leonarski_fandClaude Opus 5
b8fa8e67d5
An audit of docs/ against the code at HEAD, concentrating on what landed after the previous documentation audit: the balanced half-set split and CCanom, the declared-range completeness denominator, the one rule for a quantity nobody measured, and the PONI the calibration now refuses to write. Five statements the code had made false: - The rotation merge's CCref column shows a dash, not "nan". - Two pages still promised unweighted 2Fo-Fc / Fo-Fc maps; they have been sigma_A-weighted since the rigid-body work, and one of the two sat six lines from a paragraph that said so. - Inserting the CCanom prose into the SigAno paragraph left the sentence about the PDBx items and the SigAno column with CCanom as its subject, so it read as a claim about a quantity that is in neither. CCanom is also rotation-only and is not in the mmCIF, which nothing said. - Two cross-references did not resolve - a heading that was renumbered, and a slug spelled without the hyphen MyST puts in "TCP/IP". Added where the behaviour is new and a user meets it: the report's contract for a quantity a run did not measure - no key, and a dash in the table, which is not the same claim as a measured zero; the half-set rule behind CC1/2, which is why a CUDA and a non-CUDA build now agree on it and on CCanom; and the second reason a calibration writes no .poni, a detector whose stored image is mirrored or quarter-turned, which the PONI format cannot state. The rc.166 changelog stays a release note. One entry is widened from the shell table to the rule it is a case of, and two are added for output that was wrong rather than merely undocumented: FITTED_RESOLUTION was the P1 cross-check's, and the unmerged MTZ carried the reference setting where the merged file carried the adopted one. Sphinx builds clean with -W on the pinned docs/requirements.txt, and every intra-doc anchor resolves against the generated HTML. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
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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 <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, 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.