Merge pull request #694 from chrisfilo/enh/custom_output_names

Added support for custom output names

Author: satra

doc/devel/cmd_interface_devel.rst

@@ -193,6 +193,10 @@ hash_files
 
 name_template (optional)
      overrides the default ``_generated`` suffix
+     
+output_name (optional)
+     name of the output (if this is not set same name as the input will be 
+     assumed)
 
 keep_extension (optional - not used)
      if you want the extension from the input to be kept

nipype/interfaces/base.py

@@ -1466,7 +1466,10 @@ def _filename_from_source(self, name):
                         break
             else:
                 name_source = trait_spec.name_source
-            _, base, _ = split_filename(getattr(self.inputs, name_source))
+            source = getattr(self.inputs, name_source)
+            while isinstance(source, list):
+                source = source[0]
+            _, base, _ = split_filename(source)
             retval = name_template % base
             _, _, ext = split_filename(retval)
             if trait_spec.keep_extension and ext:
@@ -1482,11 +1485,14 @@ def _overload_extension(self, value):
 
     def _list_outputs(self):
         metadata = dict(name_source=lambda t: t is not None)
-        out_names = self.inputs.traits(**metadata).keys()
-        if out_names:
+        traits = self.inputs.traits(**metadata)
+        if traits:
             outputs = self.output_spec().get()
-            for name in out_names:
-                outputs[name] = \
+            for name, trait_spec in traits.iteritems():
+                out_name = name
+                if trait_spec.output_name != None:
+                    out_name = trait_spec.output_name
+                outputs[out_name] = \
                     os.path.abspath(self._filename_from_source(name))
             return outputs
 

nipype/interfaces/mrtrix/preprocess.py

@@ -84,8 +84,8 @@ def _gen_outfilename(self):
 class DWI2TensorInputSpec(CommandLineInputSpec):
     in_file = InputMultiPath(File(exists=True), argstr='%s', mandatory=True,
                              position=-2, desc='Diffusion-weighted images')
-    out_filename = File(genfile=True, argstr='%s', position=-1,
-                        desc='Output tensor filename')
+    out_filename = File(name_template="%s_tensor.mif", name_source="in_file", output_name="tensor",
+                        argstr='%s', posidesc='Output tensor filename', position=-1)
     encoding_file = File(argstr='-grad %s', position= 2,
                          desc=('Encoding file supplied as a 4xN text file with '
                                'each line is in the format [ X Y Z b ], where '
@@ -114,27 +114,15 @@ class DWI2Tensor(CommandLine):
     >>> dwi2tensor = mrt.DWI2Tensor()
     >>> dwi2tensor.inputs.in_file = 'dwi.mif'
     >>> dwi2tensor.inputs.encoding_file = 'encoding.txt'
+    >>> dwi2tensor.cmdline
+    'dwi2tensor -grad encoding.txt dwi.mif dwi_tensor.mif'
     >>> dwi2tensor.run()                                   # doctest: +SKIP
     """
 
     _cmd = 'dwi2tensor'
     input_spec=DWI2TensorInputSpec
     output_spec=DWI2TensorOutputSpec
 
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['tensor'] = op.abspath(self._gen_outfilename())
-        return outputs
-
-    def _gen_filename(self, name):
-        if name is 'out_filename':
-            return self._gen_outfilename()
-        else:
-            return None
-    def _gen_outfilename(self):
-        _, name , _ = split_filename(self.inputs.in_file[0])
-        return name + '_tensor.mif'
-
 class Tensor2VectorInputSpec(CommandLineInputSpec):
     in_file = File(exists=True, argstr='%s', mandatory=True, position=-2,
         desc='Diffusion tensor image')