Suggested changes to nipy/nipype#2502

nipype/interfaces/afni/preprocess.py

@@ -218,7 +218,8 @@ class AllineateInputSpec(AFNICommandInputSpec):
     out_file = File(
         desc='output file from 3dAllineate',
         argstr='-prefix %s',
-        genfile=True,
+        name_template='%s_allineate',
+        name_source='in_file',
         hash_files=False,
         xor=['allcostx'])
     out_param_file = File(
@@ -425,11 +426,11 @@ class AllineateInputSpec(AFNICommandInputSpec):
     _dirs = ['X', 'Y', 'Z', 'I', 'J', 'K']
     nwarp_fixmot = traits.List(
         traits.Enum(*_dirs),
-        argstr='-nwarp_fixmot%s',
+        argstr='-nwarp_fixmot%s...',
         desc='To fix motion along directions.')
     nwarp_fixdep = traits.List(
         traits.Enum(*_dirs),
-        argstr='-nwarp_fixdep%s',
+        argstr='-nwarp_fixdep%s...',
         desc='To fix non-linear warp dependency along directions.')
     verbose = traits.Bool(
         argstr='-verb', desc='Print out verbose progress reports.')
@@ -466,50 +467,43 @@ class Allineate(AFNICommand):
     '3dAllineate -source functional.nii -prefix functional_allineate.nii -1Dmatrix_apply cmatrix.mat'
     >>> res = allineate.run()  # doctest: +SKIP
 
-    >>> from nipype.interfaces import afni
     >>> allineate = afni.Allineate()
     >>> allineate.inputs.in_file = 'functional.nii'
     >>> allineate.inputs.reference = 'structural.nii'
     >>> allineate.inputs.allcostx = 'out.allcostX.txt'
     >>> allineate.cmdline
     '3dAllineate -source functional.nii -base structural.nii -allcostx |& tee out.allcostX.txt'
     >>> res = allineate.run()  # doctest: +SKIP
+
+    >>> allineate = afni.Allineate()
+    >>> allineate.inputs.in_file = 'functional.nii'
+    >>> allineate.inputs.reference = 'structural.nii'
+    >>> allineate.inputs.nwarp_fixmot = ['X', 'Y']
+    >>> allineate.cmdline
+    '3dAllineate -source functional.nii -nwarp_fixmotX -nwarp_fixmotY -prefix functional_allineate -base structural.nii'
+    >>> res = allineate.run()  # doctest: +SKIP
     """
 
     _cmd = '3dAllineate'
     input_spec = AllineateInputSpec
     output_spec = AllineateOutputSpec
 
-    def _format_arg(self, name, trait_spec, value):
-        if name == 'nwarp_fixmot' or name == 'nwarp_fixdep':
-            arg = ' '.join([trait_spec.argstr % v for v in value])
-            return arg
-        return super(Allineate, self)._format_arg(name, trait_spec, value)
-
-    def _gen_outfilename(self):
-        out_file = self.inputs.out_file
-        if not isdefined(out_file) and isdefined(self.inputs.in_file) and not isdefined(self.inputs.allcostx):
-            out_file = op.abspath(self._gen_fname(self.inputs.in_file,op.dirname(self.inputs.in_file),suffix='_allineate'))
-        return out_file
-
     def _list_outputs(self):
-        outputs = self.output_spec().get()
-
-        outputs['out_file'] = self._gen_outfilename()
+        outputs = super(Allineate, self)._list_outputs()
 
-        if isdefined(self.inputs.out_weight_file):
+        if self.inputs.out_weight_file:
             outputs['out_weight_file'] = op.abspath(
                 self.inputs.out_weight_file)
 
-        if isdefined(self.inputs.out_matrix):
+        if self.inputs.out_matrix:
             path, base, ext = split_filename(self.inputs.out_matrix)
             if ext.lower() not in ['.1d', '.1D']:
                 outputs['out_matrix'] = self._gen_fname(
                     self.inputs.out_matrix, suffix='.aff12.1D')
             else:
                 outputs['out_matrix'] = op.abspath(self.inputs.out_matrix)
 
-        if isdefined(self.inputs.out_param_file):
+        if self.inputs.out_param_file:
             path, base, ext = split_filename(self.inputs.out_param_file)
             if ext.lower() not in ['.1d', '.1D']:
                 outputs['out_param_file'] = self._gen_fname(
@@ -518,16 +512,10 @@ def _list_outputs(self):
                 outputs['out_param_file'] = op.abspath(
                     self.inputs.out_param_file)
 
-        if isdefined(self.inputs.allcostx):
-            outputs['allcostX'] = os.path.abspath(
-                os.path.join(os.getcwd(), self.inputs.allcostx))
+        if self.inputs.allcostx:
+            outputs['allcostX'] = os.path.abspath(self.inputs.allcostx)
         return outputs
 
-    def _gen_filename(self, name):
-        if name == 'out_file':
-            return self._gen_outfilename()
-        return None
-
 
 class AutoTcorrelateInputSpec(AFNICommandInputSpec):
     in_file = File(

nipype/interfaces/base/core.py

@@ -1072,6 +1072,12 @@ def _filename_from_source(self, name, chain=None):
         if not isdefined(retval) or "%s" in retval:
             if not trait_spec.name_source:
                 return retval
+
+            # Do not generate filename when excluded by other inputs
+            if trait_spec.xor and any(isdefined(getattr(self.inputs, field))
+                                      for field in trait_spec.xor):
+                return retval
+
             if isdefined(retval) and "%s" in retval:
                 name_template = retval
             else: