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

#pragma once

#include <vector>

#include "gemmi/unitcell.hpp"

// One reflection as the sigma_A estimate sees it: an observed and a calculated amplitude, already on
// a common scale, plus what the likelihood needs to know about the reflection itself.
struct SigmaAReflection {
    double f_obs = 0;
    double f_calc = 0;
    double inv_d2 = 0;
    int epsilon = 1;
    bool centric = false;
    bool free = false;
};

// The weights of one reflection's map coefficients: 2mFo - DFc and mFo - DFc.
struct SigmaAWeight {
    double m = 1.0;   // figure of merit
    double d = 1.0;   // D, carried on the observed amplitudes' scale
};

struct SigmaAResult {
    std::vector<SigmaAWeight> weight;   // one per input reflection, in the input order
    int shells = 0;
    int free_reflections = 0;
    double mean_fom = 1.0;
    double sigma_a_lowest_shell = 0.0;   // for a log line: sigma_A at the low- and high-resolution ends
    double sigma_a_highest_shell = 0.0;
};

// Per-resolution-shell sigma_A by maximum likelihood, and from it the figure of merit m and the
// scale D of each reflection. Estimated on the FREE reflections only - on the working set the model
// has been fitted to the data, so sigma_A would come out too high and the weighting would under-state
// the model's error where the map is meant to reveal it.
//
// Following Read (1986) Acta Cryst. A42, 140-149
SigmaAResult EstimateSigmaA(const std::vector<SigmaAReflection> &refl, const gemmi::UnitCell &cell);