BF - merge Stephans py3 port changes

Author: matthew-brett

nibabel/gifti/__init__.py

@@ -17,5 +17,5 @@
    gifti
 """
 
-from giftiio import read, write
-from gifti import *
+from .giftiio import read, write
+from .gifti import *

nibabel/gifti/gifti.py

@@ -7,7 +7,12 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 
+import sys
 from StringIO import StringIO
+if sys.version_info[0] >= 3:
+    from io import BytesIO
+else:
+    BytesIO = StringIO
 
 import numpy as np
 
@@ -162,11 +167,11 @@ def to_xml(self):
 \t<TransformedSpace><![CDATA[%s]]></TransformedSpace>\n""" % (xform_codes.niistring[self.dataspace], \
                 xform_codes.niistring[self.xformspace])
 
-        e = StringIO()
+        e = BytesIO()
         np.savetxt(e, self.xform, '%10.6f')
         e.seek(0)
         res = res + "<MatrixData>\n"
-        res = res + e.read()
+        res = res + e.read().decode()
         e.close()
         res = res + "</MatrixData>\n"
         res = res + "</CoordinateSystemTransformMatrix>\n" 
@@ -192,7 +197,7 @@ def data_tag(dataarray, encoding, datatype, ordering):
         ord = 'C'
 
     if encoding == "GIFTI_ENCODING_ASCII":
-        c = StringIO()
+        c = BytesIO()
         # np.savetxt(c, dataarray, format, delimiter for columns)
         np.savetxt(c, dataarray, datatype, ' ')
         c.seek(0)
@@ -207,11 +212,8 @@ def data_tag(dataarray, encoding, datatype, ordering):
     elif encoding == "GIFTI_ENCODING_B64GZ":        
         # first compress
         comp = zlib.compress(dataarray.tostring(ord))
-        c = StringIO(comp)
-        out = StringIO()
-        base64.encode(c, out)
-        out.seek(0)
-        da = out.read()
+        da = base64.encodestring(comp)
+        da = da.decode()
 
     elif encoding == "GIFTI_ENCODING_EXTBIN":
         raise NotImplementedError("In what format are the external files?")

nibabel/gifti/parse_gifti_fast.py

@@ -41,7 +41,7 @@ def read_data_block(encoding, endian, ordering, datatype, shape, data):
 
     elif encoding == 2:
         # GIFTI_ENCODING_B64BIN
-        dec = base64.decodestring(data)
+        dec = base64.decodestring(data.encode('ascii'))
         dt = data_type_codes.type[datatype]
         sh = tuple(shape)
         newarr = np.fromstring(zdec, dtype = dt, sep = '\n', count = c)
@@ -52,7 +52,9 @@ def read_data_block(encoding, endian, ordering, datatype, shape, data):
 
     elif encoding == 3:
         # GIFTI_ENCODING_B64GZ
-        dec = base64.decodestring(data)
+        # convert to bytes array for python 3.2
+        # http://diveintopython3.org/strings.html#byte-arrays
+        dec = base64.decodestring(data.encode('ascii'))
         zdec = zlib.decompress(dec)
         dt = data_type_codes.type[datatype]
         sh = tuple(shape)
@@ -292,7 +294,6 @@ def CharacterDataHandler(self, data):
             self.coordsys.xformspace = xform_codes.code[data]
         elif self.write_to == 'MatrixData':
             # conversion to numpy array
-            from StringIO import StringIO
             c = StringIO(data)
             self.coordsys.xform = np.loadtxt(c)
             c.close()
@@ -307,7 +308,7 @@ def CharacterDataHandler(self, data):
 
 def parse_gifti_file(fname, buffer_size = 35000000):
 
-    datasource = open(fname,'r')
+    datasource = open(fname,'rb')
 
     parser = ParserCreate()
     parser.buffer_text = True