leonarski_f
54c0100e8e
This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`. * rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling. * rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics. * rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1. * rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group. * rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix. * jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation. * jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning. * jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint. * jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed). * jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types. * jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails. * jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak. * Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation. * CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
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Naming
The software is Swiss, and so are its names: both halves of the system are named after places in the Alps that are, in one way or another, about moving a lot of something up a steep mountain as efficiently as possible — usually by train. Throughput, in other words.
| Part | Name | What it does |
|---|---|---|
| Streaming / acquisition | Jungfraujoch | Receives detector data at high data rates, runs the FPGA/GPU pipeline, and streams images out for writing. |
| Data processing | Rugnux | Offline crystallographic analysis of a stored dataset — indexing, integration, scaling and merging (the rugnux tool). |
Jungfraujoch
The Jungfraujoch is a high mountain col in the Bernese Alps, the saddle (Joch is German for "yoke" or "col") between the peaks Jungfrau and Mönch, at 3,466 m. It is the site of the High Altitude Research Station Jungfraujoch, whose long-running atmospheric measurements are co-operated by the Paul Scherrer Institute — the same institute that develops this software and the JUNGFRAU detector.
The name is also a small piece of word-play. PSI's JUNGFRAU detector and DECTRIS's EIGER detector are both named after Bernese Alps peaks (the famous trio is Eiger, Mönch, Jungfrau). The Jungfraujoch — the pass between Jungfrau and Mönch — is where those two detector worlds meet.
And it fits the theme of the whole project: the Jungfraujoch is reached by the Jungfraubahn, whose terminus is the highest railway station in Europe (3,454 m, the "Top of Europe"). It is the closest you can get to that summit in a genuinely high-throughput way — by train, moving crowds up the mountain — which is exactly what the streaming side of this software does with detector frames.
Pronunciation (German): Jungfraujoch ≈ YUNG-frow-yokh. "Jung" as in young, "frau" rhymes with cow, and the final "joch" ends in the guttural ch of Scottish loch or German Bach — not a hard k.
Rugnux
Piz Rugnux is a mountain in the Rhaetian Alps of canton Graubünden, in south-eastern Switzerland. (Piz is the Romansh word for "peak".) It rises above the Albula line of the Rhaetian Railway (Rhätische Bahn), part of the "Rhaetian Railway in the Albula / Bernina Landscapes" — a UNESCO World Heritage Site (Welterbe).
That stretch of line is a masterpiece of throughput engineering: to climb a great deal of altitude in very little horizontal distance, it corkscrews through a series of helical (spiral) tunnels looping back inside the mountains. It is, again, the Swiss art of getting an enormous amount up a steep mountain efficiently — the same idea the data-processing side of this software is built around: pushing a large volume of diffraction data through the analysis pipeline.
So the theme is consistent — Swiss mountains, trains, and throughput — while keeping the two subsystems clearly distinct: Jungfraujoch streams, Rugnux processes.
Pronunciation (Romansh): Piz Rugnux ≈ peets roo-NYOOKS. The "gn" is a soft palatal ñ, as in canyon or Italian gnocchi, not two separate sounds.
What is Romansh?
Romansh (Rumantsch) is the fourth national language of Switzerland, alongside German, French and Italian. It is a Romance language — a direct descendant of the spoken Latin left behind in the Alpine valleys — today spoken by only a few tens of thousands of people, almost all in the canton of Graubünden. It survives in several regional idioms, brought together in a standard form called Rumantsch Grischun. Naming the processing engine with a Romansh mountain is a small nod to the least-spoken but no-less-Swiss corner of the country.