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diff --git a/relnotes-0.6.0 b/relnotes-0.6.0 deleted file mode 100644 index 22efa56d..00000000 --- a/relnotes-0.6.0 +++ /dev/null @@ -1,257 +0,0 @@ -CrystFEL - Crystallography with a FEL -------------------------------------- - -Release notes for version 0.6.0 - -Copyright © 2012-2015 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> - -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 multi-event HDF5 files (e.g. CXI format as used by CXIDB) - -- geoptimiser: a new tool for precisely optimising the detector geometry - -- Removal of beam files / automatic determination of spot prediction parameters - -- whirligig: a new tool for finding clusters of similarly-oriented - crystal snapshots, e.g. for finding "mini rotation series" in data - from slow extrusion sample delivery methods. - -- Introduction of "CrystFEL unit cell files". - -These new features have individual sections below. In addition, there are many -other new developments. See the ChangeLog or the changes page on the website -for more details. There were, of course, the usual large number of smaller -refinements and bug fixes. - - -Support for multi-event HDF5 files ----------------------------------- - -CrystFEL's handling of HDF5 files has been made much more flexible. Most -importantly, it now offers the ability to handle HDF5 files which contain more -than one event (frame). Until now, CrystFEL has required that each event be -contained in its own file, which can place a lot of unnecessary strain on -filesystems. Recent versions of Cheetah allow you to create larger files which -contain many events each using the CXI format (see http://www.cxidb.org for more -details). CrystFEL now supports this as well as almost any reasonable -multi-event HDF5 layout. - -If you choose to continue using many small files, you should not notice much -difference. However, some small updates will be required. Firstly, -indexamajig's "-e" and "--image" command-line parameters have been removed. -Instead, you need to edit your geometry file and add a line such as this near -the top: - - data = /data/rawdata - -Geometry files now contain all the information needed to interpret the contents -of the HDF5 files as a physical setup, including the photon energy. Beam -parameter files have been removed. See below for more information about this. - -When using multi-event files in CXI format, the peak lists are read differently. -Use --peaks=cxi to retrieve peak lists from CXI files. - -hdfsee has been extended to support multi-event files, including navigation -between events. You should always provide a geometry file on the command line, -otherwise it won't know how to interpret the contents of your HDF5 file. - -A new tool in CrystFEL 0.6.0, list_events, is provided to simplify the process -of creating lists of individual events. However, most users will simply be -able to list the multi-event filenames themselves in the input to indexamajig, -which will then process all of the events in the file. See "man indexamajig" -and "man list_events" for more details. - -Finally, it may be necessary to update your check-near-bragg and -check-peak-detection scripts. Simply make a fresh copy from the CrystFEL -"scripts" folder or download them from the website. - - -geoptimiser: a tool for optimising the detector geometry --------------------------------------------------------- - -CrystFEL 0.6.0 introduces a new tool, geoptimiser, for optimising the detector -geometry. You simply give it a stream containing indexing results obtained with -the approximate geometry, and it gives you a refined geometry. It can refine -panel translations, rotations and camera lengths. - -To use geoptimiser, you need to add some extra information about the -mechanical construction of your detector. This is used to constrain the -refinement appropriately, for example to ensure that panels which share sensor -silicon do not move relative to one another. If you're processing CSPAD data, -you can simply copy all the rigid_group lines from one of the CSPAD geometry -file examples (folder doc/examples) into your own geometry file. - -Refer to "man geoptimiser" and "man crystfel_geometry" for more information. - - -Removal of beam files / automatic determination of spot prediction parameters ------------------------------------------------------------------------------ - -As of version 0.6.0, "beam files" have been removed completely. This should -simplify usage for most people and remove a lot of ambiguity. Programs which -need X-ray beam parameters, such as pattern_sim, now have additional command- --line arguments to provide them. indexamajig now determines these parameters -automatically for the purposes of spot prediction. - -We are interested in feedback about the automatic spot prediction parameter -determination. If it appears not to work well for you, you can restore the old -behaviour by using the new command-line options for indexamajig: ---fix-profile-radius, --fix-bandwidth and --fix-divergence. Simply set these -parameters to the values you had in your old beam file. - -The photon energy, or information about where to get it, now needs to be in the -geometry file. This can be done with a line like this: - - photon_energy = /LCLS/photon_energy_eV - -or, for a fixed value: - - photon_energy = 8300 - - -whirligig: a tool for finding "mini rotation series" ----------------------------------------------------- - -CrystFEL 0.6.0 introduces yet another tool, whirligig, which can be used for -locating "mini rotation series" in the output from indexamajig. This might be -used to perform an experiment similar to that described by Gati et al., IUCrJ -1 (2014) p87. In this initial version, whirligig finds runs of consecutive -frames which contain crystals in similar orientations. It writes the -corresponding filenames and event/crystal identifiers to log files, which might -be useful for further analysis. - -This is the program described by Nogly et al., IUCrJ 2 (2015). Refer to "man -whirligig" for usage information. - - -Introduction of CrystFEL unit cell files ----------------------------------------- - -CrystFEL offers you the ability to index patterns using Bravais lattice -information but without unit cell parameters, for example: "index these using -only tetragonal primitive lattices, but any parameters". However, it's awkward -to give this information using a PDB file: you essentially have to "trick" it -into interpreting the parameters correctly, then throw away the parameter -information. - -Version 0.6.0 of CrystFEL introduces a new way of specifying unit cell -information. These new unit cell files look like this: - - CrystFEL unit cell file version 1.0 - - lattice_type = cubic - centering = I - - a = 66.2 A - b = 66.2 A - c = 66.2 A - - al = 90.0 deg - be = 90.0 deg - ga = 90.0 deg - -In the event that you want to specify the lattice type information alone, you -can simply omit the cell parameters: - - CrystFEL unit cell file version 1.0 - - lattice_type = tetragonal - centering = P - unique_axis = c - -Note that a unique axis must be specified for all types of cell where this makes -sense, and can be omitted otherwise. This was done in the first example above, -which is cubic and therefore has no unique axis. - -You can, of course, continue to use PDB files just like before. - - -API changes ------------ - -The following changes have been made to the libcrystfel API: - -New functions: - - The event API (see libcrystfel/src/events.h) - - load_cell_from_file() - - cell_has_parameters() - - find_orig_panel() - - crystal_{get,set}_num_implausible_reflections() were added - - panel_is_in_rigid_group() - - rigid_group_is_in_collection() - - single_panel_data_source() - - find_rigid_group_collection_by_name() - - write_detector_geometry_2() - - find_intersections_to_res() - - sphere_fraction() - - gaussian_fraction() - - hdf5_read2() - - check_path_existence() - - get_peaks_cxi() - - hdfile_get_value() - - fill_event_list() - - image_reflection_closest() - - intmat_identity() - - extract_f_from_stuff() - -Removed functions: - - cell_set_cartesian_{a,b,c}() - - cell_{get,set}_pointgroup() - - twod_mapping() - - get_value() - -Changed function prototypes: - - record_image() - - get_detector_geometry() - - fill_in_values() - - write_detector_geometry() - - hdf5_write_image() - - hdf5_read() - - hdfile_set_image() - - hdfile_get_string_value() - - {get,set}_partial() - - write_chunk() - - prepare_indexing() and {dirax,mosflm,reax,grainspotter,xds}_prepare() - -beam-parameters.h was removed, and "struct beam_params" is now defined in -image.h. |