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
72 lines
3.0 KiB
Markdown
72 lines
3.0 KiB
Markdown
# Tools
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Besides the main services ([`jfjoch_broker`](JFJOCH_BROKER.md),
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[`jfjoch_writer`](JFJOCH_WRITER.md), [`jfjoch_viewer`](JFJOCH_VIEWER.md)), the repository ships a
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number of command-line tools. Each prints its own usage when run with `-h` or without arguments.
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## Data analysis
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### rugnux
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Offline CLI tool that runs the full crystallographic analysis pipeline (spot finding, indexing,
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integration, scaling/merging) on a stored HDF5 dataset, producing a `_process.h5` file and, when
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merging, reflection files. Merging is on by default (`--no-merge` disables it). `--mode` picks what a
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run does: `mx` (the above, the default), `azint` (only azimuthal integration, no spot
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finding/indexing), `scale` (re-scale/merge the already-integrated reflections in a `_process.h5`
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without re-integrating) or `calibration` (detector geometry from a calibrant's powder rings, written
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as `<prefix>.poni` and `<prefix>.json`). See [rugnux](RUGNUX.md).
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`rugnux` installs on its own, as the `rugnux` package or as a standalone archive — see
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[Installing rugnux](RUGNUX_INSTALL.md).
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### jfjoch_extract_hkl
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Extracts reflections (HKL list) from a Jungfraujoch master file; can sum the same HKL across
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neighbouring images and compare against an XDS `INTEGRATE.HKL` reference. A developer utility: it is
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built from source but, like `jfjoch_recompress`, is not installed into any package.
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## FPGA / PCIe card management
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### jfjoch_pcie_status
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Prints detailed status information about the card. Safe to run during data collection:
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```
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./jfjoch_pcie_status /dev/jfjoch0
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```
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### jfjoch_pcie_net_cfg
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Reads and modifies the network configuration of the card's interfaces:
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```
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jfjoch_pcie_net_cfg <device name>
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Read configuration for all network interfaces of a device
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jfjoch_pcie_net_cfg <device name> <if number>|fgen
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Read configuration for a particular network interface / internal frame generator
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jfjoch_pcie_net_cfg <device name> <if number>|fgen ipv4 <IPv4 address>
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Set IPv4 address for a particular network interface / internal frame generator
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jfjoch_pcie_net_cfg <device name> <if number>|fgen direct 0|1
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Set direct mode for a particular network interface / internal frame generator
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jfjoch_pcie_net_cfg <device name> <if number>|fgen clear
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Clear Ethernet counters for a particular network interface / internal frame generator
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```
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### jfjoch_pcie_clear_net_counters
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Resets the card's Ethernet, UDP and ICMP packet counters (which otherwise run from power-on):
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```
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./jfjoch_pcie_clear_net_counters /dev/jfjoch0
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```
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## Testing, benchmarking and simulation
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### jfjoch_udp_simulator
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UDP packet simulator used to test the Jungfraujoch FPGA receiver.
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### jfjoch_fpga_test
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Exercises and benchmarks the FPGA data path and receiver. With `-H` it runs the high-level
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synthesis C model on the CPU, so no FPGA device is required.
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### jfjoch_lite_perf_test
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Performance test of the lite (CPU/GPU) analysis path — indexing, integration and optional file
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writing.
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### jfjoch_hdf5_test
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Tests single-threaded HDF5 writer performance.
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### jfjoch_simplon_test
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Minimal test client for a DECTRIS SIMPLON detector API. |