[IUCr Home Page] [CIF Home Page] [CBF/imgCIF] [CBFlib] Get CBFlib at SourceForge.net. Fast, secure and Free Open Source software downloads

| 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 |

CBFlib

README

Information for CBFlib 0.9.3 release of 15 October 2013
Revised as CBFlib 0.9.3.1 16 October 2013
Revised as CBFlib 0.9.3.2 29 October 2013
Revised as CBFlib 0.9.3.3 7 November 2013

by
Paul J. Ellis
Stanford Synchrotron Radiation Laboratory

and
Herbert J. Bernstein
Bernstein + Sons

© Copyright 2006 -- 2013 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
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. Recent work on integration among CBF, HDF5 and NeXus supported in part by Pandata ODI (EU 7th Framework Programme)


CBFlib 0.9.3.3 adds examples of the description of a multi-module FEL detector, thanks to Aaron Brewster of LCLS. New convenience accessor functions have been added to expose the details of axes field by field. Corrections have been made to the handling of _axis.rotation and _axis.rotation_axis. This is an interim release. The API version and dictionary will be updated on the next release.

CBFlib 0.9.3.2 has a revised API version, and, otherwise, the same code as CBFlib 0.9.3.1, but with further update to the imgCIF dictionary to avoid issues with the PDB validation software. Because of the revised API version, many of the data files changed to update the version in the file comments.

CBFlib 0.9.3.1 has the same code as CBFlib 0.9.3, but with an update to the imgCIF dictionary reflecting a major technical cleanup by John Westbrook. An explanation of the choices of regex versions has been added to the README.

CBFlib 0.9.3 is the formal base release integrating CBF, HDF5 and NeXus. It also includes changes to support the description of FEL detectors. More details on the integration and the new dctionary including both NeXus information and the new FEL detector tags, _axis.rotation_axis and _axis.rotation are avialable at https://sites.google.com/site/nexuscbf/. The commulative changes in releases 0.9.1, 0.9.2 and 0.9.3 since CBFlib 0.9.0 are:

The changes for FEL support involve major changes to the positioner logic used in computing goniometer and detector positions. This code should be used with caution.

Please report all difficulties you may encounter with this release to

Our thanks to Jonathan Sloan, Tobias Richter and Graeme Winter of Diamond Light Source and Robert M. Sweet of Brookhaven National Laboratory for their major contributions to this release. Without their efforts it would not have happened.

CBFlib 0.9.2.5 in October 2012 through CBFlib 0.9.2.12 in June 2013 were an accumulation of minor revisions to the CBFlib 0.0.2.4 release, plus the testbed for HDF5/NeXus support and preliminary Eiger support, now released in CBFlib 0.9.3.

CBFlib 0.9.2.4 was 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 was 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 was 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 was 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 was the recommended release of CBFlib of February 2011.

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-0.9.3.3.tar.gz

In addition, http://downloads.sf.net/cbflib/CBFlib_0.9.3.2_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_0.9.3.2_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_0.9.3.2_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_0.9.3.2.tar.gz file in the directory that is intended to contain up to 4 new directories, named CBFlib_0.9.3.2 (the "top-level" directory), CBFlib_0.9.3.2_Data_Files_Input and either CBFlib_0.9.3.2_Data_Files_Output or CBFlib_0.9.3.2_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_0.9.3.3.tar.gz with gunzip and unpack it with tar:

     gunzip CBFlib_0.9.3.3.tar.gz
     tar xvf CBFLIB_0.9.3.3.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_0.9.3_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.

In building this release there is an enviroment variable you may need to set if you are building on an older machine with a broken dlfnc that cannot support the HDF5 filter plugin mechanism:

HDF5REGISTER

which should be set to the string "--register manual" to disable the automatic plugin search.

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

regex

CBFlib makes can optionally use a system regular expression library to assist in validation of CIFS. The feature is controlled by two compile-time defines. The possible choices are

The default in the supplied Makefiles is to use regex.h. The default in the CMakeLists.txt is to use pcreposix.h.

Cmake

A partial preliminary CMakeLists.txt has been included in this kit. It is not yet complete, but on machines for which the Makefiles are not appropriate, it is worth a try. To use in, create a directory named CBFlib-0.9.3.1-build on the same level as CBFlib-0.9.3.1, and in the new, empty build directory, try

    cmake ../CBFlib-0.9.3.1
    make all
    make test
    

Work on improving cmake support will continue, and comments, corrections and suggestions would be appreciated.

Please refer to the manual doc/CBFlib.html for more detailed information.



Updated 16 October 2013.