CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2017-10-18	indexamajig: Auto-detection of available indexing methods	Thomas White

2017-10-18	Add probe functions to 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.
2017-10-17	felix: Set nsigmas=1	Thomas White

2017-10-12	indexamajig: Simplify Felix options	Thomas White

2017-10-12	Remove write_reflections_to_file() from API	Thomas White
	It's there because it used to be used to write the reflections into the stream. Therefore there was a need for a function to write a bare list of reflections to a file, with no headers. Since then, the stream and merged reflection file formats have diverged, so there's no use for this other than to confuse people.
2017-10-12	hdfsee: Add "peaks", "preds" or "rings" to export filename, as applicable	Thomas White

2017-10-12	hdfsee: Add event ID to exported image filename	Thomas White

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

2017-10-09	configure.ac: Fix CBFlib path variable name	Thomas White
	Whoops.
2017-10-02	indexamajig: Tidy up --help	Thomas White

2017-10-02	indexamajig(1): Add --temp-dir	Thomas White

2017-10-02	Formatting fussiness	Thomas White

2017-10-02	indexamajig: Add missing documentation for --check-peaks	Thomas White

2017-09-27	Fix check for CBF files in event enumeration	Thomas White
	-1 means the check failed.
2017-09-27	remove_flagged_crystals(): Remove multiple bad crystals	Thomas White
	A silly bug
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	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