RF: Use name_source for Allineate.inputs.out_file

Author: effigies

nipype/interfaces/afni/preprocess.py

@@ -218,7 +218,8 @@ class AllineateInputSpec(AFNICommandInputSpec):
     out_file = File(
         desc='output file from 3dAllineate',
         argstr='-prefix %s',
-        genfile=True,
+        name_template='%s_allineate',
+        name_source='in_file',
         hash_files=False,
         xor=['allcostx'])
     out_param_file = File(
@@ -486,16 +487,8 @@ def _format_arg(self, name, trait_spec, value):
             return arg
         return super(Allineate, self)._format_arg(name, trait_spec, value)
 
-    def _gen_outfilename(self):
-        out_file = self.inputs.out_file
-        if not isdefined(out_file) and isdefined(self.inputs.in_file) and not isdefined(self.inputs.allcostx):
-            out_file = op.abspath(self._gen_fname(self.inputs.in_file,op.dirname(self.inputs.in_file),suffix='_allineate'))
-        return out_file
-
     def _list_outputs(self):
-        outputs = self.output_spec().get()
-
-        outputs['out_file'] = self._gen_outfilename()
+        outputs = super(Allineate, self)._list_outputs()
 
         if isdefined(self.inputs.out_weight_file):
             outputs['out_weight_file'] = op.abspath(
@@ -523,11 +516,6 @@ def _list_outputs(self):
                 os.path.join(os.getcwd(), self.inputs.allcostx))
         return outputs
 
-    def _gen_filename(self, name):
-        if name == 'out_file':
-            return self._gen_outfilename()
-        return None
-
 
 class AutoTcorrelateInputSpec(AFNICommandInputSpec):
     in_file = File(