Merge branch 'maint/1.x' into v1.13

CHANGELOG.rst

@@ -2,6 +2,20 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+1.13.3 (Friday February 8th 2019)
+---------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue with the `.dicom.loadSeries` using memory-mapping for
+  image files that would subsequently be deleted.
+* Fixed an issue in the :class:`.GiftiMesh` class, where
+  ``numpy``/``nibabel`` was returning read-only index arrays.
+
+
 1.13.2 (Friday November 30th 2018)
 ----------------------------------
 

fsl/data/dicom.py

@@ -236,9 +236,13 @@ def loadSeries(series):
             sp.call(cmd.split(), stdout=devnull, stderr=devnull)
 
         files  = glob.glob(op.join(td, '{}*.nii'.format(snum)))
-        images = [nib.load(f) for f in files]
-
-        # Force-load images into memory
-        [i.get_data() for i in images]
+        images = [nib.load(f, mmap=False) for f in files]
+
+        # 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)
+                  for i in images]
 
         return [DicomImage(i, series, dcmdir, name=desc) for i in images]

fsl/data/gifti.py

@@ -195,8 +195,8 @@ def loadGiftiMesh(filename):
         raise ValueError('{}: GIFTI surface files must contain '
                          'exactly one triangle array'.format(filename))
 
-    vertices = pointsets[0].data
-    indices  = triangles[0].data
+    vertices = np.array(pointsets[0].data)
+    indices  = np.array(triangles[0].data)
 
     return gimg, vertices, indices
 

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '1.13.2'
+__version__ = '1.13.3'
 """Current version number, as a string. """