RF: Local absolute imports to file-level relative

Author: effigies

nipype/interfaces/dipy/preprocess.py

@@ -13,6 +13,8 @@
 import nibabel as nb
 import numpy as np
 
+from ...utils import NUMPY_MMAP
+
 from ... import logging
 from ..base import (traits, TraitedSpec, File, isdefined)
 from .base import DipyBaseInterface
@@ -179,7 +181,6 @@ 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.reslice import reslice
-    from nipype.utils import NUMPY_MMAP
 
     if out_file is None:
         fname, fext = op.splitext(op.basename(in_file))
@@ -223,7 +224,6 @@ def nlmeans_proxy(in_file, settings,
     from dipy.denoise.nlmeans import nlmeans
     from scipy.ndimage.morphology import binary_erosion
     from scipy import ndimage
-    from nipype.utils import NUMPY_MMAP
 
     if out_file is None:
         fname, fext = op.splitext(op.basename(in_file))

nipype/interfaces/petpvc.py

@@ -13,7 +13,8 @@
 import os
 
 from .base import TraitedSpec, CommandLineInputSpec, CommandLine, File, isdefined, traits
-from ..external.due import due, Doi, BibTeX
+from ..utils.filemanip import fname_presuffix
+from ..external.due import BibTeX
 
 pvc_methods = ['GTM',
                'IY',
@@ -200,8 +201,6 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
             New filename based on given parameters.
 
         """
-        from nipype.utils.filemanip import fname_presuffix
-
         if basename == '':
             msg = 'Unable to generate filename for command %s. ' % self.cmd
             msg += 'basename is not set!'

nipype/interfaces/utility/wrappers.py

@@ -21,7 +21,7 @@
 
 from ... import logging
 from ..base import (traits, DynamicTraitedSpec, Undefined, isdefined, runtime_profile,
-                    BaseInterfaceInputSpec)
+                    BaseInterfaceInputSpec, get_max_resources_used)
 from ..io import IOBase, add_traits
 from ...utils.filemanip import filename_to_list
 from ...utils.misc import getsource, create_function_from_source
@@ -138,7 +138,6 @@ def _add_output_traits(self, base):
 
     def _run_interface(self, runtime):
         # Get workflow logger for runtime profile error reporting
-        from nipype import logging
         logger = logging.getLogger('workflow')
 
         # Create function handle
@@ -163,7 +162,6 @@ def _function_handle_wrapper(queue, **kwargs):
 
         # Profile resources if set
         if runtime_profile:
-            from nipype.interfaces.base import get_max_resources_used
             import multiprocessing
             # Init communication queue and proc objs
             queue = multiprocessing.Queue()

nipype/workflows/dmri/fsl/artifacts.py

@@ -9,6 +9,8 @@
 from ....interfaces import ants
 from ....interfaces import fsl
 from ....pipeline import engine as pe
+from ...data import get_flirt_schedule
+
 from .utils import (b0_indices, time_avg, apply_all_corrections, b0_average,
                     hmc_split, dwi_flirt, eddy_rotate_bvecs, rotate_bvecs,
                     insert_mat, extract_bval, recompose_dwi, recompose_xfm,
@@ -352,8 +354,6 @@ def hmc_pipeline(name='motion_correct'):
         outputnode.out_xfms - list of transformation matrices
 
     """
-    from nipype.workflows.data import get_flirt_schedule
-
     params = dict(dof=6, bgvalue=0, save_log=True, no_search=True,
                   # cost='mutualinfo', cost_func='mutualinfo', bins=64,
                   schedule=get_flirt_schedule('hmc'))
@@ -454,7 +454,6 @@ def ecc_pipeline(name='eddy_correct'):
         outputnode.out_xfms - list of transformation matrices
     """
 
-    from nipype.workflows.data import get_flirt_schedule
     params = dict(dof=12, no_search=True, interp='spline', bgvalue=0,
                   schedule=get_flirt_schedule('ecc'))
     # cost='normmi', cost_func='normmi', bins=64,

nipype/workflows/smri/freesurfer/recon.py

@@ -206,7 +206,6 @@ def setconfig(reg_template=None,
                   awk_file=None,
                   rb_date=None):
         """Set optional configurations to the default"""
-        from nipype.workflows.smri.freesurfer.utils import getdefaultconfig
         def checkarg(arg, default):
             """Returns the value if defined; otherwise default"""
             if arg: