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README
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CBFlib
README
Information for CBFlib 0.9.5 release of 27 April 2014
by
Paul J. Ellis
Stanford Synchrotron Radiation Laboratory
and
Herbert J. Bernstein
Bernstein + Sons
yaya at bernstein-plus-sons dot com
(c) Copyright 2006 -- 2014 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.
All functions in the src, include and examples directories are included
in the term "API" unless explicitly placed under a diferent license in
the header comments of that particular source code.
----------------------------------------------------------------------
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 0.9.5 is the full release resulting from the interim effort on
0.9.4, reflecting significant and unfortunately somewhat disruptive
changes resulting from changes to the agreed CBF-NeXus mapping. Axis data
on the NeXus side is now in a new tranformations:NXtransformations group.
Polarization is now handled with Stokes vectors with optional esds.
Further changes are expected for full support of mapping multi-module
detectors such as FELs where module positioning may be refined, but this
mapping should work for unitary detectors.
CBFlib 0.9.4.1 has further refactoring by Jonathan Sloan, and partial
documentation with an updated dictionary. This is an interim release,
expected to be become a full release with 0.9.4.2.
CBFlib 0.9.4 provides a reasonably functional mapping of CBF files to
NeXus files that carries all essential information for monchromatic MX
processing in the NeXus file, and extends the cmake build capabilities and
refactors a lot of the mapping code. Our thanks to Jonathan Sloan for this
effort.
CBFlib 0.9.3.3 added examples of the description of a multi-module FEL
detector, thanks to Aaron Brewster of LCLS. New convenience accessor
functions were been added to expose the details of axes field by field.
Corrections were been made to the handling of _axis.rotation and
_axis.rotation_axis. This was an interim release. The API version and
dictionary were to 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 were:
* 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.
* Addition of nibble offset compression trial code.
* Addition of support for full axis poise calculations.
* Incorporation of hdf5-1.8.11 and the first phase of code in CBFlib to
support NeXus, including mincbf2nexus and cbf2nexus by Jonathan Sloan
of DLS
* Cleanup and fixes to Makefiles for more reliable builds, and a partial
preliminary CMakeLists.txt
* Fixes to support newer DECTRIS minicbf headers in convertminicbf
* The first phase of code to support
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.
The changes for the CBF-HDF5 mappings are extensive and should be used
with caution.
Please report all difficulties you may encounter with this release to
yayahjb at gmail dot com
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 0.9.2.4 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 500 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-0.9.5.tar.gz
In addition,
http://downloads.sf.net/cbflib/CBFlib_0.9.5_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_0.9.5_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_0.9.5_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_0.9.5.tar.gz file in the
directory that is intended to contain up to 4 new directories, named
CBFlib_0.9.5 (the "top-level" directory), CBFlib_0.9.5_Data_Files_Input
and either CBFlib_0.9.5_Data_Files_Output or
CBFlib_0.9.5_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_0.9.5.tar.gz with gunzip and unpack it with tar:
gunzip CBFlib_0.9.5.tar.gz
tar xvf CBFLIB_0.9.5.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, and several files related to
NeXus and FEL testing. All these files will be dowloaded and extracted by
the Makefile from CBFlib_0.9.5_Data_Files_Input. Do not download copies
into the top level directory.
After unpacking the archives, the top-level directory should contain a
makefile and a cmake file.:
Makefile Makefile for Linux
CMakeLists.txt Top level data file for cmake builds
and several alternate makefiles for other systems
and the subdirectories:
doc/ Documentation
src/ CBFLIB source files
include/ CBFLIB header files
external_packages/ For additional support kits
bin/ Executable example programs
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
ply-3.2/ A support kit needed for dREL code
drel-ply/ A support kit needed for dREL code
dREL-ply-0.5/ A support kit needed for dREL code
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
* Not to use regex. If CBF_NO_REGEX is defined, no regex will be used.
* To used the tradition unix regex. If CBF_REGEXLIB_REGEX is defined,
regex.h is used.
* To use the newer and more popular POSIX pcre regex. If neither
CBF_NO_REGEX nor CBF_REGEXLIB_REGEX is defined, pcreposix.h is used.
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-0.9.5-build on the same level as CBFlib-0.9.5, and in the new,
empty build directory, try
cmake ../CBFlib-0.9.5
make all
make test
Work on improving cmake support will continue, and comments, corrections
and suggestions would be appreciated.
Depending on your system, some tests may fail mysteriously under cmake.
The most likely cause is a failure to link example programs to the HDF5
shared library or other shared libraries when tests are run prior to those
libraries having been installed in locations known to your system's
loader. This is handled automatically in the Makefiles, but we do not yet
have a reliable way to do so for cmake ctest tests. Until this is
resolved, you may need to set various system-dependent environment
variables such as DYLD_LIBRARY_PATH, LD_LIBRARY_PATH or PATH. We hope to
resolve this for an upcoming release.
Please refer to the manual doc/CBFlib.html for more detailed information.
----------------------------------------------------------------------
----------------------------------------------------------------------
Updated 27 April 2014. yayahjb at gmail dot com