Merge branch 'rf/protect_nifti_header' into 'master'

Rf/protect nifti header

See merge request fsl/fslpy!200

.ci/test_template.sh

@@ -2,6 +2,13 @@
 
 set -e
 
+# Temporary: this should be done
+# in docker image definition
+apt install -y locales
+locale-gen en_US.UTF-8
+locale-gen en_GB.UTF-8
+update-locale
+
 # If running on a fork repository, we merge in the
 # upstream/master branch. This is done so that merge
 # requests from fork to the parent repository will
@@ -59,4 +66,4 @@ if [[ $CI_COMMIT_REF_NAME == v* ]]; then
     python setup.py test --addopts="$TEST_OPTS -m 'longtest'"
 fi
 
-python -m coverage report
+python -m coverage report -i

CHANGELOG.rst

@@ -2,6 +2,16 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+2.8.3 (Friday 28th February 2020)
+---------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug in the :meth:`.Image.save` method.
+
 
 2.8.2 (Thursday 27th February 2020)
 -----------------------------------

fsl/data/image.py

@@ -254,7 +254,7 @@ class Nifti(notifier.Notifier, meta.Meta):
                                                          shape,
                                                          pixdim)
 
-        self.header           = header
+        self.__header         = header
         self.__shape          = shape
         self.__origShape      = origShape
         self.__pixdim         = pixdim
@@ -262,6 +262,11 @@ class Nifti(notifier.Notifier, meta.Meta):
         self.__isNeurological = isneuro
 
 
+    def __del__(self):
+        """Clears the reference to the ``nibabel`` header object. """
+        self.__header = None
+
+
     @staticmethod
     def determineShape(header):
         """This method is called by :meth:`__init__`. It figures out the actual
@@ -492,6 +497,24 @@ class Nifti(notifier.Notifier, meta.Meta):
         return ''.join([c for c in val if c in string.printable]).strip()
 
 
+    @property
+    def header(self):
+        """Return a reference to the ``nibabel`` header object. """
+        return self.__header
+
+
+    @header.setter
+    def header(self, header):
+        """Replace the ``nibabel`` header object managed by this ``Nifti``
+        with a new header. The new header must have the same dimensions,
+        voxel size, and orientation as the old one.
+        """
+        new = Nifti(header)
+        if not (self.sameSpace(new) and self.ndim == new.ndim):
+            raise ValueError('Incompatible header')
+        self.__header = header
+
+
     @property
     def niftiVersion(self):
         """Returns the NIFTI file version:
@@ -1180,8 +1203,7 @@ class Image(Nifti):
 
     def __del__(self):
         """Closes any open file handles, and clears some references. """
-
-        self.header         = None
+        Nifti.__del__(self)
         self.__nibImage     = None
         self.__imageWrapper = None
 
@@ -1411,12 +1433,6 @@ class Image(Nifti):
 
             nib.save(self.__nibImage, tmpfname)
 
-            # nibabel should close any old
-            # file handles when the image/
-            # header refs are deleted
-            self.__nibImage = None
-            self.header     = None
-
             # Copy to final destination,
             # and reload from there
             imcp.imcp(tmpfname, filename, overwrite=True)