RF,BF: Modify read_data_block so that the GiftiDataArray is passed in, rather

than all of its attributes as separate args. Also pass in name of file being
parsed, in case data is to be loaded from an external file

Author: pauldmccarthy

nibabel/gifti/parse_gifti_fast.py

@@ -11,6 +11,7 @@
 import sys
 import warnings
 import zlib
+import os.path as op
 from io import StringIO
 from xml.parsers.expat import ExpatError
 
@@ -30,16 +31,27 @@ class GiftiParseError(ExpatError):
     """ Gifti-specific parsing error """
 
 
-def read_data_block(encoding,
-                    endian,
-                    ordering,
-                    datatype,
-                    shape,
-                    data,
-                    darray):
-    """ Tries to unzip, decode, parse the funny string data """
-    enclabel = gifti_encoding_codes.label[encoding]
-    dtype = data_type_codes.type[datatype]
+def read_data_block(darray, fname, data):
+    """Parses data from a <Data> element, or loads from an external file.
+
+    Parameters
+    ----------
+    darray : GiftiDataArray
+         GiftiDataArray object representing the parent <DataArray> of this
+         <Data> element
+
+    fname : str or None
+         Name of GIFTI file being loaded, or None if in-memory
+
+    data : str or None
+         Data to parse, or None if data is in an external file
+
+    Returns
+    -------
+    numpy.ndarray containing the parsed data
+    """
+    enclabel = gifti_encoding_codes.label[darray.encoding]
+    dtype = data_type_codes.type[darray.datatype]
 
     if enclabel == 'ASCII':
         # GIFTI_ENCODING_ASCII
@@ -54,9 +66,15 @@ def read_data_block(encoding,
     # the data type/endianness/ordering specified by the other DataArray
     # attributes
     if enclabel == 'External':
-        with open(darray.ext_fname, 'rb') as f:
+        if fname is None:
+            raise GiftiParseError('ExternalFileBinary is not supported '
+                                  'when loading from in-memory XML')
+        ext_fname = op.join(op.dirname(fname), darray.ext_fname)
+        if not op.exists(ext_fname):
+            raise GiftiParseError('Cannot locate external file ' + ext_fname)
+        with open(ext_fname, 'rb') as f:
             f.seek(darray.ext_offset)
-            nbytes = np.prod(shape) * dtype().itemsize
+            nbytes = np.prod(darray.dims) * dtype().itemsize
             buff = f.read(nbytes)
 
     # Numpy arrays created from bytes objects are read-only.
@@ -75,13 +93,14 @@ def read_data_block(encoding,
             buff = bytearray(zlib.decompress(dec))
         del dec
 
-    sh = tuple(shape)
+    sh = tuple(darray.dims)
     newarr = np.frombuffer(buff, dtype=dtype)
     if len(newarr.shape) != len(sh):
-        newarr = newarr.reshape(sh, order=array_index_order_codes.npcode[ordering])
+        newarr = newarr.reshape(
+            sh, order=array_index_order_codes.npcode[darray.ind_ord])
 
     # check if we need to byteswap
-    required_byteorder = gifti_endian_codes.byteorder[endian]
+    required_byteorder = gifti_endian_codes.byteorder[darray.endian]
     if (required_byteorder in ('big', 'little') and
             required_byteorder != sys.byteorder):
         newarr = newarr.byteswap()
@@ -339,10 +358,7 @@ def flush_chardata(self):
             c.close()
 
         elif self.write_to == 'Data':
-            da_tmp = self.img.darrays[-1]
-            da_tmp.data = read_data_block(da_tmp.encoding, da_tmp.endian,
-                                          da_tmp.ind_ord, da_tmp.datatype,
-                                          da_tmp.dims, data, self.da)
+            self.da.data = read_data_block(self.da, self.fname, data)
             # update the endianness according to the
             # current machine setting
             self.endian = gifti_endian_codes.code[sys.byteorder]