Jungfraujoch/image_analysis/scale_merge/ScaleAndMerge.cpp

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

#include "ScaleAndMerge.h"

#include <ceres/ceres.h>

#include <thread>
#include <iostream>
#include <algorithm>
#include <cmath>
#include <limits>
#include <stdexcept>
#include <tuple>
#include <unordered_map>
#include <utility>
#include <vector>

namespace {

struct HKLKey {
    int64_t h = 0;
    int64_t k = 0;
    int64_t l = 0;
    bool is_positive = true; // only relevant if opt.merge_friedel == false

    bool operator==(const HKLKey& o) const noexcept {
        return h == o.h && k == o.k && l == o.l && is_positive == o.is_positive;
    }
};

struct HKLKeyHash {
    size_t operator()(const HKLKey& key) const noexcept {
        auto mix = [](uint64_t x) {
            x ^= x >> 33;
            x *= 0xff51afd7ed558ccdULL;
            x ^= x >> 33;
            x *= 0xc4ceb9fe1a85ec53ULL;
            x ^= x >> 33;
            return x;
        };
        const uint64_t a = static_cast<uint64_t>(key.h);
        const uint64_t b = static_cast<uint64_t>(key.k);
        const uint64_t c = static_cast<uint64_t>(key.l);
        const uint64_t d = static_cast<uint64_t>(key.is_positive ? 1 : 0);
        return static_cast<size_t>(mix(a) ^ (mix(b) << 1) ^ (mix(c) << 2) ^ (mix(d) << 3));
    }
};

inline int RoundImageId(float image_number, double rounding_step) {
    if (!(rounding_step > 0.0))
        rounding_step = 1.0;
    const double x = static_cast<double>(image_number) / rounding_step;
    const double r = std::round(x) * rounding_step;
    return static_cast<int>(std::llround(r / rounding_step));
}

inline double SafeSigma(double s, double min_sigma) {
    if (!std::isfinite(s) || s <= 0.0)
        return min_sigma;
    return std::max(s, min_sigma);
}

inline double SafeD(double d) {
    if (!std::isfinite(d) || d <= 0.0)
        return std::numeric_limits<double>::quiet_NaN();
    return d;
}

inline int SafeToInt(int64_t x) {
    if (x < std::numeric_limits<int>::min() || x > std::numeric_limits<int>::max())
        throw std::out_of_range("HKL index out of int range for Gemmi");
    return static_cast<int>(x);
}

inline double SafeInv(double x, double fallback) {
    if (!std::isfinite(x) || x == 0.0)
        return fallback;
    return 1.0 / x;
}

inline HKLKey CanonicalizeHKLKey(const Reflection& r, const ScaleMergeOptions& opt) {
    HKLKey key{};
    key.h = r.h;
    key.k = r.k;
    key.l = r.l;
    key.is_positive = true;

    if (!opt.space_group.has_value()) {
        if (!opt.merge_friedel) {
            const HKLKey neg{-r.h, -r.k, -r.l, true};
            const bool pos = std::tie(key.h, key.k, key.l) >= std::tie(neg.h, neg.k, neg.l);
            if (!pos) {
                key.h = -key.h;
                key.k = -key.k;
                key.l = -key.l;
                key.is_positive = false;
            }
        }
        return key;
    }

    const gemmi::SpaceGroup& sg = *opt.space_group;
    const gemmi::GroupOps gops = sg.operations();
    const gemmi::ReciprocalAsu rasu(&sg);

    const gemmi::Op::Miller in{{SafeToInt(r.h), SafeToInt(r.k), SafeToInt(r.l)}};
    const auto [asu_hkl, sign_plus] = rasu.to_asu_sign(in, gops);

    key.h = asu_hkl[0];
    key.k = asu_hkl[1];
    key.l = asu_hkl[2];
    key.is_positive = opt.merge_friedel ? true : sign_plus;
    return key;
}

