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leonarski_fandClaude Opus 5 376aa0a2e0 docs: split RUGNUX.md into one page per job, and put rugnux first

The 1274-line page becomes a landing page (quick start, the page map, where it
fits) plus seven pages a reader can answer one question from: installing,
what rugnux reads, running it, integration with other programs, the results
report, advanced usage, and powder calibration. Content is moved, not
rewritten - only the connective sentences at each page top are new. Every
internal anchor is remapped to its new page and every inbound link
(DEPLOYMENT, TOOLS, HDF5, CPU_DATA_ANALYSIS) updated; the built site has zero
Sphinx warnings and an anchor check over the rendered HTML finds no dead
link. index.rst leads with the rugnux group, then acquisition, FPGA,
reference and project.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N

2026-09-02 09:18:36 +02:00

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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). --mode picks what a run does: mx (the above, the default), azint (only azimuthal integration, no spot finding/indexing), scale (re-scale/merge the already-integrated reflections in a _process.h5 without re-integrating) or calibration (detector geometry from a calibrant's powder rings, written as a .poni file). See rugnux.

rugnux installs on its own, as the rugnux package or as a standalone archive — see Installing 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. A developer utility: it is built from source but, like jfjoch_recompress, is not installed into any package.

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.

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