leonarski_fandClaude Opus 5
376aa0a2e0
The 1274-line page becomes a landing page (quick start, the page map, where it fits) plus seven pages a reader can answer one question from: installing, what rugnux reads, running it, integration with other programs, the results report, advanced usage, and powder calibration. Content is moved, not rewritten - only the connective sentences at each page top are new. Every internal anchor is remapped to its new page and every inbound link (DEPLOYMENT, TOOLS, HDF5, CPU_DATA_ANALYSIS) updated; the built site has zero Sphinx warnings and an anchor check over the rendered HTML finds no dead link. index.rst leads with the rugnux group, then acquisition, FPGA, reference and project. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
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What rugnux reads
Which data rugnux opens, before anything is typed. The short answer: an HDF5 master (NXmx or
DECTRIS, from any facility) or a PILATUS miniCBF sweep — nothing else is read, so any other format
has to be converted to one of these two first.
Input is either an HDF5 master file or a directory of PILATUS miniCBF frames. One input is
one sweep of one crystal — rugnux does not combine sweeps or crystals in a run; process each
sweep to its own _unmerged.mtz and merge them downstream
(see Taking the data onward).
- HDF5 master (NXmx-based) — a file written by
jfjoch_writer, a DECTRIS EIGER master, or an NXmx master written by another facility's toolchain. Lengths are taken in the unit the file declares, the image size from the image array's own shape, and each data file's images at the path the master's own link names, so masters that state single values as one-element arrays, compose their images as a virtual dataset over the master itself, or keep them somewhere other than/entry/data/dataall open. Where the NXmx spellings are absent the pre-NXmx ones are tried, so a DECTRIS firmware 1.x master opens too — including its goniometer, which used to be missed and the sweep read as stills. Images may bebitshuffle+LZ4/Zstd or the HDF Group's plain LZ4 (filter 32004); any other filter is named in the error. - PILATUS miniCBF sweep — one frame per file, read natively with no conversion and no libcbf.
Name any frame of the sweep, or the directory holding it, and the whole sweep is processed:
the frames are the ones matching that frame's template (prefix plus digit count), so a directory
holding two sweeps is not spliced into one crystal, and naming a directory takes the sweep with
the most frames in it. The geometry, the rotation axis and the detector mounting come from the
header, including the imgCIF axis table where the header carries one (see
Detector geometry). A raw CBF carries no analysis results, so
--mode scale— which re-scales the reflections stored in a_process.h5— does not accept one.
Spots are always found by rugnux itself, including for the two-pass rotation first pass — the
spot lists a dataset may already carry were found online, at the acquisition's threshold and with
its ice-band spots already discarded, so reusing them would hide the spot-finding settings from
the lattice search.