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diff --git a/relnotes-0.9.0 b/relnotes-0.9.0 new file mode 100644 index 00000000..43c5f147 --- /dev/null +++ b/relnotes-0.9.0 @@ -0,0 +1,214 @@ +CrystFEL - Data processing for serial crystallography +----------------------------------------------------- + +Release notes for version 0.9.0 + +Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY, + a research centre of the Helmholtz Association. + +Authors: + Thomas White <taw@physics.org> + Richard Kirian <rkirian@asu.edu> + Kenneth Beyerlein <kenneth.beyerlein@desy.de> + Andrew Aquila <andrew.aquila@cfel.de> + Andrew Martin <andrew.martin@desy.de> + Lorenzo Galli <lorenzo.galli@desy.de> + Chun Hong Yoon <chun.hong.yoon@desy.de> + Karol Nass <karol.nass@desy.de> + Nadia Zatsepin <nadia.zatsepin@asu.edu> + Anton Barty <anton.barty@desy.de> + Cornelius Gati <cornelius.gati@desy.de> + Fedor Chervinskii <fedor.chervinskii@gmail.com> + Alexandra Tolstikova <alexandra.tolstikova@desy.de> + Wolfgang Brehm <wolfgang.brehm@gmail.com> + Valerio Mariani <valerio.mariani@desy.de> + Parker de Waal <Parker.deWaal@vai.org> + Takanori Nakane <nakane.t@gmail.com> + Keitaro Yamashita <k.yamashita@spring8.or.jp> + Oleksandr Yefanov <oleksandr.yefanov@cfel.de> + Steve Aplin <steve.aplin@desy.de> + Helen Ginn <helen@strubi.ox.ac.uk> + Thomas Grant <tgrant@hwi.buffalo.edu> + Mamoru Suzuki <mamoru.suzuki@protein.osaka-u.ac.jp> + Nicolas Riebesel <nicolas.riebesel@tuhh.de> + Yaroslav Gevorkov <yaroslav.gevorkov@desy.de> + Omri Mor <omor1@asu.edu> + +CrystFEL is free software: you can redistribute it and/or modify it under the +terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY +WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A +PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +CrystFEL. If not, see <http://www.gnu.org/licenses/>. + + +Overview +-------- + +The most important new features in this version of CrystFEL are: + +- Features for wide bandwidth and electron diffraction processing + +- Introduction of cell_tool + +- New unit cell comparison algorithm (eliminating --no-cell-combinations) + +- CBF files now handled natively (CBFlib not required) + +- Resolution limits no longer needed for ambigator + +See below for information about each of these features. + +In addition, there were many bug fixes and other improvements. See the +"ChangeLog" or the changes page on the CrystFEL website for details. + + +Features for wide bandwidth and electron diffraction processing +--------------------------------------------------------------- + +A new indexing method has been added: PinkIndexer. This is a new indexing +algorithm which can index wide bandwidth data as well as flat Ewald sphere +(i.e. electron diffraction) data. For more information, see: +Gevorkov et al., Acta Cryst. A72 (2020) doi:10.1107/S2053273319015559 + +To accompany the new indexing algorithm, the reflection position calculation +("prediction") has also been improved. The results should be better for all +types of data, particularly at low resolution. + +Further improvements for wide bandwidth and electron data are planned for future +releases of CrystFEL. + + +Introduction of cell_tool +------------------------- + +A new CrystFEL core program has been added: cell_tool. This program can perform +a variety of operations on unit cell files, similar to how get_hkl can do things +with reflection data files. The tasks include: finding indexing ambiguities, +turning a centered cell into a primitive one, calculating power ring positions, +comparing unit cells, transforming unit cells, and working out all the possible +cell choices for centered monoclinic cells. + + +New unit cell comparison algorithm +---------------------------------- + +The way that indexamajig compares indexing results