the last nibabel.load without NUMPY_MMAP

Author: oesteban

examples/fmri_fsl.py

@@ -106,10 +106,11 @@ def pickfirst(files):
 
 def getmiddlevolume(func):
     from nibabel import load
+    from nipype.utils import NUMPY_MMAP
     funcfile = func
     if isinstance(func, list):
         funcfile = func[0]
-    _, _, _, timepoints = load(funcfile).shape
+    _, _, _, timepoints = load(funcfile, mmap=NUMPY_MMAP).shape
     return int(timepoints / 2) - 1
 
 preproc.connect(inputnode, ('func', getmiddlevolume), extract_ref, 't_min')

nipype/algorithms/rapidart.py

@@ -29,6 +29,7 @@
 from scipy import signal
 import scipy.io as sio
 
+from ..utils import NUMPY_MMAP
 from ..interfaces.base import (BaseInterface, traits, InputMultiPath,
                                OutputMultiPath, TraitedSpec, File,
                                BaseInterfaceInputSpec, isdefined)
@@ -352,12 +353,12 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
 
         # read in functional image
         if isinstance(imgfile, (str, bytes)):
-            nim = load(imgfile)
+            nim = load(imgfile, mmap=NUMPY_MMAP)
         elif isinstance(imgfile, list):
             if len(imgfile) == 1:
-                nim = load(imgfile[0])
+                nim = load(imgfile[0], mmap=NUMPY_MMAP)
             else:
-                images = [load(f) for f in imgfile]
+                images = [load(f, mmap=NUMPY_MMAP) for f in imgfile]
                 nim = funcs.concat_images(images)
 
         # compute global intensity signal
@@ -394,7 +395,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
                     mask[:, :, :, t0] = mask_tmp
                     g[t0] = np.nansum(vol * mask_tmp) / np.nansum(mask_tmp)
         elif masktype == 'file':  # uses a mask image to determine intensity
-            maskimg = load(self.inputs.mask_file)
+            maskimg = load(self.inputs.mask_file, mmap=NUMPY_MMAP)
             mask = maskimg.get_data()
             affine = maskimg.affine
             mask = mask > 0.5

nipype/interfaces/spm/base.py

@@ -28,7 +28,7 @@
 
 # Local imports
 from ... import logging
-from ...utils import spm_docs as sd
+from ...utils import spm_docs as sd, NUMPY_MMAP
 from ..base import (BaseInterface, traits, isdefined, InputMultiPath,
                     BaseInterfaceInputSpec, Directory, Undefined)
 from ..matlab import MatlabCommand
@@ -45,7 +45,7 @@ def func_is_3d(in_file):
     if isinstance(in_file, list):
         return func_is_3d(in_file[0])
     else:
-        img = load(in_file)
+        img = load(in_file, mmap=NUMPY_MMAP)
         shape = img.shape
         if len(shape) == 3 or (len(shape) == 4 and shape[3] == 1):
             return True
@@ -73,7 +73,7 @@ def scans_for_fname(fname):
         for sno, f in enumerate(fname):
             scans[sno] = '%s,1' % f
         return scans
-    img = load(fname)
+    img = load(fname, mmap=NUMPY_MMAP)
     if len(img.shape) == 3:
         return np.array(('%s,1' % fname,), dtype=object)
     else: