CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2021-03-12	FromFile indexer: Move to libcrystfel/src/indexers	Thomas White
	Also adds to meson.build
2021-03-11	indexamajig: Add --max-indexer-threads	Thomas White
	This is a more general replacement for --pinkIndexer-thread-count.
2021-03-11	PinkIndexer: Allocate peak lists when indexing	Thomas White
	There doesn't seem to be any point in allocating them earlier, except to make space for some nice bugs.
2021-03-11	PinkIndexer: Remove unnecessary cast	Thomas White

2021-03-11	PinkIndexer: Remove wide bandwidth stuff	Thomas White
	This will return later in a more centralised form, if we decide to work further on wide bandwidth.
2021-03-11	PinkIndexer: Use fake camera length for detector refinement	Thomas White
	... and calculate the real value afterwards, checking that the detector is really flat enough for it to work.
2021-03-11	PinkIndexer: Remove custom indexing checks	Thomas White
	These conflict badly with CrystFEL's own checks, creating a horrible user and developer experience. Later, if we want to handle wide bandwidth beams, we will improve the central CrystFEL checks to support it.
2021-03-11	detgeom_transform_coords: Take an additional detector shift	Thomas White
	This allows the refined detector position to be used in a lot of places.
2021-03-11	Update copyright dates in libcrystfel/src/indexers	Thomas White

2021-03-11	PinkIndexer: Don't use ImageFeature->rx,ry,rz	Thomas White
	This brings it up to date after e7cf3911104f.
2021-03-11	setup_indexing: Remove dtempl	Thomas White
	There is absolutely nothing useful that an indexing algorithm can do with the opaque DataTemplate object.
2021-03-11	indexamajig: Add --wavelength-estimate	Thomas White
	This is a more sensible non-indexer-specific and non-Xray-specific replacement for --pinkIndexer-override-photon-energy
2021-03-05	Mosflm: Add -n option	Thomas White
	This tells Mosflm not to try to load environ.def and defaults.def. We don't need either.
2020-12-07	Get rid of ImageFeature->rx,ry,rz	Thomas White
	These needed to be kept up to date with a call to map_all_peaks every time anything changed - wavelength, detector position etc. Not doing so has already led to bugs in another branch, and probably already causes problems on this branch. This patch eliminates the rx,ry,rz completely. Anyone who needs reciprocal space coordinates for a peak is now responsible for calling detgeom_transform_coords themselves.
2020-10-15	TakeTwo: Limit number of seeds to 10, and reduce MAX_OBS_VECTORS to 300	Thomas White
	This gives a huge speed improvement, without sacrificing very much in indexing rate.
2020-10-07	asdf: Fix incorrect units conversion for cell volume	Thomas White

2020-10-07	Fussiness	Thomas White
	Commented out debug message is no longer relevant
2020-10-07	TakeTwo: Set tp->opts	Thomas White

2020-10-07	TakeTwo: Fix get_chiral_holohedry for "hexagonal H"	Thomas White
	Fixes CRYS-240
2020-10-01	asdf: Replace weird loop syntax	Thomas White

2020-09-11	xgandalf: Remove C99-style 'for' declarations	Thomas White

2020-08-27	TakeTwo: Remove internal declarations	Thomas White

2020-08-20	Add default_method_options()	Thomas White
	This allows the indexing method private options structures to be set up easily.
2020-08-10	Start on converting pinkIndexer to DataTemplate	Thomas White

2020-08-10	pinkIndexer: Remove detector update	Thomas White
	Overall detector offsets can now be done via the geometry file, and this is labelled as a hack. It doesn't actually do very much anyway, because the "updated" detector is thrown away for the next pattern. The updated detector is used only for subsequent indexing attempts on the same pattern.
2020-08-07	Move indexers out of API	Thomas White