CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
24 hours	data_template_write_to_fh: Fix bad region outputHEAD master	Thomas White
	Two problems: 1. Didn't take into account that bad->name already includes the prefix "bad". 2. Didn't convert the panel-relative coordinates back to slab-relative. Fixes: https://github.com/taw10/crystfel/issues/11
24 hours	tests/geom_roundtrip: Check bad regions	Thomas White

3 days	indexamajig: Reduce ASAP::O verbosity	Thomas White

4 days	indexamajig: Send ASAP::O acknowledgement only after process_image	Thomas White
	Otherwise, we end up acknowledging the previous message ID after receiving something like kEndOfStream.
4 days	indexamajig: Report ASAP::O message ID for acknowledgement	Thomas White
	Something strange is going on here, need to debug.
7 days	Further clarification about ordering of panel group directives	Thomas White
	See 79bda19687e425818888ce17cc6e2239744ee640
7 days	DataTemplate: Add an "all" group if no panel definitions are given	Thomas White
	Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/96
7 days	Whitespace	Thomas White

7 days	crystfel_geometry(5): Mention that group definitions must come after panels	Thomas White
	Also mention this when complaining about the geometry file. Fixes: https://github.com/taw10/crystfel/issues/10
8 days	indexamajig: Avoid writing empty Mille records	Thomas White
	Fixes: https://github.com/taw10/crystfel/issues/9
9 days	Julia: Add 'setreflections!' to add a RefList for a Crystal in an image	Thomas White

9 days	Julia: Avoid making a list of Nothing	Thomas White
	The type of the list needs to be correct, otherwise we can't push to it later.
9 days	indexamajig: Add ASAP::O acknowledgements	Thomas White

10 days	align_detector: Add missing argument in warning message	Thomas White
	Fixes: https://github.com/taw10/crystfel/issues/8
11 days	asdf: Force cell to be right-handed after refinement	Thomas White
	In some rare cases, the cell changes from right to left handed during the vector refinement stage of asdf, while ending up at an apparently correct indexing solution. This commit just flips the axis round when necessary, in the same way that asdf already does in an earlier stage. I haven't done a proper survey, but I can say that the image I used to isolate and test this issue had very low resolution while still being what we would call "indexable". The left-handed cells appeared for six out of the 12173 hits in that run, or slightly below 0.05%. So, it's rare but not totally impossible.
11 days	asdf: Don't store cell volume	Thomas White
	It's hardly needed for re-use, and invites problems with the volume going out of sync with the vectors. Better just to calculate it when needed.
11 days	Minor documentation tweaks	Thomas White

14 days	GUI: Fix buffer overflow in "delete_gui_tempdir"	Philipp Middendorf

14 days	CI: Better way of restricting build-centos7 to mainline only	Thomas White

14 days	CI: Run build-centos7 only for "main" project (not for e.g. MRs)	Thomas White

2024-04-18	Merge branch 'julia'	Thomas White

2024-04-18	Address pipeline performance improvement changes which Tom requested.	Parthasarathy Tirumalai
	1) Remove MacOS native build job and build-brew-macos the only job for MacOS. 2) Make container builds manual.
2024-04-18	Reorder job stages so that maxwell deployment can start as soon as centos7 ↵	Parthasarathy Tirumalai
	build is done.
2024-04-17	CONTRIBUTING.md: Fix DOI link	Thomas White

2024-04-17	Update Homebrew formula to 0.11.0	Thomas White

2024-04-17	This is CrystFEL 0.11.00.11.0	Thomas White

2024-04-17	Add -f option to brew upgrade commands in the MacOS jobs.	Parthasarathy Tirumalai

2024-04-17	INSTALL.md: Fix link to crystfel.rb	Thomas White
	Needs to be a raw download.
2024-04-17	Update crystfel(7)	Thomas White

2024-04-17	Update INSTALL.md	Thomas White

2024-04-17	Update README.md	Thomas White

2024-04-16	Update INSTALL.md	Thomas White

2024-04-16	Update AUTHORS	Thomas White

2024-04-16	Tweak prediction refinement weightings	Thomas White

2024-04-16	alignment-test.jl: Plot shift/sigma (pull value)	Thomas White

2024-04-16	alignment-test.jl: Round peak coordinates to one pixel, to get realistic errors	Thomas White

2024-03-07	ASAP::O: Do not free image->data_block until we get the callback	Thomas White

2024-03-07	ASAP::O: Add even more debug for producer	Thomas White

2024-03-07	ASAP::O: Fix ingest flags for placeholders	Thomas White

2024-02-27	alignment_test.jl: Break plotting routine into 3	Thomas White

2024-02-27	Julia: Do polarisation correction via CrystFEL function	Thomas White
	The Julia-native correction was 50% slower.
2024-02-27	Julia: Move merging utils to separate module	Thomas White

2024-02-26	process_hkl.jl: Add polarisation correction	Thomas White

2024-02-26	Julia: RefList: Return indices as vectors, not tuples	Thomas White
	We're going to be doing a lot of linear algebra with these numbers, so this makes more sense.
2024-02-26	Julia: UnitCell: Add accessors for cell parameters and basis vectors	Thomas White

2024-02-26	stream_read_chunk: Set kpred to nominal wavelength	Thomas White
	This avoids having to awkwardly pass the wavelength separately, e.g. to the polarisation correction.
2024-02-22	julia/process_hkl.jl: Abstract stable running mean/variance	Thomas White

2024-02-21	Julia: Set finalizers for RefList and Crystal when taken from image	Thomas White

2024-02-21	Julia: chunkread: Expose option for reconstructing image data arrays/detgeom	Thomas White
	It makes a big performance difference to avoid creating these arrays. We will just need to deal with the fact that an Image might not have a DetGeom or data arrays. This commit also sets sensible chunkread options for allcrystals().
2024-02-21	Julia: RefList: Return nothing if no reflections in list	Thomas White