CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2019-09-12	Increase indexing timeout when using pinkIndexer	Thomas White

2019-09-12	Add indexing_methods() to examine the actual list of methods	Thomas White

2019-09-12	Remove message directing to old option	Thomas White

2019-09-12	Avoid duplication of beam and detector parameters for pinkIndexer	Thomas White

2019-09-12	Accept --indexing=pinkindexer (lower case)	Thomas White

2019-09-12	Set task name for PinkIndexer	Thomas White

2019-09-12	Whitespace	Thomas White

2019-09-12	Add pinkIndexer interface	Yaroslav Gevorkov

2019-09-06	Use new peak check only when doing multi-lattice indexing	Thomas White

2019-09-03	Fix memory leaks in cell comparison	Thomas White

2019-08-29	Use compare_cell_parameters for after-refinement cell check	Thomas White
	No need to do all the cell reduction stuff again.
2019-08-29	indexamajig: Remove --no-cell-combinations	Thomas White
	Also remove all the related API stuff. We now have a much better way of checking indexing results.
2019-08-22	Tidy up comparison function definitions	Thomas White
	Especially, remove the last ltl/atl tolerance values.
2019-08-22	Framework for new unit cell comparison function	Thomas White

2019-08-16	Clarify cell vs reference in comparison functions. Also reindexed vs permuted	Thomas White

2019-08-16	Use new cell comparison functions for indexing	Thomas White

2019-08-16	indexamajig: Accept six values for unit cell tolerance	Thomas White

2019-05-07	Update all source code comments to Doxygen format	Thomas White

2019-03-11	Change horribly confusing names of unit cell comparison functions	Thomas White
	cells_are_similar -> compare_cell_parameters_and_orientation compare_cells -> compare_reindexed_cell_parameters_and_orientation cell_tool.c:cells_the_same -> cellutils.c:compare_cell_parameters All comparisons now done in real space, checking that centering is the same, and without uncentering anything.
2019-01-22	Fix some small memory leaks	Thomas White

2018-11-15	indexamajig: Name and shame slow processing stages	Thomas White

2018-11-02	Change a couple of important asserts to if statements	Thomas White

2018-07-11	reduce minimum angle separation for similarity check of lattices	Yaroslav Gevorkov

2018-07-09	Add number of indexing attempts to stream	Thomas White

2018-06-18	Add interface to XGANDALF indexer	Yaroslav Gevorkov

2018-05-25	Fix incorrect loop in cleanup_indexing	Thomas White

2018-04-20	Restore peak alignment check and unset multi-lattice indexing as default	Thomas White
	Unfortunately, they seem to be severely reducing data quality. Partially reverts 60c48f3876b0d3c30bf729ce691dbd3f56665c4c
2018-04-20	Remove TakeTwo from default indexing method probes	Thomas White
	At least until it can be made faster.
2018-02-27	Read debug indexing from file	Thomas White

2017-11-28	Fix check for cell parameters at start	Thomas White

2017-10-27	Merge branch 'tom/simpler_felix'	Thomas White

2017-10-19	Add probe for TakeTwo	Thomas White

2017-10-18	indexamajig: Auto-detection of available indexing methods	Thomas White

2017-10-17	Handle old indexing methods	Thomas White
	There are limits to how well they can be handled, but this avoids screwing users over too much.
2017-10-12	indexamajig: Simplify Felix options	Thomas White

2017-10-09	indexer_str(): Don't return "none-nolatt-nocell"	Thomas White

2017-09-27	Add an assertion	Thomas White

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	Set --no-check-cell if cell is given, but has no parameters	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

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

2017-09-15	Perform peak alignment check if requested	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	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.