CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
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

2017-06-19	Add observed angle check back in...	cppxfel

2017-06-19	Compile error sorted and some code re-added	cppxfel

2017-06-19	Theoretical speed improvements by replacing acos with comparison of cosines ↵	cppxfel
	for the quick check, but not necessarily good
2017-06-14	More fiddling	Helen Ginn

2017-06-14	Memory leak fixes and various tweaks	Helen Ginn

2017-06-14	Added symmetry checking - better indexing rate but something's holding back ↵	Helen Ginn
	a number of crystals
2017-05-18	Implement get_chiral_holohedry()	Thomas White

2017-05-18	Small fixes	Thomas White

2017-05-18	Formatting	Thomas White

2017-05-18	Formatting	Thomas White

2017-05-18	Fix uninitialised variable	Thomas White

2017-05-18	Various fiddles to add symmetry operations but not functional	Helen Ginn

2017-05-09	Allow reading CBF without geometry (only for simple viewing)	Thomas White

2017-05-09	Add missing checks	Thomas White

2017-05-05	Show filename of CBF file if it can't be read	Thomas White

2017-05-05	Fill in photon energy, clen and adu for CBFs	Thomas White
	This needed a bit of reorganisation and clarification of who is repsonsible for loading what. The low-level file loaders, e.g. hdf5_read and hdf5_read2 in hdf5-file.c or cbf_read in image.c, are responsible. There is a helper function adjust_centering_for_rail in detector.h which they can use. It seems like this could be done more cleanly at the imagefile layer. However, we need to make sure that the "old" hdfile API still works on its own, even when not accessed via the new imagefile API.
2017-05-05	Allow location of photon energy (eg in HDF5 file) to start with any character	Thomas White

2017-05-05	Read CBF data	Thomas White

2017-05-03	Detect CBF files, interface bits	Thomas White

2017-05-03	hdfile_set_image(): Remove panel argument	Thomas White
	Seems to have been added in 2014 and is not used at the moment
2017-05-03	HDF5 reading under new API	Thomas White