2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	6140de7249	rugnux: the unmerged MTZ carries the sensor efficiency in its own column, not inside LP ... LP is a column other programs read and un-apply. It is documented as the Lorentz-polarization factor, and until the sensor efficiency was folded into the same product that is what it held. Measured on our own unmerged file, LP spanned a factor of 1.1343 across the detector where pure L/P spans nothing of the sort - the excess is the efficiency, 13% end to end at 13 keV and 34% at 18 keV. Both reference implementations keep it out. Recomputing pure L/P from a stored XDS file's own geometry over its 124k reflections leaves RLP flat to 0.1% from 8.6 to 33.7 degrees, where a folded-in efficiency would have shown a 7% trend - and XDS has the sensor numbers in hand. DIALS fills LP from lorentz and polarization alone and writes QE as a separate column, even a column of ones. Split them: LP is L/P again, QE is the efficiency, and the intensity is unchanged, so a reader that un-applies LP recovers what it expects and one that wants raw counts divides by LP and multiplies by QE. Only the unmerged file moves - every other column is bit-identical and the file grows by exactly one float per reflection plus one header record. The merged files are byte for byte what they were. The process file gains an optional qe dataset beside the existing one rather than changing what that one means, so a file written before the efficiency existed still loads, and reads back as a correction of exactly one - which is what it was. It is stored rather than recomputed on read because the writer has no geometry to recompute it from, and because recomputing would have written a radial trend into every stored file that never had one. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-05 14:29:45 +02:00
leonarski_f	680c36c20d	v1.0.0-rc.166 (#76) ... * `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>	2026-09-02 21:17:31 +02:00