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Commit 25b46b1

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Merge pull request #1831 from effigies/bug/mmap
FIX: Import NUMPY_MMAP inside functions
2 parents 102d8d7 + 72cb924 commit 25b46b1

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6 files changed

+26
-7
lines changed

6 files changed

+26
-7
lines changed

‎nipype/interfaces/dipy/preprocess.py‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,6 @@
1616
from ... import logging
1717
from ..base import (traits, TraitedSpec, File, isdefined)
1818
from .base import DipyBaseInterface
19-
from ...utils import NUMPY_MMAP
2019

2120
IFLOGGER = logging.getLogger('interface')
2221

@@ -180,6 +179,7 @@ def resample_proxy(in_file, order=3, new_zooms=None, out_file=None):
180179
Performs regridding of an image to set isotropic voxel sizes using dipy.
181180
"""
182181
from dipy.align.reslice import reslice
182+
from nipype.utils import NUMPY_MMAP
183183

184184
if out_file is None:
185185
fname, fext = op.splitext(op.basename(in_file))
@@ -223,6 +223,7 @@ def nlmeans_proxy(in_file, settings,
223223
from dipy.denoise.nlmeans import nlmeans
224224
from scipy.ndimage.morphology import binary_erosion
225225
from scipy import ndimage
226+
from nipype.utils import NUMPY_MMAP
226227

227228
if out_file is None:
228229
fname, fext = op.splitext(op.basename(in_file))

‎nipype/workflows/dmri/dipy/denoise.py‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,6 @@
44
# vi: set ft=python sts=4 ts=4 sw=4 et:
55

66
from builtins import range
7-
from nipype.utils import NUMPY_MMAP
87
from ....pipeline import engine as pe
98
from ....interfaces import utility as niu
109
from ....interfaces import dipy
@@ -57,6 +56,7 @@ def csf_mask(in_file, in_mask, out_file=None):
5756
from scipy.ndimage import binary_erosion, binary_opening, label
5857
import scipy.ndimage as nd
5958
import os.path as op
59+
from nipype.utils import NUMPY_MMAP
6060

6161
if out_file is None:
6262
fname, ext = op.splitext(op.basename(in_file))
@@ -100,6 +100,7 @@ def bg_mask(in_file, in_mask, out_file=None):
100100
from scipy.ndimage import binary_dilation
101101
import scipy.ndimage as nd
102102
import os.path as op
103+
from nipype.utils import NUMPY_MMAP
103104

104105
if out_file is None:
105106
fname, ext = op.splitext(op.basename(in_file))

‎nipype/workflows/dmri/fsl/epi.py‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,6 @@
55

66
import warnings
77

8-
from nipype.utils import NUMPY_MMAP
98
from ....pipeline import engine as pe
109
from ....interfaces import utility as niu
1110
from ....interfaces import fsl as fsl
@@ -722,6 +721,7 @@ def _prepare_phasediff(in_file):
722721
import nibabel as nb
723722
import os
724723
import numpy as np
724+
from nipype.utils import NUMPY_MMAP
725725
img = nb.load(in_file, mmap=NUMPY_MMAP)
726726
max_diff = np.max(img.get_data().reshape(-1))
727727
min_diff = np.min(img.get_data().reshape(-1))
@@ -741,6 +741,7 @@ def _dilate_mask(in_file, iterations=4):
741741
import nibabel as nb
742742
import scipy.ndimage as ndimage
743743
import os
744+
from nipype.utils import NUMPY_MMAP
744745
img = nb.load(in_file, mmap=NUMPY_MMAP)
745746
img._data = ndimage.binary_dilation(img.get_data(), iterations=iterations)
746747

