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diff --git a/relnotes-0.9.0 b/relnotes-0.9.0 deleted file mode 100644 index 43c5f147..00000000 --- a/relnotes-0.9.0 +++ /dev/null @@ -1,214 +0,0 @@ -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] |