/// CrystFEL-like log-scaling residual
///
///   residual = w * [ ln(I_obs) - ln(G) - ln(partiality) - ln(lp) - ln(I_true) ]
///
/// Only observations with I_obs > 0 should be fed in (the caller skips the rest).
/// G and I_true are constrained to be positive via Ceres lower bounds.
struct LogIntensityResidual {
    LogIntensityResidual(const Reflection& r, double sigma_obs, double wedge_deg, bool refine_partiality)
        : log_Iobs_(std::log(std::max(static_cast<double>(r.I), 1e-30))),
          weight_(SafeInv(sigma_obs / std::max(static_cast<double>(r.I), 1e-30), 1.0)),
          delta_phi_(r.delta_phi_deg),
          log_lp_(std::log(std::max(SafeInv(static_cast<double>(r.rlp), 1.0), 1e-30))),
          half_wedge_(wedge_deg / 2.0),
          c1_(r.zeta / std::sqrt(2.0)),
          partiality_(r.partiality),
          refine_partiality_(refine_partiality) {}

    template<typename T>
    bool operator()(const T* const G,
                    const T* const mosaicity,
                    const T* const Itrue,
                    T* residual) const {
        T partiality;
        if (refine_partiality_ && mosaicity[0] != 0.0) {
            const T arg_plus  = T(delta_phi_ + half_wedge_) * T(c1_) / mosaicity[0];
            const T arg_minus = T(delta_phi_ - half_wedge_) * T(c1_) / mosaicity[0];
            partiality = (ceres::erf(arg_plus) - ceres::erf(arg_minus)) / T(2.0);
        } else {
            partiality = T(partiality_);
        }

        // Clamp partiality away from zero so log is safe
        const T min_p = T(1e-30);
        if (partiality < min_p)
            partiality = min_p;

        // ln(I_pred) = ln(G) + ln(partiality) + ln(lp) + ln(Itrue)
        const T log_Ipred = ceres::log(G[0]) + ceres::log(partiality) + T(log_lp_) + ceres::log(Itrue[0]);
        residual[0] = (log_Ipred - T(log_Iobs_)) * T(weight_);
        return true;
    }

    double log_Iobs_;
    double weight_;       // w_i ≈ I_obs / sigma_obs  (relative weight in log-space)
    double delta_phi_;
    double log_lp_;
    double half_wedge_;
    double c1_;
    double partiality_;
    bool refine_partiality_;
};
    
struct IntensityResidual {
    IntensityResidual(const Reflection& r, double sigma_obs, double wedge_deg, bool refine_partiality)
        : Iobs_(static_cast<double>(r.I)),
          inv_sigma_(SafeInv(sigma_obs, 1.0)),
          delta_phi_(r.delta_phi_deg),
          lp_(SafeInv(static_cast<double>(r.rlp), 1.0)),
          half_wedge_(wedge_deg / 2.0),
          c1_(r.zeta / std::sqrt(2.0)),
          partiality_(r.partiality),
          refine_partiality_(refine_partiality) {}

    template<typename T>
    bool operator()(const T* const G,
                    const T* const mosaicity,
                    const T* const Itrue,
                    T* residual) const {
        T partiality;
        if (refine_partiality_ && mosaicity[0] != 0.0) {
            const T arg_plus  = T(delta_phi_ + half_wedge_) * T(c1_) / mosaicity[0];
            const T arg_minus = T(delta_phi_ - half_wedge_) * T(c1_) / mosaicity[0];
            partiality = (ceres::erf(arg_plus) - ceres::erf(arg_minus)) / T(2.0);
        } else
            partiality = T(partiality_);

        const T Ipred = G[0] * partiality * T(lp_) * Itrue[0];
        residual[0] = (Ipred - T(Iobs_)) * T(inv_sigma_);
        return true;
    }

    double Iobs_;
    double inv_sigma_;
    double delta_phi_;
    double lp_;
    double half_wedge_;
    double c1_;
    double partiality_;
    bool refine_partiality_;
};

struct ScaleRegularizationResidual {
    explicit ScaleRegularizationResidual(double sigma_k)
        : inv_sigma_(SafeInv(sigma_k, 1.0)) {}

    template <typename T>
    bool operator()(const T* const k, T* residual) const {
        residual[0] = (k[0] - T(1.0)) * T(inv_sigma_);
        return true;
    }

    double inv_sigma_;
};

