leonarski_f
cfcd4c9e56
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Full-jet R-free showed the factored model regressed vs the traditional pipeline (R-free 0.34 vs 0.26, CCref 58 vs 76), traced to Term 2 using the raw measured profile width: it is too tight (~0.002 A^-1), so the template sits off the ~0.4 px centroid-floor scatter and underestimates the intensity (box-sum is immune). Fix, XDS-style (integrate over ~6 sigma): multiply the measured R1 by r1_multiplier (default 6) before use. On the jet at 1.3 A this recovers CCref 55.2 -> 59.3 (~ traditional's 60.5); crystal 2 -0.7. Tunable via env PR_RMULT for R-free. Also reinstates the pre-factored per-image orientation refinement (per-pixel ShoeboxResidual against the shoebox, regularised to the spot-centroid orientation, re-predict), behind env PR_ORIENT (off by default), to A/B its effect on serial-data R-free. On the jet CCref it is a no-op (XtalOptimizer orientation already at the optimum), but CCref is a weak R-free proxy here, so it is left for R-free validation. NOTE: PR_RMULT / PR_ORIENT are temporary diagnostic env knobs; the final multiplier value and the orientation-refine decision are to be fixed against R-free, then baked. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>