CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
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
2017-07-04	Add a missing newline	Thomas White

2017-07-04	Switch CBF support on by default	Thomas White

2017-07-04	pattern_sim: Try all OpenCL platforms to find one with a GPU device	Thomas White

2017-07-04	Check for CBF headers, even if they're somewhere weird	Thomas White

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	indexamajig: Add --no-non-hits-in-stream	Thomas White

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	Update ChangeLog	Thomas White

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.
2017-06-21	indexamajig: Add --min-peaks (basic hitfinder functionality)	Thomas White

2017-06-21	Merge branch 'tom/cbf'	Thomas White

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

2017-05-18	Update ChangeLog	Thomas White

2017-05-17	Actually add scripts/sum-peaks	Thomas White

2017-05-16	check_hkl: Calculate resolution of reflection with asymmetric indices for ↵	Thomas White
	both possible and measured reflections Previously, it used whichever indices it found first. This made the resolutions different enough to fall into different bins, and screwed up the completeness (fortunately, rarely).
2017-05-16	Add scripts/sum-peaks	Thomas White

2017-05-12	Make all Python scripts compatible with Python 2 and 3	Thomas White
	It would be nice to upgrade completely to Python 3, but this may create problems at SLAC because psana only supports Python 2 (Python 3 is available, but means that users have to jump through hoops to run a simple CrystFEL script). None of our scripts do anything complicated, so they can all be compatible with both so far. If anyone adds a script which requires a particular version, make sure to specify the version in the first line, consistent with PEP 394.
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