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

#include "XtalOptimizer.h"
#include "ceres/ceres.h"
#include "ceres/rotation.h"

struct XtalResidual {
    XtalResidual(double x, double y,
                 double beam_x, double beam_y,
                 double lambda,
                 double pixel_size, double distance_mm,
                 double rot1, double rot2,
                 double exp_h, double exp_k,
                 double exp_l, gemmi::CrystalSystem symmetry)
        : obs_x(x), obs_y(y),
          lambda(lambda),
          pixel_size(pixel_size),
          exp_h(exp_h),
          exp_k(exp_k),
          exp_l(exp_l),
          distance(distance_mm),
          rot1(rot1),
          rot2(rot2),
          beam_x(beam_x),
          beam_y(beam_y),
          symmetry(symmetry) {
    }

    template<typename T>
    bool operator()(const T *const corr_x,
                    const T *const corr_y,
                    const T *const p0,
                    const T *const p1,
                    const T *const p2,
                    T *residual) const {
        T c1 = ceres::cos(T(rot1));
        T c2 = ceres::cos(T(rot2));
        T s1 = ceres::sin(T(rot1));
        T s2 = ceres::sin(T(rot2));

        // x_lab in mm
        T x_lab = (T(obs_x) - beam_x - corr_x[0]) * T(pixel_size);
        T y_lab = (T(obs_y) - beam_y - corr_y[0]) * T(pixel_size);
        T z_lab = T(distance);

        // apply rotations
        T x = x_lab * c1 + z_lab * s1;
        T y = y_lab * c2 + (-x_lab * s1 + z_lab * c1) * s2;
        T z = -y_lab * s2 + (-x_lab * s1 + z_lab * c1) * c2;

        // convert to recip space
        T lab_norm = ceres::sqrt(x * x + y * y + z * z);

        T recip[3];
        recip[0] = x / (lab_norm * T(lambda));
        recip[1] = y / (lab_norm * T(lambda));
        recip[2] = (z / lab_norm - T(1.0)) / T(lambda);

        Eigen::Map<const Eigen::Matrix<T, 3, 1>> e_obs_recip(recip);

        Eigen::Matrix<T, 3, 1> e_pred;
        Eigen::Matrix<T, 3, 3> e_latt;

        T uc_rot_matrix[9];
        ceres::AngleAxisToRotationMatrix(p0, uc_rot_matrix);

        Eigen::Map<const Eigen::Matrix<T, 3, 3>> e_uc_rot_matrix(uc_rot_matrix);
        Eigen::Matrix<T, 3, 1> e_uc_len = Eigen::Matrix<T, 3, 1>::Zero();
        Eigen::Matrix<T, 3, 3> B = Eigen::Matrix<T, 3, 3>::Identity();

        if (symmetry == gemmi::CrystalSystem::Hexagonal) {
            e_uc_len << p1[0], p1[0], p1[2];
            B(0, 1) = T(-0.5); // cos(120)
            B(1, 1) = T(sqrt(3.0) / 2.0); // sin(120)
        } else if (symmetry == gemmi::CrystalSystem::Orthorhombic) {
            e_uc_len << p1[0], p1[1], p1[2];
        } else if (symmetry == gemmi::CrystalSystem::Tetragonal) {
            e_uc_len << p1[0], p1[0], p1[2];
        } else if (symmetry == gemmi::CrystalSystem::Cubic) {
            e_uc_len << p1[0], p1[0], p1[0];
        } else if (symmetry == gemmi::CrystalSystem::Monoclinic) {
            // Unique axis b: alpha = gamma = 90°, beta free (angle between a and c)
            e_uc_len << p1[0], p1[1], p1[2];
            B(0, 2) = ceres::cos(p2[0]);
            B(2, 2) = ceres::sin(p2[0]);
        } else {
            // Triclinic: p1 = (a,b,c), p2 = (alpha, beta, gamma) in radians
            const T ca = ceres::cos(p2[0]);
            const T cb = ceres::cos(p2[1]);
            const T cg = ceres::cos(p2[2]);
            const T sg = ceres::sin(p2[2]);

            e_uc_len << p1[0], p1[1], p1[2];

            // B_triclinic builds lattice from lengths+angles in crystallographic convention
            // columns correspond to a, b, c in Cartesian frame prior to global rotation
            B(0, 0) = T(1);
            B(1, 0) = T(0);
            B(2, 0) = T(0);
            B(0, 1) = cg;
            B(1, 1) = sg;
            B(2, 1) = T(0);
            // c vector components:
            T cx = cb;
            T cy = (ca - cb * cg) / sg;
            T cz = ceres::sqrt(T(1) - cx * cx - cy * cy);
            B(0, 2) = cx;
            B(1, 2) = cy;
            B(2, 2) = cz;
        }

        e_latt = e_uc_rot_matrix * e_uc_len.asDiagonal() * B;


        Eigen::Matrix<T, 3, 1> e_hkl;
        e_hkl << T(exp_h), T(exp_k), T(exp_l);

        auto e_pred_hkl = e_latt.transpose() * e_obs_recip;

        residual[0] = exp_h - e_pred_hkl[0];
        residual[1] = exp_k - e_pred_hkl[1];
        residual[2] = exp_l - e_pred_hkl[2];

        return true;
    }

    const double obs_x, obs_y;
    const double lambda;
    const double pixel_size;
    const double exp_h;
    const double exp_k;
    const double exp_l;
    const double distance;
    const double rot1, rot2;
    const double beam_x, beam_y;
    gemmi::CrystalSystem symmetry;
};

inline void LatticeToRodriguesAndLengths_GS(const CrystalLattice &latt,
                                            double rod[3],
                                            double lengths[3]) {
    // Load lattice columns
    const Coord a = latt.Vec0();
    const Coord b = latt.Vec1();
    const Coord c = latt.Vec2();

    Eigen::Vector3d A(a[0], a[1], a[2]);
    Eigen::Vector3d B(b[0], b[1], b[2]);
    Eigen::Vector3d C(c[0], c[1], c[2]);

    // Lengths = column norms (orthorhombic assumption)
    lengths[0] = A.norm();
    lengths[1] = B.norm();
    lengths[2] = C.norm();

    auto safe_unit = [](const Eigen::Vector3d &v, double eps = 1e-15) -> Eigen::Vector3d {
        double n = v.norm();
        return (n > eps) ? (v / n) : Eigen::Vector3d(1.0, 0.0, 0.0);
    };

    // Gram–Schmidt with original order: x from A, y from B orthogonalized vs x
    Eigen::Vector3d e1 = safe_unit(A);
    Eigen::Vector3d y = B - (e1.dot(B)) * e1;
    Eigen::Vector3d e2 = safe_unit(y);

    // z from cross to ensure right-handed basis
    Eigen::Vector3d e3 = e1.cross(e2);
    double n3 = e3.norm();
    if (n3 < 1e-15) {
        // Degenerate case: B nearly collinear with A → use C instead
        y = C - (e1.dot(C)) * e1;
        e2 = safe_unit(y);
        e3 = e1.cross(e2);
        n3 = e3.norm();
        if (n3 < 1e-15) {
            // Still degenerate: pick any perpendicular to e1
            e2 = safe_unit((std::abs(e1.x()) < 0.9)
                               ? Eigen::Vector3d::UnitX().cross(e1)
                               : Eigen::Vector3d::UnitY().cross(e1));
            e3 = e1.cross(e2);
        }
    } else {
        e3 /= n3;
    }

    Eigen::Matrix3d R;
    R.col(0) = e1;
    R.col(1) = e2;
    R.col(2) = e3;

    // Convert rotation to Rodrigues (axis * angle)
    Eigen::AngleAxisd aa(R);
    Eigen::Vector3d r = aa.angle() * aa.axis();
    rod[0] = r.x();
    rod[1] = r.y();
    rod[2] = r.z();
}

void LatticeToRodriguesAndLengths_Hex(const CrystalLattice &latt, double rod[3], double ac[3]) {
    const Coord a = latt.Vec0();
    const Coord b = latt.Vec1();
    const Coord c = latt.Vec2();

    Eigen::Vector3d A(a[0], a[1], a[2]);
    Eigen::Vector3d B(b[0], b[1], b[2]);
    Eigen::Vector3d C(c[0], c[1], c[2]);

    const double a_len = A.norm();
    const double b_len = B.norm();
    const double c_len = C.norm();

    ac[0] = (a_len + b_len) / 2.0;
    ac[1] = (a_len + b_len) / 2.0;
    ac[2] = c_len;

    Eigen::Vector3d e1;
    Eigen::Vector3d e3;

    if (a_len > 0.0)
        e1 = A / a_len;
    else
        e1 = Eigen::Vector3d::UnitX();

    if (c_len > 0.0)
        e3 = C / c_len;
    else
        e3 = Eigen::Vector3d::UnitZ();

    Eigen::Vector3d e2 = e3.cross(e1);
    if (e2.norm() < 1e-15) {
        e2 = (std::abs(e1.x()) < 0.9)
                 ? Eigen::Vector3d::UnitX().cross(e1)
                 : Eigen::Vector3d::UnitY().cross(e1);
    }
    e2.normalize();
    e3 = e1.cross(e2).normalized();

