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                                     CBFlib

                                     README

            Information for CBFlib 0.9.6 release of 4 December 2018

                                       by
                                 Paul J. Ellis
                   Stanford Synchrotron Radiation Laboratory

                                      and
                              Herbert J. Bernstein
                                Bernstein + Sons
                      yaya at bernstein-plus-sons dot com

                 © Copyright 2006 -- 2018 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) and Dectris, Ltd. The content is solely the
   responsibility of the authors and does not necessarily represent the
   official views of DOE, NSF, NIH, NIGMS, NCRR, IUCr or Dectris. Recent work
   on integration among CBF, HDF5 and NeXus supported in part by Pandata ODI
   (EU 7th Framework Programme)

     ----------------------------------------------------------------------

   CBFlib 0.9.6 is the full release supporting the integration of CBF and
   NeXus, including support for the NeXus NXpdb embedding of CIF files in
   NeXus files. *** IMPORTANT: Because of the requirements of dynamic loading
   to support the compressions used by the Dectris NeXus/HDF5 format, all
   applications require setting of library and plugin paths. See the
   initialization file cbflib.ini, which should be sourced before running any
   applications ***. The primary development source is at
   https://github.com/yayahjb/cbflib. The branch pdb_in_nexus, which was used
   for much of this development has been merged, is now deprecated, and will
   be removed in the near future.

   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.

   You may download clone the git repository with
   git clone https://github.com/yayahjb/cbflib.git
   or a gizpped tarball of this release is available on sourceforge at

   http://downloads.sf.net/cbflib/CBFlib-0.9.6.tar.gz

   In addition,
   http://downloads.sf.net/cbflib/CBFlib_0.9.6_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_0.9.6_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_0.9.6_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_0.9.6.tar.gz file in the
   directory that is intended to contain up to 4 new directories, named
   CBFlib_0.9.6 (the "top-level" directory), CBFlib_0.9.6_Data_Files_Input
   and either CBFlib_0.9.6_Data_Files_Output or
   CBFlib_0.9.6_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_0.9.6.tar.gz with gunzip and unpack it with tar:

      gunzip CBFlib_0.9.6.tar.gz
      tar xvf CBFLIB_0.9.6.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_0.9.6_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.

  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-0.9.6-build on the same level as CBFlib-0.9.6, and in the new,
   empty build directory, try

     cmake ../CBFlib-0.9.6
     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. You may need to set
   various system-dependent environment variables such as DYLD_LIBRARY_PATH,
   LD_LIBRARY_PATH or PATH. The bash script in the kit cbflib.ini should be
   sourced before testing.

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

     ----------------------------------------------------------------------

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   Updated 4 December 2018. yayahjb at gmail dot com