[FIX]: AFNI Allineate conflicts with master

Edited AFNI Allineate interface to accommodate updated master branch. Updated
xor options for allcostx.

Author: rmarkello

nipype/interfaces/afni/preprocess.py

@@ -220,14 +220,12 @@ class AllineateInputSpec(AFNICommandInputSpec):
     out_file = File(
         desc='output file from 3dAllineate',
         argstr='-prefix %s',
-        name_source='in_file',
-        name_template='%s_allineate',
         genfile=True,
         xor=['allcostx'])
     out_param_file = File(
         argstr='-1Dparam_save %s',
         desc='Save the warp parameters in ASCII (.1D) format.',
-        xor=['in_param_file'])
+        xor=['in_param_file','allcostx'])
     in_param_file = File(
         exists=True,
         argstr='-1Dparam_apply %s',
@@ -237,7 +235,7 @@ class AllineateInputSpec(AFNICommandInputSpec):
     out_matrix = File(
         argstr='-1Dmatrix_save %s',
         desc='Save the transformation matrix for each volume.',
-        xor=['in_matrix'])
+        xor=['in_matrix','allcostx'])
     in_matrix = File(
         desc='matrix to align input file',
         argstr='-1Dmatrix_apply %s',
@@ -247,14 +245,12 @@ class AllineateInputSpec(AFNICommandInputSpec):
         desc='overwrite output file if it already exists',
         argstr='-overwrite')
 
-    # TODO: implement sensible xors for allcostx and suppres prefix in command when allcosx is used
     allcostx= File(
         desc='Compute and print ALL available cost functionals for the un-warped inputs'
              'AND THEN QUIT. If you use this option none of the other expected outputs will be produced',
         argstr='-allcostx |& tee %s',
         position=-1,
-        xor=['out_file'])
-
+        xor=['out_file', 'out_matrix', 'out_param_file', 'out_weight_file'])
     _cost_funcs = [
         'leastsq', 'ls',
         'mutualinfo', 'mi',
@@ -365,7 +361,8 @@ class AllineateInputSpec(AFNICommandInputSpec):
              'Must be defined on the same grid as the base dataset')
     out_weight_file = traits.File(
         argstr='-wtprefix %s',
-        desc='Write the weight volume to disk as a dataset')
+        desc='Write the weight volume to disk as a dataset',
+        xor=['allcostx'])
     source_mask = File(
         exists=True,
         argstr='-source_mask %s',
@@ -445,7 +442,7 @@ class Allineate(AFNICommand):
     >>> allineate.inputs.out_file = 'functional_allineate.nii'
     >>> allineate.inputs.in_matrix = 'cmatrix.mat'
     >>> allineate.cmdline  # doctest: +ALLOW_UNICODE
-    '3dAllineate -source functional.nii -1Dmatrix_apply cmatrix.mat -prefix functional_allineate.nii'
+    '3dAllineate -source functional.nii -prefix functional_allineate.nii -1Dmatrix_apply cmatrix.mat'
     >>> res = allineate.run()  # doctest: +SKIP
 
     >>> from nipype.interfaces import afni
@@ -454,7 +451,7 @@ class Allineate(AFNICommand):
     >>> allineate.inputs.reference = 'structural.nii'
     >>> allineate.inputs.allcostx = 'out.allcostX.txt'
     >>> allineate.cmdline  # doctest: +ALLOW_UNICODE
-    '3dAllineate -source functional.nii -prefix functional_allineate -base structural.nii -allcostx |& tee out.allcostX.txt'
+    '3dAllineate -source functional.nii -base structural.nii -allcostx |& tee out.allcostX.txt'
     >>> res = allineate.run()  # doctest: +SKIP
     """
 
@@ -493,8 +490,8 @@ def _list_outputs(self):
             else:
                 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(),\
+        if isdefined(self.inputs.allcostx):
+            outputs['allcostX'] = os.path.abspath(os.path.join(os.getcwd(),
                                          self.inputs.allcostx))
         return outputs
 

nipype/interfaces/afni/tests/test_auto_Allineate.py

@@ -6,7 +6,7 @@
 def test_Allineate_inputs():
     input_map = dict(allcostx=dict(argstr='-allcostx |& tee %s',
     position=-1,
-    xor=['out_file'],
+    xor=['out_file', 'out_matrix', 'out_param_file', 'out_weight_file'],
     ),
     args=dict(argstr='%s',
     ),
@@ -69,17 +69,16 @@ def test_Allineate_inputs():
     ),
     out_file=dict(argstr='-prefix %s',
     genfile=True,
-    name_source='in_file',
-    name_template='%s_allineate',
     xor=['allcostx'],
     ),
     out_matrix=dict(argstr='-1Dmatrix_save %s',
-    xor=['in_matrix'],
+    xor=['in_matrix', 'allcostx'],
     ),
     out_param_file=dict(argstr='-1Dparam_save %s',
-    xor=['in_param_file'],
+    xor=['in_param_file', 'allcostx'],
     ),
     out_weight_file=dict(argstr='-wtprefix %s',
+    xor=['allcostx'],
     ),
     outputtype=dict(),
     overwrite=dict(argstr='-overwrite',