    Eigen::Matrix3d R;
    R.col(0) = e1;
    R.col(1) = e2;
    R.col(2) = e3;

    Eigen::AngleAxisd aa(R);
    Eigen::Vector3d r = aa.angle() * aa.axis();
    rod[0] = r.x();
    rod[1] = r.y();
    rod[2] = r.z();
}

// Extract rotation (Rodrigues), lengths (a,b,c) and beta (rad) for monoclinic (unique axis b).
// Frame choice: e2 aligned with b; e1 from a projected orthogonal to e2; e3 = e1 x e2.
inline void LatticeToRodriguesLengthsBeta_Mono(const CrystalLattice &latt,
                                               double rod[3],
                                               double lengths[3],
                                               double &beta_rad) {
    const Coord a = latt.Vec0();
    const Coord b = latt.Vec1();
    const Coord c = latt.Vec2();

    Eigen::Vector3d A(a[0], a[1], a[2]);
    Eigen::Vector3d B(b[0], b[1], b[2]);
    Eigen::Vector3d C(c[0], c[1], c[2]);

    const double a_len = A.norm();
    const double b_len = B.norm();
    const double c_len = C.norm();

    lengths[0] = a_len;
    lengths[1] = b_len;
    lengths[2] = c_len;

    // beta = angle between a and c
    double cos_beta = 0.0;
    if (a_len > 0.0 && c_len > 0.0)
        cos_beta = std::max(-1.0, std::min(1.0, A.dot(C) / (a_len * c_len)));
    beta_rad = std::acos(cos_beta);
    Eigen::Vector3d e2, ax;

    // e2 along b (unique axis)
    if (b_len > 0.0)
        e2 = B / b_len;
    else
        e2 = Eigen::Vector3d::UnitY();

    if (a_len > 0.0)
        ax = A / a_len;
    else
        ax = Eigen::Vector3d::UnitX();

    Eigen::Vector3d e1 = ax - (ax.dot(e2)) * e2;
    double n1 = e1.norm();
    if (n1 < 1e-15) {
        // Fallback: use any perpendicular to e2
        e1 = (std::abs(e2.x()) < 0.9
                  ? Eigen::Vector3d::UnitX().cross(e2)
                  : Eigen::Vector3d::UnitY().cross(e2));
    }
    e1.normalize();
    // e3 completes the right-handed frame
    Eigen::Vector3d e3 = e1.cross(e2).normalized();

    Eigen::Matrix3d R;
    R.col(0) = e1;
    R.col(1) = e2;
    R.col(2) = e3;

    Eigen::AngleAxisd aa(R);
    Eigen::Vector3d r = aa.angle() * aa.axis();
    rod[0] = r.x();
    rod[1] = r.y();
    rod[2] = r.z();
}

CrystalLattice AngleAxisAndLengthsToLattice(const double rod[3], const double lengths[3], bool hex) {
    const Eigen::Vector3d r(rod[0], rod[1], rod[2]);
    const double angle = r.norm();
    Eigen::Matrix3d R = Eigen::Matrix3d::Identity();
    if (angle > 0.0)
        R = Eigen::AngleAxisd(angle, r / angle).toRotationMatrix();
    const Eigen::DiagonalMatrix<double, 3> D(lengths[0], lengths[1], lengths[2]);

    Eigen::Matrix3d Bhex = Eigen::Matrix3d::Identity();
    if (hex) {
        Bhex(0, 1) = -1 / 2.0;
        Bhex(1, 1) = sqrt(3) / 2;
    }

    auto latt = R * D * Bhex;
    return CrystalLattice(Coord(latt(0, 0), latt(1, 0), latt(2, 0)),
                          Coord(latt(0, 1), latt(1, 1), latt(2, 1)),
                          Coord(latt(0, 2), latt(1, 2), latt(2, 2)));
}

inline CrystalLattice AngleAxisLengthsBetaToLattice_Mono(const double rod[3],
                                                         const double lengths[3],
                                                         double beta_rad) {
    const Eigen::Vector3d r(rod[0], rod[1], rod[2]);
    const double angle = r.norm();
    Eigen::Matrix3d R = Eigen::Matrix3d::Identity();
    if (angle > 0.0)
        R = Eigen::AngleAxisd(angle, r / angle).toRotationMatrix();

    const Eigen::DiagonalMatrix<double, 3> D(lengths[0], lengths[1], lengths[2]);

