CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2019-03-07	indexamajig: Status message improvements	Thomas White
	1. Show the number of hits 2. Keep producing updates while the last patterns are being processed 3. Don't duplicate the code for displaying the status messages
2019-03-06	indexamajig: Rename --min-gradient to --min-squared-gradient	Thomas White
	The eventual aim of this is to deprecate the "--min-gradient" option, resolving the long-standing confusion about whether this option is the gradient or the squared gradient.
2018-12-03	indexamajig: Add --wait-for-file	Thomas White

2018-11-15	indexamajig: Name and shame slow processing stages	Thomas White

2018-09-27	Write in stream whether crystal was selected as a "hit" or not	Thomas White

2018-09-10	indexamajig: read pink beam spectrum from file	Alexandra Tolstikova

2018-07-27	indexamajig: Complain if profile radius determination fails	Thomas White

2018-06-10	indexamajig: Estimate resolution based on peaks only	Thomas White

2018-05-30	Whitespace fussiness	Thomas White

2018-05-30	Use only one min-snr option	Thomas White

2018-05-30	Changed parameter window-radius -> local-bg-radius	Yaroslav Gevorkov

2018-05-30	Changed sig_fac to min_snr	Yaroslav Gevorkov

2018-05-24	Generalise peakfinder9 error messages, and fail if not compiled in	Thomas White

2018-05-24	Update authorship and copyright dates	Thomas White

2018-05-24	Formatting	Thomas White

2018-05-24	Add "peakfinder9"	Yaroslav Gevorkov

2018-04-20	Set default bandwidth very small	Thomas White
	This seems to have been reducing data quality by overpredicting.
2018-02-27	New partiality model from Ginn et al.	Thomas White

2018-02-27	Formatting	Thomas White

2018-02-27	indexamajig: Add --overpredict	Thomas White

2017-06-27	indexamajig: Add --no-non-hits-in-stream	Thomas White

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

2017-05-02	Initial CBF stuff	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 'valerio/peakfinder8'	Thomas White

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

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

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

2016-03-01	indexamajig: Wall clock profiling	Thomas White

2016-01-29	Perform prediction refinement straight after indexing	Thomas White
	This allows indexing to be attempted again (either a new method or with "retry") if the prediction refinement fails, increasing overall indexing rate. Side-effect: there are some hoops which would need to be jumped through to store the profile radius before refinement and hence enable scripts/plot-predict-refine to work. For now, we'll ignore this as it's clear that the prediction refinement is working.
2015-12-18	Saturation map fixes	Thomas White

2015-10-05	process_image(): Remove image->data	Thomas White

2015-07-13	Re-work im-sandbox	Thomas White
	... it certainly needed it.
2015-07-09	indexamajig: Fix noise filter backup/restore	Thomas White

2015-06-18	Replace semaphore with a mutex	Thomas White
	A mutex (in a shared memory segment) is the correct synchronisation primitive here. I had confused myself...
2015-06-17	Use a POSIX semaphore for synchronising terminal access during indexing	Thomas White
	Nice side-effect: indexamajig -j and --int-diag can now be used together
2015-04-28	Remove unnecessary rejection tests	Thomas White

2015-04-20	Tweak rejection	Thomas White

2015-04-20	Add a simple rejection criterion to the prediction refinement	Thomas White

2015-04-20	indexamajig: Reset indexing method if all crystals fail integration	Thomas White

2015-04-20	indexamajig: Add --no-refine	Thomas White

2015-04-20	Refine detector position in prediction refinement	Thomas White

2015-04-20	refine_{radius,prediction}: unite common code (pair_peaks), avoid ↵	Thomas White
	preliminary integration round
2015-04-20	Remove debugging statements	Thomas White

2015-04-20	Record profile radius before and after refinement	Thomas White

2015-04-20	Throw out crystals which could not be refined	Thomas White

2015-04-20	Tweak weightings and cutoffs	Thomas White

2015-04-20	Add prediction refinement	Thomas White

2015-04-01	Initialise indexed_by to INDEXING_NONE	Thomas White
	Not entirely sure how this was missed for so long.