fix: automask bug when apply_mask is not specified

Author: satra

nipype/interfaces/afni/preprocess.py

@@ -562,7 +562,9 @@ class AutomaskInputSpec(AFNITraitedSpec):
         hash_files=False)
 
     apply_mask = File(desc="output file from 3dAutomask",
-        argstr='-apply_prefix %s')
+                      argstr='-apply_prefix %s',
+                      genfile=True,
+                      hash_files=False)
 
     clfrac = traits.Float(desc='sets the clip level fraction' +
         ' (must be 0.1-0.9). ' +
@@ -610,8 +612,10 @@ class Automask(AFNICommand):
     output_spec = AutomaskOutputSpec
 
     def _gen_filename(self, name):
-        if name == 'out_file' or name == 'brain_file':
+        if name == 'out_file':
             return self._list_outputs()[name]
+        if name == 'apply_mask':
+            return self._list_outputs()['brain_file']
         return None
 
     def _list_outputs(self):
@@ -623,8 +627,8 @@ def _list_outputs(self):
             outputs['out_file'] = os.path.abspath(self.inputs.out_file)
 
         if not isdefined(self.inputs.apply_mask):
-            outputs['brain_file'] = self._gen_fname(
-                self.inputs.in_file, suffix=self.inputs.apply_suffix)
+            outputs['brain_file'] = self._gen_fname(self.inputs.in_file,
+                                                suffix=self.inputs.apply_suffix)
         else:
             outputs['brain_file'] = os.path.abspath(self.inputs.apply_mask)
         return outputs

nipype/interfaces/afni/tests/test_preprocess.py

@@ -356,17 +356,20 @@ def test_maskave():
             yield assert_equal, getattr(instance.inputs.traits()[key], metakey), value
 
 def test_automask():
-    input_map = dict(apply_mask = dict(argstr='-apply_prefix %s',),
+    input_map = dict(apply_mask = dict(argstr='-apply_prefix %s',
+                                       hash_files=False,genfile=True,),
+                     apply_suffix = dict(usedefault=True,),
                      args = dict(argstr='%s',),
                      clfrac = dict(argstr='-dilate %s',),
                      dilate = dict(argstr='-dilate %s',),
                      environ = dict(usedefault=True,),
                      erode = dict(argstr='-erode %s',),
                      ignore_exception = dict(usedefault=True,),
                      in_file = dict(argstr='%s',mandatory=True,),
-                     out_file = dict(argstr='-prefix %s',),
+                     mask_suffix = dict(usedefault=True,),
+                     out_file = dict(hash_files=False,genfile=True,
+                                     argstr='-prefix %s',),
                      outputtype = dict(),
-                     suffix = dict(),
                      )
     instance = afni.Automask()
     for key, metadata in input_map.items():