@@ -756,6 +757,7 @@ def _fill_phase(in_file):
756757
import nibabel as nb
757758
import os
758759
import numpy as np
760+
from nipype.utils import NUMPY_MMAP
759761
img = nb.load(in_file, mmap=NUMPY_MMAP)
760762
dumb_img = nb.Nifti1Image(np.zeros(img.shape), img.affine, img.header)
761763
out_nii = nb.funcs.concat_images((img, dumb_img))
@@ -772,6 +774,7 @@ def _vsm_remove_mean(in_file, mask_file, in_unwarped):
772774
import os
773775
import numpy as np
774776
import numpy.ma as ma
777+
from nipype.utils import NUMPY_MMAP
775778
img = nb.load(in_file, mmap=NUMPY_MMAP)
776779
msk = nb.load(mask_file, mmap=NUMPY_MMAP).get_data()
777780
img_data = img.get_data()
@@ -794,6 +797,7 @@ def _ms2sec(val):
794797
def _split_dwi(in_file):
795798
import nibabel as nb
796799
import os
800+
from nipype.utils import NUMPY_MMAP
797801
out_files = []
798802
frames = nb.funcs.four_to_three(nb.load(in_file, mmap=NUMPY_MMAP))
799803
name, fext = os.path.splitext(os.path.basename(in_file))

‎nipype/workflows/dmri/fsl/tbss.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,14 +5,14 @@
55
import os
66
from warnings import warn
77

8-
from nipype.utils import NUMPY_MMAP
98
from ....pipeline import engine as pe
109
from ....interfaces import utility as util
1110
from ....interfaces import fsl as fsl
1211

1312

1413
def tbss1_op_string(in_files):
1514
import nibabel as nb
15+
from nipype.utils import NUMPY_MMAP
1616
op_strings = []
1717
for infile in in_files:
1818
img = nb.load(infile, mmap=NUMPY_MMAP)

‎nipype/workflows/dmri/fsl/utils.py‎

Lines changed: 12 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,8 +6,6 @@
66
from __future__ import print_function, division, unicode_literals, absolute_import
77
from builtins import zip, next, range, str
88

9-
from nipype.utils import NUMPY_MMAP
10-
119
from ....pipeline import engine as pe
1210
from ....interfaces import utility as niu
1311
from ....interfaces import fsl
@@ -209,6 +207,7 @@ def extract_bval(in_dwi, in_bval, b=0, out_file=None):
209207
import numpy as np
210208
import nibabel as nb
211209
import os.path as op
210+
from nipype.utils import NUMPY_MMAP
212211

213212
if out_file is None:
214213
fname, ext = op.splitext(op.basename(in_dwi))
@@ -244,6 +243,7 @@ def hmc_split(in_file, in_bval, ref_num=0, lowbval=5.0):
244243
import nibabel as nb
245244
import os.path as op
246245
from nipype.interfaces.base import isdefined
246+
from nipype.utils import NUMPY_MMAP
247247

248248
im = nb.load(in_file, mmap=NUMPY_MMAP)
249249
data = im.get_data()
@@ -288,6 +288,7 @@ def remove_comp(in_file, in_bval, volid=0, out_file=None):
288288
import numpy as np
289289
import nibabel as nb
290290
import os.path as op
291+
from nipype.utils import NUMPY_MMAP
291292

292293
if out_file is None:
293294
fname, ext = op.splitext(op.basename(in_file))
@@ -337,6 +338,7 @@ def recompose_dwi(in_dwi, in_bval, in_corrected, out_file=None):
337338
import numpy as np
338339
import nibabel as nb
339340
import os.path as op
341+
from nipype.utils import NUMPY_MMAP
340342

341343
if out_file is None:
342344
fname, ext = op.splitext(op.basename(in_dwi))
@@ -397,6 +399,7 @@ def time_avg(in_file, index=[0], out_file=None):
397399
import numpy as np
398400
import nibabel as nb
399401
import os.path as op
402+
from nipype.utils import NUMPY_MMAP
400403

