aboutsummaryrefslogtreecommitdiff
path: root/relnotes-0.6.1
diff options
context:
space:
mode:
authorThomas White <taw@physics.org>2015-08-02 23:53:22 +0200
committerThomas White <taw@physics.org>2015-08-03 14:38:58 +0200
commitab770f18ff2740c3c1aa94c25eb547f0d60bc4c5 (patch)
treed99c73d6887906e5e38ef08ffd57111d91c1b749 /relnotes-0.6.1
parente216e29cf182e933a9b7852cb69efec46fc526cb (diff)
This is CrystFEL 0.6.10.6.1
Diffstat (limited to 'relnotes-0.6.1')
-rw-r--r--relnotes-0.6.1165
1 files changed, 165 insertions, 0 deletions
diff --git a/relnotes-0.6.1 b/relnotes-0.6.1
new file mode 100644
index 00000000..4c189cd6
--- /dev/null
+++ b/relnotes-0.6.1
@@ -0,0 +1,165 @@
+CrystFEL - Crystallography with a FEL
+-------------------------------------
+
+Release notes for version 0.6.1
+
+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:
+
+- Introduction of "prediction refinement".
+
+- Scaling and post-refinement with "partialator".
+
+- New indexing methods: mosflm-cell and asdf.
+
+- process_hkl --even-only and --odd-only instead of "alternate-stream".
+
+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.
+
+
+Introduction of "prediction refinement"
+---------------------------------------
+
+A new refinement step has been introduced between the indexing and prediction/
+integration stages of indexamajig. The refinement aims to maximise the
+agreement between the predicted spot positions and the peak positions found by
+the peak search step, at the same time as putting the peaks as close to the
+Bragg condition as possible. This increases the accuracy of spot prediction,
+which has positive effects on the downstream processing stages.
+
+The prediction refinement stage allows the central beam position to move
+relative to the entire detector. The required offset for each crystal is
+recorded in the stream and can be visualised using scripts/detector-shift.
+
+If, somehow, the prediction refinement causes problems for you, you can disable
+it using the indexamajig option "--no-refine".
+
+
+Scaling and post-refinement with "partialator"
+----------------------------------------------
+
+The scaling and post-refinement program partialator is no longer considered
+experimental in this version. Many users are already finding significant
+improvements in their data simply by applying scaling without partiality:
+
+$ partialator -i my.stream -o my.hkl -y mypg --model=unity --iterations=3
+
+A further improvement is sometimes obtained by applying partialities and doing
+full post-refinement:
+
+$ partialator -i my.stream -o my.hkl -y mypg --model=scsphere --iterations=3
+
+Note that partialator applies a per-crystal resolution cutoff to stabilise the
+scaling calculation. Therefore, you should experiment with different values
+for "--push-res".
+
+Further improvements to partiality modelling, scaling and merging will be
+included in the near future.
+
+
+New indexing methods
+--------------------
+
+This version of CrystFEL can make use of the known unit cell algorithm included
+with very recent (7.2.0 or later) versions of mosflm. The known unit cell
+algorithm is used by default if you provide lattice parameters to indexamajig.
+If this isn't what you want, or if it doesn't work well for you, use
+"mosflm-nocell" as your indexing method to restore the old behaviour.
+
+A new indexing method, asdf, has been added. This algorithm is built into
+CrystFEL directly, so no temporary files or external programs are needed.
+
+The old indexing methods "grainspotter" and "reax" have been removed.
+
+
+process_hkl --even-only and --odd-only
+--------------------------------------
+
+When using process_hkl for merging, you no longer need to use "alternate-stream"
+to split the stream into two parts in order to calculate figures of merit such
+as Rsplit. Instead, simply use the "--even-only" and "--odd-only" options to
+merge only even-numbered and odd-numbered crystals from the stream:
+
+$ process_hkl -i my.stream -o my.hkl1 -y mypg --even-only
+$ process_hkl -i my.stream -o my.hkl2 -y mypg --odd-only
+$ compare_hkl my.hkl1 my.hkl2 -y mypg --fom=rsplit [..etc..]
+
+Note that the numbering of crystals for this purpose is simply according to the
+order they appear in the stream. For most purposes, this is effectively random.
+
+Note further that partialator writes the ".hkl1" and ".hkl2" split-merged
+datasets for you automatically.
+
+
+API changes
+-----------
+
+The following changes have been made to the libcrystfel API:
+
+New functions:
+ - asdf_prepare(), run_asdf(), asdf_cleanup()
+ - cell_get_volume()
+ - crystal_{get,set}_Bfac()
+ - crystal_{get,set,add}_notes()
+ - detector_has_clen_references()
+ - {x,y,r}_gradient()
+ - refine_prediction()
+ - refine_radius()
+ - {get,set}_panel()
+ - {get,set}_flag()
+ - solve_svd()
+
+Removed functions:
+ - select_intersections()
+ - update_partialities_2()
+ - get_excitation_error()
+ - extract_f_from_stuff()
+ - grainspotter_{prepare,index,cleanup}()
+ - reax_{prepare,index,cleanup}()
+
+Changed function prototypes:
+ - integrate_all_4()
+ - set_detector_pos()