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authorThomas White <taw@physics.org>2024-04-16 17:11:35 +0200
committerThomas White <taw@physics.org>2024-04-17 16:01:10 +0200
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tree61d5454d16193087fcf4a6b28f87ab64727aa213 /relnotes-0.10.2.md
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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`