[MAINT] Reorganize nipype.interfaces.base

nipype/interfaces/ants/registration.py

@@ -1303,7 +1303,7 @@ class MeasureImageSimilarity(ANTSCommand):
     >>> sim.inputs.fixed_image_mask = 'mask.nii'
     >>> sim.inputs.moving_image_mask = 'mask.nii.gz'
     >>> sim.cmdline
-    u'MeasureImageSimilarity --dimensionality 3 --masks ["mask.nii","mask.nii.gz"] \
+    'MeasureImageSimilarity --dimensionality 3 --masks ["mask.nii","mask.nii.gz"] \
 --metric MI["T1.nii","resting.nii",1.0,5,Regular,1.0]'
     """
     _cmd = 'MeasureImageSimilarity'

nipype/interfaces/ants/segmentation.py

@@ -13,9 +13,8 @@
 
 import os
 from ...external.due import BibTeX
-from ...utils.filemanip import split_filename, copyfile
-from ..base import (TraitedSpec, File, traits, InputMultiPath, OutputMultiPath, isdefined,
-                    _exists_in_path)
+from ...utils.filemanip import split_filename, copyfile, which
+from ..base import TraitedSpec, File, traits, InputMultiPath, OutputMultiPath, isdefined
 from .base import ANTSCommand, ANTSCommandInputSpec
 
 
@@ -724,7 +723,7 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
         if ants_path is None:
             # Check for antsRegistration, which is under bin/ (the $ANTSPATH) instead of
             # checking for antsBrainExtraction.sh which is under script/
-            _, cmd_path = _exists_in_path('antsRegistration', runtime.environ)
+            cmd_path = which('antsRegistration', env=runtime.environ)
             if not cmd_path:
                 raise RuntimeError(
                     'The environment variable $ANTSPATH is not defined in host "%s", '
@@ -1326,7 +1325,7 @@ class KellyKapowski(ANTSCommand):
     >>> kk.inputs.number_integration_points = 10
     >>> kk.inputs.thickness_prior_estimate = 10
     >>> kk.cmdline
-    u'KellyKapowski --convergence "[45,0.0,10]" \
+    'KellyKapowski --convergence "[45,0.0,10]" \
 --output "[segmentation0_cortical_thickness.nii.gz,segmentation0_warped_white_matter.nii.gz]" \
 --image-dimensionality 3 --gradient-step 0.025000 --number-of-integration-points 10 \
 --segmentation-image "[segmentation0.nii.gz,2,3]" --smoothing-variance 1.000000 \

nipype/interfaces/base/__init__.py

@@ -0,0 +1,31 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+Nipype base interfaces
+----------------------
+
+This module defines the API of all nipype interfaces.
+
+"""
+from .core import (
+    Interface, BaseInterface, SimpleInterface,
+    CommandLine, StdOutCommandLine,
+    MpiCommandLine, SEMLikeCommandLine, PackageInfo
+)
+
+from .specs import (
+    BaseTraitedSpec, TraitedSpec, DynamicTraitedSpec,
+    BaseInterfaceInputSpec, CommandLineInputSpec,
+    StdOutCommandLineInputSpec
+)
+
+from .traits_extension import (
+    traits, Undefined, TraitDictObject, TraitListObject, TraitError, isdefined,
+    File, Directory, Str, DictStrStr, has_metadata, ImageFile,
+    MultiPath, OutputMultiPath, InputMultiPath)
+
+from .support import (
+    Bunch, InterfaceResult, load_template,
+    NipypeInterfaceError
+)