    Eigen::Matrix3d B = Eigen::Matrix3d::Identity();
    // Bmono = [[1,0,cosβ],[0,1,0],[0,0,sinβ]]
    B(0, 2) = std::cos(beta_rad);
    B(2, 2) = std::sin(beta_rad);

    Eigen::Matrix3d latt = R * D * B;
    return CrystalLattice(Coord(latt(0, 0), latt(1, 0), latt(2, 0)),
                          Coord(latt(0, 1), latt(1, 1), latt(2, 1)),
                          Coord(latt(0, 2), latt(1, 2), latt(2, 2)));
}

bool XtalOptimizerInternal(XtalOptimizerData &data,
                           const std::vector<SpotToSave> &spots,
                           const float tolerance) {
    try {
        data.latt.Regularize(data.crystal_system);

        Coord vec0 = data.latt.Vec0();
        Coord vec1 = data.latt.Vec1();
        Coord vec2 = data.latt.Vec2();
        double beta = data.latt.GetUnitCell().beta;

        // Initial guess for the parameters
        double corr_x = 0;
        double corr_y = 0;

        ceres::Problem problem;

        double latt_vec0[3], latt_vec1[3], latt_vec2[3];

        switch (data.crystal_system) {
            case gemmi::CrystalSystem::Orthorhombic:
                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
                break;
            case gemmi::CrystalSystem::Tetragonal:
                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
                latt_vec1[0] = (latt_vec1[0] + latt_vec1[1]) / 2.0;
                break;
            case gemmi::CrystalSystem::Cubic:
                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
                latt_vec1[0] = (latt_vec1[0] + latt_vec1[1] + latt_vec1[2]) / 3.0;
                break;
            case gemmi::CrystalSystem::Hexagonal:
                LatticeToRodriguesAndLengths_Hex(data.latt, latt_vec0, latt_vec1);
                break;
            case gemmi::CrystalSystem::Monoclinic:
                LatticeToRodriguesLengthsBeta_Mono(data.latt, latt_vec0, latt_vec1, beta);
                latt_vec2[0] = beta;
                latt_vec2[1] = 0.0;
                latt_vec2[2] = 0.0;
                break;
            default:
                // Triclinic: initialize a,b,c and α,β,γ from current unit cell
                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
                auto uc = data.latt.GetUnitCell();
                latt_vec2[0] = uc.alpha * M_PI / 180.0;
                latt_vec2[1] = uc.beta * M_PI / 180.0;
                latt_vec2[2] = uc.gamma * M_PI / 180.0;
                break;
        }

        // Add residuals for each point
        for (const auto &pt: spots) {
            Coord recip = data.geom.DetectorToRecip(pt.x, pt.y);
            double h_fp = recip * vec0;
            double k_fp = recip * vec1;
            double l_fp = recip * vec2;

            double h = std::round(h_fp);
            double k = std::round(k_fp);
            double l = std::round(l_fp);

            double norm_sq = (h - h_fp) * (h - h_fp) + (k - k_fp) * (k - k_fp) + (l - l_fp) * (l - l_fp);

            if (norm_sq > tolerance * tolerance)
                continue;

            problem.AddResidualBlock(
                new ceres::AutoDiffCostFunction<XtalResidual, 3, 1, 1, 3, 3, 3>(
                    new XtalResidual(pt.x, pt.y,
                                     data.geom.GetBeamX_pxl(),
                                     data.geom.GetBeamY_pxl(),
                                     data.geom.GetWavelength_A(),
                                     data.geom.GetPixelSize_mm(),
                                     data.geom.GetDetectorDistance_mm(),
                                     data.geom.GetPoniRot1_rad(),
                                     data.geom.GetPoniRot2_rad(),
                                     h, k, l,
                                     data.crystal_system)),
                nullptr,
                &corr_x,
                &corr_y,
                latt_vec0,
                latt_vec1,
                latt_vec2
            );
        }

        if (problem.NumResidualBlocks() < data.min_spots)
            return false;

        if (!data.refine_beam_center) {
            problem.SetParameterBlockConstant(&corr_x);
            problem.SetParameterBlockConstant(&corr_y);
        }

