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authorThomas White <taw@physics.org>2023-02-15 15:59:55 +0100
committerThomas White <taw@physics.org>2023-02-20 16:26:49 +0100
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This is CrystFEL 0.10.20.10.2
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+Release notes for CrystFEL version 0.10.2
+=========================================
+
+Copyright © 2012-2023 Deutsches Elektronen-Synchrotron DESY,
+ a research centre of the Helmholtz Association.
+
+See AUTHORS as well as the individual source code files for full contributor details.
+
+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 release is primarily a bug-fixing update to CrystFEL, and there have been
+improvements around the entire suite. The most important changes are detailed
+below. See the ChangeLog or the Git history for a comprehensive list of all
+changes.
+
+
+Graphical user interface (GUI)
+------------------------------
+
+This version adds a colour scale widget to the GUI, which can be used to
+manually adjust the colours used to display the image. The colour scale is
+found directly to the right of the image. Click and drag to move
+the histogram of image values relative to the colour scale, and use the scroll
+wheel to compress and expand the range.
+
+Resolution rings can now be added to the image. Enable them in the "View" menu.
+There are also menu items for running `detector-shift` and `peakogram`, found
+under the "Tools" menu.
+
+The figure of merit calculation tool has been improved, and now displays the
+results as a graph. The graph values can be exported as a CSV file for further
+processing.
+
+This release also adds specially-designed icons to the GUI, which fixes
+problems with "broken" icons on some systems.
+
+
+Performance
+-----------
+
+Speed has been improved in many areas of CrystFEL. The profiling option
+(`--profile`) of `indexamajig` has been re-implemented and can help you to find
+bottlenecks in processing on your data. In addition, some new options were
+added to `indexamajig`:
+
+New option `--peakfinder8-fast` tells peakfinder8 to calculate some values in
+advance, approximately halving the time taken by the peak search.
+
+Another new option `--asdf-fast` slightly alters some thresholds within asdf,
+resulting in a large speedup. Since this changes the behaviour from before, we
+decided to make it optional.
+
+Finally, `--cell-parameters-only` completely circumvents the spot prediction and
+integration calculations, which can make a very large speedup as long as you're
+not interested in spot positions. Note that this isn't the same as the
+existing option ``--integration=none``, where the spot positions are predicted
+but the intensity integration is skipped. For very large unit cells, which are
+often produced by unconstrained indexing (e.g. for online monitoring), the spot
+prediction can take signficant time.
+
+For advice about making CrystFEL faster, see this page:
+<https://gitlab.desy.de/thomas.white/crystfel/-/blob/master/doc/articles/speed.rst>
+
+
+Documentation improvements
+--------------------------
+
+Two long-form documentation articles have been added, on top of the other two
+mentioned in other sections of this page.
+
+A completely new tutorial has been added, describing how to process data using
+the graphical user interface:
+<https://gitlab.desy.de/thomas.white/crystfel/-/blob/master/doc/articles/tutorial.rst>
+
+The following new article has been added, to help with the common question of
+choosing the correct point group for merging data:
+<https://gitlab.desy.de/thomas.white/crystfel/-/blob/master/doc/articles/pointgroup.rst>
+
+
+Streaming interfaces
+--------------------
+
+ZeroMQ and ASAP::O interfaces have been added, to allow data to be streamed
+directly to CrystFEL without any intermediate file storage. For some
+information on how to get started, read the following document:
+<https://gitlab.desy.de/thomas.white/crystfel/-/blob/master/doc/articles/online.rst>
+
+
+Refuses to overwrite stream
+---------------------------
+
+Starting from this version, `indexamajig` and other CrystFEL tools will refuse to
+create a new stream if a file already exists with the same name. This is meant
+to avoid the possibility of losing valuable results by (e.g.) re-running a
+processing script. This becomes particularly important in a streaming data
+situation, where the original data might no longer be available. If you really
+want to overwrite the results, you'll need to move or delete the old file
+yourself.
+
+
+Installation
+------------
+
+CrystFEL has become easier to install because of several developments. First,
+the Slurm API headers are no longer needed for the GUI to submit Slurm jobs.
+In this version, it uses the Slurm commands directly
+(`sbatch/scontrol/scancel`).
+
+For environments based totally on CBFs or other types of files, it's now
+possible to compile CrystFEL without any reference to the HDF5 library,
+avoiding a lot of possible complications.
+
+There is a new script (`scripts/install-indexers`) which helps with installing
+Mosflm, DirAx and XDS. After downloading CrystFEL, run the script with
+`--help` to get started.
+
+Finally, Docker images are now available. These can be used with various
+container tools (not just Docker). For example, using Apptainer (the new name
+for Singularity):
+```
+$ apptainer pull docker://gitlab.desy.de:5555/thomas.white/crystfel/crystfel:latest
+$ apptainer run -B /path/to/data crystfel_latest.sif
+```
+
+More details can be found on the installation page:
+<https://www.desy.de/~twhite/crystfel/install.html>
+
+
+API changes
+-----------
+
+Added routines:
+* `data_template_slabby_file_to_panel_coords`
+* `data_template_get_2d_detgeom_if_possible`
+* `data_template_get_clen_if_possible`
+* `image_create_dp_bad_sat`
+* `profile_{init,start,end,print_and_reset}`
+
+Removed routines:
+* `image_set_zero_mask`
+
+Changed routine prototypes:
+* `default_method_options` - addition of `asdf_opts`
+* `peakfinder8` - addition of `fast_mode` and `private_data`
+
+Changed enumerations:
+* `DataSourceType` - addition of `DATA_SOURCE_TYPE_SEEDEE`