leonarski_fandClaude Opus 4.8
e4b3064254
Reference dataset (a): LoadReferenceMtz adds column selection + cell/SG/resolution + a data-vs-reference consistency check; jfjoch_process/jfjoch_scale gain --reference-column; the viewer gets a Reference section in the MX settings dock (worker-owned, independent of the loaded dataset) that flows into reprocessing jobs. 3D combine (-P rot3d): Combine3D weight-sums a reflection's per-frame partials into one counting-limited full before merging (orthogonal ScalingSettings::combine_3d flag, not a partiality model), with a de-biased Poisson variance. Crystal 2: ISa 1.7->8.4, R-meas ~67%->18.9%, intensities unchanged (CCref held). Quality metrics (b): R-meas (Diederichs-Karplus) + redundancy columns in MergeStats; ISa logged. jfjoch fulls 18.9% vs XDS 4.5% (same ASU/run). Profile-fit integrator (experimental): ProfileIntegrate2D (--integrator gaussian|empirical) is a reference-free, rot3d-compatible profile-fit extraction (the decomposed PixelRefine intensity step). Gaussian: R-meas 18.9->14.6%, ISa ->9.5. Anisotropy/per-region add nothing (the discriminating info is in the discarded rocking direction). See NEXTGEN_INTEGRATOR.md. --dump-observations exports the unmerged fulls for XDS comparison. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
53 lines
3.2 KiB
C++
53 lines
3.2 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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// =============================================================================
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// ProfileIntegrate2D — profile-fitting 2D integrator (DRAFT / not yet wired in)
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// =============================================================================
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//
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// A drop-in alternative to BraggIntegrate2D that replaces uniform box summation with
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// profile-fitted extraction - the part of PixelRefine that does NOT need reference
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// intensities (PixelRefine = this extraction + a reference-based scaling step; here only
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// the extraction is kept). See NEXTGEN_INTEGRATOR.md for the rationale: the residual ~4x
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// R-meas/ISa gap to XDS is the box-sum method (a fixed disk captures a width-dependent
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// fraction of each spot -> ~18% multiplicative per-observation floor on strong reflections).
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//
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// Output is a vector<Reflection> with I, sigma, partiality, d - IDENTICAL in shape to
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// BraggIntegrate2D - so ScaleOnTheFly, Combine3D (-P rot3d) and the merge consume it
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// unchanged, and it works for both stills and rotation.
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//
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// Algorithm (per frame):
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// A. Box-sum every reflection (rough I + observed centroid); pick strong spots (signif>=5).
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// B. Build the profile per resolution shell from the strong spots: a Gaussian of the measured
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// second moment (ProfileGaussian, the keeper) or the empirical average grid (ProfileEmpirical).
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// NOTE (measured 2026-06): radial/tangential ANISOTROPY and per-detector-region profiles were
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// tried and add nothing - the 2D detector-plane spots are ~round, the real anisotropy is in the
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// discarded rocking direction - so an isotropic per-shell width is kept. The empirical grid
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// under-performs the Gaussian as built (per-frame, integer-binned -> sub-pixel-smeared + noisy).
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// C. Profile-fit each reflection (Kabsch): I = sum P(c-B)/v over sum P^2/v, de-biased
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// variance v = B + max(I,0)*P (iterate), sigma = sqrt(1/sum P^2/v). Carry the rotation
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// partiality exactly as BraggIntegrate2D does.
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//
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// Staging: v1 = measured-R1 Gaussian (lifts PixelRefine's extraction out, proves the
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// decomposition + rot3d-combine compatibility); v2 = empirical per-shell (the expected win);
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// v3 = empirical per detector-region x shell (XDS-grade).
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//
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// EXPERIMENTAL: selected by BraggIntegrationSettings::Integrator (ProfileGaussian = v1,
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// ProfileEmpirical = v2); jfjoch_process exposes it as `--integrator gaussian|empirical` (default
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// box-sum). For A/B vs XDS_ASCII.HKL via --dump-observations. Not yet exposed in the OpenAPI / viewer.
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// =============================================================================
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#include <vector>
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#include "../../common/DiffractionExperiment.h"
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#include "../../common/Reflection.h"
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#include "../../common/CompressedImage.h"
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std::vector<Reflection> ProfileIntegrate2D(const DiffractionExperiment &experiment,
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const CompressedImage &image,
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const std::vector<Reflection> &predicted,
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size_t npredicted,
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int64_t image_number);
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