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2025-01-03GUI: Add cancellation mechanism for single-image indexingThomas White
2025-01-03Add a private pointer to debug functionsThomas White
2025-01-02smallcell: Reduce verbosityThomas White
2024-12-20Fix memory allocation routinesThomas White
2024-12-20Merge branch 'smallcell'Thomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/merge_requests/35
2024-12-19CrystFEL support for the ffbidx indexer (implementation of the TORO algorithm)Hans-Christian Stadler
Repository and description: https://github.com/paulscherrerinstitute/fast-feedback-indexer TORO algorithm paper: https://journals.iucr.org/j/issues/2024/04/00/jo5098/index.html Please cite the paper if you do research with this algorithm. Use --help-ffbidx to see options and --indexing=ffbidx to use it with indexamajig.
2024-12-12Shorten long set_last_task namesThomas White
2024-12-12indexamajig: Add a load of set_last_task callsThomas White
"indexing:finalisation" covers a lot of steps, and jobs seem to have been hanging there recently. This should help unblock the pipeline.
2024-11-14indexamajig: Avoid duplicate indexer infoThomas White
A consequence of fork-exec is that each worker process prints the indexer info at startup. We often have >100 processes, so that's a lot of spam. With this commit, the indexer info is printed by a separate routine which has to be called explicitly by the top level. Indexamajig only does this for worker 0. If worker 0 gets re-spawned, we'll see the message again. That seems to be an acceptable trade-off. The indexer info now won't get printed by the GUI, unless we go back and add the call to print_indexing_info.
2024-11-14Remove image->idThomas White
It wasn't used anywhere, and never got set to the correct value anyway.
2024-10-28peakfinder8: Disable max-res cutoff by defaultThomas White
This changes the behaviour of peakfinder8 such that --max-res=0 disables the high-resolution cutoff completely. It then sets this value as the default for indexamajig and in the GUI. When peakfinder8 was first created, 1200 pixels was a generous cutoff. These days, we have many detectors that are much bigger and the default value for --max-res seems to create confusion.
2024-10-28all_panels_perpendicular_to_beam: Fix units problemThomas White
fsz and ssz are in units of pixels (of clen) per pixel (of pixel index). Therefore, the difference calculation result is in pixels. The limit is 10 pixels (of whatever panel). The old version was therefore far too conservative with what constitutes "flat"
2024-10-28Clarify that coffset/cnz_offset is in metresThomas White
2024-10-22Add u1 format for SeedeeThomas White
2024-10-18Fix memory leak in powder_rings()Thomas White
2024-10-18smallcell: Fix memory leaksThomas White
2024-10-18smallcell: Simplify fit_cellThomas White
2024-10-18smallcell: Keep list of biggest cliquesThomas White
Instead of complaining when we run out of space, replace the smallest clique with the latest one (but only if the latest one is bigger).
2024-10-18smallcell: Add missing check for right-handed cellThomas White
2024-10-18smallcell: Replace list manipulation with qsortThomas White
2024-10-18smallcell: Move find_max_cliques into separate functionThomas White
2024-10-17smallcell: Tweak debugging messagesThomas White
2024-10-17FormattingThomas White
2024-10-17smallcell: Move tolerances into respective proceduresThomas White
No need to have these magic numbers far away.
2024-10-17smallcell: Move link_nodes into separate routineThomas White
2024-10-17smallcell: Break associate_to_rings out into separate functionThomas White
2024-10-17smallcell: Reduce comment verbosityThomas White
2024-10-16smallcell: Fix double freeThomas White
These are copies of Nodelists already in Max_cliques.
2024-10-16smallcell: Formatting and elimination of redundant variablesThomas White
2024-10-16smallcell: Move SymOpMask outside loopThomas White
2024-10-16smallcell: Move d_2 calculation to separate functionThomas White
2024-10-16smallcell: Fix array size and potential overrun of clique listThomas White
2024-10-16smallcell: Free pivot pool earlierThomas White
2024-10-16smallcell: Factorise creation of NodelistsThomas White
2024-10-16smallcell: Move find_pivot to separate routine (+ fix it)Thomas White
2024-10-16smallcell: Fix help messageThomas White
2024-10-16smallcell: Simplify tolerance calculationThomas White
2024-10-16smallcell: Factorise avg_weightThomas White
2024-10-16Fix up indentation style and commentsThomas White
2024-10-15smallcell: Code tidy-up part 1Thomas White
2024-10-15Move powder ring enumeration routine into libcrystfelThomas White
It's now shared between cell_tool and smallcell
2024-10-15smallcell: Replace C99-style loop declarationsThomas White
Should enable build on CentOS7 without messing around with the compiler options.
2024-10-15Implement smallcell indexing algorithmIsabel Costello
2024-10-15Increase maximum number of panel groupsThomas White
LPD already ran into the old limit.
2024-10-15Merge branch 'fork-exec' into 'master'Thomas White
indexamajig: exec() after fork() Closes #92 See merge request thomas.white/crystfel!36
2024-10-14Move set_last_task and sandbox ping into global routinesThomas White
This breaks the dependency of libcrystfel routines on the indexamajig sandbox. This also adds the missing queue_lock needed in set_last_task().
2024-10-14Replace stream_get_fd() with stream_get_fh()Thomas White
This is only used in one place, not really necessary, and encourages mixing stdio with OS-level writes.
2024-10-14indexamajig: New memory-based data pumpThomas White
This simplifies the code somewhat, removes some old cruft, and allows most of the same pump code to be used for Mille data as well as stream data. Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/92
2024-10-14Remove old MEASURE_INDEX_TIME codeThomas White
We don't need this because we have the proper profiling code now. To be honest, I'd forgotten this code was still there.
2024-09-27Allow panel group definitions to come at the top of the geometry fileThomas White
Nasty code, but will save a lot of hassle. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/115
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