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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) |