CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2017-09-27	Don't reset user flag to zero	Thomas White
	Some indexing methods may set it to 1 already, in which case we should take the hint.
2017-09-26	Remove unnecessary counting	Thomas White

2017-09-22	Don't send detector and tolerance to indexing methods	Thomas White
	The detector isn't used for anything, and the tolerance is none of their business.
2017-09-22	Fix silly mistake in friendly_indexer_name()	Thomas White

2017-09-22	Remove "latt" from asdf	Thomas White
	For consistency with other algorithms, let's standardise on an interpretation where just using the centering information in combination with the cell parameters, which is always necessary, doesn't qualify as "cell-latt", only "cell-nolatt". "Using lattice type as prior information" implies that asdf would behave differently with cell-nolatt, if it were allowed, than with cell-latt. It wouldn't. It just needs the centering to calculate the cell volume correctly. Note that TakeTwo, by contrast, would behave differently in this hypothetical case, because it uses the lattice type to exclude certain solutions by symmetry. Mosflm allows all four combinations of no/cell and no/latt, and does indeed behave differently between them.
2017-09-22	asdf uses prior information for its volume constraint, so add "cell" to the ↵	Thomas White
	method
2017-09-22	cell_explorer: Also count cells excluded by the choice of indexing method	Thomas White

2017-09-22	Set --no-check-cell if cell is given, but has no parameters	Thomas White

2017-09-22	cell_new_from_cell(): Don't try to duplicate non-existent parameters	Thomas White

2017-09-22	Mosflm: Recognise P3 as hexagonal P lattice	Thomas White

2017-09-22	Don't write cell parameters to the stream if we don't have them	Thomas White

2017-09-22	If no cell params or lattice type, set nocell/nolatt at top level	Thomas White
	Another thing that the indexing engines don't need to be repsonsible for.
2017-09-22	Stop if an indexing method can't be prepared	Thomas White

2017-09-22	indexamajig: Avoid segfault when no unit cell given	Thomas White

2017-09-21	hdfsee: Increase ring thickness	Thomas White

2017-09-21	indexamajig: Friendlier display of indexing engines	Thomas White

2017-09-21	indexamajig: Hide indexing setup messages if we are not indexing anything	Thomas White

2017-09-21	Improve error message when using CBF files and a multi-event geometry	Thomas White

2017-09-21	Remove old warning for XDS indexing	Thomas White

2017-09-21	Fix crash in XDS indexing	Thomas White

2017-09-21	Group the options in indexamajig(1) according to processing stage	Thomas White

2017-09-21	Update man page for new indexing options	Thomas White

2017-09-19	geoptimiser: Remove deprecated option from --help	Thomas White

2017-09-19	get_ev_based_value(): Allow integer types	Thomas White
	Just an oversight in the test
2017-09-17	Fix logic for new indexing options	Thomas White

2017-09-17	indexamajig: --help documentation for new indexing options	Thomas White

2017-09-16	Fix return of unit cells from asdf and dirax	Thomas White

2017-09-15	Merge branch 'tom/index'	Thomas White

2017-09-15	Perform peak alignment check if requested	Thomas White

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