From d8231fe28494a3d0f2a3461fe49d7dbf8dd8d4be Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 12 Dec 2019 10:26:40 +0000
Subject: [PATCH] RF: Don't use get_data
---
fsl/data/dicom.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py
index d38d2081d..51c750385 100644
--- a/fsl/data/dicom.py
+++ b/fsl/data/dicom.py
@@ -36,6 +36,7 @@ import shlex
import logging
import binascii
+import numpy as np
import nibabel as nib
import fsl.utils.tempdir as tempdir
@@ -279,9 +280,11 @@ def loadSeries(series):
# copy images so nibabel no longer
# refs to the files (as they will
- # be deleted), and use get_data()
- # to force-load the image data.
- images = [nib.Nifti1Image(i.get_data(), None, i.header)
+ # be deleted), and force-load the
+ # the image data into memory (to
+ # avoid any disk accesses due to
+ # e.g. memmap)
+ images = [nib.Nifti1Image(np.asanyarray(i.dataobj), None, i.header)
for i in images]
return [DicomImage(i, series, dcmdir, name=desc) for i in images]
--
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