FIX: make check-before-commit

Author: David Ellis

nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py

@@ -19,6 +19,7 @@ def test_Aparc2Aseg_inputs():
     environ=dict(nohash=True,
     usedefault=True,
     ),
+    filled=dict(),
     hypo_wm=dict(argstr='--hypo-as-wm',
     mandatory=False,
     ),

nipype/interfaces/freesurfer/tests/test_auto_Curvature.py

@@ -19,6 +19,7 @@ def test_Curvature_inputs():
     usedefault=True,
     ),
     in_file=dict(argstr='%s',
+    copyfile=True,
     mandatory=True,
     position=-2,
     ),

nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py

@@ -35,6 +35,7 @@ def test_MakeSurfaces_inputs():
     in_orig=dict(argstr='-orig %s',
     mandatory=True,
     ),
+    in_white=dict(),
     in_wm=dict(mandatory=True,
     ),
     longitudinal=dict(argstr='-long',
@@ -66,6 +67,8 @@ def test_MakeSurfaces_inputs():
     subjects_dir=dict(),
     terminal_output=dict(nohash=True,
     ),
+    white=dict(argstr='-white %s',
+    ),
     white_only=dict(argstr='-whiteonly',
     mandatory=False,
     ),

nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py

@@ -10,6 +10,7 @@ def test_SegStatsReconAll_inputs():
     ),
     args=dict(argstr='%s',
     ),
+    aseg=dict(),
     avgwf_file=dict(argstr='--avgwfvol %s',
     ),
     avgwf_txt_file=dict(argstr='--avgwf %s',
@@ -85,8 +86,7 @@ def test_SegStatsReconAll_inputs():
     ),
     partial_volume_file=dict(argstr='--pv %s',
     ),
-    presurf_seg=dict(mandatory=True,
-    ),
+    presurf_seg=dict(),
     rh_orig_nofix=dict(mandatory=True,
     ),
     rh_pial=dict(mandatory=True,

nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py

@@ -6,6 +6,8 @@
 def test_VolumeMask_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
+    aseg=dict(xor=['in_aseg'],
+    ),
     copy_inputs=dict(mandatory=False,
     ),
     environ=dict(nohash=True,
@@ -16,6 +18,7 @@ def test_VolumeMask_inputs():
     ),
     in_aseg=dict(argstr='--aseg_name %s',
     mandatory=False,
+    xor=['aseg'],
     ),
     left_ribbonlabel=dict(argstr='--label_left_ribbon %d',
     mandatory=True,

nipype/interfaces/freesurfer/utils.py

@@ -2315,14 +2315,14 @@ class VolumeMaskInputSpec(FSTraitedSpec):
     rh_white = File(mandatory=True, exists=True,
                     desc="Implicit input right white matter surface")
     aseg = File(exists=True,
-                xor=['in_aseg'], 
-                desc="Implicit aseg.mgz segmentation. " + 
+                xor=['in_aseg'],
+                desc="Implicit aseg.mgz segmentation. " +
                 "Specify a different aseg by using the 'in_aseg' input.")
     subject_id = traits.String('subject_id', usedefault=True,
                                position=-1, argstr="%s", mandatory=True,
                                desc="Subject being processed")
     # optional
-    in_aseg = File(argstr="--aseg_name %s", mandatory=False, 
+    in_aseg = File(argstr="--aseg_name %s", mandatory=False,
                    exists=True, xor=['aseg'],
                    desc="Input aseg file for VolumeMask")
     save_ribbon = traits.Bool(argstr="--save_ribbon", mandatory=False,
@@ -2383,7 +2383,7 @@ def run(self, **inputs):
             copy2subjdir(self, self.inputs.rh_white, 'surf', 'rh.white')
             copy2subjdir(self, self.inputs.in_aseg, 'mri')
             copy2subjdir(self, self.inputs.aseg, 'mri', 'aseg.mgz')
-            
+
         return super(VolumeMask, self).run(**inputs)
 
     def _format_arg(self, name, spec, value):

nipype/workflows/smri/freesurfer/autorecon1.py

@@ -345,7 +345,7 @@ def awkfile(in_file, log_file):
         intensity_correction.inputs.iterations = 2
         ar1_wf.connect([(add_xform_to_orig, intensity_correction, [('out_file', 'in_file')]),
                         (copy_transform, intensity_correction, [('out_file', 'transform')])])
-        
+
 
         add_to_header_nu = pe.Node(AddXFormToHeader(), name="Add_XForm_to_NU")
         add_to_header_nu.inputs.copy_name = True
@@ -356,7 +356,7 @@ def awkfile(in_file, log_file):
                          [('out_file', 'transform')])
                     ])
 
