CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
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

2017-05-02	Skeleton image file API	Thomas White

2017-05-02	Initial CBF stuff	Thomas White

2017-04-13	Add half-pixel offset for peakfinder8	Thomas White
	Like zaef, the pixel indices need to be converted to geometrical coordinates. This increases the indexing rate by about 5% in my test.
2017-04-13	hdf5_read2(): Free buffers when read fails	Thomas White

2017-03-31	Offset peak locations from HDF5 or CXI files by 0.5,0.5	Thomas White
	CrystFEL considers all peak locations to be distances from the corner of the detector panel, in pixel units, consistent with its description of detector geometry. In contrast, Cheetah considers the peak locations to be pixel indices in the data array. Therefore, a half-pixel offset is needed when importing the peak lists. For users who need the old behaviour, this commit adds a new option indexamajig --no-half-pixel-shift to deactivate this offset.
2017-03-24	Merge branch 'taketwo' of ssh://git.bitwiz.org.uk/crystfel into taketwo	Helen Ginn

2017-03-24	Now tries the shortest vectors first.	Helen Ginn

2017-03-24	Remove an old debugging message	Thomas White

2017-03-24	Propagate error if indexing method is unrecognised	Thomas White

2017-03-24	Merge branch 'valerio/peakfinder8'	Thomas White

2017-03-24	Mostly fussiness	Thomas White

2017-03-22	Completely revamped implementation of peakfinder8	Valerio Mariani

2017-03-15	largest_q(): Handle NULL detector	Thomas White

2017-03-13	Added management of max_num_peaks per image instead of per panel	Valerio Mariani

2017-03-13	Added saturated peak management to peakfinder8	Valerio Mariani

2017-03-13	Ask for C99 in configure.ac, remove weird C99 declarations	Thomas White

2017-03-11	Fixed some more bugs reported by Yaroslav	Valerio Mariani

2017-03-10	Fixed a couple of bugs reported by Tom	Valerio Mariani

2017-03-10	cell_print(): Show reciprocal angles	Thomas White