        // Parameter bounds
        // Lengths
        for (int i = 0; i < 3; ++i) {
            problem.SetParameterLowerBound(latt_vec1, i, data.min_length_A);
            problem.SetParameterUpperBound(latt_vec1, i, data.max_length_A);
        }

        if (data.crystal_system == gemmi::CrystalSystem::Monoclinic) {
            const double beta_lo = std::max(1e-6, M_PI * (data.min_angle_deg / 180.0));
            const double beta_hi = std::min(M_PI - 1e-6, M_PI * (data.max_angle_deg / 180.0));
            problem.SetParameterLowerBound(latt_vec2, 0, beta_lo);
            problem.SetParameterUpperBound(latt_vec2, 0, beta_hi);
        } else if (data.crystal_system == gemmi::CrystalSystem::Triclinic) {
            // α, β, γ bounds (radians)
            const double alo = M_PI * (data.min_angle_deg / 180.0);
            const double ahi = M_PI * (data.max_angle_deg / 180.0);
            for (int i = 0; i < 3; ++i) {
                problem.SetParameterLowerBound(latt_vec2, i, alo);
                problem.SetParameterUpperBound(latt_vec2, i, ahi);
            }
        }

        // Configure solver
        ceres::Solver::Options options;
        options.linear_solver_type = ceres::DENSE_QR;
        options.minimizer_progress_to_stdout = false;
        options.logging_type = ceres::LoggingType::SILENT;
        ceres::Solver::Summary summary;

        // Run optimization
        ceres::Solve(options, &problem, &summary);

        if (data.refine_beam_center) {
            data.beam_corr_x = corr_x;
            data.beam_corr_y = corr_y;
            data.geom.BeamX_pxl(data.geom.GetBeamX_pxl() + corr_x)
                    .BeamY_pxl(data.geom.GetBeamY_pxl() + corr_y);
        }

        if (data.crystal_system == gemmi::CrystalSystem::Orthorhombic)
            data.latt = AngleAxisAndLengthsToLattice(latt_vec0, latt_vec1, false);
        else if (data.crystal_system == gemmi::CrystalSystem::Tetragonal) {
            latt_vec1[1] = latt_vec1[0];
            data.latt = AngleAxisAndLengthsToLattice(latt_vec0, latt_vec1, false);
        } else if (data.crystal_system == gemmi::CrystalSystem::Cubic) {
            latt_vec1[1] = latt_vec1[0];
            latt_vec1[2] = latt_vec1[0];
            data.latt = AngleAxisAndLengthsToLattice(latt_vec0, latt_vec1, false);
        } else if (data.crystal_system == gemmi::CrystalSystem::Hexagonal) {
            latt_vec1[1] = latt_vec1[0];
            data.latt = AngleAxisAndLengthsToLattice(latt_vec0, latt_vec1, true);
        } else if (data.crystal_system == gemmi::CrystalSystem::Monoclinic) {
            data.latt = AngleAxisLengthsBetaToLattice_Mono(latt_vec0, latt_vec1, latt_vec2[0]);
        } else {
            // Triclinic: reconstruct with generic B from α,β,γ
            const Eigen::Vector3d r(latt_vec0[0], latt_vec0[1], latt_vec0[2]);
            const double angle = r.norm();
            Eigen::Matrix3d R = Eigen::Matrix3d::Identity();
            if (angle > 0.0)
                R = Eigen::AngleAxisd(angle, r / angle).toRotationMatrix();

            Eigen::Matrix3d B = Eigen::Matrix3d::Identity();
            const double ca = std::cos(latt_vec2[0]);
            const double cb = std::cos(latt_vec2[1]);
            const double cg = std::cos(latt_vec2[2]);
            const double sg = std::sin(latt_vec2[2]);

            // a along x, b in x-y, c general
            B(0,0) = 1.0;  B(1,0) = 0.0;  B(2,0) = 0.0;
            B(0,1) = cg;   B(1,1) = sg;   B(2,1) = 0.0;

            const double cx = cb;
            const double cy = (ca - cb*cg) / sg;
            const double cz = std::sqrt(std::max(0.0, 1.0 - cx*cx - cy*cy));

            B(0,2) = cx;
            B(1,2) = cy;
            B(2,2) = cz;

            Eigen::DiagonalMatrix<double,3> D(latt_vec1[0], latt_vec1[1], latt_vec1[2]);
            Eigen::Matrix3d latt = R * D * B;

            data.latt = CrystalLattice(Coord(latt(0, 0), latt(1, 0), latt(2, 0)),
                                       Coord(latt(0, 1), latt(1, 1), latt(2, 1)),
                                       Coord(latt(0, 2), latt(1, 2), latt(2, 2)));
        }
        data.latt.Regularize(data.crystal_system);

        return true;
    } catch (...) {
        // Convergence problems, likely not updated
        return false;
    }
}

bool XtalOptimizer(XtalOptimizerData &data, const std::vector<SpotToSave> &spots) {
    if (!XtalOptimizerInternal(data, spots, 0.3))
        return false;
    return XtalOptimizerInternal(data, spots, 0.1);
}