diff options
Diffstat (limited to 'relnotes-0.10.0')
| -rw-r--r-- | relnotes-0.10.0 | 181 |
1 files changed, 0 insertions, 181 deletions
diff --git a/relnotes-0.10.0 b/relnotes-0.10.0 deleted file mode 100644 index 2ebeebe6..00000000 --- a/relnotes-0.10.0 +++ /dev/null @@ -1,181 +0,0 @@ -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) |