-        
+
     # Intensity Normalization
     # Performs intensity normalization of the orig volume and places the result in mri/T1.mgz.
     # Attempts to correct for fluctuations in intensity that would otherwise make intensity-based
@@ -368,7 +368,7 @@ def awkfile(in_file, log_file):
     mri_normalize.inputs.out_file = 'T1.mgz'
 
     if fsvernum < 6:
-        ar1_wf.connect([(add_to_header_nu, mri_normalize, [('out_file', 'in_file')])])        
+        ar1_wf.connect([(add_to_header_nu, mri_normalize, [('out_file', 'in_file')])])
     else:
         ar1_wf.connect([(add_xform_to_orig_nu, mri_normalize, [('out_file', 'in_file')])])
 
@@ -390,7 +390,7 @@ def awkfile(in_file, log_file):
             ar1_wf.connect(add_to_header_nu, 'out_file', mri_em_register, 'in_file')
         else:
             ar1_wf.connect(add_xform_to_orig_nu, 'out_file', mri_em_register, 'in_file')
-            
+
         ar1_wf.connect([(inputspec, mri_em_register, [('num_threads', 'num_threads'),
                                                       ('reg_template_withskull', 'template')])])
 

nipype/workflows/smri/freesurfer/autorecon2.py

@@ -61,7 +61,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
         ar2_wf.connect([(inputspec, intensity_correction, [('orig', 'in_file'),
                                                            ('brainmask', 'mask'),
                                                            ('transform', 'transform')])])
-        
+
         # intensity correction parameters are more specific in 6+
         intensity_correction.inputs.iterations = 1
         intensity_correction.inputs.protocol_iterations = 1000
@@ -70,7 +70,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
         if shrink:
             intensity_correction.inputs.shrink =  shrink
         intensity_correction.inputs.distance = distance
-        
+
         add_to_header_nu = pe.Node(AddXFormToHeader(), name="Add_XForm_to_NU")
         add_to_header_nu.inputs.copy_name = True
         add_to_header_nu.inputs.out_file = 'nu.mgz'
@@ -108,7 +108,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
             ar2_wf.connect([(add_to_header_nu, align_transform, [('out_file', 'in_file')])])
         else:
             ar2_wf.connect([(inputspec, align_transform, [('nu', 'in_file')])])
-            
+
 
     # CA Normalize
     """
@@ -698,7 +698,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
         # add to outputspec to perserve datasinking
         ar2_wf.connect([(inputspec, outputspec, [('nu', 'nu')])])
 
-    
+
     ar2_wf.connect([(align_transform, outputspec, [('out_file', 'tal_lta')]),
                     (ca_normalize, outputspec, [('out_file', 'norm')]),
                     (ca_normalize, outputspec, [('control_points', 'ctrl_pts')]),

nipype/workflows/smri/freesurfer/autorecon3.py

@@ -621,10 +621,10 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
                                        out_aseg),
                               name="Aseg")
         ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_aparcaseg')]),
-                        (inputspec, apas_2_aseg, [('aseg_presurf', 'in_aseg')])])       
+                        (inputspec, apas_2_aseg, [('aseg_presurf', 'in_aseg')])])
 
     apas_2_aseg.inputs.out_file = "aseg.mgz"
-                                       
+
 
     # Segmentation Stats
     """

nipype/workflows/smri/freesurfer/ba_maps.py

@@ -85,7 +85,7 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
                         out_file = '{0}.{1}_exvivo.label'.format(hemisphere, label)
                     else:
                         out_file = '{0}.{1}.label'.format(hemisphere, label)
-                        
+
                     out_files.append(out_file)
                     field_template[label] = 'label/' + out_file
                     source_fields.append(label)