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authorThomas White <taw@physics.org>2022-01-14 15:25:22 +0100
committerThomas White <taw@physics.org>2022-01-14 15:25:22 +0100
commit5566d02188f11e41a3cb4391597394f0fc122417 (patch)
tree28d4943aab98535ff1c132083f0d97d05cf8edb4 /relnotes-0.10.0
parent2a966a1d7cc5ff8d50312870cd3045949e55841e (diff)
This is CrystFEL 0.10.10.10.1
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-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)