Remove XmlBasedImage, xmlbasedimages.py=>xmlutils.py

Author: Ben Cipollini

nibabel/gifti/gifti.py

@@ -12,7 +12,8 @@
 
 import numpy as np
 
-from .. import xmlbasedimages as xml
+from .. import xmlutils as xml
+from ..filebasedimages import FileBasedImage
 from ..nifti1 import data_type_codes, xform_codes, intent_codes
 from .util import (array_index_order_codes, gifti_encoding_codes,
                    gifti_endian_codes, KIND2FMT)
@@ -385,7 +386,7 @@ def metadata(self):
         return self.meta.metadata
 
 
-class GiftiImage(xml.XmlBasedImage):
+class GiftiImage(xml.XmlSerializable, FileBasedImage):
     """
     The Gifti spec suggests using the following suffixes to your
     filename when saving each specific type of data:
@@ -564,3 +565,42 @@ def to_xml(self, enc='utf-8'):
         return b"""<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/115/gifti.dtd">
 """ + xml.XmlSerializable.to_xml(self, enc)
+
+    def to_file_map(self, file_map=None):
+        """ Save the current image to the specified file_map
+
+        Parameters
+        ----------
+        file_map : string
+
+        Returns
+        -------
+        None
+        """
+        if file_map is None:
+            file_map = self.file_map
+        f = file_map['image'].get_prepare_fileobj('wb')
+        f.write(self.to_xml())
+
+    @classmethod
+    def from_file_map(klass, file_map, buffer_size=35000000):
+        """ Load a Gifti image from a file_map
+
+        Parameters
+        file_map : string
+
+        Returns
+        -------
+        img : GiftiImage
+            Returns a GiftiImage
+         """
+        parser = klass.parser(buffer_size=buffer_size)
+        parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb'))
+        img = parser.img
+        return img
+
+    @classmethod
+    def from_filename(klass, filename, buffer_size=35000000):
+        file_map = klass.filespec_to_file_map(filename)
+        img = klass.from_file_map(file_map, buffer_size=buffer_size)
+        return img

nibabel/gifti/parse_gifti_fast.py

@@ -22,7 +22,7 @@
 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
+from ..xmlutils import XmlParser
 
 
 def read_data_block(encoding, endian, ordering, datatype, shape, data):
@@ -72,12 +72,14 @@ def read_data_block(encoding, endian, ordering, datatype, shape, data):
     return newarr
 
 
-class GiftiImageParser(XmlImageParser):
+class GiftiImageParser(XmlParser):
 
     def __init__(self, encoding=None, buffer_size=35000000, verbose=0):
         super(GiftiImageParser, self).__init__(encoding=encoding,
                                                buffer_size=buffer_size,
                                                verbose=verbose)
+        # output
+        self.img = None
 
         # finite state machine stack
         self.fsm_state = []
@@ -333,7 +335,6 @@ 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.")

nibabel/xmlbasedimages.py nibabel/xmlutils.pynibabel/xmlbasedimages.py renamed to nibabel/xmlutils.py

@@ -35,8 +35,8 @@ class XmlBasedHeader(FileBasedHeader, XmlSerializable):
     pass
 
 
-class XmlImageParser(object):
-    """ Base class for defining how to parse xml-based images.
+class XmlParser(object):
+    """ Base class for defining how to parse xml-based image snippets.
 
     Image-specific parsers should define:
         StartElementHandler
@@ -62,10 +62,9 @@ def __init__(self, encoding=None, buffer_size=35000000, verbose=0):
         verbose : int, optional
             amount of output during parsing (0=silent, by default).
         """
-        self.encoding=encoding
+        self.encoding = encoding
         self.buffer_size = buffer_size
         self.verbose = verbose
-        self.img = None
 
     def _create_parser(self):
         """Internal function that allows subclasses to mess
@@ -88,11 +87,7 @@ def parse(self, string=None, fname=None, fptr=None):
             file name of an xml document.
 
         fptr : file pointer
-            open file pointer to an xml document
-
-        Returns
-        -------
-        img : XmlBasedImage
+            open file pointer to an xml documents
         """
         if int(string is not None) + int(fptr is not None) + int(fname is not None) != 1:
             raise ValueError('Exactly one of fptr, fname, string must be specified.')
@@ -107,12 +102,6 @@ def parse(self, string=None, fname=None, fptr=None):
             setattr(parser, name, getattr(self, name))
         parser.ParseFile(fptr)
 
-        if fname is not None:
-            fptr.close()
-            self.img.set_filename(fname)
-
-        return self.img
-
     def StartElementHandler(self, name, attrs):
         raise NotImplementedError
 
@@ -121,53 +110,3 @@ def EndElementHandler(self, name):
 
     def CharacterDataHandler(self, data):
         raise NotImplementedError
-
-
-class XmlBasedImage(FileBasedImage, XmlSerializable):
-    """Basic convenience wrapper around FileBasedImage and XmlSerializable.
-
-        Properties
-        ----------
-        parser : XmlImageParser
-            class name of the XML parser associated with this image type.
-    """
-
-    parser = XmlImageParser
-    header = XmlBasedHeader
-
-    def to_file_map(self, file_map=None):
-        """ Save the current image to the specified file_map
-
-        Parameters
-        ----------
-        file_map : string
-
-        Returns
-        -------
-        None
-        """
-        if file_map is None:
-            file_map = self.file_map
-        f = file_map['image'].get_prepare_fileobj('wb')
-        f.write(self.to_xml())
-
-    @classmethod
-    def from_file_map(klass, file_map, buffer_size=35000000):
-        """ Load a Gifti image from a file_map
-
-        Parameters
-        file_map : string
-
-        Returns
-        -------
-        img : GiftiImage
-            Returns a GiftiImage
-         """
-        img = klass.parser(buffer_size=buffer_size).parse(
-            fptr=file_map['image'].get_prepare_fileobj('rb'))
-        return img
-
-    @classmethod
-    def from_filename(klass, filename, buffer_size=35000000):
-        file_map = klass.filespec_to_file_map(filename)
-        return klass.from_file_map(file_map, buffer_size=buffer_size)