CrystFEL - release notes for version 0.5.0 ------------------------------------------ Copyright (c) 2012-2013 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. Authors: Thomas White Richard Kirian Andrew Aquila Andrew Martin Lorenzo Galli Chun Hong Yoon Kenneth Beyerlein Karol Nass Nadia Zatsepin Cornelius Gati Please read the AUTHORS file for a full list of contributions and contributors. See the COPYING file for licence conditions. Summary: GPLv3+. CrystFEL is a suite of programs for processing (and simulating) Bragg diffraction data acquired with a free electron laser. This version, 0.5.0, is the sixth officially packaged release of CrystFEL. The most significant changes since the previous release (version 0.4.3) are as follows: - The indexing pipeline has been completely revamped. The options "--cell-reduction" and "--insane" have been removed, and the equivalent information is now given in the list of indexing methods via --indexing. You can specify a combination of different methods, such as trying to index using a known unit cell and then indexing "freely" for the patterns where this doesn't work. The indexing method which was successful for a particular pattern is included in the stream so you can separate things out later. - The stream format and internal architecture have been updated to allow there to be more than one crystal per diffraction pattern. - Indexamajig's filtering of the image data has been improved. There is a new option "--median-filter", which applies the same "local background filter" as Cheetah. - XDS and GrainSpotter can now be used for indexing, although some optimisation of the parameters is still required. The following smaller changes were made, in addition to small bug fixes and documentation improvements: - The option "--filter-cm" to indexamajig has been removed. It was very specific to the pnCCD anyway, to the point of having hardcoded pixel ranges. - An error in the solid angle calculation was fixed, affecting simulation with pattern_sim (Chun Hong Yoon). - Saturated peaks and integrated reflections are now counted and the number included in the stream. - Lattice type, centering and unique axis information is now included in the stream. - The "--nshells" argument was added to check_hkl. - check-near-bragg and check-peak-detection can now be given extra command-line options which will be passed through to hdfsee. Changes to the libcrystfel API and ABI were made to accommodate these changes: - In "struct image", "indexed_cell", "candidate_cells" and related fields have been removed and replaced with an array of "Crystal". - All crystal parameters are now stored in Crystal, not in "struct image". - The Crystal API was added (libcrystfel/src/crystal.h). - The indexing API (libcrystfel/src/index.h) has been completely reworked, along with the APIs of all the individual indexing methods (libcrystfel/src/dirax.h, libcrystfel/src/reax.h and libcrystfel/src/mosflm.h). - New indexing APIs for XDS and GrainSpotter were added (libcrystfel/src/xds.h and libcrystfel/src/grainspotter.h). - integrate_reflections() has a new parameter "res_cutoff". - peak_sanity_check() now takes a list of Crystals as an argument, instead of using image->indexed_cell. - The stream API (libcrystfel/src/stream.h) has been reworked and rationalised. - set_symmetry_name() was added. - lattice_from_str() was added. Shared library versioning should mean that any external programs using the library should continue to work after you install the new version, even though they were compiled and linked against the previous version. Known problems with this version of CrystFEL are as follows: - ReAx autoindexing remains experimental and unstable. - "partialator" remains experimental and unstable. - Simulation with pattern_sim is not accurate. Comments, suggestions, bug reports and requests for assistance should be addressed to Thomas White (taw@physics.org). Thomas White, 19th April 2013