add NUMPY_MMAP import

oesteban · oesteban · commit 671fc0358d55 · 2017-02-15T14:59:04.000-08:00
diff --git a/examples/dmri_camino_dti.py b/examples/dmri_camino_dti.py
@@ -18,14 +18,15 @@
 Import necessary modules from nipype.
 """
 
+import os                                    # system functions
 import nipype.interfaces.io as nio           # Data i/o
 import nipype.interfaces.utility as util     # utility
 import nipype.pipeline.engine as pe          # pypeline engine
 import nipype.interfaces.camino as camino
 import nipype.interfaces.fsl as fsl
 import nipype.interfaces.camino2trackvis as cam2trk
 import nipype.algorithms.misc as misc
-import os                                    # system functions
+from nipype.utils import NUMPY_MMAP
 
 """
 We use the following functions to scrape the voxel and data dimensions of the input images. This allows the
diff --git a/examples/dmri_connectivity.py b/examples/dmri_connectivity.py
@@ -47,6 +47,10 @@
 First, we import the necessary modules from nipype.
 """
 
+import inspect
+
+import os.path as op                      # system functions
+import cmp                                    # connectome mapper
 import nipype.interfaces.io as nio           # Data i/o
 import nipype.interfaces.utility as util     # utility
 import nipype.pipeline.engine as pe          # pypeline engine
@@ -56,10 +60,7 @@
 import nipype.interfaces.freesurfer as fs    # freesurfer
 import nipype.interfaces.cmtk as cmtk
 import nipype.algorithms.misc as misc
-import inspect
-
-import os.path as op                      # system functions
-import cmp                                    # connectome mapper
+from nipype.utils import NUMPY_MMAP
 
 """
 We define the following functions to scrape the voxel and data dimensions of the input images. This allows the
diff --git a/examples/fmri_ants_openfmri.py b/examples/fmri_ants_openfmri.py
@@ -36,6 +36,8 @@
 from nipype.workflows.fmri.fsl import (create_featreg_preproc,
                                        create_modelfit_workflow,
                                        create_fixed_effects_flow)
+from nipype.utils import NUMPY_MMAP
+
 
 config.enable_provenance()
 version = 0
diff --git a/examples/fmri_spm_auditory.py b/examples/fmri_spm_auditory.py
@@ -28,6 +28,8 @@
 import nipype.pipeline.engine as pe          # pypeline engine
 import nipype.algorithms.modelgen as model   # model specification
 import os                                    # system functions
+from nipype.utils import NUMPY_MMAP
+
 
 """
 
diff --git a/examples/fmri_spm_face.py b/examples/fmri_spm_face.py
@@ -20,13 +20,14 @@
 from __future__ import division
 from builtins import range
 
+import os                                    # system functions
 import nipype.interfaces.io as nio           # Data i/o
 import nipype.interfaces.spm as spm          # spm
 import nipype.interfaces.matlab as mlab      # how to run matlab
 import nipype.interfaces.utility as util     # utility
 import nipype.pipeline.engine as pe          # pypeline engine
 import nipype.algorithms.modelgen as model   # model specification
-import os                                    # system functions
+from nipype.utils import NUMPY_MMAP
 
 """
 
diff --git a/examples/rsfmri_vol_surface_preprocessing.py b/examples/rsfmri_vol_surface_preprocessing.py
@@ -75,6 +75,8 @@
 import numpy as np
 import scipy as sp
 import nibabel as nb
+from nipype.utils import NUMPY_MMAP
+
 
 imports = ['import os',
            'import nibabel as nb',
diff --git a/examples/rsfmri_vol_surface_preprocessing_nipy.py b/examples/rsfmri_vol_surface_preprocessing_nipy.py
@@ -75,6 +75,7 @@
 import numpy as np
 import scipy as sp
 import nibabel as nb
+from nipype.utils import NUMPY_MMAP
 
 imports = ['import os',
            'import nibabel as nb',
diff --git a/nipype/algorithms/confounds.py b/nipype/algorithms/confounds.py
@@ -16,21 +16,21 @@
 
 import os
 import os.path as op
-from distutils.version import LooseVersion
 
 import nibabel as nb
 import numpy as np
 from numpy.polynomial import Legendre
-from scipy import linalg, signal
+from scipy import linalg
 
 from .. import logging
 from ..external.due import BibTeX
 from ..interfaces.base import (traits, TraitedSpec, BaseInterface,
                                BaseInterfaceInputSpec, File, isdefined,
                                InputMultiPath)
+from nipype.utils import NUMPY_MMAP
+
 IFLOG = logging.getLogger('interface')
 
