iwarp'],
+ ),
+ quiet=dict(
+ argstr='-quiet',
+ xor=['verb'],
+ ),
+ resample=dict(argstr='-resample', ),
  source_file=dict(
  argstr='-source %s',
  copyfile=False,
- mandatory=True,
+ deprecated='1.1.2',
+ new_name='in_file',
+ ),
+ verb=dict(
+ argstr='-verb',
+ xor=['quiet'],
+ ),
+ wball=dict(argstr='-wball %s', ),
+ weight=dict(argstr='-weight %s', ),
+ wmask=dict(argstr='-wpass %s %f', ),
+ workhard=dict(
+ argstr='-workhard',
+ xor=['boxopt', 'ballopt'],
  ),
  )
  inputs = QwarpPlusMinus.input_spec()
@@ -37,6 +166,7 @@ def test_QwarpPlusMinus_outputs():
  source_warp=dict(),
  warped_base=dict(),
  warped_source=dict(),
+ weights=dict(),
  )
  outputs = QwarpPlusMinus.output_spec()
 

nipype/interfaces/elastix/registration.py

@@ -178,21 +178,36 @@ def _list_outputs(self):
  return outputs
 
 
-class AnalyzeWarpInputSpec(ElastixBaseInputSpec):
- transform_file = File(
+class AnalyzeWarpInputSpec(ApplyWarpInputSpec):
+ points = traits.Enum(
+ 'all',
+ usedefault=True,
+ position=0,
+ argstr='-def %s',
+ desc='transform all points from the input-image, which effectively'
+ ' generates a deformation field.')
+ jac = traits.Enum(
+ 'all',
+ usedefault=True,
+ argstr='-jac %s',
+ desc='generate an image with the determinant of the spatial Jacobian')
+ jacmat = traits.Enum(
+ 'all',
+ usedefault=True,
+ argstr='-jacmat %s',
+ desc='generate an image with the spatial Jacobian matrix at each voxel')
+ moving_image = File(
  exists=True,
- mandatory=True,
- argstr='-tp %s',
- desc='transform-parameter file, only 1')
-
+ argstr='-in %s',
+ desc='input image to deform (not used)')
 
 class AnalyzeWarpOutputSpec(TraitedSpec):
  disp_field = File(desc='displacements field')
  jacdet_map = File(desc='det(Jacobian) map')
  jacmat_map = File(desc='Jacobian matrix map')
 
 
-class AnalyzeWarp(CommandLine):
+class AnalyzeWarp(ApplyWarp):
  """
  Use transformix to get details from the input transform (generate
  the corresponding deformation field, generate the determinant of the
@@ -210,7 +225,6 @@ class AnalyzeWarp(CommandLine):
 
  """
 
- _cmd = 'transformix -def all -jac all -jacmat all'
  input_spec = AnalyzeWarpInputSpec
  output_spec = AnalyzeWarpOutputSpec