leonarski_fandClaude Opus 5
52f0e58cae
SmoothGeometry de-rotates each frame's lattice to a common reference, averages in frame order and rotates back. A frame that never indexed keeps a default-constructed CrystalLattice whose vectors are all ZERO - and zero is finite, so the isfinite guard let it through. Those zero vectors were averaged into their neighbours' smoothed orientation, pulling it toward the origin, and they were scored in the leave-one-out cross-validation that picks the smoothing window. On a crystal where 374 of 900 frames fail to index, the effect on the window choice is not subtle. Measured: before n_scored 900 (only 526 indexed) CV score ~504-542 A^2 window +-12 after n_scored 516-526 CV score 0.160-0.175 window +-2 The score was inflated ~3000x and the choice among windows was noise. It settled on +-12 frames - 9.6 degrees of goniometer rotation - on a crystal whose orientation genuinely drifts by ~8 degrees over the sweep, so every partial's delta_phi was recomputed from an orientation averaged across that drift. Require a real cell. Exactly inert when every frame indexes, and no threshold is touched. The crystal that exposed it goes P1 -> P2_1, observations 60107 -> 77021, completeness 64.1% -> 93.0%, multiplicity 1.10 -> 2.0, CC1/2 70.0% -> 84.9%, R_meas low shell 37.3% -> 22.1%, and its 2-fold operator CC 0.330 -> 0.669, comfortably clear of the 0.5 gate. Battery over 37 crystals: space groups 33/37 -> 34/37, and that crystal is the ONLY flip - no losses. Another crystal is rescued from near-total collapse (4402 -> 139213 observations) because the two-pass "going back to the header geometry" fallback stops firing. Anomalous peak height +0.043 +- 0.022 sigma over 7 crystals, so the background clip's gain is intact. Merged quality is otherwise neutral (CC1/2 6 better/6 worse, R_meas_lo 9/6) with observations up on 18 crystals. 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.