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leonarski_fandClaude Opus 5 b8fa8e67d5 docs: the pages catch up with the last day on rc166

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

2026-09-02 17:44:20 +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 <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.

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