3 Commits

Include renames

Author	SHA1	Message	Date
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