From e6a1cc71fbbc650f4e64d8fae78a4b801d23d386 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Mon, 7 Oct 2019 16:16:53 -0700
Subject: [PATCH] FIX: Restore ``AFNICommand._get_fname``, required by some
 interfaces

In #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).

Also remove a definition of the same function for ``Deconvolve``.

This PR restores the missing function. Closes #3070.
---
 nipype/interfaces/afni/base.py  | 51 +++++++++++++++++++++++++++++++-
 nipype/interfaces/afni/model.py | 52 ---------------------------------
 2 files changed, 50 insertions(+), 53 deletions(-)

diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py
index 815f0619c8..1a21dcb2cf 100644
--- a/nipype/interfaces/afni/base.py
+++ b/nipype/interfaces/afni/base.py
@@ -11,7 +11,7 @@
 from distutils import spawn
 
 from ... import logging, LooseVersion
-from ...utils.filemanip import split_filename
+from ...utils.filemanip import split_filename, fname_presuffix
 from ..base import (CommandLine, traits, CommandLineInputSpec, isdefined, File,
                     TraitedSpec, PackageInfo)
 from ...external.due import BibTeX
@@ -237,6 +237,55 @@ 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 not 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:
+            suffix = ''.join((suffix, ext)) if suffix else 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."""
diff --git a/nipype/interfaces/afni/model.py b/nipype/interfaces/afni/model.py
index 96afbe7320..ff6994b374 100644
--- a/nipype/interfaces/afni/model.py
+++ b/nipype/interfaces/afni/model.py
@@ -309,58 +309,6 @@ def _list_outputs(self):
         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.
-
-        """
-        from nipype.utils.filemanip import fname_presuffix
-
-        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
-
-
 class RemlfitInputSpec(AFNICommandInputSpec):
     # mandatory files
     in_files = InputMultiPath(