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leonarski_fandClaude Opus 4.8 100fe7b7e7 PixelRefine: make factored Terms 1+2 the model, remove old wiring
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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 6f2033db00 PixelRefine: checkpoint before cleanup (factored model + all diagnostic levers) 
Snapshot of the messy state: factored likelihood Terms 1+2+3 behind PR_*
env flags (PR_INTENSITY/PR_SHAPE/PR_RECENTER) alongside the old per-pixel
ShoeboxResidual, plus diagnostic scaffolding (PR_R0/R1/COV/FIX_R0/FIX_R/
ADAPT_R1/CENTROID/RECENTER) and the FACTORED_MODEL.md spec. Next commit
makes Terms 1+2 the model and strips all of this.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
 2026-06-13 21:34:33 +02:00