@@ -152,7 +152,7 @@ class SimpleThreshold(BaseInterface):
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def _run_interface (self , runtime ):
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for fname in self .inputs .volumes :
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- img = nb .load (fname , mmap = NUMPY_MMAP )
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+ img = nb .load (fname )
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data = img .get_fdata ()
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active_map = data > self .inputs .threshold
@@ -1269,7 +1269,7 @@ def normalize_tpms(in_files, in_mask=None, out_files=None):
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out_file = op .abspath ("%s_norm_%02d%s" % (fname , i , fext ))
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out_files += [out_file ]
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- imgs = [nb .load (fim , mmap = NUMPY_MMAP ) for fim in in_files ]
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+ imgs = [nb .load (fim ) for fim in in_files ]
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if len (in_files ) == 1 :
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img_data = imgs [0 ].get_fdata (dtype = np .float32 )
@@ -1290,7 +1290,7 @@ def normalize_tpms(in_files, in_mask=None, out_files=None):
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msk [weights <= 0 ] = 0
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if in_mask is not None :
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- msk = np .asanyarray (nb .load (in_mask , mmap = NUMPY_MMAP ).dataobj )
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+ msk = np .asanyarray (nb .load (in_mask ).dataobj )
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msk [msk <= 0 ] = 0
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msk [msk > 0 ] = 1
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@@ -1328,7 +1328,7 @@ def split_rois(in_file, mask=None, roishape=None):
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droishape = (roishape [0 ], roishape [1 ], roishape [2 ], nvols )
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if mask is not None :
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- mask = np .asanyarray (nb .load (mask , mmap = NUMPY_MMAP ).dataobj )
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+ mask = np .asanyarray (nb .load (mask ).dataobj )
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mask [mask > 0 ] = 1
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mask [mask < 1 ] = 0
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else :
@@ -1432,7 +1432,7 @@ def merge_rois(in_files, in_idxs, in_ref, dtype=None, out_file=None):
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for cname , iname in zip (in_files , in_idxs ):
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f = np .load (iname )
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idxs = np .squeeze (f ["arr_0" ])
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- cdata = np .asanyarray (nb .load (cname , mmap = NUMPY_MMAP ).dataobj ).reshape (
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+ cdata = np .asanyarray (nb .load (cname ).dataobj ).reshape (
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- 1 , ndirs
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)
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nels = len (idxs )
@@ -1464,10 +1464,10 @@ def merge_rois(in_files, in_idxs, in_ref, dtype=None, out_file=None):
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idxs = np .squeeze (f ["arr_0" ])
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for d , fname in enumerate (nii ):
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- data = np .asanyarray (nb .load (fname , mmap = NUMPY_MMAP ).dataobj ).reshape (
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+ data = np .asanyarray (nb .load (fname ).dataobj ).reshape (
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- 1
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)
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- cdata = nb .load (cname , mmap = NUMPY_MMAP ).dataobj [..., d ].reshape (- 1 )
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+ cdata = nb .load (cname ).dataobj [..., d ].reshape (- 1 )
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nels = len (idxs )
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idata = (idxs ,)
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data [idata ] = cdata [0 :nels ]
@@ -1547,7 +1547,7 @@ def _run_interface(self, runtime):
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total = None
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self ._median_files = []
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for idx , fname in enumerate (ensure_list (self .inputs .in_files )):
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- img = nb .load (fname , mmap = NUMPY_MMAP )
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+ img = nb .load (fname )
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data = np .median (img .get_fdata (), axis = 3 )
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if self .inputs .median_per_file :
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self ._median_files .append (self ._write_nifti (img , data , idx ))
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