401404
if out_file is None:
402405
fname, ext = op.splitext(op.basename(in_file))
@@ -444,6 +447,7 @@ def b0_average(in_dwi, in_bval, max_b=10.0, out_file=None):
444447
import numpy as np
445448
import nibabel as nb
446449
import os.path as op
450+
from nipype.utils import NUMPY_MMAP
447451

448452
if out_file is None:
449453
fname, ext = op.splitext(op.basename(in_dwi))
@@ -623,6 +627,7 @@ def rads2radsec(in_file, delta_te, out_file=None):
623627
import nibabel as nb
624628
import os.path as op
625629
import math
630+
from nipype.utils import NUMPY_MMAP
626631

627632
if out_file is None:
628633
fname, fext = op.splitext(op.basename(in_file))
@@ -644,6 +649,7 @@ def demean_image(in_file, in_mask=None, out_file=None):
644649
import nibabel as nb
645650
import os.path as op
646651
import math
652+
from nipype.utils import NUMPY_MMAP
647653

648654
if out_file is None:
649655
fname, fext = op.splitext(op.basename(in_file))
@@ -674,6 +680,7 @@ def add_empty_vol(in_file, out_file=None):
674680
import os.path as op
675681
import numpy as np
676682
import math
683+
from nipype.utils import NUMPY_MMAP
677684

678685
if out_file is None:
679686
fname, fext = op.splitext(op.basename(in_file))
@@ -696,6 +703,7 @@ def reorient_bvecs(in_dwi, old_dwi, in_bvec):
696703
import os
697704
import numpy as np
698705
import nibabel as nb
706+
from nipype.utils import NUMPY_MMAP
699707

700708
name, fext = os.path.splitext(os.path.basename(in_bvec))
701709
if fext == '.gz':
@@ -721,6 +729,7 @@ def copy_hdr(in_file, in_file_hdr, out_file=None):
721729
import numpy as np
722730
import nibabel as nb
723731
import os.path as op
732+
from nipype.utils import NUMPY_MMAP
724733

725734
if out_file is None:
726735
fname, fext = op.splitext(op.basename(in_file))
@@ -744,6 +753,7 @@ def enhance(in_file, clip_limit=0.010, in_mask=None, out_file=None):
744753
import nibabel as nb
745754
import os.path as op
746755
from skimage import exposure, img_as_int
756+
from nipype.utils import NUMPY_MMAP
747757

748758
if out_file is None:
749759
fname, fext = op.splitext(op.basename(in_file))

‎nipype/workflows/misc/utils.py‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,11 +4,11 @@
44
from __future__ import print_function, division, unicode_literals, absolute_import
55

66
from builtins import map, range
7-
from nipype.utils import NUMPY_MMAP
87

98

109
def get_vox_dims(volume):
1110
import nibabel as nb
11+
from nipype.utils import NUMPY_MMAP
1212
if isinstance(volume, list):
1313
volume = volume[0]
1414
nii = nb.load(volume, mmap=NUMPY_MMAP)
@@ -19,6 +19,7 @@ def get_vox_dims(volume):
1919

2020
def get_data_dims(volume):
2121
import nibabel as nb
22+
from nipype.utils import NUMPY_MMAP
2223
if isinstance(volume, list):
2324
volume = volume[0]
2425
nii = nb.load(volume, mmap=NUMPY_MMAP)
@@ -29,6 +30,7 @@ def get_data_dims(volume):
2930

3031
def get_affine(volume):
3132
import nibabel as nb
33+
from nipype.utils import NUMPY_MMAP
3234
nii = nb.load(volume, mmap=NUMPY_MMAP)
3335
return nii.affine
3436

@@ -50,6 +52,7 @@ def select_aparc_annot(list_of_files):
5052
def region_list_from_volume(in_file):
5153
import nibabel as nb
5254
import numpy as np
55+
from nipype.utils import NUMPY_MMAP
5356
segmentation = nb.load(in_file, mmap=NUMPY_MMAP)
5457
segmentationdata = segmentation.get_data()
5558
rois = np.unique(segmentationdata)

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