CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
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	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	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

2016-12-09	New polarisation correction	Thomas White

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

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.
2016-11-04	Add (more) warnings about unique axes	Thomas White

2016-10-14	validate_peaks(): Remove drifting and proximity checks, and use original ↵	Thomas White
	coordinates We trust the HDF5 peaks, even if we can't see a peak there. That means we can't reliably take a centroid and "improve" the coordinates. In some cases, the centroiding procedure seems to be making the peak coordinates worse than they were originally. Now, the only remaining checks are: 1. Is the peak in a bad region of the detector? 2. Is it saturated? (but --use-saturated is the default) 3. If --check-hdf5-snr, is it above the minimum SNR?
2016-10-10	Fix bad regions	Thomas White
	Previously, this was broken when not using a mask
2016-10-10	Add missing newline	Thomas White

2016-10-10	Fussiness / boilerplate	Thomas White

2016-10-10	Added detector shift to crystal structure, wrote get and get functions	Valerio Mariani

2016-10-07	XDS: Clean up open files	Thomas White

2016-10-06	hdf5_write_image(): Write the correct data	Thomas White

2016-10-06	hdf5_write_image(): Use correct dataspace for writing	Thomas White

2016-10-06	pattern_sim: Fix loop bounds in record_image()	Thomas White

2016-09-12	Add newline at end of geometry file in stream, if not already present	Thomas White

2016-09-12	Restore loading of saturation map	Thomas White

2016-09-12	Restore loading of bad pixel map	Thomas White

2016-09-07	XDS: Create fake coordinates taking detector z into account	Thomas White

2016-09-07	Mosflm: Create fake coordinates taking detector z into account	Thomas White

2016-08-16	Add reflist_add_command_and_version()	Thomas White

2016-08-16	Read and write RefList notes to reflection list files	Thomas White

2016-08-16	Add notes to RefList	Thomas White

2016-08-11	Take rail direction as a vector rather than individual x,y,z values	Thomas White
	Just to make it more consistent with fs/ss directions
2016-08-11	Use whole of 'value' field when parsing top-level geometry options	Thomas White
	This is a long-standing bug, which we got away with up to now because top-level options with more than just a single number or location were rare or possibly never used at all.
2016-08-10	Ensure z component is set in dir_conv()	Thomas White