further cleanup

Author: chrisgorgo

nipype/interfaces/afni/base.py

@@ -6,7 +6,7 @@
 import os
 import warnings
 
-from ...utils.filemanip import fname_presuffix, split_filename
+from ...utils.filemanip import split_filename
 from ..base import (
     CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec)
 
@@ -98,25 +98,26 @@ def standard_image(img_name):
         return os.path.join(basedir, img_name)
 
 
-class AFNIBaseCommandInputSpec(CommandLineInputSpec):
+class AFNICommandInputSpec(CommandLineInputSpec):
     outputtype = traits.Enum('AFNI', Info.ftypes.keys(),
                              desc='AFNI output filetype')
+    out_file = File(name_template="%s_afni", desc='output image file name',
+                    argstr='-prefix %s',
+                    name_source=["in_file"])
+    
+class AFNICommandOutputSpec(TraitedSpec):
+    out_file = File(desc='output file',
+                    exists=True)
 
-class AFNITraitedSpec(AFNIBaseCommandInputSpec):
-    pass
-
-
-class AFNIBaseCommand(CommandLine):
-    """General support for AFNI commands. Every AFNI command accepts 'outputtype' input. For example:
-    afni.Threedsetup(outputtype='NIFTI_GZ')
-    """
 
-    input_spec = AFNIBaseCommandInputSpec
+class AFNICommand(CommandLine):
+    
+    input_spec = AFNICommandInputSpec
     _outputtype = None
 
 
     def __init__(self, **inputs):
-        super(AFNIBaseCommand, self).__init__(**inputs)
+        super(CommandLine, self).__init__(**inputs)
         self.inputs.on_trait_change(self._output_update, 'outputtype')
 
         if self._outputtype is None:
@@ -148,58 +149,8 @@ def set_default_output_type(cls, outputtype):
             cls._outputtype = outputtype
         else:
             raise AttributeError('Invalid AFNI outputtype: %s' % outputtype)
+        
 
-#     def _gen_fname(self, basename, cwd=None, suffix='_afni', change_ext=True, prefix=''):
-#         """Generate a filename based on the given parameters.
-# 
-#         The filename will take the form: cwd/basename<suffix><ext>.
-#         If change_ext is True, it will use the extensions specified in
-#         <instance>inputs.outputtype.
-# 
-#         Parameters
-#         ----------
-#         basename : str
-#             Filename to base the new filename on.
-#         cwd : str
-#             Path to prefix to the new filename. (default is os.getcwd())
-#         suffix : str
-#             Suffix to add to the `basename`.  (default is '_fsl')
-#         change_ext : bool
-#             Flag to change the filename extension to the FSL output type.
-#             (default True)
-# 
-#         Returns
-#         -------
-#         fname : str
-#             New filename based on given parameters.
-# 
-#         """
-# 
-#         if basename == '':
-#             msg = 'Unable to generate filename for command %s. ' % self.cmd
-#             msg += 'basename is not set!'
-#             raise ValueError(msg)
-#         if cwd is None:
-#             cwd = os.getcwd()
-#         ext = Info.outputtype_to_ext(self.inputs.outputtype)
-#         if change_ext:
-#             if suffix:
-#                 suffix = ''.join((suffix, ext))
-#             else:
-#                 suffix = ext
-#         fname = fname_presuffix(basename, suffix=suffix,
-#                                 use_ext=False, newpath=cwd, prefix=prefix)
-#         return fname
-
-
-class AFNICommandInputSpec(AFNIBaseCommandInputSpec):
-    out_file = File(name_template="%s_afni", desc='output image file name',
-                    argstr='-prefix %s',
-                    name_source=["in_file"])
-
-
-class AFNICommand(AFNIBaseCommand):
-    input_spec = AFNICommandInputSpec
 
     def _overload_extension(self, value):
         path, base, _ = split_filename(value)
@@ -216,7 +167,3 @@ def _list_outputs(self):
                     if ext == "":
                         outputs[name] = outputs[name] + "+orig.BRIK" 
         return outputs
-
-class AFNICommandOutputSpec(TraitedSpec):
-    out_file = File(desc='output file',
-                    exists=True)