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authorThomas White <taw@physics.org>2018-12-19 10:16:58 +0100
committerThomas White <taw@physics.org>2018-12-19 11:28:31 +0100
commit1ccb8c35a27d1e714b8c3caacc1a68307ff12ada (patch)
tree2adcdb3957bc2a863a0df4737b43fc8da90c1fbd /relnotes-0.8.0
parentc20df5bc54645acdec7ba3babcc252641a589d3b (diff)
This is CrystFEL 0.8.00.8.0
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+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