Corrected Camino interface out_file auto-naming

Author: mick-d

nipype/algorithms/metrics.py

@@ -572,7 +572,7 @@ def _run_interface(self, runtime):
  nb.Nifti1Image(errmap.astype(np.float32), nii_ref.get_affine(),
  hdr).to_filename(self._out_file)
 
- return runtime 
+ return runtime
 
  def _list_outputs(self):
  outputs = self.output_spec().get()

nipype/algorithms/tests/test_auto_ErrorMap.py

@@ -23,7 +23,8 @@ def test_ErrorMap_inputs():
  yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 def test_ErrorMap_outputs():
- output_map = dict(out_map=dict(),
+ output_map = dict(distance=dict(),
+ out_map=dict(),
  )
  outputs = ErrorMap.output_spec()
 

nipype/algorithms/tests/test_errormap.py

@@ -32,7 +32,7 @@ def test_errormap():
 errmap.inputs.in_ref = os.path.join(tempdir, 'alan.nii.gz')
 errmap.out_map = os.path.join(tempdir, 'out_map.nii.gz')
 result = errmap.run()
-yield assert_equal, result.outputs.distance, 1.125 
+yield assert_equal, result.outputs.distance, 1.125
 
 # Square metric
 errmap.inputs.metric = 'sqeuclidean'
@@ -42,9 +42,9 @@ def test_errormap():
 # Linear metric
 errmap.inputs.metric = 'euclidean'
 result = errmap.run()
-yield assert_equal, result.outputs.distance, 0.875 
+yield assert_equal, result.outputs.distance, 0.875
 
-# Masked 
+# Masked
 errmap.inputs.mask = os.path.join(tempdir, 'mask.nii.gz')
 result = errmap.run()
 yield assert_equal, result.outputs.distance, 1.0

nipype/interfaces/ants/registration.py

@@ -395,7 +395,7 @@ class Registration(ANTSCommand):
  >>> outputs = reg4._list_outputs()
  >>> print outputs #doctest: +ELLIPSIS
  {'reverse_invert_flags': [], 'inverse_composite_transform': ['.../nipype/testing/data/output_InverseComposite.h5'], 'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz', 'inverse_warped_image': <undefined>, 'forward_invert_flags': [], 'reverse_transforms': [], 'composite_transform': ['.../nipype/testing/data/output_Composite.h5'], 'forward_transforms': []}
- 
+
  >>> # Test collapse transforms flag
  >>> reg4b = copy.deepcopy(reg4)
  >>> reg4b.inputs.write_composite_transform = False

nipype/interfaces/camino/dti.py

@@ -549,7 +549,11 @@ class Track(CommandLine):
 
  def _list_outputs(self):
  outputs = self.output_spec().get()
- outputs['tracked'] = os.path.abspath(self._gen_outfilename())
+ if isdefined(self.inputs.out_file):
+ out_file_path = os.path.abspath(self.inputs.out_file)
+ else:
+ out_file_path = os.path.abspath(self._gen_outfilename())
+ outputs['tracked'] = out_file_path
  return outputs
 
  def _gen_filename(self, name):