} // namespace

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

    struct ObsRef {
        const Reflection* r = nullptr;
        int img_id = 0;
        int img_slot = -1;
        int hkl_slot = -1;
        double sigma = 0.0;
    };

    std::vector<ObsRef> obs;
    obs.reserve(observations.size());

    std::unordered_map<int, int> imgIdToSlot;
    imgIdToSlot.reserve(256);

    std::unordered_map<HKLKey, int, HKLKeyHash> hklToSlot;
    hklToSlot.reserve(observations.size());

    for (const auto& r : observations) {
        const double d = SafeD(r.d);
        if (!std::isfinite(d))
            continue;
        if (!std::isfinite(r.I))
            continue;

        if (!std::isfinite(r.zeta) || r.zeta <= 0.0f)
            continue;
        if (!std::isfinite(r.rlp) || r.rlp == 0.0f)
            continue;

        const double sigma = SafeSigma(static_cast<double>(r.sigma), opt.min_sigma);

        const int img_id = RoundImageId(r.image_number, opt.image_number_rounding);

        int img_slot;
        {
            auto it = imgIdToSlot.find(img_id);
            if (it == imgIdToSlot.end()) {
                img_slot = static_cast<int>(imgIdToSlot.size());
                imgIdToSlot.emplace(img_id, img_slot);
            } else {
                img_slot = it->second;
            }
        }

        int hkl_slot;
        try {
            const HKLKey key = CanonicalizeHKLKey(r, opt);
            auto it = hklToSlot.find(key);
            if (it == hklToSlot.end()) {
                hkl_slot = static_cast<int>(hklToSlot.size());
                hklToSlot.emplace(key, hkl_slot);
            } else {
                hkl_slot = it->second;
            }
        } catch (...) {
            continue;
        }

        ObsRef o;
        o.r = &r;
        o.img_id = img_id;
        o.img_slot = img_slot;
        o.hkl_slot = hkl_slot;
        o.sigma = sigma;
        obs.push_back(o);
    }

    const int nimg = static_cast<int>(imgIdToSlot.size());
    const int nhkl = static_cast<int>(hklToSlot.size());

    out.image_scale_g.assign(nimg, 1.0);
    out.image_ids.assign(nimg, 0);

    for (const auto& kv : imgIdToSlot) {
        out.image_ids[kv.second] = kv.first;
    }

    std::vector<double> g(nimg, 1.0);
    std::vector<double> Itrue(nhkl, 0.0);

    // Mosaicity: always per-image
    std::vector<double> mosaicity(nimg, opt.mosaicity_init_deg);

    // Initialize Itrue from per-HKL median of observed intensities
    {
        std::vector<std::vector<double>> per_hkl_I(nhkl);
        for (const auto& o : obs) {
            per_hkl_I[o.hkl_slot].push_back(static_cast<double>(o.r->I));
        }
        for (int h = 0; h < nhkl; ++h) {
            auto& v = per_hkl_I[h];
            if (v.empty()) {
                Itrue[h] = std::max(opt.min_sigma, 1e-6);
                continue;
            }
            std::nth_element(v.begin(), v.begin() + static_cast<long>(v.size() / 2), v.end());
            double med = v[v.size() / 2];
            if (!std::isfinite(med) || med <= opt.min_sigma)
                med = opt.min_sigma;
            Itrue[h] = med;
        }
    }

    ceres::Problem problem;

    const bool refine_partiality = opt.wedge_deg > 0.0;

    for (const auto& o : obs) {
        if (opt.log_scaling_residual) {
            // Log residual requires positive I_obs
            if (o.r->I <= 0.0f)
                continue;

            auto* cost = new ceres::AutoDiffCostFunction<LogIntensityResidual, 1, 1, 1, 1>(
                new LogIntensityResidual(*o.r, o.sigma, opt.wedge_deg, refine_partiality));

            problem.AddResidualBlock(cost,
                                     nullptr,
                                     &g[o.img_slot],
                                     &mosaicity[o.img_slot],
                                     &Itrue[o.hkl_slot]);
        } else {
            auto* cost = new ceres::AutoDiffCostFunction<IntensityResidual, 1, 1, 1, 1>(
                new IntensityResidual(*o.r, o.sigma, opt.wedge_deg, refine_partiality));

            problem.AddResidualBlock(cost,
                                     nullptr,
                                     &g[o.img_slot],
                                     &mosaicity[o.img_slot],
                                     &Itrue[o.hkl_slot]);
        }
    }

