CBFlib

| IUCr Home Page | CIF Home Page | CBF/imgCIF | CBFlib |
| NOTICE | doc/GPL | doc/LGPL | imgCIF dictionary | SourceForge CBFlib site |
| Click Here to Make a Donation |

## 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

by
Paul J. Ellis
Stanford Synchrotron Radiation Laboratory

and
Herbert J. Bernstein
Bernstein + Sons

© Copyright 2006, 2007, 2008, 2010, 2011 Herbert J. Bernstein

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.

### Before using this software, please read the
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.

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-0.9.2.2.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_0.9.2.2.tar.gz file in the directory that is intended to contain up to 4 new directories, named CBFlib_0.9.2.2 (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.tar.gz with gunzip and unpack it with tar:

         gunzip CBFlib_0.9.2.tar.gz
         tar xvf CBFLIB_0.9.2.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.

Updated 2 July 2011.