CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
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

2017-09-07	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

2017-08-31	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.
2017-07-24	Update docs	Thomas White

2017-07-24	Make struct taketwo_options const	Thomas White

2017-07-24	Ensure TakeTwo arrays get freed	Thomas White

2017-07-24	TakeTwo options again	Thomas White

2017-07-24	Formatting/copyright dates	Thomas White

2017-07-21	Add a warning about mask_file when mask is not set	Thomas White

2017-07-20	Change units for TakeTwo parameters	Thomas White

2017-07-18	Crashy for unknown reason, but have added the code for using custom params.	cppxfel

2017-07-06	indexamajig: Add TakeTwo-specific options	Thomas White

2017-07-06	Fix typo	Thomas White

2017-07-06	Merge branch 'master' into taketwo	Thomas White

2017-07-06	Indexing engine private pointers should be void *	Thomas White

2017-07-06	Remove unnecessary headers and move an include	Thomas White

2017-07-06	Use void pointers for indexing engine private stuff	Thomas White

2017-07-06	Update to peakfinder8, with bug fixed and new functionality. Code synced ↵	Valerio Mariani
	with OnDA and Oleksandr's programs
2017-07-05	Update docs	Thomas White

2017-07-05	Rearrange quaternion declarations so that gtk-doc can cope	Thomas White
	The utils file contains two gtk-doc sections, "utils" and "quaternion", with a change of section halfway through. It seems that gtk-doc doesn't like it if the declarations are all mixed together.
2017-07-05	Shoved a bunch of the stuff being passed from function to function into ↵	cppxfel
	TakeTwoCell, and shoved gsl_vector allocation into it as well to reduce alloc events
2017-07-01	Adding a cutoff for maximum allowed vectors (100,000) to stop Tom's computer ↵	cppxfel
	(and others) falling apart again.
2017-06-30	Ridiculous ASCII art to increase prominance of citation	cppxfel

2017-06-30	Removed unnecessary returns and set functions to void, and removed ↵	cppxfel
	superfluous integer declaration
2017-06-30	Didn't use C99 code, fixing	cppxfel

2017-06-30	Yet more speed fiddles	cppxfel

2017-06-30	Removed some code, fixed some code, and so on and so forth	cppxfel

2017-06-29	WARNING - profanity - uploading to my server so I can gvalgrind	cppxfel

2017-06-29	Disable a check which wasn't acted upon to measure impact on speed	cppxfel

2017-06-29	Should not limit to proceeding vectors only when a new spot may have been ↵	cppxfel
	included\!
2017-06-29	Relaxation of tolerances	cppxfel

2017-06-27	Dummy setup bits for INDEXING_NONE	Thomas White
	This doesn't do much except for preventing a possibly confusing warning message about "Failed to prepare indexing method none". You can actually do --indexing=none,asdf, but don't tell anyone...
2017-06-27	If prediction refinement fails, don't carry on and check the cell	Thomas White
	Doing so results in one crystal being counted as bad twice, which messes up the logic which follows.
2017-06-23	Accept either cbf/cbf.h or cbflib/cbf.h	Thomas White
	You get cbflib/cbf.h if you install CBFlib from source, and cbf/cbf.h if using the package manager in Fedora, probably other systems as well. We definitely don't want to include the cbf or cbflib folder in the include path, because CBFlib may bring its own HDF5 headers, which we don't want to touch with a bargepole.
2017-06-21	Close more leftover HDF5 handles	Thomas White

2017-06-21	Don't compile CBF stuff without CBFlib	Thomas White

2017-06-21	Close leftover HDF5 handles	Thomas White

2017-06-21	hdf5_read2(): Fix exit path	Thomas White
	Bad pixel map is not allocated at this point.
2017-06-19	Reduced amount of gsl_matrix reallocation	cppxfel

2017-06-19	Changing cosine of angle to be most sensitive to 0.5 degrees	cppxfel