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yayahjb / cbflib

CBFlib repository cloned from SF CBFlib repository as of 1 Dec 15
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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

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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.

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.

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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) 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)

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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: