CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
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.
2015-02-20	indexamajig: Show event ID if there are implausible reflections	Thomas White

2015-02-20	indexamajig: Take a copy of the geometry structure	Thomas White
	There are already things which alter this structure during processing, and probably more to come. Taking a copy avoids problems down the line and fixes a serious bug when using coffset and a fixed clen.
2015-02-18	Fix profile radius determination	Thomas White

2015-02-16	indexamajig: --peaks=cxi instead of --peaks=hdf5 --cxi-hdf5-peaks	Thomas White

2015-02-12	Increase max radius to 0.02e9 m^-1	Thomas White

2015-02-12	indexamajig: Add --fix-{profile-radius,bandwidth,divergence}	Thomas White

2015-02-12	Improved determination of profile radius	Thomas White

2015-02-10	Formatting and comments	Thomas White

2014-12-14	Fussiness	Thomas White

2014-12-14	Read cxidb peak info	Valerio Mariani

2014-12-09	Capitalise all warnings	Thomas White

2014-12-09	Update warning	Thomas White

2014-12-02	Count very strong reflections instead of intensity when calculating profile ↵	Thomas White
	radius
2014-11-28	indexamajig: Only do int-diag on second integration pass	Thomas White

2014-11-28	indexamajig: Report implausibly negative reflections only after final ↵	Thomas White
	integration
2014-11-26	Formatting	Thomas White

2014-11-24	Fixed stream I/O across different versions	Valerio Mariani