Properly deprecate Outputter, parse_gifti_file

Author: Ben Cipollini

nibabel/gifti/parse_gifti_fast.py

@@ -16,12 +16,12 @@
 
 import numpy as np
 
-from ..nifti1 import data_type_codes, xform_codes, intent_codes
 from .gifti import (GiftiMetaData, GiftiImage, GiftiLabel,
                     GiftiLabelTable, GiftiNVPairs, GiftiDataArray,
                     GiftiCoordSystem)
 from .util import (array_index_order_codes, gifti_encoding_codes,
                    gifti_endian_codes)
+from ..nifti1 import data_type_codes, xform_codes, intent_codes
 from ..xmlbasedimages import XmlImageParser
 
 DEBUG_PRINT = False
@@ -94,6 +94,7 @@ def __init__(self):
 
         # Collecting char buffer fragments
         self._char_blocks = None
+        self.buffer_size = None
 
     def StartElementHandler(self, name, attrs):
         self.flush_chardata()
@@ -311,3 +312,42 @@ def flush_chardata(self):
     def pending_data(self):
         " True if there is character data pending for processing "
         return not self._char_blocks is None
+
+    def _create_parser(self):
+        parser = super(GiftiImageParser, self)._create_parser()
+        if self.buffer_size is not None:
+            parser.buffer_text = True
+            parser.buffer_size = self.buffer_size
+        return parser
+
+    def parse(self, string=None, fname=None, fptr=None, buffer_size=None):
+        """ Parse gifti file named `fname`, return image
+
+        Parameters
+        ----------
+        fname : str
+            filename of gifti file
+        buffer_size: None or int, optional
+            size of read buffer. None gives default of 35000000 unless on python <
+            2.6, in which case it is read only in the parser.  In that case values
+            other than None cause a ValueError on execution
+
+        Returns
+        -------
+        img : gifti image
+        """
+        self.buffer_size = buffer_size
+        return super(GiftiImageParser, self).parse(string=string, fname=fname,
+                                                   fptr=fptr)
+
+
+class Outputter(GiftiImageParser):
+    @np.deprecate_with_doc("Use GiftiImageParser instead.")
+    def __init__(self, *args, **kwargs):
+        super(Outputter, self).__init__(*args, **kwargs)
+        self.img = None
+
+
+@np.deprecate_with_doc("Use GiftiImageParser.parse() instead.")
+def parse_gifti_file(fname=None, fptr=None, buffer_size=None):
+    GiftiImageParser().parse(fname=fname, fptr=fptr, buffer_size=buffer_size)

nibabel/xmlbasedimages.py

@@ -10,7 +10,7 @@
 Thin layer around xml.etree.ElementTree, to abstract nibabel xml support.
 """
 from xml.etree.ElementTree import Element, SubElement, tostring
-from xml.parsers.expat import ParserCreate, ExpatError
+from xml.parsers.expat import ParserCreate
 
 from .filebasedimages import FileBasedHeader, FileBasedImage
 
@@ -43,6 +43,9 @@ def __init__(self, encoding=None):
         self.encoding = encoding
         self.img = None
 
+    def _create_parser(self):
+        return ParserCreate()  # from xml package
+
     def parse(self, string=None, fname=None, fptr=None):
         """
         Parameters
@@ -68,7 +71,7 @@ def parse(self, string=None, fname=None, fptr=None):
         elif fname is not None:
             fptr = open(fname, 'r')
 
-        parser = ParserCreate()  # from xml package
+        parser = self._create_parser()
         for name in self.HANDLER_NAMES:
             setattr(parser, name, getattr(self, name))
         parser.ParseFile(fptr)