leonarski_fandClaude Opus 5
e77b96c4ce
jfjoch_broker's own page did not mention the analysis mode at all, and its "example with all fields" configuration was missing the three blocks that carry it. Both fixed, with a table of what each mode runs and a note that rotation MX is not offered online. The viewer page did not mention the grid-scan map. The rugnux mode tables in RUGNUX_ADVANCED.md and TOOLS.md were missing raster, and the advanced page was missing mx_rotation and mx_stills; its --raster-max-crystals default was stale, since an absent cap replaced 0 meaning "all". The changelog entries this work added were pruned to the house rule - one line, what changed, no rationale and no measurements - and the three that were missing were added: the two per-image detection scores, the viewer map, and the ice_ring_ratio rename with its accepted older spelling. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
3.2 KiB
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), calibration (detector geometry from a calibrant's powder rings, written
as <prefix>.poni and <prefix>.json) or raster (score every image of a stored grid scan and
report the crystals in it, written as <prefix>_raster_report.txt and <prefix>_raster.json).
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.