2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	093069be29	rugnux stills: a given cell is matched in any setting, and per-image reindexing moves the lattice with the indices ... Three defects that stopped known-cell stills runs: - The consensus cell compared every frame's cell to -C axis by axis. A run whose frames index in another setting of the same lattice (axes in another order, another monoclinic choice) had no frame accepted, no consensus cell and no output ("No crystal lattice was determined"), although it merged fine. A frame whose lattice contains the given cell now counts on the given cell's axes (CellOnReference, the same FindSublatticeBases the merge-stage relabel uses). - The per-image ambiguity resolver relabelled a frame's reflections but left its lattice on the old axes. Everything after it predicts from index and lattice: the sublattice relabel put such a frame through a second transformation, and on a monoclinic cell with a near-symmetry (a+c nearly as long as a) the merge came out at indices finer than anything measured, shells over 100% complete. The lattice now follows the indices (ReindexLattice, B' = R^-1 B). - With -C/-S the stills path replaced the known-cell indexer's lattice, already on the given axes, by LatticeSearch's conventional choice, which on that near-symmetric cell is the other description on half the frames. The indexer's lattice is now kept when it is close to the given cell. Measured (cell + space group given, dimple against the deposited model and free set): - monoclinic MbCO-type still set: was over-complete/broken with --model; now 2.06 A, R/Rfree 0.233/0.314 at 2.11 A (P1 merge before: 0.275/0.306). - C-centred orthorhombic set: no MTZ before; now 3.27 A, R/Rfree 0.298/0.403 at 3.68 A (de novo 0.336/0.448). - monoclinic two-form set, one form: cell P 1 21 1 with beta (was alpha); Rfree 0.310 -> 0.260, 3.05 -> 2.72 A. - No change on seven other stills sets, nor on two rotation battery sets (5reo, lyso_x10sa_90deg_1). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>	2026-10-20 20:56:07 +02:00
leonarski_fandFilip Leonarski	19b135186d	v1.0.0-rc.175 (#85) ... * Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`). * Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection. * Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS). * Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead. * Rugnux: On macOS, Bragg integration runs on the Apple GPU. * Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand. * Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`. * Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit. * Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed. * Rugnux: The beam-stop shadow is found correctly on tilted detectors. * Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement. * jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps. * jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection. * jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images. * Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges. --------- Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home> Reviewed-on: #85 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-16 15:34:43 +02:00