Jungfraujoch/docs/TOOLS.md

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 without arguments (rugnux has no -h).

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 <prefix>.poni and <prefix>.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 is not installed into any package.

jfjoch_recompress

Re-compresses /entry/data/data of a Jungfraujoch _data_NNNNNN.h5 file from bitshuffle/LZ4 to bitshuffle/Zstandard; every other object in the file is reproduced unchanged.

rugnux_refine_test

Runs the restrained refinement of a model against a rugnux merged MTZ without processing anything, for measuring the refinement on finished runs against another program on the same files. Prints the outcome and one JSON line for scripts.

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 — spot finding, indexing 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.

jfjoch_stream2_replay

Replays a stored dataset as the image stream of a DECTRIS detector (a ZeroMQ PUSH socket the broker's DECTRIS receiver connects to): start message, every image at the given rate, end message. With a stand-in for the detector's control interface the broker then runs a real collection with no detector.

jfjoch_stills_gpu_replay

Replays the frames of a stored serial collection through the broker's GPU analysis of converted JUNGFRAU frames: the pre-pass on the first images, then every frame analysed with the beam centre and mask it decided. Reports the pre-pass, the indexed fraction and the sustained rate.