diff options
| -rw-r--r-- | AUTHORS | 3 | ||||
| -rw-r--r-- | CMakeLists.txt | 2 | ||||
| -rw-r--r-- | ChangeLog | 41 | ||||
| -rw-r--r-- | announcement-0.10.0 | 43 | ||||
| -rw-r--r-- | announcement-0.9.0 | 34 | ||||
| -rw-r--r-- | announcement-0.9.1 | 39 | ||||
| -rw-r--r-- | meson.build | 2 | ||||
| -rw-r--r-- | relnotes-0.10.0 | 181 | ||||
| -rw-r--r-- | relnotes-0.9.0 | 214 | ||||
| -rw-r--r-- | relnotes-0.9.1 | 90 |
10 files changed, 269 insertions, 380 deletions
@@ -103,3 +103,6 @@ * Troy D. Hanson uthash (http://troydhanson.github.com/uthash/) + +* Philipp Middendorf <philipp.middendorf@desy.de> + Gitlab continuous integration diff --git a/CMakeLists.txt b/CMakeLists.txt index 87ddfc23..78bcce10 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required(VERSION 3.6) -set(CRYSTFEL_SHORT_VERSION 0.9.1) +set(CRYSTFEL_SHORT_VERSION 0.10.0) set(CRYSTFEL_VERSION ${CRYSTFEL_SHORT_VERSION}) set(CRYSTFEL_API_VERSION 14) project(crystfel VERSION ${CRYSTFEL_VERSION} LANGUAGES C) @@ -1,5 +1,44 @@ +CrystFEL version 0.10.0, 16th August 2021 +----------------------------------------- + +- New GUI ('crystfel') added, replacing 'hdfsee' which has been removed +- Added ZeroMQ interface for streaming data processing +- Added Meson build system +- get_hkl can now write XDS and MTZ directly +- Removed geoptimiser +- Removed wide-bandwidth features +- Added 'parameter harvest files' to indexamajig and partialator +- Better handling of static masks with multi-event files +- Added 'FromFile' indexing +- Added scripts/display-hdf5 and scripts/make-csplit +- New DataTemplate API +- New Stream API, allowing random access and better recreation of processing +- Bug fix for asdf indexing, vastly increasing speed and success rate +- Big speed improvement for TakeTwo +- Speed improvement for detector pixel coordinate transformation +- Speed improvement for UnitCell +- Speed improvement for creation of bad pixel maps from bad regions +- Fixed a large memory leak in cell_tool +- Fix large number of "rejected" reflections +- Support for units in geometry file distances (eg 'clen = 43 mm') +- Support for wavelength and electron accelerating voltage in geometry file +- Added detector_shift_x/y to geometry file +- Added peak_list_type to geometry file +- Added flag_{lessthan,morethan,equal} to geometry file +- Added peak_list to geometry file (no more --hdf5-peaks) +- Added requirement for fs/ss bad regions to name a panel +- indexamajig: Added --no-image-data and --no-mask-data +- partialator, process_hkl: Handle multiple input streams +- partialator: Reject crystals with large profile radii +- indexamajig: Added --wavelength-estimate and --camera-length-estimate +- indexamajig: Added --max-indexer-threads +- Figure of merit calculations moved to libcrystfel +- Removed badrow culling +- compare_hkl: Removed --intensity-shells + + CrystFEL version 0.9.1, 22nd June 2020 -------------------------------------- +-------------------------------------- - indexamajig: Fixed default unit cell tolerance (was 1.5 rad, now 1.5 deg) - Fixed bug in unit cell reduction/comparison diff --git a/announcement-0.10.0 b/announcement-0.10.0 new file mode 100644 index 00000000..75122e68 --- /dev/null +++ b/announcement-0.10.0 @@ -0,0 +1,43 @@ +Dear CrystFEL users and interested crystallographers, + +CrystFEL version 0.10.0 has been released! + +This is a huge update to CrystFEL, adding a completely new graphical user +interface (GUI) which makes it much easier to interact with your data, guiding +you through the processing steps. To give a preview of the GUI and help you +get started, I've made a video tutorial to accompany this release: +https://www.desy.de/~twhite/crystfel/presentations.html + +Electron diffraction is fully supported in this version of CrystFEL. Amongst +other things, you can now specify an electron accelerating voltage (instead of +an X-ray photon energy) in the geometry file. Combined with the 'diffractem' +pre-processing software developed by the Max Planck Institute for the Structure +and Dynamics of Matter, you have a complete solution for processing data from +serial electron diffraction crystallography. For more details, see: +https://gitlab.desy.de/thomas.white/crystfel/-/blob/master/doc/articles/electrons.rst + +In addition, I've taken advantage of the extended quiet time to work on many +internal parts of CrystFEL. The most noticable benefit of this is that several +parts of CrystFEL are now much faster. + +Some command-line parameters and geometry file directives have changed, but you +should find that the error messages will direct you towards what needs to be +updated. + +See the release notes and the ChangeLog for full details of the other +improvements. + +Release notes for version 0.10.0: +https://www.desy.de/~twhite/crystfel/relnotes-0.10.0 + +Change log: +https://www.desy.de/~twhite/crystfel/changes.html + +CrystFEL website: +https://www.desy.de/~twhite/crystfel + +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. + +Tom diff --git a/announcement-0.9.0 b/announcement-0.9.0 deleted file mode 100644 index 7915cece..00000000 --- a/announcement-0.9.0 +++ /dev/null @@ -1,34 +0,0 @@ -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/announcement-0.9.1 b/announcement-0.9.1 deleted file mode 100644 index 6ddda6cb..00000000 --- a/announcement-0.9.1 +++ /dev/null @@ -1,39 +0,0 @@ -Dear CrystFEL users and interested crystallographers, - -CrystFEL version 0.9.1 has been released! - -This is a maintenance and bug-fixing release which fixes a few problems which -crept into version 0.9.0. The most important fixes are: - -1. The unit cell comparision function, which was completely re-written for - CrystFEL 0.9.0, was updated to fix a mis-indexing problem with certain - types of unit cell. This may increase indexing rate or fix wrong output - cells in those cases. - -2. The default unit cell angle tolerance, which was accidentally set to - 1.5 radians in CrystFEL 0.9.0 as a result of the above changes, - was re-set to 1.5 degrees. - -3. Build compatability was added with very new HDF5 versions (>= 1.12) and - older versions of zlib (< 1.2.3.5). - -See the release notes and the ChangeLog for full details of the other -improvements. - -Release notes for version 0.9.1: -https://www.desy.de/~twhite/crystfel/relnotes-0.9.1 - -Change log: -https://www.desy.de/~twhite/crystfel/changes.html - -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 - -CrystFEL tutorial: -https://www.desy.de/~twhite/crystfel/tutorial - -Tom diff --git a/meson.build b/meson.build index c4df5b42..acb33250 100644 --- a/meson.build +++ b/meson.build @@ -1,6 +1,6 @@ # Meson file for CrystFEL project('crystfel', 'c', - version: '0.9.1', + version: '0.10.0', license: 'GPL3+', meson_version: '>=0.50.0', default_options: ['buildtype=debugoptimized']) diff --git a/relnotes-0.10.0 b/relnotes-0.10.0 new file mode 100644 index 00000000..2ebeebe6 --- /dev/null +++ b/relnotes-0.10.0 @@ -0,0 +1,181 @@ +CrystFEL - Data processing for serial crystallography +----------------------------------------------------- + +Release notes for version 0.10.0 + +Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY, + a research centre of the Helmholtz Association. + +See AUTHORS as well as individual source code files for full details of contributors. + +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 changes in this version of CrystFEL are: + +- New graphical user interface + +- Support for electron diffraction + +- Temporary removal of geoptimiser and pink beam support + +- Improved MTZ and XDS output + +- Big speed improvements + +- Improved options for bad pixel masking + +See below for information about each of these changes. + +In addition, there were many bug fixes and other improvements. See the +"ChangeLog" or the changes page on the CrystFEL website for details. + + +New graphical user interface +---------------------------- + +This release adds a new graphical user interface to CrystFEL. The old image +viewer "hdfsee" has been removed entirely. To start the GUI, simply run +"crystfel" at the command line. The GUI guides you through the stages of +processing a dataset, from importing image data all the way to exporting +merged data. To help you get started, there is a video introduction: + +https://www.desy.de/~twhite/crystfel/presentations.html + +The "old" command-line way of processing data is still available. The only +difference is that you should now use the GUI to view the results graphically, +instead of hdfsee and the old "check-near-bragg" and "check-peak-detection" +programs. Simply run the GUI, giving the stream filename as an argument, for +example: "crystfel results-output.stream". + + +Support for electron diffraction +-------------------------------- + +This release adds support for serial crystallography using electrons. For more +information, see doc/articles/electrons.rst in the CrystFEL distribution: +https://gitlab.desy.de/thomas.white/crystfel/-/blob/master/doc/articles/electrons.rst + + +Temporary removal of geoptimiser and pink beam support +------------------------------------------------------ + +A lot of internal re-organisation and cleaning-up has taken place in this +release cycle. Due to a lack of development resources, two things fell by the +wayside in order to make the release in a reasonable timescale: this release +does not include "geoptimiser", nor support for wide bandwidth ("pink-beam") +diffraction. + +But don't worry! The next release will include an improved replacement for +geoptimiser. For the time being, note that the data formats used by CrystFEL +have not changed much, so an older CrystFEL version (e.g. 0.9.1) can still be +used for fine-grained geometry refinement in almost all cases. + +If you previously installed CrystFEL 0.9.1, you should find that geoptimiser +from the old installation is still present and working. Therefore, you might +not even notice the difference! + +Features for processing data acquired with wide bandwidth radiation will be +developed further if there is demand. + + +Improved MTZ and XDS output +--------------------------- + +This CrystFEL version can export directly to MTZ (CCP4) or XDS-ASCII format. +Export to MTZ and XDS format can also