conform to PEP8, add deprecated field for ROIStats interface

Author: rciric

nipype/interfaces/afni/preprocess.py

@@ -1807,6 +1807,8 @@ class ROIStatsInputSpec(CommandLineInputSpec):
         position=-2,
         mandatory=True,
         exists=True)
+    mask = File(desc='input mask', argstr='-mask %s', position=3, exists=True,
+                deprecated='1.1.5', new_name='mask_file')
     mask_file = File(desc='input mask', argstr='-mask %s', exists=True)
     mask_f2short = traits.Bool(
         desc='Tells the program to convert a float mask to short integers, '
@@ -1925,24 +1927,22 @@ class ROIStats(AFNICommandBase):
     output_spec = ROIStatsOutputSpec
 
     def _format_arg(self, name, spec, value):
-
-        _stat_dict  =   {
-                            'mean': '-nzmean',
-                            'median': '-nzmedian',
-                            'mode': '-nzmode',
-                            'minmax': '-nzminmax',
-                            'sigma': '-nzsigma',
-                            'voxels': '-nzvoxels',
-                            'sum': '-nzsum',
-                            'summary': '-summary',
-                            'zerominmax': '-minmax',
-                            'zeromedian': '-median',
-                            'zerosigma': '-sigma',
-                            'zeromode': '-mode'
-                        }
+        _stat_dict = {
+            'mean': '-nzmean',
+            'median': '-nzmedian',
+            'mode': '-nzmode',
+            'minmax': '-nzminmax',
+            'sigma': '-nzsigma',
+            'voxels': '-nzvoxels',
+            'sum': '-nzsum',
+            'summary': '-summary',
+            'zerominmax': '-minmax',
+            'zeromedian': '-median',
+            'zerosigma': '-sigma',
+            'zeromode': '-mode'
+            }
         if name == 'stat':
             value = [_stat_dict[v] for v in value]
-
         return super(ROIStats, self)._format_arg(name, spec, value)
 
 

nipype/interfaces/afni/tests/test_auto_ROIStats.py

@@ -24,6 +24,12 @@ def test_ROIStats_inputs():
             mandatory=True,
             position=-2,
         ),
+        mask=dict(
+            argstr='-mask %s',
+            deprecated='1.1.5',
+            new_name='mask_file',
+            position=3,
+        ),
         mask_f2short=dict(argstr='-mask_f2short', ),
         mask_file=dict(argstr='-mask %s', ),
         nobriklab=dict(argstr='-nobriklab', ),

nipype/interfaces/afni/tests/test_auto_ReHo.py

@@ -21,7 +21,7 @@ def test_ReHo_inputs():
             position=1,
         ),
         label_set=dict(argstr='-in_rois %s', ),
-        mask=dict(argstr='-mask %s', ),
+        mask_file=dict(argstr='-mask %s', ),
         neighborhood=dict(
             argstr='-nneigh %s',
             xor=['sphere', 'ellipsoid'],

nipype/interfaces/afni/utils.py

@@ -2318,8 +2318,10 @@ class ReHoInputSpec(CommandLineInputSpec):
     chi_sq = traits.Bool(
         argstr='-chi_sq',
         desc='Output the Friedman chi-squared value in addition to the '
-             'Kendall\'s W.')
-    mask = traits.File(
+             'Kendall\'s W. This option is currently compatible only with '
+             'the AFNI (BRIK/HEAD) output type; the chi-squared value will '
+             'be the second sub-brick of the output dataset.')
+    mask_file = traits.File(
         desc='Mask within which ReHo should be calculated voxelwise',
         argstr='-mask %s')
     neighborhood = traits.Enum(
@@ -2403,24 +2405,19 @@ class ReHo(AFNICommandBase):
     output_spec = ReHoOutputSpec
 
     def _list_outputs(self):
-
         outputs = super(ReHo, self)._list_outputs()
-
         if self.inputs.label_set:
             outputs['out_vals'] = outputs['out_file'] + '_ROI_reho.vals'
-
         return outputs
 
     def _format_arg(self, name, spec, value):
-
-        _neigh_dict =   {
-                            'faces': 7,
-                            'edges': 19,
-                            'vertices': 27,
-                        }
+        _neigh_dict = {
+            'faces': 7,
+            'edges': 19,
+            'vertices': 27,
+            }
         if name == 'neighborhood':
             value = _neigh_dict[value]
-
         return super(ReHo, self)._format_arg(name, spec, value)