diff options
| -rw-r--r-- | CMakeLists.txt | 4 | ||||
| -rw-r--r-- | ChangeLog | 4 | ||||
| -rw-r--r-- | announcement-0.8.0 | 32 | ||||
| -rw-r--r-- | announcement-0.9.0 | 34 | ||||
| -rw-r--r-- | relnotes-0.8.0 | 194 | ||||
| -rw-r--r-- | relnotes-0.9.0 | 214 |
6 files changed, 252 insertions, 230 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt index 08e3905b..ec944a5a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,7 +1,7 @@ cmake_minimum_required(VERSION 3.6) -set(CRYSTFEL_SHORT_VERSION 0.8.0) +set(CRYSTFEL_SHORT_VERSION 0.9.0) set(CRYSTFEL_VERSION ${CRYSTFEL_SHORT_VERSION}) -set(CRYSTFEL_API_VERSION 11) +set(CRYSTFEL_API_VERSION 12) project(crystfel VERSION ${CRYSTFEL_VERSION} LANGUAGES C) cmake_policy(SET CMP0074 NEW) @@ -1,5 +1,5 @@ -Changes in this development version ------------------------------------ +CrystFEL version 0.9.0, 6th February 2020 +----------------------------------------- - Introduction of cell_tool - Addition of PinkIndexer interface diff --git a/announcement-0.8.0 b/announcement-0.8.0 deleted file mode 100644 index 2666da94..00000000 --- a/announcement-0.8.0 +++ /dev/null @@ -1,32 +0,0 @@ -Dear CrystFEL users and interested crystallographers, - -An early Christmas present for you all, as CrystFEL version 0.8.0 has been -released. - -This new version adds a powerful new indexing algorithm, more stable B-factors -when merging and rejection of rogue patterns via "delta CChalf". Besides those, -there are several other exciting features such as an option to wait for files -to appear on disk (useful for certain automated processing environments). -In addition, the pixelmap creation utility (make_pixelmap) has become a core -CrystFEL program with this release. - -Note that the build system has changed from GNU autotools ("./configure") to -CMake. The README file has instructions for how to compile and install. - -See the release notes for more discussion of these improvements, and the -ChangeLog for full details of the other improvements. - -Thanks for all of your past and future feedback and contributions, and -your continued use of CrystFEL. As ever, please contact me directly if -you would prefer to be unsubscribed from this mailing list. - -CrystFEL website: -https://www.desy.de/~twhite/crystfel - -Release notes for version 0.8.0: -https://www.desy.de/~twhite/crystfel/relnotes-0.8.0 - -CrystFEL tutorial: -https://www.desy.de/~twhite/crystfel/tutorial - -Tom diff --git a/announcement-0.9.0 b/announcement-0.9.0 new file mode 100644 index 00000000..7915cece --- /dev/null +++ b/announcement-0.9.0 @@ -0,0 +1,34 @@ +Dear CrystFEL users and interested crystallographers, + +CrystFEL version 0.9.0 has been released! + +This release adds a new indexing method ("PinkIndexer") and improvements to +reflection prediction which will enable data processing for wide bandwidth and +electron diffraction experiments. + +A new core program has been added, "cell_tool", which can perform several +useful tasks on unit cells such as transformation, finding indexing ambiguities +and calculating power ring positions. + +There have been many other improvements across the whole suite. Notably, +CBFlib is no longer required by CrystFEL, manual resolution limits are no +longer needed by ambigator, and "--no-cell-combinations" is no longer needed by +indexamajig. + +See the release notes for more discussion of these improvements, and the +ChangeLog for full details of the other improvements. + +Thanks for all of your past and future feedback and contributions, and +your continued use of CrystFEL. As ever, please contact me directly if +you would prefer to be unsubscribed from this mailing list. + +CrystFEL website: +https://www.desy.de/~twhite/crystfel + +Release notes for version 0.9.0: +https://www.desy.de/~twhite/crystfel/relnotes-0.9.0 + +CrystFEL tutorial: +https://www.desy.de/~twhite/crystfel/tutorial + +Tom diff --git a/relnotes-0.8.0 b/relnotes-0.8.0 deleted file mode 100644 index ed05d678..00000000 --- a/relnotes-0.8.0 +++ /dev/null @@ -1,194 +0,0 @@ -CrystFEL - Data processing for serial crystallography ------------------------------------------------------ - -Release notes for version 0.8.0 - -Copyright © 2012-2018 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: - -- Switch of build system to CMake from autotools - -- Support for peakfinder9 and XGANDALF - -- More stable B factors during merging - -- Rejection of patterns during merging according to deltaCCHalf - -- Introduction of make_pixelmap as a core CrystFEL program - -- indexamajig --wait-for-file - -- Support for gzipped CBF files - -These changes have sections below. In addition, there were many bug fixes and -other improvements. See the "ChangeLog" or the changes page on the CrystFEL -website for details. - - -Switch of build system to CMake from autotools ----------------------------------------------- - -The build system has been changed from GNU autotools (./configure etc) to CMake. -The README file contains updated instructions for how to compile and install. -Briefly: - $ mkdir build - $ cd build - $ cmake .. - $ make - $ sudo make install -To set the installation path, add the option -DCMAKE_INSTALL_PREFIX to the cmake -command. To manually set the paths to external libraries, there are options -such as -DOpenCL_INCLUDE_DIR and -DCBF_LIBRARIES. - -Note that there will be no further development snapshots in .tar.gz format made -available on the CrystFEL website. These are now unnecessary, since a version -from the Git repository is now structurally identical to a packaged release -version. If you want to try out the latest features (and possibly the latest -bugs!), simply follow the instructions on the website "download" page to check -out a Git version. - - -Support for peakfinder9 and XGANDALF ------------------------------------- - -The new peak finding algorithm, peakfinder9, is based on local background -estimates, similar to peakfinder8 which uses radial background estimates. -It's implemented in the Fast Diffraction Image Processing library by Yaroslav -Gevorkov. You can download it from here: -https://stash.desy.de/users/gevorkov/repos/fastdiffractionimageprocessing - -The new indexing algorithm, "eXtended GrAdient Descent Algorithm for Lattice -Finding", XGANDALF for short, is also implemented as a separate library written -by Yaroslav Gevorkov. Download it here: -https://stash.desy.de/users/gevorkov/repos/xgandalf/ - -Once they are installed, the CrystFEL build system should detect these librares -and enable you to use respectively "indexamajig --peaks=peakfinder9" and -"indexamajig --indexing=xgandalf". See the indexamajig manual page for details -of the advanced options. - - -More stable B factors during merging ------------------------------------- - -Previously, it was very easy for the relative Debye-Waller factors for all -crystals to drift downwards during merging, resulting in reduced intensity at -high resolution. In this new version, the merging algorithm has been changed so -that, while the scaling factors are being determined, logarithms of the -intensities are merged rather than the intensities themselves. This makes the -calculation more stable and avoids the drifting B-factors. Although the actual -information content of the merged dataset is not affected very much, this -usually produces a higher apparent resolution in the electron density maps. -(Credit: Ken Beyerlein) - - -Rejection of patterns during merging according to deltaCChalf -------------------------------------------------------------- - -The rogue dataset rejection algorithm from Assmann, Brehm and Diederichs, -J. Appl. Cryst. 49 (2016) p1021, has been implemented in partialator. It is -enabled by default. To turn it off, use the option "--no-deltacchalf". - - -Introduction of make_pixelmap as a core CrystFEL program --------------------------------------------------------- - -make_pixelmap is now a core CrystFEL program, so you no longer need to install -a separate program if you need to make pixel maps for Cheetah, OnDA and others. -The program is largely unchanged from the previous standalone version, except -that the functionality of make_badmap is now accessed using "make_pixelmap ---badmap". You can use --good-pixel and --bad-pixel to set the values for good -and bad pixels respectively. - - -indexamajig --wait-for-file ---------------------------- - -This option behaves similarly to XDS's "SECONDS" parameter. When set to a value -other than zero, this causes indexamajig to wait this number of seconds for each -image file to appear. This can be useful when using CrystFEL as part of an -automated processing pipeline. - - -Support for gzipped CBF files ------------------------------ - -Finally, CBF files compressed using gzip (.cbf.gz) can now be read directly by -CrystFEL, without any need to temporarily uncompress them. - - -API changes ------------ - -The following changes have been made to the libcrystfel API. - -New functions: - - index_pattern_3() - - search_peaks_peakfinder9() - - estimate_peak_resolution() - - free_contribs() - - {set,get}_contributions() - - ph_eV_to_k (macro) - - strip_extension() - - run_xgandalf, xgandalf_{probe,prepare,cleanup} - -Removed functions: - (none) - -Changed function prototypes: - - set_dim_structure_entry() - - setup_indexing() - - refine_radius() - -Changed structure/enum definitions: - - enum SpectrumType: new value SPECTRUM_FROMFILE - - enum imagefile_file: new value IMAGEFILE_CBFGZ - - struct image: new members "hit", "n_indexing_tries", "spectrum0" and - peak_resolution - - enum IndexingMethod: new value INDEXING_XGANDALF 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] |