Bugfix in FUGUE and doctest added

CHANGES

@@ -1,6 +1,7 @@
 Next Release
 ============
 
+* FIX: FUGUE interface was adding wrong parameter in forward warping mode.
 * API: Interfaces to external packages are no longer available in the top-level ``nipype`` namespace, and must be imported directly (e.g. ``from nipype.interfaces import fsl``).
 * ENH: New ANTs interface: ApplyTransformsToPoints
 * ENH: New FreeSurfer workflow: create_skullstripped_recon_flow()

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')
@@ -1159,9 +1159,8 @@ def _gen_filename(self, name):
 class FUGUEInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr='--in=%s',
                    desc='filename of input volume')
-    unwarped_file = File(
-        argstr='--unwarp=%s', genfile=True,
-        desc='apply unwarping and save as filename', hash_files=False)
+    unwarped_file = File(argstr='--unwarp=%s', desc='apply unwarping and save as filename',
+                         hash_files=False)
     forward_warping = traits.Bool(
         False, usedefault=True,
         desc='apply forward warping instead of unwarping')
@@ -1242,7 +1241,16 @@ class FUGUE(FSLCommand):
     Examples
     --------
 
-    Please insert examples for use of this command
+    >>> from nipype.interfaces.fsl.preprocess import FUGUE
+    >>> fugue = FUGUE()
+    >>> fugue.inputs.forward_warping = True
+    >>> fugue.inputs.in_file = 'epi.nii'
+    >>> fugue.inputs.mask_file = 'epi_mask.nii'
+    >>> fugue.inputs.shift_in_file = 'image.nii'  # Previously computed with fugue as well
+    >>> fugue.inputs.unwarp_direction = 'y'
+    >>> fugue.cmdline #doctest: +ELLIPSIS
+    'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=image.nii --unwarpdir=y --warp=.../epi_warped.nii.gz'
+    >>> fugue.run() #doctest: +SKIP
 
     """
 
@@ -1257,10 +1265,14 @@ def __init__(self, **kwargs):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        if self.inputs.forward_warping:
+
+        if isdefined(self.inputs.forward_warping) and self.inputs.forward_warping:
             out_field = 'warped_file'
+            self.inputs.unwarped_file = Undefined
+            outputs.pop('unwarped_file')
         else:
             out_field = 'unwarped_file'
+            outputs.pop('warped_file')
 
         out_file = getattr(self.inputs, out_field)
         if not isdefined(out_file):
@@ -1279,10 +1291,11 @@ def _list_outputs(self):
         return outputs
 
     def _gen_filename(self, name):
-        if name == 'unwarped_file' and not self.inputs.forward_warping:
-            return self._list_outputs()['unwarped_file']
-        if name == 'warped_file' and self.inputs.forward_warping:
-            return self._list_outputs()['warped_file']
+        is_fwd = isdefined(self.inputs.forward_warping) and self.inputs.forward_warping
+
+        if (is_fwd and name=='warped_file') or (not is_fwd and name=='unwarped_file'):
+            return self._list_outputs()[name]
+
         return None
 
     def _parse_inputs(self, skip=None):

nipype/interfaces/fsl/tests/test_auto_FUGUE.py

@@ -79,7 +79,6 @@ def test_FUGUE_inputs():
     unwarp_direction=dict(argstr='--unwarpdir=%s',
     ),
     unwarped_file=dict(argstr='--unwarp=%s',
-    genfile=True,
     hash_files=False,
     ),
     warped_file=dict(argstr='--warp=%s',