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+CrystFEL - Crystallography with a FEL
+-------------------------------------
+
+Release notes for version 0.6.2
+
+Copyright © 2012-2016 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:
+
+- Stability improvements to the scaling algorithm in partialator.
+
+- Addition of "custom dataset splitting" in partialator.
+
+- "retry" indexing.
+
+- Per-pixel saturation values
+
+These changes have sections below.  In addition, there were many bug fixes and
+smaller improvements.
+
+
+Stability improvements in partialator
+-------------------------------------
+
+The scaling algorithm in partialator has been altered such that only the strong
+reflections contribute to the scaling factors at all.  This reduces the
+"drifting" of scale factors which happened before, and helps avoid the situation
+where a very large number of crystals get rejected with large B factors.
+Of course, all reflections contribute to the final merged data set as before.
+
+In CrystFEL 0.6.1, we needed to reduce the amount of noise going into the
+scaling algorithm to make it work.  This was done by including reflections only
+up to the apparent (conservative) resolution limit of each crystal made by
+indexamajig, and could be overridden by using the "--push-res" option of
+partialator.  The default --push-res value was zero, which meant to ignore any
+reflections higher than the limit.  With the stabilised algorithm, this is no
+longer necessary, and hence the default --push-res value has been changed to
+infinity, i.e. no cutoff at all.  You can restore the old behaviour with
+--push-res=0.
+
+
+Custom dataset splitting in partialator
+---------------------------------------
+
+When performing a time-resolved or isomorphous replacement experiment (plus some
+other types of experiment), it is preferable to ensure that the data for all
+time points has been processed identically.  Rather than processing each time
+point independently with separate runs of partialator, it is better to process
+them all together and do the splitting into time points just before the final
+output.  Consider, for example, the case of simple scaling (without a B
+factor): when merging independently, the resulting datasets would probably end
+up with different overall scaling factors.  When comparing the results, you
+would need to take this difference into account.  In practice, most programs
+can do that job easily, but what about if a B factor is included?  And what if
+partialities are included - how unique is the solution?
+
+Partialator's new "custom dataset splitting" option allows you to provide a
+text file containing a list of filenames, event numbers and dataset
+names, one event (detector frame) per line.  All crystals will be refined
+together, but they will be merged according to the dataset names you give.  The
+parameters (scaling factors, partialities etc) determined during the joint
+refinement will be applied.  For each dataset, a separate pair of split
+half-datasets will also be written, allowing you to calculate figures of merit
+such as Rsplit and CC1/2 for each one.
+
+
+"retry" indexing
+----------------
+
+If an indexing method fails to index a pattern (or if the solution doesn't get
+through the prediction refinement stage), this version of CrystFEL will delete
+the weakest few peaks and try again.  This can increase the indexing yield a lot
+(sometimes a factor of two!), but decreases the speed.  If you'd rather keep
+things fast, add "-noretry" to each of your indexing methods.
+
+
+Per-pixel saturation values
+---------------------------
+
+When using dual-gain mode on the CSPAD (or any other detector which offers a
+similar feature), our current advice is to correct the pixel values in one of
+the regions by multiplying them by the relative gain factor.  This will give
+image data which looks good, but the saturation values will be different in the
+two regions.  To handle this, CrystFEL 0.6.2 allows you to prepare a map, in
+HDF5 format, giving the saturation value for each pixel individually.  The
+script "gaincal-to-saturation-map" can be used to create a suitable file from
+the gain map (e.g. as generated and used by Cheetah).  Specify the filename and
+HDF5 path of the saturation map using saturation_map and saturation_map_file
+in the geometry file - these work exactly like the bad pixel map.  Reflections
+containing any pixel above this value will be rejected, in addition to any
+reflections which get rejected by the usual saturation criteria (so remove any
+max_adu directives if you want the saturation map to be the only decider!).
+
+
+API changes
+-----------
+
+The following changes have been made to the libcrystfel API:
+
+New functions:
+	- write_cell()
+	- find_orig_panel_number()
+	- felix_{prepare,index,cleanup}()
+	- sort_peaks()
+	- remove_flagged_crystals()
+	- open_stream_for_write_3()
+
+Removed functions:
+	(none)
+
+Changed function prototypes:
+	- prepare_indexing()
+
+"data", "flags" and "twotheta" were removed from "struct image", and "sat" was
+added.