3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	e3da313c84	reader: a goniometer whose inner circle is inclined says so in its axis table ... A fixed-chi stage carries phi at a standing angle to the base circle, and states that angle in the CBF _axis table and nowhere else - its "# Chi" line reads 0.0000, because no chi circle is driven. ParseAxisTable kept only rotation axes hanging off nothing, so the inclination was discarded and RotationAxis() fell back to that zero: a phi scan was run about the base axis, tens of degrees from the one the crystal actually turned about. Measured on a magic-angle head 54.74 degrees off omega: the axis goes from 1 0 0 to 0.577382 -0.707087 -0.408237, against dxtbx's 0.5774 -0.7071 -0.4083, and the first pass from a P-centred triclinic 27.2 58.1 126.2 that indexes nothing to P-orthorhombic 5.16 14.05 14.81, which is the cell DIALS and XDS both reach on these frames. The mirrored inclination returns to nothing, so it is that angle and not any perturbation of the axis. Every other header in the corpus states one rotation axis, which is every Eulerian head, and is untouched. The two that share this table were written three days later by a template that puts the same angle on the "# Chi" line, agreeing to 0.03 degrees - they read identically either way. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011GxZqDiFP3KqriBhNdcR56	2026-09-13 15:02:04 +02:00
leonarski_f	77bc0cfe52	v1.0.0-rc.168 (#78) ... * rugnux is substantially faster - a corpus of 145 rotation datasets processes in about two thirds of the time - with identical results. * A crystal whose lattice looks more symmetric than it is because the beam centre is off is no longer processed on the wrong cell. * rugnux prints at startup, and writes at the foot of every results report, a short acknowledgement of the X-ray research community whose methods it implements and of the open-source projects it builds on; `ACKNOWLEDGEMENT.md` now ships in every package beside `LICENSE` and `THIRD_PARTY_NOTICES.md`. Reviewed-on: #78 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-10 13:51:16 +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