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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.
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