5 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	4f3153d6c7	rugnux: automatic CC1/2-logistic high-resolution cutoff ... Merge/report/write to the CC1/2 fall-off instead of the detector edge. After the final merge, fit a logistic to a fine-binned CC1/2 profile and cut one shell past cc_target (default 0.30) - generous, DIALS-style. Only the written MTZ/CIF and the reported shell table are trimmed; scaling, the 3D combine and the error model still run over the full range, and the per-image _process.h5 keeps full data for re-scaling. The de-novo P1 merge that feeds the space-group search is never cut (gated on the final merge). - ScalingSettings: resolution_cutoff {Off,CCHalfLogistic}, resolution_cc_target, report_shell_count (report shell count is now configurable). - New ResolutionCutoff.{h,cpp}: ComputeCCHalfLogisticCutoff (fine-bin CC1/2 + grid/refine logistic fit + one-shell extension + degeneracy/low-res guards). - Wired into RotationScaleMerge (rotation) and MergeOnTheFly/Rugnux (stills), plus the rugnux --scale path. - CLI: --resolution-cutoff cc-logistic|off, --resolution-cc-target, --resolution-shells. --scaling-high-resolution stays the manual override (wins and disables the auto-cut). Validated on the 24-crystal battery: no crashes (incl. Benas/cytC_10/Thau_9); --resolution-cutoff off is bit-identical to baseline; cutoffs reproduce the design table within ~0.05 A (lysoC 1.30, Ins_I 1.43, cytC_2 1.68, EcwtCQ244-E3 1.54); good-to-edge datasets (lyso_ref, EP_cs_02-10) correctly keep the full range. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-09 17:34:49 +02:00
leonarski_fandClaude Fable 5	dc8a80f3e0	viewer: fix HTTP live-follow OOM via datasetLoaded backpressure + shared pixel mask ... The viewer could grow to ~100 GB RAM when live-following an HTTP broker. The rc.153 images_in_flight backpressure only throttled imageLoaded; the heavy per-frame payload rides datasetLoaded, fanned out over ~10 queued cross-thread connections with no cap. In HTTPSyncDataset follow mode (entered when an operator clicks an image while following live) RefreshDatasetOnly_i emits a fresh full dataset every autoload tick with no imageLoaded, so the gate never engaged and the queued events - each pinning a full JFJochReaderDataset (full-detector PixelMask + per-image plots) - accumulated without bound. Backpressure datasetLoaded the same way as imageLoaded: a datasets_in_flight counter (cap 2), all emits routed through EmitDatasetLoaded_i, and AutoLoadTimerExpired gated on it (covers HTTPSyncDataset). The window routes the worker's datasetLoaded through a single OnDatasetReady sink that fans out synchronously via datasetReady and acks with datasetConsumed. Under load stale datasets are dropped; the next tick sends the latest. Share the pixel mask instead of deep-copying it: JFJochReaderDataset::pixel_mask is now shared_ptr<const PixelMask>, so per-frame dataset copies share the ~72 MB mask. UpdateUserMask does copy-on-write; JFJochHttpReader caches the mask by arm_date so a live refresh reuses one shared mask per acquisition. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-09 10:58:10 +02:00
leonarski_fandClaude Fable 5	51bfdd2b35	Fix acquisition error-handling and rugnux CLI issues from branch review ... Broker acquisition failure paths: - Report a truncated writer output / missing packets as errors ahead of the queue-full warning, so an incomplete dataset is no longer masked as a "reduce frame rate" warning. - Route PCIe/FPGA hardware faults to the Error state: make PCIeDeviceException a JFJochCriticalException, and stop JFJochServices::Stop() from slicing the caught exception (capture/rethrow via exception_ptr) so the critical type survives to the state machine. - Stop the (possibly partially-armed) detector, not just the receiver, when a detector arm fails, so the next start does not see it BUSY. - Return structured Error_message JSON for bind_json operation failures (e.g. a failed synchronous /start), matching the no-arg endpoints. rugnux CLI: - Default -N to all hardware threads, resolved once after parsing so full analysis, --azint-only and --scale behave the same. - Parse numeric option arguments strictly (reject non-numeric input and trailing garbage) instead of atof/stod, which silently yielded 0 or aborted the process; require --wavelength > 0. - Emit -R attached (-R100) in the reproduced command line so it re-parses. - Compare the reference MTZ against the cell that actually drives the merge in the --scale path. - Correct the --scaling-high-resolution help text and de-duplicate the offline-output experiment setup. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-08 15:48:01 +02:00
leonarski_fandClaude Fable 5	01e4f81e44	Consolidate offline tools into rugnux; merge on by default ... Fold jfjoch_azint and rugnux_scale into the single rugnux CLI, and flip scaling/merging from opt-in to on-by-default. - rugnux --azint-only replaces jfjoch_azint (reuses ProcessMode:: AzimuthalIntegration; adds the correction toggles and geometry overrides the old tool carried). - rugnux --scale replaces rugnux_scale (re-scale/merge stored reflections, same simpler scale/merge as before: no space-group search or rot3d defaults). Its workflow is folded into the CLI verbatim. - Merging is now on by default for rotation and stills; --no-merge disables it, replacing -M/--scale-merge. Also fix the batch ReadReflections reader so it works on rugnux's own NXmxIntegrated _process.h5: read per-image reflections/mosaicity/lattice from the master (global index) first, falling back to the source-data locator for legacy/VDS datasets. Without this, both --scale and the former rugnux_scale read zero reflections from an integrated snapshot. RugnuxCommandLine now emits `rugnux --azint-only` and `--no-merge`; docs and tests updated to match. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-08 14:09:15 +02:00
leonarski_fandClaude Opus 4.8	1caa57744a	Rebrand offline processing as rugnux (jfjoch_process -> rugnux) ... Split the naming: rugnux = data-processing subsystem, Jungfraujoch = streaming/acquisition. Executables jfjoch_process -> rugnux (source tools/rugnux_cli.cpp) and jfjoch_scale -> rugnux_scale; the processing library process/ -> rugnux/ with class/target JFJochProcess -> Rugnux (JFJochProcessObserver -> RugnuxObserver, JFJochProcessCommandLine -> RugnuxCommandLine). Doc JFJOCH_PROCESS.md -> RUGNUX.md, reconciled with the live usage message (drop dead -P/--partiality, -w/--wedge; --process-as-stills -> --force-still; add the real rot3d scaling knobs). New docs/NAMING.md explains both names, with pronunciation and a note on Romansh. rugnux now scales and merges rotation data automatically (implicit -M); stills still require an explicit -M. jfjoch_viewer and its classes keep their names (rename deferred); only their references to the renamed library are updated. The _process.h5 output suffix and ProcessConfig/Mode/Result are kept. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-07 22:46:58 +02:00