CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2017-09-15	Add restraints to prediction refinement	Thomas White

2017-09-15	Remove debugging statement	Thomas White

2017-09-15	Better way of displaying cell check option	Thomas White

2017-09-15	Record indices in write_pairs() (debugging function)	Thomas White

2017-09-15	Factorise cell parameter check	Thomas White

2017-09-15	Simplify indexing options	Thomas White
	mosflm-cell-nolatt-multi-refine-bad-retry.... it's all getting a bit too much. This commit removes all the options from the indexing methods except for the prior information flags (cell/nocell and latt/nolatt). All the other options are now given at the top level with new indexamajig options, e.g. --no-multi and --no-retry. They are applied to all the methods, with no option to (say) use retry for one method and not for another. This also makes the "peak alignment test" default to OFF, and multi-lattice indexing ON. I think that the prediction refinement does a good enough job of checking the validity of indexing solutions, allowing us to turn off the alignment check which filters out most multi-lattice solutions.
2017-09-15	Fix uninitialised peak counts (for info in stream only)	Thomas White

2017-09-15	hdfsee(1): Document --rigid-groups	Thomas White

2017-09-07	Use compare_cells() for multi-lattice indexing	Thomas White

2017-09-07	remove_flagged_crystals(): Return the number of crystals removed	Thomas White

2017-09-07	Add compare_cells() (and use it in whirligig)	Thomas White

2017-09-07	Add scripts/peakogram-stream to Makefile.am	Thomas White

2017-09-06	tests/transformation_check: Check lots more things	Thomas White

2017-09-05	cell_explorer: Display number of matching cells (on terminal)	Thomas White

2017-09-04	pattern_sim: Add crystal orientation and basis vectors	Thomas White

2017-08-31	Set first argument when running external indexing programs	Thomas White
	This makes sure they have names in process displays.
2017-08-31	setup_indexing(): Honour no_refine	Thomas White
	Fixes a regression caused by 61565336125, which broke indexamajig --no-refine.
2017-08-09	partial_sim: Add missing bracket in parameter list	Thomas White

2017-08-09	Fix extra bracket in configure.ac	Thomas White

2017-08-03	configure: Fix option name for --with-cbflib	Thomas White

2017-07-25	create-mtz: Tidy up create-mtz.temp.hkl file	Thomas White

2017-07-25	Fix typo in author name	Thomas White
	Whoops. Sorry Suzuki-san!
2017-07-24	This is CrystFEL 0.6.30.6.3	Thomas White

2017-07-24	Update docs	Thomas White

2017-07-24	Make struct taketwo_options const	Thomas White

2017-07-24	Ensure TakeTwo arrays get freed	Thomas White

2017-07-24	TakeTwo options again	Thomas White

2017-07-24	Formatting/copyright dates	Thomas White

2017-07-21	Tidy up some warnings	Thomas White

2017-07-21	Fix option names for TakeTwo parameters	Thomas White

2017-07-21	Add a warning about mask_file when mask is not set	Thomas White

2017-07-20	indexamajig(1): Give default values for TakeTwo options	Thomas White

2017-07-20	Merge branch 'taketwo'	Thomas White

2017-07-20	Change units for TakeTwo parameters	Thomas White

2017-07-18	Merge params code with whatever this git pull thingy contains because I ↵	cppxfel
	didn't pull first. Merge branch 'taketwo' of ssh://git.bitwiz.org.uk/crystfel into taketwo
2017-07-18	Crashy for unknown reason, but have added the code for using custom params.	cppxfel

2017-07-07	Update ChangeLog	Thomas White

2017-07-07	Convert angle_tol to radians	Thomas White

2017-07-07	Documentation for TakeTwo indexamajig options	Thomas White

2017-07-06	indexamajig: Add TakeTwo-specific options	Thomas White

2017-07-06	Fix typo	Thomas White

2017-07-06	Merge branch 'master' into taketwo	Thomas White

2017-07-06	Indexing engine private pointers should be void *	Thomas White

2017-07-06	Remove unnecessary headers and move an include	Thomas White

2017-07-06	Use void pointers for indexing engine private stuff	Thomas White

2017-07-06	Update docs	Thomas White

2017-07-06	Temporary fix for the geomptimiser not being able to optimize whole quadrants	Valerio Mariani

2017-07-06	Update to peakfinder8, with bug fixed and new functionality. Code synced ↵	Valerio Mariani
	with OnDA and Oleksandr's programs
2017-07-05	Update docs	Thomas White

2017-07-05	Rearrange quaternion declarations so that gtk-doc can cope	Thomas White
	The utils file contains two gtk-doc sections, "utils" and "quaternion", with a change of section halfway through. It seems that gtk-doc doesn't like it if the declarations are all mixed together.