leonarski_f
680c36c20d
Build Packages / Unit tests (push) Successful in 1h22m15s
Build Packages / build:windows:nocuda (push) Successful in 18m0s
Build Packages / build:windows:cuda (push) Successful in 20m30s
Build Packages / build:viewer-tgz:cpu (push) Successful in 10m32s
Build Packages / build:viewer-tgz:cuda (push) Successful in 11m39s
Build Packages / build:rugnux-tgz (x86_64) (push) Successful in 8m55s
Build Packages / build:rugnux:windows (push) Successful in 11m25s
Build Packages / build:rpm (rocky8_nocuda) (push) Successful in 20m6s
Build Packages / build:rpm (rocky9_nocuda) (push) Successful in 16m27s
Build Packages / build:rpm (ubuntu2204_nocuda) (push) Successful in 20m19s
Build Packages / build:rpm (ubuntu2404_nocuda) (push) Successful in 15m34s
Build Packages / build:rpm (rocky8_sls9) (push) Successful in 20m25s
Build Packages / build:rpm (rocky9_sls9) (push) Successful in 19m36s
Build Packages / build:rpm (rocky8) (push) Successful in 17m43s
Build Packages / build:rpm (rocky9) (push) Successful in 13m34s
Build Packages / build:rpm (ubuntu2204) (push) Successful in 21m28s
Build Packages / build:rpm (ubuntu2404) (push) Successful in 18m19s
Build Packages / DIALS test (push) Successful in 12m36s
Build Packages / XDS test (durin plugin) (push) Successful in 6m56s
Build Packages / XDS test (JFJoch plugin) (push) Successful in 6m48s
Build Packages / XDS test (neggia plugin) (push) Successful in 6m7s
Build Packages / Generate python client (push) Successful in 11s
Build Packages / Build documentation (push) Successful in 36s
Build Packages / Create release (push) Skipped
Build Packages / build:rugnux:aarch64 (cross) (push) Successful in 5m11s
* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands. * `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion. * Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants. * `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing. * A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed. * `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing. * Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences. * The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to. * The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after. * The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution. * `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have. * Twinning is no longer reported when the L-test contradicts it. * The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's. * `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots. * The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area. Reviewed-on: #76 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2.5 KiB
2.5 KiB
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.