On the LysozymeJet5 serial stills the default Gaussian profile-fit
integrator (ProfileIntegrate2D) + reference scaling matched or beat
whole-PixelRefine on every per-shell CC1/2 (overall 95.7% vs 91.9%), ISa
(1.6 vs 1.2) and R-meas (98.5% vs 175%), with CCref a tie -- so PixelRefine
has no remaining advantage. Reference-based per-image scaling is
integrator-agnostic (IndexAndRefine::ReferenceIntensities builds a
ScaleOnTheFly(experiment, reference) applied to any integrator's output),
so the reference-dataset feature (CCref + reference scaling) is kept.
Delete image_analysis/pixel_refinement/, GeomRefinementAlgorithmEnum::
PixelRefine and its gates, BraggIntegrationSettings::ProfileMultiplier
(PixelRefine-only; R1 is shared and kept), and the -r pixelrefine /
--profile-multiplier CLI. The inherited lessons (mean background, de-biased
variance, tight-profile-loses / centroid floor, R-refinement futile) are
folded into NEXTGEN_INTEGRATOR.md.
NOTE: this transiently breaks the viewer build -- the committed viewer
still references the removed enum and ProfileMultiplier. It is fixed in the
next commit (the viewer feature work), held separate while the viewer UI is
being tested.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
leonarski_f
38ea0ec237