be done via the "Export" function of the +new CrystFEL GUI. Alternatively, use get_hkl to convert the file, for example: + +$ get_hkl -i my-data.hkl -o my-data.mtz --output-format=mtz -p my-data.cell + +This replaces the old "create-mtz" and "create-xscale" scripts, and the +resulting files are more consistent with the expectations of other software. + + +Big speed improvements +---------------------- + +Several significant speed improvements have been made. In particular, these +affect 'asdf' and 'TakeTwo' indexing, unit cell transformations and loading +image data. You should notice a greatly reduced number of "timeouts" during +indexing. + + +Improved options for bad pixel masking +-------------------------------------- + +More ways to mask bad pixels have been added. You can now use one or more of +the following directives in the geometry file to flag pixels with values lower +than, equal or more than a given value: "flag_lessthan", "flag_morethan", +"flag_equal". + +In addition, this version of CrystFEL is better able to handle the situation +where a single bad pixel mask applies to multiple frames in a "multi-event" +data file. For example: with data in HDF5 format, if the location of the bad +pixel mask contains fewer "placeholder" characters ("%") than the image data, +only the required number of placeholders will be filled in when calculating the +location of the mask. This means that you can do something like this: + +data = /data/image/%/frames/%/pixel_values +mask = /data/image/%/bad_pixel_mask + +In this case, one "bad_pixel_mask" would apply to everything under each set of +"frames". + + +API changes +----------- + +The following changes have been made to the libcrystfel API. + +Additions: + - DataTemplate API (data_template_*, see datatemplate.h) + - Figure of merit API (fom_*, see fom.h) + - Stream API (stream_*, see stream.h) + - Image API (image_*, see image.h) + - 'struct detgeom' and associated API (detgeom_*) + - str_peaksearch and parse_peaksearch + - intcontext_new, integrate_rings_once, intcontext_free + - write_to_mtz, write_to_xds, libcrystfel_can_write_mtz + - parse_indexing_methods + - base_indexer_str + - default_method_options + - cell_print_oneline + - has_unique_axis + - lowest_reflection + - colscale_lookup (replaces 'render_scale') + - crystal_copy_deep + - Miscellaneous utility functions: compare_double, safe_strdup, + load_entire_file, file_exists, filename_extension, + set_log_message_func, el_v_to_lambda, CLEAR_BIT, convert_int, + convert_float, ELECTRON_MASS + +Removals: + - 'struct detector' and associated API + - 'struct event' and associated API + - 'struct hdfile' and associated API (hdf5-file.h) + - 'struct beam_params' + - All direct interfaces to indexing engines, e.g. xds_prepare + - render_scale (renamed to colscale_lookup) + - stderr_lock + - {get,set}_panel (replaced by {get,set}_panel_number) + - INDEXING_DEBUG (use INDEXING_FILE instead) + +Changes: + - cell_get_* and cell_has_parameters (changes to 'const' qualifiers) + - struct image: removed 'parent', 'p', 'rx,ry,rz', added 'pn' + - estimate_peak_resolution (added 'det' arg) + - setup_indexing (added lots of new args) 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] diff --git a/relnotes-0.9.1 b/relnotes-0.9.1 deleted file mode 100644 index 2d451cf0..00000000 --- a/relnotes-0.9.1 +++ /dev/null @@ -1,90 +0,0 @@ -CrystFEL - Data processing for serial crystallography ------------------------------------------------------ - -Release notes for version 0.9.1 - -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 --------- - -This is a maintenance and bug-fixing release which fixes a few issues which -crept into CrystFEL 0.9.0. Here are the detils, in roughly decreasing -order of importance: - -1. The unit cell comparision function, which was completely re-written for - CrystFEL 0.9.0, was updated to fix a mis-indexing problem with certain - types of unit cell. This may increase indexing rate or fix wrong output - cells in those cases. - -2. The default unit cell angle tolerance, which was accidentally set to - 1.5 radians in CrystFEL 0.9.0, was re-set to 1.5 degrees. - -3. Build compatability was added with very new HDF5 versions (>= 1.12) and - older versions of zlib (< 1.2.3.5). - -4. A problem was fixed in indexamajig when reading metadata from certain - HDF5 structures (arrays of fixed length strings). - -5. The sigma(I) estimates for very weakly negative (unmerged) reflections - were improved. - -6. PinkIndexer logic fixes and documentation improvements, and addition of - "--pinkIndexer-max-refinement-disbalance" option to indexamajig. - -7. General documentation improvements. - -For your convenience, the announcement and release notes for the previous -version (CrystFEL 0.9.0) have been included with version 0.9.1. If you're -upgrading from CrystFEL 0.8.0, you should check those files as well. -As always, you can find more details in the "ChangeLog" or the changes page -on the CrystFEL website. - - -API changes ------------ - -"maxRefinementDisbalance" was added to "struct pinkIndexer_options". -No other API changes. |