    // For log residual, G and Itrue must stay positive
    if (opt.log_scaling_residual) {
        for (int i = 0; i < nimg; ++i)
            problem.SetParameterLowerBound(&g[i], 0, 1e-12);
        for (int h = 0; h < nhkl; ++h)
            problem.SetParameterLowerBound(&Itrue[h], 0, 1e-12);
    }

    // Optional Kabsch-like regularization for k

    // Mosaicity refinement + bounds
    if (!opt.refine_mosaicity) {
        for (int i = 0; i < nimg; ++i)
            problem.SetParameterBlockConstant(&mosaicity[i]);
    } else {
        for (int i = 0; i < nimg; ++i) {
            problem.SetParameterLowerBound(&mosaicity[i], 0, opt.mosaicity_min_deg);
            problem.SetParameterUpperBound(&mosaicity[i], 0, opt.mosaicity_max_deg);
        }
    }

    // use all available threads
    unsigned int hw = std::thread::hardware_concurrency();
    if (hw == 0)
        hw = 1; // fallback

    ceres::Solver::Options options;

    options.linear_solver_type = ceres::SPARSE_NORMAL_CHOLESKY;
    options.minimizer_progress_to_stdout = true;
    options.max_num_iterations = opt.max_num_iterations;
    options.max_solver_time_in_seconds = opt.max_solver_time_s;
    options.num_threads = static_cast<int>(hw);

    ceres::Solver::Summary summary;
    ceres::Solve(options, &problem, &summary);

    // --- Export per-image results ---
    for (int i = 0; i < nimg; ++i)
        out.image_scale_g[i] = g[i];

    out.mosaicity_deg.resize(nimg);
    for (int i = 0; i < nimg; ++i)
        out.mosaicity_deg[i] = mosaicity[i];

    // --- Compute goodness-of-fit (reduced chi-squared) ---
    const int n_obs = static_cast<int>(obs.size());
    // Count free parameters: nhkl Itrue + per-image (k + mosaicity) minus fixed ones
    int n_params = nhkl;
    for (int i = 0; i < nimg; ++i) {
        n_params += 1; // k
        if (opt.refine_mosaicity)
            n_params += 1; // mosaicity
    }

    std::vector<HKLKey> slotToHKL(nhkl);
    for (const auto& kv : hklToSlot) {
        slotToHKL[kv.second] = kv.first;
    }

    out.merged.resize(nhkl);
    for (int h = 0; h < nhkl; ++h) {
        out.merged[h].h = slotToHKL[h].h;
        out.merged[h].k = slotToHKL[h].k;
        out.merged[h].l = slotToHKL[h].l;
        out.merged[h].I = Itrue[h];
        out.merged[h].sigma = 0.0;
        out.merged[h].d = 0.0;
    }

    // Populate d from median of observations per HKL
    {
        std::vector<std::vector<double>> per_hkl_d(nhkl);
        for (const auto& o : obs) {
            const double d_val = static_cast<double>(o.r->d);
            if (std::isfinite(d_val) && d_val > 0.0)
                per_hkl_d[o.hkl_slot].push_back(d_val);
        }
        for (int h = 0; h < nhkl; ++h) {
            auto& v = per_hkl_d[h];
            if (!v.empty()) {
                std::nth_element(v.begin(), v.begin() + static_cast<long>(v.size() / 2), v.end());
                out.merged[h].d = v[v.size() / 2];
            }
        }
    }

    std::cout << summary.FullReport() << std::endl;

    return out;
}