-NUMPY_MMAP = LooseVersion(np.__version__) >= LooseVersion('1.12.0')
 
 class ComputeDVARSInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='functional data, after HMC')
diff --git a/nipype/algorithms/icc.py b/nipype/algorithms/icc.py
@@ -8,6 +8,7 @@
 from scipy.linalg import pinv
 from ..interfaces.base import BaseInterfaceInputSpec, TraitedSpec, \
     BaseInterface, traits, File
+from nipype.utils import NUMPY_MMAP
 
 
 class ICCInputSpec(BaseInterfaceInputSpec):
diff --git a/nipype/algorithms/metrics.py b/nipype/algorithms/metrics.py
@@ -30,6 +30,8 @@
 from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
                                InputMultiPath,
                                BaseInterfaceInputSpec, isdefined)
+from nipype.utils import NUMPY_MMAP
+
 iflogger = logging.getLogger('interface')
 
 
diff --git a/nipype/algorithms/misc.py b/nipype/algorithms/misc.py
@@ -34,6 +34,8 @@
                                BaseInterfaceInputSpec, isdefined,
                                DynamicTraitedSpec, Undefined)
 from ..utils.filemanip import fname_presuffix, split_filename
+from nipype.utils import NUMPY_MMAP
+
 from . import confounds
 
 iflogger = logging.getLogger('interface')
diff --git a/nipype/algorithms/tests/test_normalize_tpms.py b/nipype/algorithms/tests/test_normalize_tpms.py
@@ -14,6 +14,7 @@
 import nipype.testing as nit
 
 from nipype.algorithms.misc import normalize_tpms
+from nipype.utils import NUMPY_MMAP
 
 
 def test_normalize_tpms(tmpdir):
diff --git a/nipype/algorithms/tests/test_splitmerge.py b/nipype/algorithms/tests/test_splitmerge.py
@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 from nipype.testing import example_data
+from nipype.utils import NUMPY_MMAP
 
 
 def test_split_and_merge(tmpdir):
diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py
@@ -22,6 +22,8 @@
 
 from ... import logging
 from ...utils.filemanip import split_filename
+from ...utils import NUMPY_MMAP
+
 from ..base import (BaseInterface, BaseInterfaceInputSpec, traits, File,
                     TraitedSpec, Directory, OutputMultiPath, isdefined)
 iflogger = logging.getLogger('interface')
diff --git a/nipype/interfaces/dcmstack.py b/nipype/interfaces/dcmstack.py
@@ -23,6 +23,7 @@
                    InputMultiPath, File, Directory,
                    traits, BaseInterface)
 from .traits_extension import isdefined, Undefined
+from ..utils import NUMPY_MMAP
 
 
 have_dcmstack = True
diff --git a/nipype/interfaces/dipy/preprocess.py b/nipype/interfaces/dipy/preprocess.py
@@ -16,6 +16,8 @@
 from ... import logging
 from ..base import (traits, TraitedSpec, File, isdefined)
 from .base import DipyBaseInterface
+from ...utils import NUMPY_MMAP
+
 IFLOGGER = logging.getLogger('interface')
 
 
diff --git a/nipype/interfaces/dipy/simulate.py b/nipype/interfaces/dipy/simulate.py
@@ -13,6 +13,7 @@
 import nibabel as nb
 
 from ... import logging
+from ...utils import NUMPY_MMAP
 from ..base import (traits, TraitedSpec, BaseInterfaceInputSpec,
                     File, InputMultiPath, isdefined)
 from .base import DipyBaseInterface
diff --git a/nipype/interfaces/freesurfer/tests/test_model.py b/nipype/interfaces/freesurfer/tests/test_model.py
@@ -7,6 +7,8 @@
 import nibabel as nb
 
 import pytest
+
+from nipype.utils import NUMPY_MMAP
 from nipype.interfaces.freesurfer import model, no_freesurfer
 import nipype.pipeline.engine as pe
 
diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py
@@ -21,6 +21,8 @@
 import warnings
 
 from ...utils.filemanip import split_filename
+from ...utils import NUMPY_MMAP
+
 from ..base import (traits, TraitedSpec, InputMultiPath, File,
                     isdefined)
 from .base import FSLCommand, FSLCommandInputSpec
diff --git a/nipype/interfaces/nipy/model.py b/nipype/interfaces/nipy/model.py
@@ -8,6 +8,8 @@
 import numpy as np
 