to your target cell has been +improved. Previously, the option --no-cell-combinations was needed for certain +unit cells. This is no longer the case, and the new comparison should be more +reliable in all cases. + + +CBF files now handled natively +------------------------------ + +The CBF library (CBFlib) is no longer used in CrystFEL. Most common types of +CBF file can now be read directly by CrystFEL. If you find a CBF file that +cannot be read, please get in touch so we can fix it. + + +Resolution limits no longer needed for ambigator +------------------------------------------------ + +Previously, a careful choice of resolution bounds (--highres and --lowres) was +needed for good results with ambigator. Now, the reflections will be compared +and correlated in three resolution bins (>10, 10-2.5 and <2.5 Angstroms). For +most datasets, this allows ambiguities to be resolved easily without any manual +adjustment. You can still override this and use your own resolution limits, +if you need to. + + +API changes +----------- + +The following changes have been made to the libcrystfel API. + +New functions: + - cell_print_full + - compare_cell_parameters + - compare_cell_parameters_and_orientation + - compare_permuted_cell_parameters_and_orientation + - compare_derivative_cell_parameters + - compare_reindexed_cell_parameters + - cell_get_G6 + - cell_transform_gsl_direct + - cell_transform_rational + - cell_transform_rational_inverse + - cell_transform_intmat + - cell_transform_intmat_inverse + - crystal_get_image_const + - get_detector_geometry_from_string + - write_detector_geometry_3 + - multi_event_geometry + - parse_polarisation + - indexing_methods + - intmat_size + - intmat_zero + - intmat_create_3x3 + - transform_indices + - intmat_times_intmat + - indexing_peak_check + - pinkIndexer_prepare/cleanup/probe/run_pinkIndexer + - rtnl_zero + - rtnl + - rtnl_as_double + - rtnl_mul/div/add/sub/cmp/abs + - rtnl_list + - rtnl_mtx_new/copy/get/set/free/print/dev + - rtnl_mtx_from_intmat + - rtnl_mtx_is_identity/perm + - intmat_from_rtnl_mtx + - rtnl_mtx_identity + - rtnlmtx_times_rtnlmtx + - rtnlmtx_times_intmat + - intmat_times_rtnlmtx + - transform_fractional_coords_rtnl + - transform_fractional_coords_rtnl_inverse + - spectrum_new/free/load + - spectrum_set_gaussians + - spectrum_get_gaussian + - spectrum_get_num_gaussians + - spectrum_set_pdf + - spectrum_get_range + - spectrum_get_density_at_k + - spectrum_generate_tophat/gaussian/sase/twocolour + - free_stuff_from_stream + - stream_geometry_file + - parse_symmetry_operation + - parse_cell_transformation + - mean_variance + +Removed functions: + - cell_transform + - cell_transform_inverse + - tfn_identity/from_intmat/combine/print/inverse/vector/free + - transform_cell_gsl [use cell_transform_ functions instead] + - match_cell + - match_cell_ab + - compare_cells [use compare_*_cell_parmeters functions instead] + - intmat_intvec_mult + - intmat_intmat_mult [use intmat_times_intmat instead] + +Changed function prototypes: + - uncenter_cell + - cell_get_parameters/cartesian/reciprocal [const added] + - panel_number [const added] + - polarisation_correction [uses new 'polarisation' structure] + - setup_indexing + - intmat_copy [const added] + - taketwo_prepare/index + +Changed structure/enum definitions: + - UnitCellTransformation [removed, use IntegerMatrix/RationalMatrix instead] + - struct rigid_group [removed unused panel position deltas] + - PartialityModel [added PMODEL_OFFSET and PMODEL_GGPM] + - struct spectrum/struct sample [removed, use Spectrum instead] + - struct image [removed num_peaks and num_saturated_peaks] + - IndexingMethod [added INDEXING_PINKINDEXER] + - IndexingFlags [removed _CHECK_CELL_COMBINATIONS/AXES, added _CHECK_CELL] + - IntegrationMethod [removed INTEGRATION_RESCUT] |