leonarski_f
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* `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>
35 lines
2.5 KiB
Markdown
35 lines
2.5 KiB
Markdown
# What rugnux reads
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Which data `rugnux` opens, before anything is typed. The short answer: an HDF5 master (NXmx or
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DECTRIS, from any facility) or a PILATUS miniCBF sweep — nothing else is read, so any other format
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has to be converted to one of these two first.
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**Input** is either an HDF5 master file or a directory of PILATUS miniCBF frames. One input is
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**one sweep of one crystal** — rugnux does not combine sweeps or crystals in a run; process each
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sweep to its own `_unmerged.mtz` and merge them downstream
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(see [Taking the data onward](RUGNUX_INTEGRATION.md#taking-the-data-onward)).
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* **HDF5 master (NXmx-based)** — a file written by [`jfjoch_writer`](JFJOCH_WRITER.md), a DECTRIS
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EIGER master, or an NXmx master written by another facility's toolchain. Lengths are taken in the
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unit the file declares, the image size from the image array's own shape, and each data file's
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images at the path the master's own link names, so masters that state single values as one-element
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arrays, compose their images as a virtual dataset over the master itself, or keep them somewhere
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other than `/entry/data/data` all open. Where the NXmx spellings are absent the pre-NXmx ones are
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tried, so a DECTRIS firmware 1.x master opens too — including its goniometer, which used to be
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missed and the sweep read as stills. Images may be `bitshuffle`+LZ4/Zstd or the HDF Group's plain
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LZ4 (filter 32004); any other filter is named in the error.
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* **PILATUS miniCBF sweep** — one frame per file, read natively with no conversion and no libcbf.
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Name **any frame of the sweep**, or the directory holding it, and the whole sweep is processed:
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the frames are the ones matching that frame's template (prefix plus digit count), so a directory
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holding two sweeps is not spliced into one crystal, and naming a directory takes the sweep with
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the most frames in it. The geometry, the rotation axis and the detector mounting come from the
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header, including the imgCIF axis table where the header carries one (see
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[Detector geometry](DETECTOR_GEOMETRY.md)). A raw CBF carries no analysis results, so
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`--mode scale` — which re-scales the reflections stored in a `_process.h5` — does not accept one.
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Spots are always found by `rugnux` itself, including for the two-pass rotation first pass — the
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spot lists a dataset may already carry were found online, at the acquisition's threshold and with
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its ice-band spots already discarded, so reusing them would hide the spot-finding settings from
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the lattice search.
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