From 10f4b70fbd27897989a8f0cecde435cd71e8a085 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 7 Sep 2018 12:31:14 +0100
Subject: [PATCH] RF: Don't try and save over a memory-mapped image file
---
fsl/data/image.py | 50 ++++++++++++++++++++++++++++++++++++++++-------
1 file changed, 43 insertions(+), 7 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 0a130dcaa..7af1e6960 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -35,8 +35,10 @@ and file names:
import os
import os.path as op
+import shutil
import string
import logging
+import tempfile
import six
import deprecation
@@ -1165,11 +1167,41 @@ class Image(Nifti):
log.debug('Saving {} to {}'.format(self.name, filename))
# If this Image is not managing its
- # own file object, nibabel does all
- # of the hard work.
- if self.__fileobj is None:
+ # own file object, and the image is not
+ # memory-mapped, nibabel does all of
+ # the hard work.
+ newnibimage = False
+ ismmap = isinstance(self[0, 0, :10], np.memmap)
+ if self.__fileobj is None and (not ismmap):
nib.save(self.__nibImage, filename)
+ # If the image is memory-mapped, we need
+ # to close and re-open the image
+ elif self.__fileobj is None:
+
+ # We save the image out to a temp file,
+ # then close the old image, move the
+ # temp file to the real destination,
+ # then re-open the file.
+ newnibimage = True
+ tmphd, tmpfname = tempfile.mkstemp(suffix=op.splitext(filename)[1])
+ os.close(tmphd)
+
+ try:
+ nib.save(self.__nibImage, tmpfname)
+
+ self.__nibImage = None
+ self.header = None
+
+ shutil.copy(tmpfname, filename)
+
+ self.__nibImage = nib.load(filename)
+ self.header = self.__nibImage.header
+
+ except Exception:
+ os.remove(tmpfname)
+ raise
+
# Otherwise we've got our own file
# handle to an IndexedGzipFile
else:
@@ -1190,15 +1222,19 @@ class Image(Nifti):
# compressed data. And then be able to
# transfer the index generated from the
# write to a new read-only file handle.
+ newnibimage = True
nib.save(self.__nibImage, filename)
self.__fileobj.close()
self.__nibImage, self.__fileobj = loadIndexedImageFile(filename)
self.header = self.__nibImage.header
- # We have to create a new ImageWrapper
- # instance too, as we have just destroyed
- # the nibabel image we gave to the last
- # one.
+ # If we've created a new nibabel image,
+ # we have to create a new ImageWrapper
+ # instance too, as we have just destroyed
+ # the nibabel image we gave to the last
+ # one.
+ if newnibimage:
+
self.__imageWrapper.deregister(self.__lName)
self.__imageWrapper = imagewrapper.ImageWrapper(
self.nibImage,
--
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