name_source can be a list, make "infolder" a deprecated name

Author: chrisgorgo

nipype/interfaces/afni/preprocess.py

@@ -24,13 +24,23 @@
 
 class To3DInputSpec(AFNICommandInputSpec):
     out_file = File("%s", desc='output image file name',
-                    argstr='-prefix %s', name_source="infolder", usedefault=True)
-
+                    argstr='-prefix %s', name_source=["in_folder", "infolder"], usedefault=True)
+    in_xor = ["infolder", "in_folder"]
+    in_folder = Directory(desc='folder with DICOM images to convert',
+                         argstr='%s/*.dcm',
+                         position=-1,
+                         mandatory=True,
+                         exists=True,
+                         xor=in_xor)
+    
     infolder = Directory(desc='folder with DICOM images to convert',
                          argstr='%s/*.dcm',
                          position=-1,
                          mandatory=True,
-                         exists=True)
+                         exists=True,
+                         deprecated=0.8,
+                         new_name="in_folder",
+                         xor=in_xor)
 
     filetype = traits.Enum('spgr', 'fse', 'epan', 'anat', 'ct', 'spct',
                            'pet', 'mra', 'bmap', 'diff',

nipype/interfaces/base.py

@@ -1205,7 +1205,17 @@ def _gen_filename(self, name):
             value = getattr(self.inputs, name)
             if isdefined(value):
                 if "%s" in value:
-                    _, base, _ = split_filename(getattr(self.inputs, trait_spec.name_source))
+                    if isinstance(trait_spec.name_source, list):
+                        for ns in trait_spec.name_source:
+                            if isdefined(getattr(self.inputs, ns)):
+                                name_source = ns
+                                break
+                    else:
+                        name_source = trait_spec.name_source
+                    if name_source.endswith(os.path.sep):
+                        name_source = name_source[:-len(os.path.sep)]
+                    _, base, _ = split_filename(getattr(self.inputs, name_source))
+                    
                     retval = value%base
                 else:
                     retval = value