leonarski_f
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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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Tools
Besides the main services (jfjoch_broker,
jfjoch_writer, jfjoch_viewer), the repository ships a
number of command-line tools. Each prints its own usage when run with -h or without arguments.
Data analysis
rugnux
Offline CLI tool that runs the full crystallographic analysis pipeline (spot finding, indexing,
integration, scaling/merging) on a stored HDF5 dataset, producing a _process.h5 file and, when
merging, reflection files. Merging is on by default (--no-merge disables it). Two extra modes
narrow the work: --azint-only runs only azimuthal integration (no spot finding/indexing), and
--scale re-scales/merges the already-integrated reflections in a _process.h5 without
re-integrating. See rugnux.
jfjoch_extract_hkl
Extracts reflections (HKL list) from a Jungfraujoch master file; can sum the same HKL across
neighbouring images and compare against an XDS INTEGRATE.HKL reference.
FPGA / PCIe card management
jfjoch_pcie_status
Prints detailed status information about the card. Safe to run during data collection:
./jfjoch_pcie_status /dev/jfjoch0
jfjoch_pcie_net_cfg
Reads and modifies the network configuration of the card's interfaces:
jfjoch_pcie_net_cfg <device name>
Read configuration for all network interfaces of a device
jfjoch_pcie_net_cfg <device name> <if number>|fgen
Read configuration for a particular network interface / internal frame generator
jfjoch_pcie_net_cfg <device name> <if number>|fgen ipv4 <IPv4 address>
Set IPv4 address for a particular network interface / internal frame generator
jfjoch_pcie_net_cfg <device name> <if number>|fgen direct 0|1
Set direct mode for a particular network interface / internal frame generator
jfjoch_pcie_net_cfg <device name> <if number>|fgen clear
Clear Ethernet counters for a particular network interface / internal frame generator
jfjoch_pcie_clear_net_counters
Resets the card's Ethernet, UDP and ICMP packet counters (which otherwise run from power-on):
./jfjoch_pcie_clear_net_counters /dev/jfjoch0
Testing, benchmarking and simulation
jfjoch_udp_simulator
UDP packet simulator used to test the Jungfraujoch FPGA receiver.
jfjoch_fpga_test
Exercises and benchmarks the FPGA data path and receiver. With -H it runs the high-level
synthesis C model on the CPU, so no FPGA device is required.
jfjoch_lite_perf_test
Performance test of the lite (CPU/GPU) analysis path — indexing, integration and optional file writing.
jfjoch_hdf5_test
Tests single-threaded HDF5 writer performance.
jfjoch_simplon_test
Minimal test client for a DECTRIS SIMPLON detector API.