CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
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

2017-03-10	Peakfinder8 in CrystFEL. Same results as Anton's Cheetah implementation	Valerio Mariani

2017-03-08	Check unit cell parameters after prediction refinement	Thomas White

2017-03-08	Allow indexing system to store its own data, independently of indexing methods	Thomas White
	Previously, the indexing system passed all the information on to the indexing engines and then forgot about it. That made it difficult to do things like check the indexing solution after prediction refinement, because the target unit cell was unavailable. Now, the indexing system itself can keep some information. Of course, that information includes the private pointers for the indexing engines themselves. I took the opportunity to streamline things a little bit. The caller can now set up the indexing system in one step, without having to separately parse the names of the indexing methods. The caller no longer has to keep track of a separate array of methods, instead just one structure which contains everything.
2017-03-03	Return error code if cell can't be inverted	Thomas White

2017-02-16	Fix mask path placeholder check	Thomas White
	The mask paths for all panels have to have the same number of placeholders, but the masks do not have to have the same number of placeholders as the panel data blocks. This also tidies up a few excess strdup() calls, and removes partial_event_substitution() because retrieve_full_path() can now handle the number of placeholders being too small.
2017-02-02	Merge branch 'master' into taketwo	Thomas White

2017-02-02	indexamajig: Add ping mechanism to avoid timing out when trying lots of indexers	Thomas White

2017-02-01	asdf.c: Divide volume constraints by number of lattice points per unit cell. ↵	Alexandra Tolstikova
	Add F centering
2017-02-01	asdf.c: Divide volume constraints by number of lattice points per unit cell ↵	Alexandra Tolstikova
	since asdf always finds primitive cell
2017-02-01	Fix malloc fail due to integer overflow in N_triplets	Alexandra Tolstikova

2017-02-01	Change volume_min, volume_max and d_max when indexing=asdf-comb	Alexandra Tolstikova

2017-02-01	Change d_max according to the provided cell	Alexandra Tolstikova

2017-01-18	Remove error messages	Helen Ginn

2017-01-18	One image has no more leaks from taketwo.c	Helen Ginn

2017-01-18	Significant reduction in leakage, not done yet.	Helen Ginn

2017-01-18	Fixed more memory errors	Helen Ginn

2017-01-18	Goodbye memory leaks!	Helen Ginn

2017-01-18	Fiddled with parameters, now nice for CPV17. Fixed a ton of bugs too	Helen Ginn

2017-01-17	Random indentation plus faffing with parameters.	Helen Ginn

2017-01-17	Removed all debug messages, nice and clean.	Helen Ginn

2017-01-17	General beginning of tidying and removing some debug statements and return ↵	Helen Ginn
	best solution if they're all too rubbish to hit the threshold - not tested
2017-01-17	Fiddles with parameters - more sensible now	Helen Ginn