fix:docstring of traits.Directory was not correctly generated

Author: oesteban

nipype/interfaces/elastix/base.py

@@ -6,23 +6,21 @@
 # @Author: oesteban - [email protected]
 # @Date:   2014-06-03 13:42:46
 # @Last Modified by:   oesteban
-# @Last Modified time: 2014-06-17 10:17:43
+# @Last Modified time: 2014-08-14 19:25:37
 """The :py:mod:`nipype.interfaces.elastix` provides the interface to
 the elastix registration software.
 
 .. note:: http://elastix.isi.uu.nl/
 
-
 """
 
-from ..base import (CommandLine, CommandLineInputSpec, isdefined,
-                    TraitedSpec, File, traits, InputMultiPath)
-from ... import logging
+from nipype.interfaces.base import CommandLineInputSpec, traits
+from nipype import logging
 logger = logging.getLogger('interface')
 
 
 class ElastixBaseInputSpec(CommandLineInputSpec):
-    output_path = traits.Directory('./', exists=True, mandatory=True, usedefault=True,
-                              argstr='-out %s', desc='output directory')
     num_threads = traits.Int(1, argstr='-threads %01d',
                              desc='set the maximum number of threads of elastix')
+    output_path = traits.Str('./', mandatory=True, usedefault=True,
+                             argstr='-out %s', desc='output directory')

nipype/interfaces/elastix/registration.py

@@ -6,7 +6,7 @@
 # @Author: oesteban - [email protected]
 # @Date:   2014-06-02 12:06:50
 # @Last Modified by:   oesteban
-# @Last Modified time: 2014-06-17 10:19:23
+# @Last Modified time: 2014-08-14 19:04:57
 """
 Interfaces to perform image registrations and to apply the resulting
 displacement maps to images and points.
@@ -18,8 +18,6 @@
 
 from ..base import (CommandLine, CommandLineInputSpec, isdefined,
                     TraitedSpec, File, traits, InputMultiPath)
-
-
 from base import ElastixBaseInputSpec
 
 from ... import logging
@@ -31,10 +29,8 @@ class RegistrationInputSpec(ElastixBaseInputSpec):
            desc='fixed image')
     moving_image = File(exists=True, mandatory=True, argstr='-m %s',
            desc='moving image')
-
     parameters = InputMultiPath(File(exists=True), mandatory=True, argstr='-p %s...',
                                 desc='parameter file, elastix handles 1 or more -p')
-
     fixed_mask = File(exists=True, argstr='-fMask %s', desc='mask for fixed image')
     moving_mask = File(exists=True, argstr='-mMask %s', desc='mask for moving image')
     initial_transform = File(exists=True, argstr='-t0 %s',
@@ -51,7 +47,8 @@ class RegistrationOutputSpec(TraitedSpec):
 
 
 class Registration(CommandLine):
-    """Elastix nonlinear registration interface
+    """
+    Elastix nonlinear registration interface
 
     Example
     -------
@@ -170,16 +167,18 @@ class AnalyzeWarpInputSpec(ElastixBaseInputSpec):
 
 
 class AnalyzeWarpOutputSpec(TraitedSpec):
-    disp_field = File(exists=True, desc='displacements field')
-    jacdet_map = File(exists=True, desc='det(Jacobian) map')
-    jacmat_map = File(exists=True, desc='Jacobian matrix map')
+    disp_field = File(desc='displacements field')
+    jacdet_map = File(desc='det(Jacobian) map')
+    jacmat_map = File(desc='Jacobian matrix map')
 
 class AnalyzeWarp(CommandLine):
-    """Use `transformix` to get details from the input transform (generate
+    """
+    Use transformix to get details from the input transform (generate
     the corresponding deformation field, generate the determinant of the
     Jacobian map or the Jacobian map itself)
 
-    Example::
+    Example
+    -------
 
     >>> from nipype.interfaces.elastix import AnalyzeWarp
     >>> reg = AnalyzeWarp()