[FIX]: AFNI Allineate

Errors in OutputSpec mapping for Allineate, where out_file name was not
successfully generated or mapped. Added xor options for some input options
that are mutually exclusive. Included new "overwrite" feature to overwrite
output if it already exists.

Author: rmarkello

nipype/interfaces/afni/preprocess.py

@@ -64,24 +64,29 @@ class AllineateInputSpec(AFNICommandInputSpec):
         desc='output file from 3dAllineate',
         argstr='-prefix %s',
         position=-2,
-        name_source='%s_allineate',
         genfile=True)
     out_param_file = File(
         argstr='-1Dparam_save %s',
-        desc='Save the warp parameters in ASCII (.1D) format.')
+        desc='Save the warp parameters in ASCII (.1D) format.',
+        xor=['in_param_file'])
     in_param_file = File(
         exists=True,
         argstr='-1Dparam_apply %s',
         desc='Read warp parameters from file and apply them to '
-             'the source dataset, and produce a new dataset')
+             'the source dataset, and produce a new dataset',
+        xor=['out_param_file'])
     out_matrix = File(
         argstr='-1Dmatrix_save %s',
-        desc='Save the transformation matrix for each volume.')
+        desc='Save the transformation matrix for each volume.',
+        xor=['in_matrix'])
     in_matrix = File(
         desc='matrix to align input file',
         argstr='-1Dmatrix_apply %s',
-        position=-3)
-
+        position=-3,
+        xor=['out_matrix'])
+    overwrite = traits.Bool(
+        desc='overwrite output file if it already exists',
+        argstr='-overwrite')
     _cost_funcs = [
         'leastsq', 'ls',
         'mutualinfo', 'mi',
@@ -250,8 +255,10 @@ class AllineateInputSpec(AFNICommandInputSpec):
 
 
 class AllineateOutputSpec(TraitedSpec):
-    out_file = File(desc='output image file name')
-    matrix = File(desc='matrix to align input file')
+    out_file = File(exists=True, desc='output image file name')
+    out_matrix = File(exists=True, desc='matrix to align input file')
+    out_param_file = File(exists=True, desc='warp parameters')
+    out_weight_file = File(exists=True, desc='weight volume')
 
 
 class Allineate(AFNICommand):
@@ -271,7 +278,6 @@ class Allineate(AFNICommand):
     >>> allineate.cmdline  # doctest: +ALLOW_UNICODE
     '3dAllineate -1Dmatrix_apply cmatrix.mat -prefix functional_allineate.nii -source functional.nii'
     >>> res = allineate.run()  # doctest: +SKIP
-
     """
 
     _cmd = '3dAllineate'
@@ -285,21 +291,23 @@ def _format_arg(self, name, trait_spec, value):
         return super(Allineate, self)._format_arg(name, trait_spec, value)
 
     def _list_outputs(self):
-        outputs = self.output_spec().get()
+        outputs = self._outputs().get()
         if not isdefined(self.inputs.out_file):
-            outputs['out_file'] = self._gen_filename(self.inputs.in_file,
-                                                     suffix=self.inputs.suffix)
+            outputs['out_file'] = self._gen_fname(self.inputs.in_file,
+                                                  suffix='_allineate.nii')
         else:
             outputs['out_file'] = os.path.abspath(self.inputs.out_file)
 
         if isdefined(self.inputs.out_matrix):
-            outputs['matrix'] = os.path.abspath(os.path.join(os.getcwd(),\
-                                         self.inputs.out_matrix +'.aff12.1D'))
+            outputs['out_matrix'] = os.path.abspath(os.path.join(os.getcwd(),
+                                                    self.inputs.out_matrix +
+                                                    '.aff12.1D'))
         return outputs
 
     def _gen_filename(self, name):
         if name == 'out_file':
             return self._list_outputs()[name]
+        return None
 
 
 class AutoTcorrelateInputSpec(AFNICommandInputSpec):
@@ -358,6 +366,7 @@ class AutoTcorrelate(AFNICommand):
     '3dAutoTcorrelate -eta2 -mask mask.nii -mask_only_targets -prefix functional_similarity_matrix.1D -polort -1 functional.nii'
     >>> res = corr.run()  # doctest: +SKIP
     """
+
     input_spec = AutoTcorrelateInputSpec
     output_spec = AFNICommandOutputSpec
     _cmd = '3dAutoTcorrelate'

nipype/interfaces/afni/tests/test_auto_Allineate.py

@@ -39,8 +39,10 @@ def test_Allineate_inputs():
     ),
     in_matrix=dict(argstr='-1Dmatrix_apply %s',
     position=-3,
+    xor=['out_matrix'],
     ),
     in_param_file=dict(argstr='-1Dparam_apply %s',
+    xor=['out_param_file'],
     ),
     interpolation=dict(argstr='-interp %s',
     ),
@@ -64,16 +66,19 @@ def test_Allineate_inputs():
     ),
     out_file=dict(argstr='-prefix %s',
     genfile=True,
-    name_source='%s_allineate',
     position=-2,
     ),
     out_matrix=dict(argstr='-1Dmatrix_save %s',
+    xor=['in_matrix'],
     ),
     out_param_file=dict(argstr='-1Dparam_save %s',
+    xor=['in_param_file'],
     ),
     out_weight_file=dict(argstr='-wtprefix %s',
     ),
     outputtype=dict(),
+    overwrite=dict(argstr='-overwrite',
+    ),
     reference=dict(argstr='-base %s',
     ),
     replacebase=dict(argstr='-replacebase',
@@ -113,8 +118,10 @@ def test_Allineate_inputs():
 
 
 def test_Allineate_outputs():
-    output_map = dict(matrix=dict(),
-    out_file=dict(),
+    output_map = dict(out_file=dict(),
+    out_matrix=dict(),
+    out_param_file=dict(),
+    out_weight_file=dict(),
     )
     outputs = Allineate.output_spec()