leonarski_fandClaude Opus 5
323c76abde
Ten places where the document and the implementation had drifted apart.
Each was checked against the source before rewriting:
* 7.5 rotation post-refinement: it is TWO separate cross-validated
steps (cell+axis from the angles, then distance+beam from the
positions with the cell fixed), not one joint fit against the merged
fulls; the held-out split is an hkl hash, not a frame split; the
bounds are +-5% on distance and +-15 px on the beam, not "under
~1%"; and only the distance and beam centre reach pass 2, which
re-indexes de novo.
* 9.2 the trimmed-mean background: it is computed in the shared
background pass, so it DOES apply to --integrator boxsum. Only the
broadband sigma-clip is excluded. The section previously said both,
contradicting itself two paragraphs apart.
* 9.3 per-reflection profile rebuild, sub-pixel centring and radial
elongation are gaussian-only; the empirical profile keeps the fixed
per-shell grid and is accumulated on rounded predicted positions,
not centroids.
* 10.5 the asymptotic ISa and the b_ISa sigma floor are rotation-only;
stills report 1/b and floor with the whole-range b.
* 8.4 centering absences are applied only when the user fixes the
space group - de novo, prediction runs in P so the search can
confirm the centering from the intensities.
* 10.6 per-batch relative-B cross-validates on ASU-group parity, not
the frame parity the other surfaces use.
* 13 the resolution cutoff sits one reported-shell width PAST the
CC1/2 = 0.30 crossing, so data below 0.30 are kept.
* 7.1 the orientation-only prior penalises all three components of the
angle-axis vector.
* 10.1 rlp is the RECIPROCAL Lorentz factor, L = 1/rlp.
* 14.3 the model scaling is fitted over work and free reflections
alike, so R-free is free of refinement, not of the scaling fit.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Jungfraujoch
Application to receive data from the PSI JUNGFRAU and EIGER detectors.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.