CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2018-02-27	indexamajig: Add --overpredict	Thomas White

2017-10-12	indexamajig: Simplify Felix options	Thomas White

2017-07-06	indexamajig: Add TakeTwo-specific options	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	Skeleton image file API	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

2017-03-11	Removed unused iarg	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.
2016-03-01	indexamajig: Wall clock profiling	Thomas White

2016-01-30	indexamajig: Restore --no-refine	Thomas White
	Adds yet another indexing option...
2015-09-15	Implement Felix Indexer	Kenneth Beyerlein

2015-07-13	Re-work im-sandbox	Thomas White
	... it certainly needed it.
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
2015-04-20	indexamajig: Add --no-refine	Thomas White

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

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

2015-02-05	Remove --element option from inxexamajig	Valerio Mariani

2014-12-14	Fussiness	Thomas White

2014-12-14	Read cxidb peak info	Valerio Mariani

2014-10-23	Add serial numbers to chunks	Thomas White

2014-09-05	Multi-event mode	Valerio Mariani

2014-08-13	indexamajig: Add --highres	Thomas White

2014-07-24	Suspend indexing statistics while --int-diag is displaying	Thomas White

2014-06-20	indexamajig: Add --peak-radius	Thomas White

2014-04-09	Remove vestigial "closer-peak" option	Thomas White

2014-04-08	indexamajig: Add --push-res	Thomas White

2014-03-26	indexamajig: Don't check SNR with --peaks=hdf5 unless given --check-hdf5-snr	Thomas White

2013-11-23	indexamajig: Add --int-diag	Thomas White

2013-10-10	indexamajig: Add --temp-dir	Thomas White

2013-05-30	indexamajig: Get rid of --min-integration-snr	Thomas White
	This functionality belongs in process_hkl.
2013-05-27	Initial integration stuff	Thomas White

2013-03-11	indexamajig: Add --median-filter	Thomas White

2013-02-22	Move processing pipeline to separate file	Thomas White