RF: ArrayProxy tells Opener whether it intends to keep the file open for

multiple accesses, so Opener knows whether it should use indexed_gzip or not.

Author: pauldmccarthy

nibabel/arrayproxy.py

@@ -265,10 +265,10 @@ def _get_fileobj(self):
         """
         if self._keep_file_open:
             if not hasattr(self, '_opener'):
-                self._opener = ImageOpener(self.file_like)
+                self._opener = ImageOpener(self.file_like, keep_open=True)
             yield self._opener
         else:
-            with ImageOpener(self.file_like) as opener:
+            with ImageOpener(self.file_like, keep_open=False) as opener:
                 yield opener
 
     def get_unscaled(self):

nibabel/openers.py

@@ -67,10 +67,10 @@ def readinto(self, buf):
             return n_read
 
 
-def _gzip_open(filename, mode='rb', compresslevel=9):
+def _gzip_open(filename, mode='rb', compresslevel=9, keep_open=False):
 
     # use indexed_gzip if possible for faster read access
-    if mode == 'rb' and HAVE_INDEXED_GZIP:
+    if keep_open and mode == 'rb' and HAVE_INDEXED_GZIP:
         gzip_file = SafeIndexedGzipFile(filename)
 
     # Fall-back to built-in GzipFile (wrapped with the BufferedGzipFile class
@@ -101,12 +101,14 @@ class Opener(object):
     \*args : positional arguments
         passed to opening method when `fileish` is str.  ``mode``, if not
         specified, is `rb`.  ``compresslevel``, if relevant, and not specified,
-        is set from class variable ``default_compresslevel``
+        is set from class variable ``default_compresslevel``. ``keep_open``, if
+        relevant, and not specified, is set from class variable
+        ``default_keep_open``.
     \*\*kwargs : keyword arguments
         passed to opening method when `fileish` is str.  Change of defaults as
         for \*args
     """
-    gz_def = (_gzip_open, ('mode', 'compresslevel'))
+    gz_def = (_gzip_open, ('mode', 'compresslevel', 'keep_open'))
     bz2_def = (bz2.BZ2File, ('mode', 'buffering', 'compresslevel'))
     compress_ext_map = {
         '.gz': gz_def,
@@ -117,6 +119,9 @@ class Opener(object):
     default_compresslevel = 1
     #: whether to ignore case looking for compression extensions
     compress_ext_icase = True
+    #: hint which tells us whether the file handle will be kept open for
+    #  multiple reads/writes, or just for one-time access.
+    default_keep_open = False
 
     def __init__(self, fileish, *args, **kwargs):
         if self._is_fileobj(fileish):
@@ -132,8 +137,16 @@ def __init__(self, fileish, *args, **kwargs):
         # Set default mode
         if 'mode' not in full_kwargs:
             kwargs['mode'] = 'rb'
+        # Default compression level
         if 'compresslevel' in arg_names and 'compresslevel' not in kwargs:
             kwargs['compresslevel'] = self.default_compresslevel
+        # Default keep_open hint
+        if 'keep_open' in arg_names:
+            if 'keep_open' not in kwargs:
+                kwargs['keep_open'] = self.default_keep_open
+        # Clear keep_open hint if it is not relevant for the file type
+        else:
+            kwargs.pop('keep_open', None)
         self.fobj = opener(fileish, *args, **kwargs)
         self._name = fileish
         self.me_opened = True