Jungfraujoch/image_analysis/scale_merge/ScaleAndMerge.h

// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#pragma once

#include <vector>
#include <cstdint>
#include <optional>

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

struct ScaleMergeOptions {
    bool refine_b_factor = true;

    bool use_huber_loss = true;
    double huber_delta = 2.0;

    int max_num_iterations = 100;
    double max_solver_time_s = 1.0;

    double image_number_rounding = 1.0;
    double min_sigma = 1e-3;

    bool fix_first_image_scale = true;

    std::optional<double> b_min = 0.0;
    std::optional<double> b_max = 200.0;

    // Symmetry canonicalization of HKL prior to merging/scaling.
    // If not set, the routine uses raw HKL as-is.
    std::optional<gemmi::SpaceGroup> space_group;

    // If true, treat Friedel mates as equivalent (merge anomalous pairs).
    // If false, keep them separate by including a sign flag in the HKL key.
    bool merge_friedel = true;
};

struct MergedReflection {
    int h;
    int k;
    int l;
    double I;
    double sigma;
};

struct ScaleMergeResult {
    std::vector<MergedReflection> merged;
    std::vector<double> image_scale_k;
    std::vector<double> image_b_factor;
    std::vector<int> image_ids;
};

ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<Reflection>& observations,
                                              const ScaleMergeOptions& opt = {});