Satra suggestion of FSLcpgeom

Author: mick-d

nipype/interfaces/fsl/utils.py

@@ -35,7 +35,8 @@ class CopyGeomInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, mandatory=True, argstr="%s", position=0,
                    desc="source image")
     dest_file = File(exists=True, mandatory=True, argstr="%s", position=1,
-                     desc="destination image", copyfile=True)
+                     desc="destination image", copyfile=True, output_name='out_file',
+                     name_source='dest_file', name_template='%s')
     ignore_dims = traits.Bool(desc=('Do not copy image dimensions'),
                               argstr='-d', position="-1")
 
@@ -44,37 +45,16 @@ class CopyGeomOutputSpec(TraitedSpec):
 
 class CopyGeom(FSLCommand):
     """Use fslcpgeom to copy the header geometry information to another image.
-
     Copy certain parts of the header information (image dimensions, voxel dimensions,
     voxel dimensions units string, image orientation/origin or qform/sform info)
     from one image to another. Note that only copies from Analyze to Analyze
     or Nifti to Nifti will work properly. Copying from different files will result
     in loss of information or potentially incorrect settings.
-
     """
     _cmd = "fslcpgeom"
     input_spec = CopyGeomInputSpec
     output_spec = CopyGeomOutputSpec
 
-    def _run_interface(self, runtime):
-        # Copy destination file to new local file to prevent overwriting
-        # and update destination file
-        out_file = self._gen_filename('out_file')
-        copyfile(self.inputs.dest_file, out_file, copy=True)
-        self.inputs.dest_file = out_file
-        return super(CopyGeom, self)._run_interface(runtime)
-
-    def _gen_filename(self, name):
-        if name == 'out_file':
-            return self._gen_fname(self.inputs.dest_file, suffix="_newhd")
-        return None
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        # Use the new destination file updated by _run_interface
-        outputs['out_file'] = self.inputs.dest_file
-        return outputs
-
 
 class RobustFOVInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True,