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diff --git a/relnotes-0.6.3 b/relnotes-0.6.3 deleted file mode 100644 index 11a1f93b..00000000 --- a/relnotes-0.6.3 +++ /dev/null @@ -1,211 +0,0 @@ -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. - |