fix: tests

Author: satra

nipype/interfaces/ants/registration.py

@@ -486,9 +486,10 @@ def _formatRegistration(self):
             for metric in self._formatMetric(ii):
                 retval.append('--metric %s' % metric)
             retval.append('--convergence %s' % self._formatConvergence(ii))
-            if self.inputs.sigma_units:
-                retval.append('--smoothing-sigmas %s%s' % (self._antsJoinList(
-                    self.inputs.smoothing_sigmas[ii], self.inputs.sigma_units[ii])))
+            if isdefined(self.inputs.sigma_units):
+                retval.append('--smoothing-sigmas %s%s' %
+                        (self._antsJoinList(self.inputs.smoothing_sigmas[ii]),
+                         self.inputs.sigma_units[ii]))
             else:
                 retval.append('--smoothing-sigmas %s' %
                     self._antsJoinList(self.inputs.smoothing_sigmas[ii]))

nipype/interfaces/ants/resampling.py

@@ -224,10 +224,10 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
                        exists=True)
     output_image = traits.Str(argstr='--output %s',
                               desc=('output file name'), genfile=True,
-                              hash_file=False, xor=['out_postfix'])
-    out_postfix = File("_trans", usedefault=True, hash_files=False,
-                       desc=('Postfix that is appended to all output '
-                             'files (default = _trans)'), xor=['output_image'])
+                              hash_file=False)
+    out_postfix = traits.Str("_trans", usedefault=True,
+                             desc=('Postfix that is appended to all output '
+                                   'files (default = _trans)'))
     reference_image = File(argstr='--reference-image %s', mandatory=True,
                            desc='reference image space that you wish to warp INTO',
                            exists=True)
@@ -289,7 +289,7 @@ def _gen_filename(self, name):
             output = self.inputs.output_image
             if not isdefined(output):
                 _, name, ext = split_filename(self.inputs.input_image)
-                output = name + '_trans' + ext
+                output = name + self.inputs.out_postfix + ext
             return output
         return None
 

nipype/pipeline/engine.py

@@ -1160,7 +1160,10 @@ def __init__(self, interface, name, iterables=None, itersource=None,
             multiprocessing pool
 
         """
-        super(Node, self).__init__(name, **kwargs)
+        base_dir = None
+        if 'base_dir' in kwargs:
+            base_dir = kwargs['base_dir']
+        super(Node, self).__init__(name, base_dir)
         if interface is None:
             raise IOError('Interface must be provided')
         if not isinstance(interface, Interface):

nipype/pipeline/utils.py

@@ -311,12 +311,14 @@ def synchronize_iterables(iterables):
     Examples
     --------
     >>> from nipype.pipeline.utils import synchronize_iterables
-    >>> iterables = dict(a=lambda: [1, 2]), b=lambda: [3, 4])
-    >>> synchronize_iterable_lists(iterables)
-    [{'a': 1, 'b': 3}, {'a': 2, 'b': 4}]
-    >>> iterables = dict(a=lambda: [1, 2]), b=lambda: [3], c=lambda: [4, 5, 6])
-    >>> synchronize_iterable_lists(iterables)
-    [{'a': 1, 'b': 3, 'c': 4}, {'a': 2, 'c': 5}, {'c': 6}]
+    >>> iterables = dict(a=lambda: [1, 2], b=lambda: [3, 4])
+    >>> synced = synchronize_iterables(iterables)
+    >>> synced == [{'a': 1, 'b': 3}, {'a': 2, 'b': 4}]
+    True
+    >>> iterables = dict(a=lambda: [1, 2], b=lambda: [3], c=lambda: [4, 5, 6])
+    >>> synced = synchronize_iterables(iterables)
+    >>> synced == [{'a': 1, 'b': 3, 'c': 4}, {'a': 2, 'c': 5}, {'c': 6}]
+    True
     """
     # Convert the (field, function) tuples into (field, value) lists
     pair_lists = [[(field, value) for value in func()]