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Merge pull request #2059 from effigies/relative_imports
ENH: Reduce within-package absolute imports
2 parents a61e455 + aaef1f3 commit ed9af31

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18 files changed

+56
-62
lines changed

18 files changed

+56
-62
lines changed

nipype/algorithms/icc.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
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from scipy.linalg import pinv
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from ..interfaces.base import BaseInterfaceInputSpec, TraitedSpec, \
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BaseInterface, traits, File
11-
from nipype.utils import NUMPY_MMAP
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from ..utils import NUMPY_MMAP
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1313

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class ICCInputSpec(BaseInterfaceInputSpec):

nipype/algorithms/metrics.py

Lines changed: 1 addition & 1 deletion
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@@ -30,7 +30,7 @@
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from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
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InputMultiPath,
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BaseInterfaceInputSpec, isdefined)
33-
from nipype.utils import NUMPY_MMAP
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from ..utils import NUMPY_MMAP
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iflogger = logging.getLogger('interface')
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nipype/algorithms/misc.py

Lines changed: 1 addition & 1 deletion
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@@ -34,7 +34,7 @@
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BaseInterfaceInputSpec, isdefined,
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DynamicTraitedSpec, Undefined)
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from ..utils.filemanip import fname_presuffix, split_filename
37-
from nipype.utils import NUMPY_MMAP
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from ..utils import NUMPY_MMAP
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from . import confounds
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nipype/interfaces/dipy/preprocess.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,8 @@
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import nibabel as nb
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import numpy as np
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from ...utils import NUMPY_MMAP
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from ... import logging
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from ..base import (traits, TraitedSpec, File, isdefined)
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from .base import DipyBaseInterface
@@ -179,7 +181,6 @@ def resample_proxy(in_file, order=3, new_zooms=None, out_file=None):
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Performs regridding of an image to set isotropic voxel sizes using dipy.
180182
"""
181183
from dipy.align.reslice import reslice
182-
from nipype.utils import NUMPY_MMAP
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if out_file is None:
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fname, fext = op.splitext(op.basename(in_file))
@@ -223,7 +224,6 @@ def nlmeans_proxy(in_file, settings,
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from dipy.denoise.nlmeans import nlmeans
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from scipy.ndimage.morphology import binary_erosion
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from scipy import ndimage
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from nipype.utils import NUMPY_MMAP
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if out_file is None:
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fname, fext = op.splitext(op.basename(in_file))

nipype/interfaces/fsl/ICA_AROMA.py

Lines changed: 4 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -10,17 +10,12 @@
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... '../../testing/data'))
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>>> os.chdir(datadir)
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"""
13-
from nipype.interfaces.base import (
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TraitedSpec,
15-
CommandLineInputSpec,
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CommandLine,
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File,
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Directory,
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traits,
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OutputMultiPath
21-
)
13+
from __future__ import print_function, division, unicode_literals, absolute_import
14+
from ..base import (TraitedSpec, CommandLineInputSpec, CommandLine,
15+
File, Directory, traits)
2216
import os
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18+
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class ICA_AROMAInputSpec(CommandLineInputSpec):
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feat_dir = Directory(exists=True, mandatory=True,
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argstr='-feat %s',

nipype/interfaces/fsl/fix.py

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
1+
# -*- coding: utf-8 -*-
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""The fix module provides classes for interfacing with the `FSL FIX
@@ -53,8 +54,9 @@
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outgraph = fix_pipeline.run()
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"""
57+
from __future__ import print_function, division, unicode_literals, absolute_import
5658

57-
from nipype.interfaces.base import (
59+
from ..base import (
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TraitedSpec,
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CommandLineInputSpec,
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CommandLine,
@@ -64,13 +66,10 @@
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BaseInterfaceInputSpec,
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traits
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)
67-
from nipype.interfaces.traits_extension import (
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Directory,
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File,
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isdefined
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)
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from ..traits_extension import Directory, File, isdefined
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import os
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class TrainingSetCreatorInputSpec(BaseInterfaceInputSpec):
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mel_icas_in = InputMultiPath(Directory(exists=True), copyfile=False,
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desc='Melodic output directories',

nipype/interfaces/niftyseg/base.py

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
1+
# -*- coding: utf-8 -*-
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
34

@@ -15,9 +16,10 @@
1516
--------
1617
See the docstrings of the individual classes for examples.
1718
"""
19+
from __future__ import print_function, division, unicode_literals, absolute_import
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19-
from nipype.interfaces.niftyreg.base import no_nifty_package
20-
from nipype.interfaces.niftyfit.base import NiftyFitCommand
21+
from ..niftyreg.base import no_nifty_package
22+
from ..niftyfit.base import NiftyFitCommand
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import subprocess
2224
import warnings
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nipype/interfaces/petpvc.py

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,8 @@
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import os
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from .base import TraitedSpec, CommandLineInputSpec, CommandLine, File, isdefined, traits
16-
from ..external.due import due, Doi, BibTeX
16+
from ..utils.filemanip import fname_presuffix
17+
from ..external.due import BibTeX
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pvc_methods = ['GTM',
1920
'IY',
@@ -200,8 +201,6 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
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New filename based on given parameters.
201202
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"""
203-
from nipype.utils.filemanip import fname_presuffix
204-
205204
if basename == '':
206205
msg = 'Unable to generate filename for command %s. ' % self.cmd
207206
msg += 'basename is not set!'

nipype/interfaces/utility/wrappers.py

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -19,9 +19,9 @@
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2020
from builtins import str, bytes
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22-
from nipype import logging
22+
from ... import logging
2323
from ..base import (traits, DynamicTraitedSpec, Undefined, isdefined, runtime_profile,
24-
BaseInterfaceInputSpec)
24+
BaseInterfaceInputSpec, get_max_resources_used)
2525
from ..io import IOBase, add_traits
2626
from ...utils.filemanip import filename_to_list
2727
from ...utils.misc import getsource, create_function_from_source
@@ -138,7 +138,6 @@ def _add_output_traits(self, base):
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139139
def _run_interface(self, runtime):
140140
# Get workflow logger for runtime profile error reporting
141-
from nipype import logging
142141
logger = logging.getLogger('workflow')
143142

144143
# Create function handle
@@ -163,7 +162,6 @@ def _function_handle_wrapper(queue, **kwargs):
163162

164163
# Profile resources if set
165164
if runtime_profile:
166-
from nipype.interfaces.base import get_max_resources_used
167165
import multiprocessing
168166
# Init communication queue and proc objs
169167
queue = multiprocessing.Queue()

nipype/pipeline/engine/utils.py

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,3 @@
1-
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
@@ -24,7 +23,7 @@
2423
import pickle
2524
from functools import reduce
2625
import numpy as np
27-
from nipype.utils.misc import package_check
26+
from ...utils.misc import package_check
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2928
package_check('networkx', '1.3')
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