Jungfraujoch/image_analysis/scale_merge/FrenchWilson.h

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#pragma once

#include <cstdint>
#include <vector>

#include "../../common/Reflection.h"
#include "gemmi/math.hpp"
#include "gemmi/symmetry.hpp"

struct FrenchWilsonOptions {
    int num_shells = 20;                 // resolution shells for the Wilson mean <I>
    int min_reflections_per_shell = 20;  // below this, fall back to the overall mean for the shell
    int integration_points = 400;        // posterior integration steps (weak reflections only)
    double strong_cutoff = 20.0;         // I/sigma above which <|F|> = sqrt(I) (FW bias negligible)
    double reject_below = -3.7;          // I/sigma below which no amplitude is given (as ctruncate)
    int num_threads = 1;                 // workers for the per-reflection integration (independent per reflection)
    // Anisotropic Wilson prior: the anisotropy tensor B (ln <I(s)> = c - 1/2 s^T B s, A^2) in the
    // Miller-index basis, Q with s^T B s = h^T Q h (AnisotropyTensorHKL). The default, zero, is the
    // isotropic prior.
    gemmi::Mat33 anisotropy_hkl = gemmi::Mat33(0.0);
};

// Fill F and sigmaF on every merged reflection with the French-Wilson estimate of the amplitude:
// the posterior mean |F| given the measured intensity I and its sigma under the Wilson prior. The
// prior uses the resolution-shell mean intensity - scaled along the reflection's direction by the
// anisotropy tensor when one is given - the correct centric/acentric form, and the reflection's
// epsilon (symmetry-enhancement) multiplicity. Strong reflections reduce to sqrt(I);
// reflections with an unusable I/sigma fall back to sqrt(max(I,0)) with propagated sigma. An
// intensity below reject_below sigmas gets no amplitude (F = NaN) and stays out of the prior; the
// intensity itself is kept.
void ApplyFrenchWilson(std::vector<MergedReflection> &merged, const gemmi::SpaceGroup &space_group,
                       const FrenchWilsonOptions &opts = {});