Merge branch 'master' into enh/ETSConfigTookit

Author: oesteban

nipype/interfaces/dipy/preprocess.py

@@ -23,9 +23,6 @@
     package_check('dipy', version='0.6.0')
 except Exception as e:
     have_dipy = False
-else:
-    from dipy.align.aniso2iso import resample
-    from dipy.core.gradients import GradientTable
 
 
 class ResampleInputSpec(TraitedSpec):
@@ -172,6 +169,7 @@ def resample_proxy(in_file, order=3, new_zooms=None, out_file=None):
     """
     Performs regridding of an image to set isotropic voxel sizes using dipy.
     """
+    from dipy.align.aniso2iso import resample
 
     if out_file is None:
         fname, fext = op.splitext(op.basename(in_file))

nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py

@@ -16,6 +16,7 @@ def test_Surface2VolTransform_inputs():
     usedefault=True,
     ),
     mkmask=dict(argstr='--mkmask',
+    xor=['source_file'],
     ),
     projfrac=dict(argstr='--projfrac %s',
     ),
@@ -26,6 +27,7 @@ def test_Surface2VolTransform_inputs():
     source_file=dict(argstr='--surfval %s',
     copyfile=False,
     mandatory=True,
+    xor=['mkmask'],
     ),
     subject_id=dict(argstr='--identity %s',
     xor=['reg_file'],

nipype/interfaces/freesurfer/utils.py

@@ -390,7 +390,7 @@ def _gen_filename(self, name):
 
 class Surface2VolTransformInputSpec(FSTraitedSpec):
     source_file = File(exists=True, argstr='--surfval %s',
-                       copyfile=False, mandatory=True,
+                       copyfile=False, mandatory=True, xor=['mkmask'],
                        desc='This is the source of the surface values')
     hemi = traits.Str(argstr='--hemi %s', mandatory=True,
                       desc='hemisphere of data')
@@ -404,7 +404,7 @@ class Surface2VolTransformInputSpec(FSTraitedSpec):
     template_file = File(exists=True, argstr='--template %s',
                          desc='Output template volume')
     mkmask = traits.Bool(desc='make a mask instead of loading surface values',
-                         argstr='--mkmask')
+                         argstr='--mkmask', xor=['source_file'])
     vertexvol_file = File(name_template="%s_asVol_vertex.nii",
                           desc=('Path name of the vertex output volume, which '
                                 'is the same as output volume except that the '

nipype/pipeline/plugins/ipython.py

@@ -13,7 +13,7 @@
 IPython_not_loaded = False
 try:
     from IPython import __version__ as IPyversion
-    from IPython.parallel.error import TimeoutError
+    from ipyparallel.error import TimeoutError
 except:
     IPython_not_loaded = True
 
@@ -47,7 +47,7 @@ class IPythonPlugin(DistributedPluginBase):
 
     def __init__(self, plugin_args=None):
         if IPython_not_loaded:
-            raise ImportError('IPython parallel could not be imported')
+            raise ImportError('ipyparallel could not be imported')
         super(IPythonPlugin, self).__init__(plugin_args=plugin_args)
         self.iparallel = None
         self.taskclient = None
@@ -56,11 +56,11 @@ def __init__(self, plugin_args=None):
 
     def run(self, graph, config, updatehash=False):
         """Executes a pre-defined pipeline is distributed approaches
-        based on IPython's parallel processing interface
+        based on IPython's ipyparallel processing interface
         """
         # retrieve clients again
         try:
-            name = 'IPython.parallel'
+            name = 'ipyparallel'
             __import__(name)
             self.iparallel = sys.modules[name]
         except ImportError:

nipype/pipeline/plugins/ipythonx.py

@@ -22,14 +22,14 @@ class IPythonXPlugin(DistributedPluginBase):
 
     def __init__(self, plugin_args=None):
         if IPython_not_loaded:
-            raise ImportError('IPython parallel could not be imported')
+            raise ImportError('ipyparallel could not be imported')
         super(IPythonXPlugin, self).__init__(plugin_args=plugin_args)
         self.ipyclient = None
         self.taskclient = None
 
     def run(self, graph, config, updatehash=False):
         """Executes a pre-defined pipeline is distributed approaches
-        based on IPython's parallel processing interface
+        based on IPython's ipyparallel processing interface
         """
         # retrieve clients again
         try: