Fixed namespace problems in cfelfabio modules

cfelfabio.py

-#    This file is part of cfelpyutils.
-#
-#    cfelpyutils is free software: you can redistribute it and/or modify
-#    it under the terms of the GNU General Public License as published by
-#    the Free Software Foundation, either version 3 of the License, or
-#    (at your option) any later version.
-#
-#    cfelpyutils is distributed in the hope that it will be useful,
-#    but WITHOUT ANY WARRANTY; without even the implied warranty of
-#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#    GNU General Public License for more details.
-#
-#    You should have received a copy of the GNU General Public License
-#    along with cfelpyutils.  If not, see <http://www.gnu.org/licenses/>.
-
-
-"""
-Utilities based on the fabio python module
-
-This module contains utilities derived from the fabio python module.
-This module allows python to understand and process several file format used in
-x-ray crystallography. The utilites in this modules expand on what the fabio
-module alread provides.
-"""
-
-
+import numpy
 import fabio.cbfimage
 
-
 def read_cbf_from_stream(stream):
-    """"Reads a cbfimage object out of a data string buffer.
+    """Reads a cbfimage object out of a data string buffer.
 
-    Read a data string buffer received as a payload from the PETRAIII P11
-    sender, and creates a cbfimage object from it (See the documentation of the
-    fabio python module).
+    Read a data string buffer received as a payload from the PETRAIII P11 sender,
+    and creates a cbfimage object from it (See the documentation of the fabio
+    python module).
 
     Args:
 
-        stream (str): a data string buffer received from the PETRAIII P11 sender.
+       stream (str): a data string buffer received from the PETRAIII P11 sender.
 
     Returns:
 
-        cbf_obj (fabio.cbfimage): a cbfimage object containing the data
-        extracted from the string buffer.
+        cbf_obj (fabio.cbfimage): a cbfimage object containing the data extracted
+            from the string buffer.
     """
 
     cbf_obj = fabio.cbfimage.cbfimage()
@@ -51,26 +25,26 @@ def read_cbf_from_stream(stream):
 
     infile = stream
     cbf_obj._readheader(infile)
-    if fabio.cbfimage.CIF_BINARY_BLOCK_KEY not in cbf_obj.fabio.cbfimage.CIF:
-        err = "Not key %s in fabio.cbfimage.CIF, no CBF image in stream" % (fabio.cbfimage.CIF_BINARY_BLOCK_KEY)
-        fabio.cbfimage.logger.error(err)
-        for kv in cbf_obj.fabio.cbfimage.CIF.items():
+    if fabio.cbfimage.CIF_BINARY_BLOCK_KEY not in cbf_obj.cif:
+        err = "Not key %s in CIF, no CBF image in stream" % (fabio.cbfimage.CIF_BINARY_BLOCK_KEY)
+        logger.error(err)
+        for kv in cbf_obj.cif.items():
             print("%s: %s" % kv)
         raise RuntimeError(err)
-    if cbf_obj.fabio.cbfimage.CIF[fabio.cbfimage.CIF_BINARY_BLOCK_KEY] == "fabio.cbfimage.CIF Binary Section":
+    if cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY] == "CIF Binary Section":
         cbf_obj.cbs += infile.read(len(fabio.cbfimage.STARTER) + int(cbf_obj.header["X-Binary-Size"]) - len(cbf_obj.cbs) + cbf_obj.start_binary)
     else:
-        if len(cbf_obj.fabio.cbfimage.CIF[fabio.cbfimage.CIF_BINARY_BLOCK_KEY]) > int(cbf_obj.header["X-Binary-Size"]) + cbf_obj.start_binary + len(fabio.cbfimage.STARTER):
-            cbf_obj.cbs = cbf_obj.fabio.cbfimage.CIF[fabio.cbfimage.CIF_BINARY_BLOCK_KEY][:int(cbf_obj.header["X-Binary-Size"]) + cbf_obj.start_binary + len(fabio.cbfimage.STARTER)]
+        if len(cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY]) > int(cbf_obj.header["X-Binary-Size"]) + cbf_obj.start_binary + len(fabio.cbfimage.STARTER):
+            cbf_obj.cbs = cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY][:int(cbf_obj.header["X-Binary-Size"]) + cbf_obj.start_binary + len(fabio.cbfimage.STARTER)]
         else:
-            cbf_obj.cbs = cbf_obj.fabio.cbfimage.CIF[fabio.cbfimage.CIF_BINARY_BLOCK_KEY]
+            cbf_obj.cbs = cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY]
     binary_data = cbf_obj.cbs[cbf_obj.start_binary + len(fabio.cbfimage.STARTER):]
 
     if "Content-MD5" in cbf_obj.header:
-            ref = fabio.cbfimage.numpy.string_(cbf_obj.header["Content-MD5"])
+            ref = numpy.string_(cbf_obj.header["Content-MD5"])
             obt = fabio.cbfimage.md5sum(binary_data)
             if ref != obt:
-                fabio.cbfimage.logger.error("Checksum of binary data mismatch: expected %s, got %s" % (ref, obt))
+                logger.error("Checksum of binary data mismatch: expected %s, got %s" % (ref, obt))
 
     if cbf_obj.header["conversions"] == "x-CBF_BYTE_OFFSET":
         cbf_obj.data = cbf_obj._readbinary_byte_offset(binary_data).astype(cbf_obj.bytecode).reshape((cbf_obj.dim2, cbf_obj.dim1))