From d083025dece726ef65708273dfcbab7217275454 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@desy.de>
Date: Mon, 2 May 2016 16:13:32 +0200
Subject: [PATCH] Fixed namespace problems in cfelfabio modules
---
cfelfabio.py | 62 +++++++++++++++-------------------------------------
1 file changed, 18 insertions(+), 44 deletions(-)
diff --git a/cfelfabio.py b/cfelfabio.py
index 936b2a3..ac7a46d 100644
--- a/cfelfabio.py
+++ b/cfelfabio.py
@@ -1,47 +1,21 @@
-# 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))
--
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