PEP8

Author: chrisgorgo

nipype/interfaces/nipy/preprocess.py

@@ -24,10 +24,10 @@
 
 class ComputeMaskInputSpec(BaseInterfaceInputSpec):
     mean_volume = File(exists=True, mandatory=True,
-    desc="mean EPI image, used to compute the threshold for the mask")
+                       desc="mean EPI image, used to compute the threshold for the mask")
     reference_volume = File(exists=True,
-                       desc=("reference volume used to compute the mask. "
-                             "If none is give, the mean volume is used."))
+                            desc=("reference volume used to compute the mask. "
+                                  "If none is give, the mean volume is used."))
     m = traits.Float(desc="lower fraction of the histogram to be discarded")
     M = traits.Float(desc="upper fraction of the histogram to be discarded")
     cc = traits.Bool(desc="Keep only the largest connected component")
@@ -69,7 +69,6 @@ def _list_outputs(self):
 
 class FmriRealign4dInputSpec(BaseInterfaceInputSpec):
 
-
     in_file = InputMultiPath(exists=True,
                              mandatory=True,
                              desc="File to realign")
@@ -144,10 +143,10 @@ def _run_interface(self, runtime):
             TR_slices = self.inputs.tr_slices
 
         R = FR4d(all_ims, tr=self.inputs.tr,
-            slice_order=self.inputs.slice_order,
-            tr_slices=TR_slices,
-            time_interp=self.inputs.time_interp,
-            start=self.inputs.start)
+                 slice_order=self.inputs.slice_order,
+                 tr_slices=TR_slices,
+                 time_interp=self.inputs.time_interp,
+                 start=self.inputs.start)
 
         R.estimate(loops=self.inputs.loops,
                    between_loops=self.inputs.between_loops,
@@ -159,11 +158,11 @@ def _run_interface(self, runtime):
 
         for j, corr in enumerate(corr_run):
             self._out_file_path.append(os.path.abspath('corr_%s.nii.gz' %
-                                (split_filename(self.inputs.in_file[j])[1])))
+                                      (split_filename(self.inputs.in_file[j])[1])))
             save_image(corr, self._out_file_path[j])
 
             self._par_file_path.append(os.path.abspath('%s.par' %
-            (os.path.split(self.inputs.in_file[j])[1])))
+                                      (os.path.split(self.inputs.in_file[j])[1])))
             mfile = open(self._par_file_path[j], 'w')
             motion = R._transforms[j]
             # nipy does not encode euler angles. return in original form of
@@ -190,19 +189,21 @@ class TrimInputSpec(BaseInterfaceInputSpec):
         exists=True, mandatory=True,
         desc="EPI image to trim")
     begin_index = traits.Int(
-        0,usedefault=True,
+        0, usedefault=True,
         desc='first volume')
     end_index = traits.Int(
-        0,usedefault=True,
+        0, usedefault=True,
         desc='last volume indexed as in python (and 0 for last)')
     out_file = File(desc='output filename')
     suffix = traits.Str(
-        '_trim',usedefault=True,
+        '_trim', usedefault=True,
         desc='suffix for out_file to use if no out_file provided')
 
+
 class TrimOutputSpec(TraitedSpec):
     out_file = File(exists=True)
 
+
 class Trim(BaseInterface):
     """ Simple interface to trim a few volumes from a 4d fmri nifti file
 
@@ -223,14 +224,14 @@ def _run_interface(self, runtime):
         out_file = self._list_outputs()['out_file']
         nii = nb.load(self.inputs.in_file)
         if self.inputs.end_index == 0:
-            s = slice(self.inputs.begin_index,nii.shape[3])
+            s = slice(self.inputs.begin_index, nii.shape[3])
         else:
-            s = slice(self.inputs.begin_index,self.inputs.end_index)
+            s = slice(self.inputs.begin_index, self.inputs.end_index)
         nii2 = nb.Nifti1Image(
-            nii.get_data()[...,s],
+            nii.get_data()[..., s],
             nii.get_affine(),
             nii.get_header())
-        nb.save(nii2,out_file)
+        nb.save(nii2, out_file)
         return runtime
 
     def _list_outputs(self):
@@ -243,5 +244,3 @@ def _list_outputs(self):
                 suffix=self.inputs.suffix)
         outputs['out_file'] = os.path.abspath(outputs['out_file'])
         return outputs
-
-