CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
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	indexamajig: Format --help and fix typos	Thomas White

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 information about max_num_peaks to documentation	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

2017-03-13	process_hkl: Add event IDs to "--stat" file	Thomas White

2017-03-11	Removed unused iarg	Valerio Mariani

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	Update ChangeLog	Thomas White

2017-03-10	compare_hkl: Add --min-measurements	Thomas White

2017-03-10	Added peakfinder8 information to the indexamajig man page	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.
2017-03-08	compare_hkl: Fix combination of sigma(I) values for d1sig and d2sig	Thomas White

2017-03-08	compare_hkl: Fix documentation	Thomas White

2017-03-08	Add SLURM version of turbo-index script	Thomas White

2017-03-08	Add example Eiger geometry file	Thomas White

2017-03-03	cell_explorer: Better handling of dodgy cells	Thomas White

2017-03-03	Return error code if cell can't be inverted	Thomas White

2017-03-03	partialator: Better handling of very small number of crystals	Thomas White

2017-03-03	geoptimiser: Call g_type_init() only if GLib is old	Thomas White

2017-02-24	get_hkl: Fix a segfault when there are no notes	Thomas White

2017-02-17	Update docs (add funding acknowledgements)	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	Cannot use stamp_response() here	Thomas White
	We have a pipe index (0 to n_read), not a process index (0 to n_proc). These are two separate lists, with no correspondence between them. See 7dbbfa4 for another fix related to this issue.
2017-02-02	indexamajig: Add ping mechanism to avoid timing out when trying lots of indexers	Thomas White

2017-02-02	cell_explorer: Fix labels once and for all	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

2017-02-01	partialator: Exit if point group is unrecognised	Thomas White

2017-01-12	indexamajig: Fix hanging on "Waiting for last patterns"	Thomas White

2016-12-13	Fix tests for new polarisation correction	Thomas White
	Actually, disable the polarisation correction in the tests.
2016-12-09	New polarisation correction	Thomas White

2016-11-25	Display line numbers at which stream is corrupted	Thomas White

2016-11-24	partialator: Fix counting of images	Thomas White

2016-11-16	partialator: Fix segfault when not using --custom-split	Thomas White
	Crash introduced by 775bbc2d. How silly of me. Thanks to Ken Beyerlein for fixing this.
2016-11-10	Fix 2theta calculation in locate_peak_on_panel()	Thomas White
	The "improved" version of this, added by 9b1374999 along with the new spot position calculation for out-of-plane panels, actually assumes that the reflection is at the exact Bragg condition. This is not a valid assumption here. The difference is small (<0.5 px), but made the prediction refinement gradients completely wrong.