CBF-ctypes is a module providing support (currently read-only) for using Crystallographic Binary Files (CBF) in Python. It is written with the Python ctypes module as a binding to the C-language library CBFlib.

The most straightforward way to read CBF files into the Python interpreter is to use the datablocks() method which returns a Python list / dictionary / numpy array -structure with the contents of the file:

>>> import cbf >>> h = cbf.CBF("testdata/agbeh_long.cbf") >>> blocks = h.datablocks() >>> blocks[0]['name'] 'e12608_1_00016_00000_00000' >>> blocks[0]['categories'][0]['name'] 'array_data' >>> blocks[0]['categories'][0].keys() ['columns~type', 'values', 'name', 'columns'] >>> blocks[0]['categories'][0]['columns'] ['header_convention', 'header_contents', 'data'] >>> blocks[0]['categories'][0]['columns~type'] ['dblq', 'text', 'bnry'] >>> blocks[0]['categories'][0]['values']['data'] #doctest: +SKIP [array([[0, 0, 0, ..., 0, 2, 1], [1, 0, 0, ..., 0, 2, 1], [0, 0, 0, ..., 3, 2, 4], ..., [0, 0, 0, ..., 1, 4, 3], [0, 0, 0, ..., 1, 2, 0], [0, 0, 0, ..., 1, 4, 4]], dtype=int32)]

A CBF object (handle) is created with the constructor:

>>> h = cbf.CBF()

The CBF object contains wrapped methods of most of the low-level CBFlib functions related to reading values and iterating through the file These have generally the same name as the corresponding CBFlib function, like rewind, next_, find, select_, count*. For example:

>>> h.read_file("testdata/agbeh_long.cbf")
>>> h.rewind_datablock()
>>> h.find_category("array_data")
>>> h.count_columns()
3

The next* methods will raise the StopIteration exception when called in the last element of their block, find* methods will raise KeyError if the given key is not found in the file, and select* methods will raise IndexError, if the given index does not exist. RuntimeErrors are raised on CBFlib errors, and IOErrors with non-existing files etc.

Also, a set of higher level functions which give the CBF-file data as values inside a Python dictionary are provided:

h.get()

Return the current value as a tuple (value, type).

h.category_asdict(key=None)

Return the current category as dictionary.

h.datablock_asdict(key=None)

Return the current datablock as dictionary.

h.datablocks()

Return a list containing all the datablocks as dictionaries.

See the code and docstrings for details.

• The CBFlib source contains a Python wrapper ('pycbf') written in SWIG.
• PyCifRW is a pure Python CIF (Crystallographic Information File) parser.

CBF-ctypes has a license similar to CBFlib, 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 2 of the License, or (at your option) any later version.

See http://www.gnu.org/licenses/gpl2.html for the license text.

CBF-ctypes was written by Teemu Ikonen <tpikonen@gmail.com>.

Copyright © 2010 Paul Scherrer Institute (http://www.psi.ch/)