fixed AutoTcorrelate and _list_outputs

Author: stymy

nipype/interfaces/afni/base.py

@@ -218,6 +218,20 @@ def _overload_extension(self, value):
         path, base, _ = split_filename(value)
         return os.path.join(path, base + Info.outputtype_to_ext(self.inputs.outputtype))
 
+    def _list_outputs(self):
+        metadata = dict(name_source=lambda t: t is not None)
+        out_names = self.inputs.traits(**metadata).keys()
+        if out_names:
+            outputs = self.output_spec().get()
+            for name in out_names:
+                out = self._gen_filename(name)
+                if out.startswith("/"):
+                    outputs[name]
+                else:
+                    path,_,_  = split_filename(getattr(self.inputs,self.inputs.trait(name).name_source))
+                    outputs[name] = os.path.join(path, self._gen_filename(name))
+            return outputs
+
 
 class AFNIPrefixOutputSpec(TraitedSpec):
     out_file = File(desc='output file',

nipype/interfaces/afni/preprocess.py

@@ -316,7 +316,16 @@ class AutoTcorrelateInputSpec(AFNIPrefixInputSpec):
         mandatory=True,
         exists=True)
 
-    out_file = File("%s_similarity_matrix", desc='output image file name',
+    polort = traits.Int(desc='Remove polynomical trend of order m or -1 for no detrending',
+        argstr="-polort %d")
+    eta2 = traits.Bool(desc='eta^2 similarity',
+        argstr="-eta2")
+    mask = File(exists=True, desc="mask of voxels", 
+        argstr="-mask %s")
+    mask_only_targets = traits.Bool(desc="use mask only on targets voxels", 
+        argstr="-mask_only_targets")
+
+    out_file = File("%s_similarity_matrix.1D", desc='output image file name',
         argstr='-prefix %s', name_source="in_file", usedefault=True)
 
 class AutoTcorrelateOutputSpec(TraitedSpec):
@@ -331,14 +340,23 @@ class AutoTcorrelate(AFNIPrefixCommand):
     >>> from nipype.interfaces import afni as afni
     >>> corr = afni.AutoTcorrelate()
     >>> corr.inputs.in_file = 'functional.nii'
-    >>> corr.inputs.outputtype = "NIFTI"
+    >>> corr.inputs.polort = -1
+    >>> corr.inputs.eta2 = True
+    >>> corr.inputs.mask = 'mask.nii'
+    >>> corr.inputs.mask_only_targets = True
     >>> corr.cmdline
-    '3dAutoTcorrelation -prefix functional_similarity_matrix.nii functional.nii'
+    '3dAutoTcorrelation -prefix functional_similarity_matrix.1D functional.nii'
     >>> res = corr.run() # doctest: +SKIP
     """
     input_spec = AutoTcorrelateInputSpec
     output_spec = AutoTcorrelateOutputSpec
-    _cmd = '3dAutoTcorrelation'
+    _cmd = '3dAutoTcorrelate'
+
+    def _overload_extension(self, value):
+        path, base, ext = split_filename(value)
+        if ext.lower() not in [".1d", ".nii.gz", ".nii"]:
+            ext = ext + ".1D"
+        return os.path.join(path, base + ext)
 
 
 class TStatInputSpec(AFNIPrefixInputSpec):

nipype/interfaces/base.py

@@ -1195,7 +1195,7 @@ def _format_arg(self, name, trait_spec, value):
             else:
                 return argstr % sep.join(str(elt) for elt in value)
         elif trait_spec.name_source:
-            return self._gen_filename(name)
+            return  argstr % self._gen_filename(name)
         else:
             # Append options using format string.
             return argstr % value
@@ -1214,9 +1214,9 @@ def _gen_filename(self, name):
                 raise NotImplementedError
 
             if trait_spec.keep_extension:
-                return argstr % retval
+                return retval
             else:
-                return argstr % self._overload_extension(retval)
+                return self._overload_extension(retval)
 
     def _overload_extension(self, value):
         return value
@@ -1227,7 +1227,7 @@ def _list_outputs(self):
         if out_names:
             outputs = self.output_spec().get()
             for name in out_names:
-                outputs[name] = os.path.abspath(self._gen_out_fname(name))
+                outputs[name] = os.path.abspath(self._gen_filename(name))
             return outputs
 
     def _parse_inputs(self, skip=None):