3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	fbebc0d56e	rugnux: run decay + absorption surfaces on the GPU and enable by default ... The decay/absorption correction surfaces previously forced the CPU 3D combine (absorption needs each full's predicted detector position, which the GPU SoA did not carry), so they could not be default-on without losing the fast GPU path. Put them on the GPU: - carry px/py (peak partial) through the GPU combine and download them with the fulls (GetFullsPxPy); - add SetFullsCorr to re-upload the host-corrected corr to the resident fulls before the merge. The surfaces themselves stay as cheap host fits on the downloaded fulls; only px/py download + corr upload are added (~two O(n_fulls) transfers). Measured +2% wall-time on lyso_ref (9.7 -> 9.9 s), and the GPU-combine and CPU-combine (--dump-observations) paths give identical results. Enable by default via a single master toggle ScalingSettings:: CorrectionSurfaces (default true; decoupled from the stills-only -B, which is rejected for rotation again). Both surfaces are cross-validated, so they no-op where their systematic is absent - safe to leave on. Off-switch wired through the rugnux CLI (--no-scaling-corrections; --absorption removed) and the viewer (a "Correction surfaces" checkbox). Documented in docs/RUGNUX.md. Battery (24 rotation crystals), default-on vs --no-scaling-corrections: EcwtCQ066S +2.4 ISa, lyso_ref +0.5 (and R-free 0.194 -> 0.185, better than XDS); every other crystal within run-to-run noise; corrections skip (CV / dB-floor) wherever there is no signal. lyso_ref anomalous S/Cl peaks are already ~45% above XDS's - the ISa gap is metric convention, not data. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-12 10:56:39 +02:00
leonarski_fandClaude Opus 4.8	bab52a8077	rugnux: optional decay + absorption correction surfaces for rotation scaling ... After scale-fulls, RotationScaleMerge can now fit two optional multiplicative corrections on the combined fulls (both off by default, rotation only): - -B (decay): a global Debye-Waller relative-B rate for radiation damage, ln(Iref/Iobs) = 2 (dB/dn)(n - nbar) s^2, folded into the per-full scale. Engages only above a physical floor (total relative-B > 2 A^2), so it is a no-op on low-dose data. (-B was previously rejected for rotation.) - --absorption[=iter]: a smooth factor over the diffracted-beam direction in the goniometer frame (predicted detector position de-rotated by the spindle, so a crystal-frame direction is sampled at many angles). Wires the existing ScalingSettings::absorption_iter scaffold. Negligible at hard X-rays; matters at low energy. On lyso_ref it is ISa-neutral (+0.5) but drops R-free 0.219 -> 0.212 against the deposited model: a smooth absorption error cancels among symmetry mates (small ISa effect) yet still biases the intensities (real R-free effect). Both are CROSS-VALIDATED: the surface is fit on even frames and applied only if it improves the held-out odd-frame equivalent agreement by a clear margin (and vice versa), so a fit to noise where the systematic is absent does not generalize and is discarded - the correction never adds scatter. Battery: EcwtCQ066S +2.4 ISa, lyso_ref R-free win, others neutral. Also fixes a latent bug this exposed: the GPU->host corr download before the CPU 3D-combine was gated on --dump-observations only, so any other forced-CPU-combine path (the new -B/--absorption) read a stale host corr and mis-scaled every full. The download condition now matches the CPU-combine condition. Predicted detector position (px, py) is carried on the combined fulls for the absorption surface (CPU combine only; unused by the GPU SoA path). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-12 10:14:00 +02:00
leonarski_fandClaude Opus 4.8	f737424bdf	rugnux: move rugnux_cli.cpp from tools/ to rugnux/ ... The offline analysis CLI belongs next to its Rugnux library. Move the source and the ADD_EXECUTABLE(rugnux ...) target (plus the Windows wingetopt link) into rugnux/CMakeLists.txt; the ../reader, ../common, ../image_analysis includes are unchanged (both dirs sit one level under the root) and ../rugnux/Rugnux.h becomes a local Rugnux.h. rugnux/ is added before tools/ in every build config, so viewer-only and Windows packages still get the CLI. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-11 22:39:12 +02:00