CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2018-05-04	Put list of indexing methods into stream header	Thomas White
	Needed for when the methods are auto-determined.
2018-04-24	Read audit information from stream	Thomas White

2017-10-17	Handle old indexing methods	Thomas White
	There are limits to how well they can be handled, but this avoids screwing users over too much.
2017-05-02	Initial CBF stuff	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.
2016-11-25	Display line numbers at which stream is corrupted	Thomas White

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

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

2016-07-01	Store all "=" fields from stream, not just HDF5 ones	Thomas White

2016-07-01	No more slab-relative coordinates in libcrystfel	Thomas White

2016-02-29	More output when reading reflections failed	Thomas White

2015-11-27	Fix documentation	Thomas White

2015-11-27	indexamajig: Write target unit cell into stream	Thomas White

2015-09-17	Improve detection of out-of-memory condition when reading stream	Thomas White

2015-09-17	Formatting	Thomas White

2015-07-17	Fix format string for num_peaks	Thomas White

2015-07-17	Load bandwidth from stream with correct units	Thomas White
	D'oh!
2015-05-19	Set panel when reading reflections from stream	Thomas White

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

2015-04-20	Make panel assignments invariant during prediction- and post-refinement	Thomas White
	Reflections appearing and disappearing are problematic when trying to do a least-squares refinement. Therefore, assume that reflections stay on panel and keep them under consideration even if their partialities go to zero (i.e. they drift off Bragg). This should stabilise both refinements, and simplifies quite a lot of code. Collateral "damage": the old "select_intersection()" is now gone.
2015-04-20	open_stream_for_read: read stream from stdin when filename is "-".	Keitaro Yamashita

2015-04-20	Fix a string overflow vulnerability, and banish extract_f_from_stuff()	Thomas White

2015-03-18	Record crystal notes in stream	Thomas White

2015-03-02	Avoid duplication of last line of geometry file in stream	Thomas White

2015-01-27	Split nested code into separate functions	Valerio Mariani

2015-01-27	Fussiness	Valerio Mariani

2015-01-27	Keep hold of HDF5 fields which came from the stream	Valerio Mariani

2015-01-27	Fix type of add_{x,y}	Valerio Mariani

2015-01-27	Formatting	Valerio Mariani

2014-12-09	Fix reading of profile_radius	Thomas White

2014-12-09	Avoid bottoming out precision for beam parameters in stream	Thomas White

2014-12-09	read_stream_reflections_2_3(): set redundancy to 1	Thomas White

2014-11-26	Fix conversion to Angstroms for diffraction_resolution_limit in stream (whoops!)	Thomas White

2014-11-25	Formatting	Thomas White

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

2014-11-21	Formatting, and fix a comment	Thomas White

2014-11-14	Ensure initialisation of as,bs,cs	Thomas White
	This is mostly just to shut the compiler up about the lack of initialisation.
2014-11-13	Remove unused variables	Thomas White

2014-11-13	Whitespace	Thomas White

2014-11-13	Fix stream reader	Takanori Nakane

2014-11-10	Fussiness	Thomas White

2014-11-10	Copy and Replace when saving geometry	Valerio Mariani

2014-11-09	Record number of implausibly negative reflections in stream	Thomas White

2014-10-24	Put write_stream_reflections_*() in the right order	Thomas White
	This changes nothing else, I promise
2014-10-24	Restore peak and background to stream reflection format 2.3	Thomas White

2014-10-24	Fix/clarify peak coordinates for rearranged panels	Thomas White

2014-10-23	read_stream_reflections_2_3(): Fix detector positions	Thomas White

2014-10-23	Fix a load of memory leaks	Thomas White