raising exception if the list provided as invert_affine doesnt make sense

Author: djarecka

nipype/interfaces/ants/resampling.py

@@ -43,9 +43,12 @@ class WarpTimeSeriesImageMultiTransformInputSpec(ANTSCommandInputSpec):
  desc='transformation file(s) to be applied',
  mandatory=True, copyfile=False)
  invert_affine = traits.List(traits.Int,
- desc=('List of Affine transformations to invert. '
+ desc=('List of Affine transformations to invert.'
  'E.g.: [1,4,5] inverts the 1st, 4th, and 5th Affines '
- 'found in transformation_series'))
+ 'found in transformation_series. Note that indexing '
+ 'starts with 1 and does not include warp fields. Affine '
+ 'transformations are distinguished '
+ 'from warp fields by the word "affine" included in their filenames.'))
 
 
 class WarpTimeSeriesImageMultiTransformOutputSpec(TraitedSpec):
@@ -67,6 +70,14 @@ class WarpTimeSeriesImageMultiTransform(ANTSCommand):
  'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz \
 ants_Affine.txt'
 
+ >>> wtsimt = WarpTimeSeriesImageMultiTransform()
+ >>> wtsimt.inputs.input_image = 'resting.nii'
+ >>> wtsimt.inputs.reference_image = 'ants_deformed.nii.gz'
+ >>> wtsimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt']
+ >>> wtsimt.inputs.invert_affine = [1] # # this will invert the 1st Affine file: ants_Affine.txt
+ >>> wtsimt.cmdline # doctest: +ALLOW_UNICODE
+ 'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz \
+-i ants_Affine.txt'
  """
 
  _cmd = 'WarpTimeSeriesImageMultiTransform'
@@ -81,13 +92,22 @@ def _format_arg(self, opt, spec, val):
  if opt == 'transformation_series':
  series = []
  affine_counter = 0
+ affine_invert = []
  for transformation in val:
  if 'Affine' in transformation and \
  isdefined(self.inputs.invert_affine):
  affine_counter += 1
  if affine_counter in self.inputs.invert_affine:
  series += ['-i']
+ affine_invert.append(affine_counter)
  series += [transformation]
+
+ if isdefined(self.inputs.invert_affine):
+ diff_inv = set(self.inputs.invert_affine) - set(affine_invert)
+ if diff_inv:
+ raise Exceptions("Review invert_affine, not all indexes from invert_affine were used, "
+ "check the description for the full definition")
+
  return ' '.join(series)
  return super(WarpTimeSeriesImageMultiTransform, self)._format_arg(opt, spec, val)
 
@@ -168,7 +188,7 @@ class WarpImageMultiTransform(ANTSCommand):
  >>> wimt.inputs.reference_image = 'functional.nii'
  >>> wimt.inputs.transformation_series = ['func2anat_coreg_Affine.txt','func2anat_InverseWarp.nii.gz', \
  'dwi2anat_Warp.nii.gz','dwi2anat_coreg_Affine.txt']
- >>> wimt.inputs.invert_affine = [1]
+ >>> wimt.inputs.invert_affine = [1] # this will invert the 1st Affine file: 'func2anat_coreg_Affine.txt'
  >>> wimt.cmdline # doctest: +ALLOW_UNICODE
  'WarpImageMultiTransform 3 diffusion_weighted.nii diffusion_weighted_wimt.nii -R functional.nii \
 -i func2anat_coreg_Affine.txt func2anat_InverseWarp.nii.gz dwi2anat_Warp.nii.gz dwi2anat_coreg_Affine.txt'
@@ -190,14 +210,24 @@ def _format_arg(self, opt, spec, val):
  if opt == 'transformation_series':
  series = []
  affine_counter = 0
+ affine_invert = []
  for transformation in val:
  if "affine" in transformation.lower() and \
  isdefined(self.inputs.invert_affine):
  affine_counter += 1
  if affine_counter in self.inputs.invert_affine:
  series += ['-i']
+ affine_invert.append(affine_counter)
  series += [transformation]
+
+ if isdefined(self.inputs.invert_affine):
+ diff_inv = set(self.inputs.invert_affine) - set(affine_invert)
+ if diff_inv:
+ raise Exceptions("Review invert_affine, not all indexes from invert_affine were used, "
+ "check the description for the full definition")
+
  return ' '.join(series)
+
  return super(WarpImageMultiTransform, self)._format_arg(opt, spec, val)
 
  def _list_outputs(self):

nipype/interfaces/ants/tests/test_resampling.py

@@ -3,7 +3,7 @@
 
 from nipype.interfaces.ants import WarpImageMultiTransform, WarpTimeSeriesImageMultiTransform
 import os
-import pytest, pdb
+import pytest
 
 
 @pytest.fixture()
@@ -47,7 +47,6 @@ def test_WarpImageMultiTransform_invaffine_2(change_dir, create_wimt):
  assert wimt.cmdline == 'WarpImageMultiTransform 3 diffusion_weighted.nii diffusion_weighted_wimt.nii -R functional.nii func2anat_coreg_Affine.txt func2anat_InverseWarp.nii.gz dwi2anat_Warp.nii.gz -i dwi2anat_coreg_Affine.txt'
 
 
-@pytest.mark.xfail(reason="dj: should it fail?")
 def test_WarpImageMultiTransform_invaffine_wrong(change_dir, create_wimt):
  wimt = create_wimt
  wimt.inputs.invert_affine = [3]
@@ -77,7 +76,6 @@ def test_WarpTimeSeriesImageMultiTransform_invaffine(change_dir, create_wtsimt):
 -R ants_deformed.nii.gz ants_Warp.nii.gz -i ants_Affine.txt'
 
 
-@pytest.mark.xfail(reason="dj: should it fail?")
 def test_WarpTimeSeriesImageMultiTransform_invaffine_wrong(change_dir, create_wtsimt):
  wtsimt = create_wtsimt
  wtsimt.inputs.invert_affine = [0]