FIX: Restore AFNICommand._get_fname, required by some interfaces

In nipy#2964 I broke some interfaces (@tsalo identified `Allineate` as one
of those) by removing the ``_get_fname`` function from the base
``AFNICommand``.

The intent was to migrate to a ``name_source``-based management of
automatically generated names, but in the case of ``Allineate``, the use
of `_get_fname` was a bit different (modifying the user-provide input
value under certain conditions to follow ANFI's ``3dAllineate``
behavior).

This PR restores the missing function. Closes nipy#3070.

nipype/interfaces/afni/base.py

@@ -237,6 +237,52 @@ def _list_outputs(self):
                         outputs[name] = outputs[name] + "+orig.BRIK"
         return outputs
 
+    def _gen_fname(self,
+                   basename,
+                   cwd=None,
+                   suffix=None,
+                   change_ext=True,
+                   ext=None):
+        """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 extentions specified in
+        <instance>intputs.output_type.
+        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`.  (defaults is '' )
+        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()
+        if ext is None:
+            ext = Info.output_type_to_ext(self.inputs.outputtype)
+        if change_ext:
+            if suffix:
+                suffix = ''.join((suffix, ext))
+            else:
+                suffix = ext
+        if suffix is None:
+            suffix = ''
+        fname = fname_presuffix(
+            basename, suffix=suffix, use_ext=False, newpath=cwd)
+        return fname
+
 
 def no_afni():
     """Check whether AFNI is not available."""