diff options
Diffstat (limited to 'relnotes-0.8.0')
| -rw-r--r-- | relnotes-0.8.0 | 194 |
1 files changed, 194 insertions, 0 deletions
diff --git a/relnotes-0.8.0 b/relnotes-0.8.0 new file mode 100644 index 00000000..ed05d678 --- /dev/null +++ b/relnotes-0.8.0 @@ -0,0 +1,194 @@ +CrystFEL - Data processing for serial crystallography +----------------------------------------------------- + +Release notes for version 0.8.0 + +Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, + a research centre of the Helmholtz Association. + +Authors: + Thomas White <taw@physics.org> + Richard Kirian <rkirian@asu.edu> + Kenneth Beyerlein <kenneth.beyerlein@desy.de> + Andrew Aquila <andrew.aquila@cfel.de> + Andrew Martin <andrew.martin@desy.de> + Lorenzo Galli <lorenzo.galli@desy.de> + Chun Hong Yoon <chun.hong.yoon@desy.de> + Karol Nass <karol.nass@desy.de> + Nadia Zatsepin <nadia.zatsepin@asu.edu> + Anton Barty <anton.barty@desy.de> + Cornelius Gati <cornelius.gati@desy.de> + Fedor Chervinskii <fedor.chervinskii@gmail.com> + Alexandra Tolstikova <alexandra.tolstikova@desy.de> + Wolfgang Brehm <wolfgang.brehm@gmail.com> + Valerio Mariani <valerio.mariani@desy.de> + Parker de Waal <Parker.deWaal@vai.org> + Takanori Nakane <nakane.t@gmail.com> + Keitaro Yamashita <k.yamashita@spring8.or.jp> + Oleksandr Yefanov <oleksandr.yefanov@cfel.de> + Steve Aplin <steve.aplin@desy.de> + Helen Ginn <helen@strubi.ox.ac.uk> + Thomas Grant <tgrant@hwi.buffalo.edu> + Mamoru Suzuki <mamoru.suzuki@protein.osaka-u.ac.jp> + Nicolas Riebesel <nicolas.riebesel@tuhh.de> + Yaroslav Gevorkov <yaroslav.gevorkov@desy.de> + Omri Mor <omor1@asu.edu> + +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 new features in this version of CrystFEL are: + +- Switch of build system to CMake from autotools + +- Support for peakfinder9 and XGANDALF + +- More stable B factors during merging + +- Rejection of patterns during merging according to deltaCCHalf + +- Introduction of make_pixelmap as a core CrystFEL program + +- indexamajig --wait-for-file + +- Support for gzipped CBF files + +These changes have sections below. In addition, there were many bug fixes and +other improvements. See the "ChangeLog" or the changes page on the CrystFEL +website for details. + + +Switch of build system to CMake from autotools +---------------------------------------------- + +The build system has been changed from GNU autotools (./configure etc) to CMake. +The README file contains updated instructions for how to compile and install. +Briefly: + $ mkdir build + $ cd build + $ cmake .. + $ make + $ sudo make install +To set the installation path, add the option -DCMAKE_INSTALL_PREFIX to the cmake +command. To manually set the paths to external libraries, there are options +such as -DOpenCL_INCLUDE_DIR and -DCBF_LIBRARIES. + +Note that there will be no further development snapshots in .tar.gz format made +available on the CrystFEL website. These are now unnecessary, since a version +from the Git repository is now structurally identical to a packaged release +version. If you want to try out the latest features (and possibly the latest +bugs!), simply follow the instructions on the website "download" page to check +out a Git version. + + +Support for peakfinder9 and XGANDALF +------------------------------------ + +The new peak finding algorithm, peakfinder9, is based on local background +estimates, similar to peakfinder8 which uses radial background estimates. +It's implemented in the Fast Diffraction Image Processing library by Yaroslav +Gevorkov. You can download it from here: +https://stash.desy.de/users/gevorkov/repos/fastdiffractionimageprocessing + +The new indexing algorithm, "eXtended GrAdient Descent Algorithm for Lattice +Finding", XGANDALF for short, is also implemented as a separate library written +by Yaroslav Gevorkov. Download it here: +https://stash.desy.de/users/gevorkov/repos/xgandalf/ + +Once they are installed, the CrystFEL build system should detect these librares +and enable you to use respectively "indexamajig --peaks=peakfinder9" and +"indexamajig --indexing=xgandalf". See the indexamajig manual page for details +of the advanced options. + + +More stable B factors during merging +------------------------------------ + +Previously, it was very easy for the relative Debye-Waller factors for all +crystals to drift downwards during merging, resulting in reduced intensity at +high resolution. In this new version, the merging algorithm has been changed so +that, while the scaling factors are being determined, logarithms of the +intensities are merged rather than the intensities themselves. This makes the +calculation more stable and avoids the drifting B-factors. Although the actual +information content of the merged dataset is not affected very much, this +usually produces a higher apparent resolution in the electron density maps. +(Credit: Ken Beyerlein) + + +Rejection of patterns during merging according to deltaCChalf +------------------------------------------------------------- + +The rogue dataset rejection algorithm from Assmann, Brehm and Diederichs, +J. Appl. Cryst. 49 (2016) p1021, has been implemented in partialator. It is +enabled by default. To turn it off, use the option "--no-deltacchalf". + + +Introduction of make_pixelmap as a core CrystFEL program +-------------------------------------------------------- + +make_pixelmap is now a core CrystFEL program, so you no longer need to install +a separate program if you need to make pixel maps for Cheetah, OnDA and others. +The program is largely unchanged from the previous standalone version, except +that the functionality of make_badmap is now accessed using "make_pixelmap +--badmap". You can use --good-pixel and --bad-pixel to set the values for good +and bad pixels respectively. + + +indexamajig --wait-for-file +--------------------------- + +This option behaves similarly to XDS's "SECONDS" parameter. When set to a value +other than zero, this causes indexamajig to wait this number of seconds for each +image file to appear. This can be useful when using CrystFEL as part of an +automated processing pipeline. + + +Support for gzipped CBF files +----------------------------- + +Finally, CBF files compressed using gzip (.cbf.gz) can now be read directly by +CrystFEL, without any need to temporarily uncompress them. + + +API changes +----------- + +The following changes have been made to the libcrystfel API. + +New functions: + - index_pattern_3() + - search_peaks_peakfinder9() + - estimate_peak_resolution() + - free_contribs() + - {set,get}_contributions() + - ph_eV_to_k (macro) + - strip_extension() + - run_xgandalf, xgandalf_{probe,prepare,cleanup} + +Removed functions: + (none) + +Changed function prototypes: + - set_dim_structure_entry() + - setup_indexing() + - refine_radius() + +Changed structure/enum definitions: + - enum SpectrumType: new value SPECTRUM_FROMFILE + - enum imagefile_file: new value IMAGEFILE_CBFGZ + - struct image: new members "hit", "n_indexing_tries", "spectrum0" and + peak_resolution + - enum IndexingMethod: new value INDEXING_XGANDALF |