The rot3d combine over-extrapolates fulls reconstructed from only a fraction f
of their rocking curve (min_partiality admits f as low as 0.02). Against XDS on
HEWL these low-capture fulls are systematically biased HIGH (+15% at f=0.8 to
+100% at f=0.3), and the bias - not random scatter - is the strong-reflection
floor that hurts anomalous accuracy.
--capture-uncertainty <coeff> (default 0 = off, baseline bit-identical) adds a
systematic uncertainty ~coeff*(1-f)*I to each full's sigma, so the merge
down-weights the over-extrapolated fulls and the error model treats their
scatter as expected. Unlike outlier rejection (which trades accuracy for CC1/2),
this fixes a real bias, so accuracy improves: at coeff=1.0 the anomalous peak
height vs XDS rises CL_CL +16%, SD_MET/SG_CYS +5-6%, ISa 10.7->11.0. Rotation-
only (no-op for stills, which never combine).
Also expose the per-image scale offline: Combine3D now carries the first-pass
per-image scale metadata (G, B, mosaicity, wedge, CC) forward instead of
dropping it, and jfjoch_process -M writes <prefix>_image.dat from it (the
offline self-scaling result was otherwise unobservable - process.h5's per-image
arrays are only filled on the online path). This enabled the XDS DECAY
comparison (jfjoch G tracks XDS, r=0.93).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
leonarski_fandClaude Opus 4.8
ed98775ba3