CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2018-01-19	Clean up indexing method probes	Thomas White

2017-10-23	Check return values from fread/fgets	Thomas White

2017-10-18	Check that dirax,felix,mosflm or xds are available at the start	Thomas White
	Avoids a confusing error message later.
2017-10-18	Add probe functions to indexing methods	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	Mosflm: Recognise P3 as hexagonal P lattice	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.
2017-09-15	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.
2017-08-31	Set first argument when running external indexing programs	Thomas White
	This makes sure they have names in process displays.
2017-07-06	Indexing engine private pointers should be void *	Thomas White

2016-09-07	Mosflm: Create fake coordinates taking detector z into account	Thomas White

2016-07-28	Check return values when writing to Mosflm or DirAx	Thomas White

2016-07-01	No more slab-relative coordinates in libcrystfel	Thomas White

2016-01-30	indexamajig: Restore --no-refine	Thomas White
	Adds yet another indexing option...
2016-01-08	Make indexing "retry" and "multi" optional	Thomas White

2015-09-14	Fix space in Mosflm command	Thomas White

2015-09-14	Revert "Use old MOSFLM indexing command when using -nocell"	Thomas White
	This reverts commit d75b852f52b244796c0386c4f21cf36ca5bfcf70.
2015-07-20	Use old MOSFLM indexing command when using -nocell	Thomas White

2015-06-25	Set MOSFLM default flags to include cell parameters, and add some checks	Thomas White

2015-06-25	Try "mosflm" first, then try "ipmosflm" if it doesn't work	Thomas White
	This allows a smooth transition from CCP4 to standalone version of mosflm, and hence an easy upgrade to newer versions.
2015-06-19	Tidy up new MOSFLM code	Thomas White

2015-06-19	Send prior cell information to MOSFLM.	Takanori Nakane
	Prior-cell algorithm will be available in the next public relase of MOSFLM. (Old version of MOSFLM simply ignores prior-cell keywords so that this change doesn't do any harm)
2014-12-01	Improve MOSFLM feedback	Thomas White

2014-11-26	Read unique axis from unit cell (.cell) files	Thomas White
	... and fix the MOSFLM logic again.
2014-11-25	Update mosflm logic for axis permutation warning, now that unit cell ↵	Thomas White
	parameters aren't compulsory
2014-11-21	Fix indexing flags check for mosflm	Thomas White

2014-09-22	Beam file removal, part I	Thomas White

2014-09-19	Introduce CrystFEL unit cell files	Thomas White

2014-08-19	Use Gnulib forkpty()	Thomas White

2014-08-18	gettimeofday() fixes	Thomas White

2014-05-08	Strip out the "prepare_filename" rubbish	Thomas White

2013-09-13	Monoclinic changes for MOSFLM	Thomas White

2013-06-02	Fix const for MOSFLM space group	Thomas White

2013-06-01	Fix multiple small memory leaks	Thomas White

2013-03-01	Warn about MOSFLM unit cell settings	Thomas White

2013-02-19	Add -cell and -nocell to indexing methods	Thomas White

2013-02-15	"mosflm-nolatt" should not be sending "SYMM P1"	Thomas White

2013-02-15	Check for lattice type should be done before calling match_cell()	Thomas White

2013-02-15	Use "CRYSTAL R" to avoid having to uncenter the unit cell from MOSFLM	Thomas White

2013-02-12	Improve handling of indexing methods	Thomas White

2013-02-11	Add comment	Thomas White

2013-02-10	Read lattice type and centering information back from MOSFLM	Thomas White

2013-02-10	Formatting	Thomas White

2013-02-09	Add cleanup functions for DirAx and MOSFLM	Thomas White

2013-02-09	Complain if a unit cell is needed and not provided	Thomas White

2013-02-09	Use H3 instead of H32 when asking for 'hexagonal H'	Thomas White

2013-02-09	MOSFLM returns 'hexagonal H' if we ask for 'rhombohedral R'. Growl.	Thomas White

2013-02-09	Clarify lattice type information	Thomas White

2013-02-08	Small tweaks	Thomas White

2013-02-05	WIP on bringing programs up to date	Thomas White