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CBFlib
README
Information for CBFlib 0.9.2 release of 12 February 2011
revised as the CBFlib 0.9.2.1 release of 20 June 2011
revised as the CBFlib 0.9.2.2 release of 2 July 2011
revised as the CBFlib 0.9.2.3 release of 9 July 2011
revised as the CBFlib 0.9.2.4 release of 1 January 2012
revised as the CBFlib 0.9.2.10 release of 19 January 2013
by
Paul J. Ellis
Stanford Synchrotron Radiation Laboratory
and
Herbert J. Bernstein
Bernstein + Sons
yaya at bernstein-plus-sons dot com
(c) Copyright 2006 -- 2013 Herbert J. Bernstein
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YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL.
ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS OF THE
LGPL.
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Before using this software, please read the
NOTICE
for important disclaimers and the IUCr Policy on the Use of the Crystallographic
Information File (CIF) and other important information.
Work on imgCIF and CBFlib supported in part by the U. S. Department of
Energy (DOE) under grants ER63601-1021466-0009501 and
ER64212-1027708-0011962, by the U. S. National Science Foundation (NSF)
under grants DBI-0610407, DBI-0315281 and EF-0312612, the U. S. National
Institutes of Health (NIH) under grants 1R15GM078077 from NIGMS and
1R13RR023192 from NCRR and funding from the International Union for
Crystallography (IUCr). The content is solely the responsibility of the
authors and does not necessarily represent the official views of DOE, NSF,
NIH, NIGMS, NCRR or IUCr.
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CBFlib 0.9.2.10 is an accumulation of minor revisions to the CBFlib
0.0.2.4 release, plus proof of concept trial code for the 0.9.3 release
that will include HDF5/NeXus support and preliminary Eiger support. The
changes made are:
* Addition of nibble offset compression trial code.
* Addition of support for full axis poise calculations.
* Incorporation of hdf5-1.8.10
* Cleanup and fixes to Makefiles for more reliable builds
* Fixes to support newer DECTRIS minicbf headers in convertminicbf
The axis poise code has been documented in the manual. The nibble offset
code and HDF5/NeXus support are subject to revision and will be documented
elsewhere to avoid confusion.
CBFlib 0.9.2.4 is a minor revision to the CBFlib 0.9.2.3 release to
support tiff2cbf for short in tiffs and to fix problems with 64 bit long
integers uncovered on Mac OSX 10.6 and 10.7 for 64 compilers.
CBFlib 0.9.2.3 is a minor revision to the CBFlib 0.9.2.2 release to allow
use of NO_CBF_REGEX to suppress use of regex for convenience in doing
visual studio builds for cctbx as requested by Ralf Ralf Grosse-Kunstleve
for cctbx builds.
CBFlib 0.9.2.2 is a minor revision to the CBFlib 0.9.2.1 release in July
2011 to update doc/cif_img.dic to the 1.6.4 revision.
CBFlib 0.9.2.1 is a minor revision to the CBFlib 0.9.2 release in June
2011 to upgrade the setup script for the pycbf Python bindings to simplify
using pycbf outside the context of the CBFlib pycbf directory.
CBFlib 0.9.2 is the recommended release of CBFlib of February 2011. The
commulative changes in releases 0.9.1 and 0.9.2 since CBFlib 0.9.0 are:
* Temporary removal of default PyCifRW support for compliance with
Fedora license requirements.
* Addition of a new tiff2cbf example program.
* Update pycbf python wraapper for CBFlib.
* Padding options added to adscimg2cbf by C. Nielsen.
* System and gnu versions of getopt replaced by cbf_getopt.
* Code to handle CIF2 bracketed constructs and quoted strings added.
* System to log errors and warnings added.
* Java wrapper by Peter Chang added.
* Dectris template code by E. Eikenberry added.
CBFlib 0.9.1 included a correction to CBFlib 0.9.0 to make axis the
cbf_simple routines apply axis rotations correctly for detectors and to
pick up corrections for byte offet compression incorporated into the
upcoming CBFlib 0.9.1 release. The earlier version had failed to apply the
rotations to the accumulated displacements. Our thanks to Joerg Kaercher
of Bruker-AXS for identifying the rotation problem.
