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diff --git a/relnotes-0.8.0 b/relnotes-0.8.0 deleted file mode 100644 index ed05d678..00000000 --- a/relnotes-0.8.0 +++ /dev/null @@ -1,194 +0,0 @@ -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 |