3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	100fe7b7e7	PixelRefine: make factored Terms 1+2 the model, remove old wiring ... PixelRefine is now an intensity-only operation: geometry is fixed (refined upstream by XtalOptimizer) and the only objective is the factored per-reflection likelihood (FACTORED_MODEL.md Terms 1+2) - measured per-resolution profile width R1 plus one Fisher-weighted intensity/scaling residual per reflection, fitting the per-image scale G and B. Validated on crystal 2 (fixed_master.h5 as stills, 1.7 A): CC1/2 84-92%, CCref 77-92%, flat - reproduces the env-flag prototype and matches the rotation path from the stills path. Removed: - the per-pixel ShoeboxResidual loss and PixelResidual cost functor; - all in-PixelRefine geometry refinement (orientation/cell/beam/distance/R), the regularised-orientation LSQ, signal-weighting, and the global sweep; - Term 3 (per-spot recentring) - a confirmed no-op on both crystals; - the diagnostic scaffolding (covariance, centroid, adaptive_R1) and the PR_* env knobs + stderr dumps in IndexAndRefine; - the PredictImage/ChiSquaredImage renderers and the entire viewer PixelRefine window/table/params + worker bindings + shoebox overlay. The sweep box-integrator background median became mean (consistency) by virtue of removing the sweep. METHODS.md rewritten for the current model; findings recorded in FINDINGS-2026-06.md. Net -2200 lines. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-13 22:02:18 +02:00
leonarski_fandClaude Opus 4.8	e6a50b45c7	Integration: mean background + global error model (trustworthy sigmas) ... Background estimate: use the mean of the local ring, not the median. For a right-skewed (Poisson) background the median sits below the mean, so subtracting it under-subtracts and biases every weak intensity positive; over multiplicity this becomes fake <I/sig> of a few in no-signal high-resolution shells. Fixed in both PixelRefine and BraggIntegrate2D (the classical route had the same bug). <I/sig> now tracks CC honestly and the true resolution limit is visible. Error model: fit a global a, b (XDS form sigma'^2 = a*sigma^2 + (b*I)^2) from the scatter of symmetry equivalents at the merge level (so both integrators benefit), and print it with ISa = 1/b in jfjoch_process. The (b*I)^2 term uses the reflection mean (not the per-observation I_i, which biases the weights and collapses CC); a,b come from a relative-weighted bin regression. Replaces the earlier per-resolution-shell variant, which was partly masking the background bias. METHODS.md: document both (Sections 6-7), integrator-agnostic. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-12 18:39:32 +02:00
leonarski_f	3cdf26232c	PixelRefine: Document on local changes	2026-06-12 17:29:28 +02:00