CBFlib 0.9.0 was a partial pre-release of CBFlib version 0.8 needed to
support changes in RasMol. This release was incomplete and used were
advided to use it with caution, but it has proven to be a reliable, stable
release for 2 years. There have been significant changes in the
input/output logic and in validation. For a ChangeLog consult the SVN of
the CBFlib project on sourceforge.
CBFLIB is a library of ANSI-C functions providing a simple mechanism for
accessing Crystallographic Binary Files (CBF files) and Image-supporting
CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API
for mmCIF files. Starting with this release, CBFLIB performs validation
checks on reading of a CBF. If a dictionary is provided, values will be
validated against dictionary ranges and enumerations. Tags missing under
parent-child relationships or category key requirements will be reported.
CBFlib provides functions to create, read, modify and write CBF binary
data files and imgCIF ASCII data files.
Installation
CBFLIB should be built on a disk with at least 350 megabytes of free
space, for a full installation with complete tests. Read the instructions
below carefully, if space is a problem.
A gizpped tarball of this release is available on sourceforge at
http://downloads.sf.net/cbflib/CBFlib-0.9.2.10.tar.gz
In addition,
http://downloads.sf.net/cbflib/CBFlib_0.9.2_Data_Files_Input.tar.gz (13
MB) is a "gzipped" tar of the input data files needed to test the API,
http://downloads.sf.net/cbflib/CBFlib_0.9.2_Data_Files_Output.tar.gz (34
MB) is a "gzipped" tar of the output data files needed to test the API,
and, if space is at a premium,
http://downloads.sf.net/cbflib/CBFlib_0.9.2_Data_Files_Output_Sigs_Only.tar.gz
(1KB) is a "gzipped" tar of only the MD5 signatures of the output data
files needed to test the API. Place the CBFlib_0.9.2.10.tar.gz file in the
directory that is intended to contain up to 4 new directories, named
CBFlib_0.9.2.10 (the "top-level" directory), CBFlib_0.9.2_Data_Files_Input
and either CBFlib_0.9.2_Data_Files_Output or
CBFlib_0.9.2_Data_Files_Output_Sigs_Only. If you have wget on your
machine, you only need to download the source tarball. If you do not have
wget, you will need to download all the tarballs into the same directory
Uncompress CBFlib_0.9.2.10.tar.gz with gunzip and unpack it with tar:
gunzip CBFlib_0.9.2.10.tar.gz
tar xvf CBFLIB_0.9.2.10.tar
To run the test programs, you will also need Paul Ellis's sample MAR345
image, example.mar2300, Chris Nielsen's sample ADSC Quantum 315 image,
mb_LP_1_001.img, and Eric Eikenberry's SLS sample Pilatus 6m image,
insulin_pilatus6m, as sample data. In addition there are is a PDB mmCIF
file, 9ins.cif, and 3 special test files testflatin.cbf,
testflatpackedin.cbf and testrealin.cbf. All these files will be dowloaded
and extracted by the Makefile from CBFlib_0.9.2_Data_Files_Input. Do not
download copies into the top level directory.
After unpacking the archives, the top-level directory should contain a
makefile:
Makefile Makefile for unix
and the subdirectories:
src/ CBFLIB source files
include/ CBFLIB header files
bin/ Executable example programs
doc/ Documentation
examples/ Example program source files
html_images/ JPEG images used in rendering the HTML files
lib/ Compiled CBFLIB (libcbf.a) and FCBLIB (libfcb.a)
libraries
m4/ CBFLIB m4 macro files (used to build .f90 files)
mswin/ An MS Windows CodeWarrior project file
pycbf/ Jon Wright's Python bindings
and additional Makefiles for other systems. All the makefiles are created
from m4/Makefile.m4. Edit the closest approximation to your system, and
then copy that variant to Makefile.
For instructions on compiling and testing the library, go to the top-level
directory and type:
make
Once you have a properly configure Makefile, compile and test the package
with
make tests
or, if space is at a premium, with
make tests_sigs_only
Please refer to the manual doc/CBFlib.html for more detailed information.
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Updated 19 January 2013. yaya at bernstein-plus-sons dot com
