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diff --git a/relnotes-0.6.3 b/relnotes-0.6.3 new file mode 100644 index 00000000..11a1f93b --- /dev/null +++ b/relnotes-0.6.3 @@ -0,0 +1,211 @@ +CrystFEL - Crystallography with a FEL +------------------------------------- + +Release notes for version 0.6.3 + +Copyright © 2012-2017 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> + Kenneth Beyerlein <kenneth.beyerlein@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> + +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: + +- Support for CBF files as input + +- TakeTwo indexing algorithm + +- Improved peak detection and basic hitfinder functionality + +- Detector panels not perpendicular to X-ray beam, and "rail direction" + +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. + + +Support for CBF files as input +------------------------------ + +Crystallographic Binary Files (CBF) can now be used as input for indexamajig +and hdfsee. To enable this functionality, you must have "CBFlib" installed. +Some distributions (eg Fedora) include CBFlib in their standard repositories - +simply install "cbflib-devel" or similar. Then compile and install CrystFEL as +usual. If CBFlib is installed somewhere non-standard, e.g. if you has to +install it manually, you will need to give the path with the "--with-cbflib-dir" +option to "./configure". + +After that, you can simply give the names of CBF files in the indexamajig input, +and everything should work as usual! There are some catches, for example you +cannot yet use a bad pixel mask with CBF files, but these will be fixed in a +future release. + + +TakeTwo indexing algorithm +-------------------------- + +This version of CrystFEL includes the TakeTwo indexing algorithm by Helen Ginn. +TakeTwo is a new indexing algorithm, designed specifically for diffraction +snapshots and operating completely differently to conventional FFT-based methods. + +To use it, simply use "taketwo" as the indexing method, or add it to the list of +indexing methods you have already: + $ indexamajig --indexing=taketwo + $ indexamajig --indexing=mosflm,taketwo,dirax + +If you use TakeTwo, please take careful note of the citation reminder which will +be shown to you, and cite the following paper in any resulting publications: + Ginn et al., Acta Cryst. (2016). D72, 956-965 + +TakeTwo is considered experimental in this version of CrystFEL. We welcome any +feedback, and will use the information to improve its performance for future +versions. + + +Improved peak detection and basic hitfinder functionality +--------------------------------------------------------- + +"Peak finder 8" from Cheetah, also used in OnDA, has been incorporated into +CrystFEL. It uses a radially varying background level to find peaks, which +works very well with most diffraction data. + +Simply use "--peaks=peakfinder8", and set --threshold, --min-snr, +--min-pix-count and --local-bg-radius. See the manual for other options. + +Indexamajig can now skip over patterns which have a small number of peaks. To +use this, use the option "--min-peaks=N", where N is the minimum number of peaks +before indexamajig will proceed to indexing (and hopefully integration) with the +pattern. + +By combining the improved peak detection with the hitfinder functionality and +CBF reading, you can process data from several different types of detector, +without converting the files to HDF5 format or using any external program for +hit finding! + +If the hit rate is very low, you might want to make CrystFEL stream smaller by +excluding non-hits from it using "--no-non-hits-in-stream". Without this +option, standard information about the non-hits (e.g. photon energy and peaks +found) will be recorded. + + +Detector panels not perpendicular to X-ray beam, and "rail direction" +---------------------------------------------------------------------- + +CrystFEL now supports three-dimensional detector geometry. The "fs" and "ss" +vectors (which are the real-space directions of the fast scan and slow scan +directions in the image data) can now contain a z component as well as x and y. + +For many detectors, the "rail" direction, along which the detector moves when +the "camera length" (sample-detector distance) is adjusted, is not perpendicular +to the detector plane. The geometry file now allows you to specify this "rail" +direction, containing x, y and z components. See the crystfel_geometry manual +page for more details. + + +API changes +----------- + +The following changes have been made to the libcrystfel API. The biggest +changes are the switch from the old "hdfile" API (which is still supported), +to the new "imagefile" API, while allows multiple file types to be used. +The indexing system was also updated, and there were changes to the detector +geometry system, which no longer uses the "data slab" representation internally. + +New functions: + - crystal_{get,set}_det_shift() + - panel_number() + - get_detector_geometry_2() + - fill_in_adu() + - adjust_centering_for_rail() + - get_peaks_2() + - get_peaks_cxi_2() + - imagefile_open() + - imagefile_read() + - imagefile_read_simple() + - imagefile_get_hdfile() + - imagefile_get_type() + - imagefile_copy_fields() + - imagefile_close() + - {new,free}_imagefile_field_list() + - add_imagefile_field() + - get_indm_from_string() + - setup_indexing() + - index_pattern_2() + - search_peaks_peakfinder8() + - reflist_add_command_and_version() + - reflist_{add,get}_notes() + - write_chunk_2() + - pointgroup_warning() + +New structure definitions: + - struct image + - struct imagefile_field_list + +Removed functions: + - get_q() + - find_panel() + - find_panel_number() + - fill_in_values() + - partial_event_substitution() + - build_indexer_list() + - prepare_indexing() + +Changed function prototypes: + - in_bad_region() + - simple_geometry() + - reverse_2d_mapping() + - hdfile_set_image() + - image_add_feature() + - image_feature_closest() + - image_reflection_closest() + - index_pattern() + - cleanup_indexing() + - write_chunk() + +Changed structure definitions: + - struct panel: removed {min,max}_{fs,ss}, added adu_per_photon, + added fsz,ssz, rail_{x,y,z} and clen_for_centering + - struct detector: removed max_{fs,ss} + - struct imagefeature: replaced "pn" with "p" + - struct beam_params: "copyme" is not an imagefile_field_list + (previously: copy_hdf5_field) + - struct image: "copyme" is not an imagefile_field_list + (previously: copy_hdf5_field). width and height remoted. + |