 from ...utils.misc import package_check
+from ...utils import NUMPY_MMAP
+
 from ..base import (BaseInterface, TraitedSpec, traits, File, OutputMultiPath,
                     BaseInterfaceInputSpec, isdefined)
 
diff --git a/nipype/interfaces/nipy/preprocess.py b/nipype/interfaces/nipy/preprocess.py
@@ -16,6 +16,8 @@
 import numpy as np
 
 from ...utils.misc import package_check
+from ...utils import NUMPY_MMAP
+
 from ...utils.filemanip import split_filename, fname_presuffix
 from ..base import (TraitedSpec, BaseInterface, traits,
                     BaseInterfaceInputSpec, isdefined, File,
diff --git a/nipype/utils/__init__.py b/nipype/utils/__init__.py
@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 from __future__ import absolute_import
 
+from nipype.utils.config import NUMPY_MMAP
 from nipype.utils.onetime import OneTimeProperty, setattr_on_read
 from nipype.utils.tmpdirs import TemporaryDirectory, InTemporaryDirectory
diff --git a/nipype/utils/config.py b/nipype/utils/config.py
@@ -10,22 +10,25 @@
 @author: Chris Filo Gorgolewski
 '''
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import str, object, open
-
-from future import standard_library
-standard_library.install_aliases()
-
-import configparser
 import os
 import shutil
 import errno
 from warnings import warn
 from io import StringIO
+from distutils.version import LooseVersion
 from simplejson import load, dump
+import numpy as np
 
+from builtins import str, object, open
+from future import standard_library
+standard_library.install_aliases()
+
+import configparser
 from ..external import portalocker
 
 
+NUMPY_MMAP = LooseVersion(np.__version__) >= LooseVersion('1.12.0')
+
 # Get home directory in platform-agnostic way
 homedir = os.path.expanduser('~')
 default_cfg = """
diff --git a/nipype/workflows/dmri/dipy/denoise.py b/nipype/workflows/dmri/dipy/denoise.py
@@ -4,6 +4,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
 from builtins import range
+from nipype.utils import NUMPY_MMAP
 from ....pipeline import engine as pe
 from ....interfaces import utility as niu
 from ....interfaces import dipy
diff --git a/nipype/workflows/dmri/fsl/artifacts.py b/nipype/workflows/dmri/fsl/artifacts.py
@@ -4,6 +4,8 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 from __future__ import division
 
+from nipype.utils import NUMPY_MMAP
+
 from ....interfaces.io import JSONFileGrabber
 from ....interfaces import utility as niu
 from ....interfaces import ants
diff --git a/nipype/workflows/dmri/fsl/epi.py b/nipype/workflows/dmri/fsl/epi.py
@@ -5,6 +5,7 @@
 
 import warnings
 
+from nipype.utils import NUMPY_MMAP
 from ....pipeline import engine as pe
 from ....interfaces import utility as niu
 from ....interfaces import fsl as fsl
diff --git a/nipype/workflows/dmri/fsl/tbss.py b/nipype/workflows/dmri/fsl/tbss.py
@@ -5,6 +5,7 @@
 import os
 from warnings import warn
 
+from nipype.utils import NUMPY_MMAP
 from ....pipeline import engine as pe
 from ....interfaces import utility as util
 from ....interfaces import fsl as fsl
diff --git a/nipype/workflows/dmri/fsl/utils.py b/nipype/workflows/dmri/fsl/utils.py
@@ -6,6 +6,8 @@
 from __future__ import print_function, division, unicode_literals, absolute_import
 from builtins import zip, next, range, str
 
+from nipype.utils import NUMPY_MMAP
+
 from ....pipeline import engine as pe
 from ....interfaces import utility as niu
 from ....interfaces import fsl
diff --git a/nipype/workflows/misc/utils.py b/nipype/workflows/misc/utils.py
@@ -4,6 +4,7 @@
 from __future__ import print_function, division, unicode_literals, absolute_import
 
 from builtins import map, range
+from nipype.utils import NUMPY_MMAP
 
 
 def get_vox_dims(volume):
diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+
+from nipype.utils import NUMPY_MMAP
 from nipype.interfaces.utility import Function,IdentityInterface
 import nipype.pipeline.engine as pe  # pypeline engine
 from nipype.interfaces.freesurfer import *
