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

#include "ModelValidation.h"

#include <cmath>
#include <complex>
#include <array>
#include <algorithm>
#include <vector>
#include <unordered_map>

#include <gemmi/pdb.hpp>       // read_pdb
#include <gemmi/gz.hpp>        // MaybeGzipped
#include <gemmi/it92.hpp>      // IT92 x-ray form factors
#include <gemmi/dencalc.hpp>   // DensityCalculator
#include <gemmi/fourier.hpp>   // transform_map_to_f_phi, get_f_phi_on_grid, transform_f_phi_grid_to_map
#include <gemmi/solmask.hpp>   // SolventMasker
#include <gemmi/scaling.hpp>   // Scaling (bulk solvent + anisotropic B)
#include <gemmi/ccp4.hpp>      // Ccp4 map I/O
#include <gemmi/mtz.hpp>       // Mtz (map-coefficient output)

#include "../common/Logger.h"
#include "../image_analysis/scale_merge/ReindexAmbiguity.h"   // ReindexReflections

namespace {

using Table = gemmi::IT92<float>;

// Stable key for a Miller index reduced into the ASU (indices are small, well within +/-512).
long hkl_key(const gemmi::Miller &h) {
    return (h[0] + 512L) * 1048576 + (h[1] + 512L) * 1024 + (h[2] + 512L);
}

// Write an FFT of ASU map coefficients as a CCP4 map; return its RMS (for reporting / sigma units).
double write_ccp4(gemmi::AsuData<std::complex<float>> &coef, const std::string &path) {
    coef.ensure_sorted();
    std::array<int, 3> size = gemmi::get_size_for_hkl(coef, {{0, 0, 0}}, 3.0);
    gemmi::Grid<float> map =
        gemmi::transform_f_phi_grid_to_map(gemmi::get_f_phi_on_grid<float>(coef, size, true));
    gemmi::Ccp4<float> ccp4;
    ccp4.grid = map;
    ccp4.update_ccp4_header(2);
    ccp4.write_ccp4_map(path);
    return ccp4.hstats.rms;
}

}  // namespace

ModelValidationResult ValidateAgainstModel(const std::vector<MergedReflection> &merged,
                                           const UnitCell &cell,
                                           const std::string &model_path,
                                           const std::string &output_prefix,
                                           Logger &logger,
                                           std::optional<int> data_space_group_number) {
    ModelValidationResult result;

    // --- read the atomic model ---
    gemmi::Structure st;
    try {
        st = gemmi::read_pdb(gemmi::MaybeGzipped(model_path));
    } catch (const std::exception &e) {
        logger.Error("Model validation: cannot read model {}: {}", model_path, e.what());
        return result;
    }
    if (st.models.empty() || !st.cell.is_crystal()) {
        logger.Error("Model validation: model {} has no atoms or no unit cell", model_path);
        return result;
    }
    const gemmi::SpaceGroup *sg = st.find_spacegroup();
    if (!sg) {
        logger.Error("Model validation: model {} has no usable space group", model_path);
        return result;
    }

    // If the data was indexed in the enantiomorph of the model's space group (e.g. data P4(1)2(1)2,
    // model P4(3)2(1)2 - the merged intensities cannot tell them apart), reindex the observed
    // reflections into the model's hand so the two settings agree. This does not change the
    // R-factors (which use |F|), but keeps the observed data consistent with the model.
    std::vector<MergedReflection> reindexed;
    const std::vector<MergedReflection> *obs_ptr = &merged;
    if (data_space_group_number && *data_space_group_number != sg->number) {
        const gemmi::SpaceGroup *dsg = gemmi::find_spacegroup_by_number(*data_space_group_number);
        if (dsg && dsg->is_enantiomorphic() && sg->is_enantiomorphic()) {
            gemmi::GroupOps eops = dsg->operations();
            eops.change_basis_forward(dsg->change_of_hand_op());
            const gemmi::SpaceGroup *enant = gemmi::find_spacegroup_by_ops(eops);
            if (enant && enant->number == sg->number) {
                reindexed = ReindexReflections(merged, dsg->change_of_hand_op());
                obs_ptr = &reindexed;
                logger.Info("Model validation: data space group {} is the enantiomorph of the model {}; "
                            "reindexed the observed reflections into the model's hand",
                            dsg->short_name(), sg->hm);
            }
        }
    }
    const std::vector<MergedReflection> &obs = *obs_ptr;

    // Resolution limit from the data (the merged set is already resolution-trimmed).
    double d_min = 0.0;
    for (const MergedReflection &r : obs)
        if (r.d > 0 && (d_min == 0.0 || r.d < d_min))
            d_min = r.d;
    if (d_min <= 0.0) {
        logger.Error("Model validation: merged reflections carry no resolution");
        return result;
    }

    // Re-fractionalize the model into the data cell (rigid cell adjustment; no refinement).
    const gemmi::UnitCell data_cell = cell;  // UnitCell -> gemmi::UnitCell
    if (data_cell.is_crystal()) {
        gemmi::UnitCell old = st.cell;
        for (gemmi::Model &m : st.models)
            for (gemmi::Chain &ch : m.chains)
                for (gemmi::Residue &r : ch.residues)
                    for (gemmi::Atom &a : r.atoms)
                        a.pos = data_cell.orthogonalize(old.fractionalize(a.pos));
        st.cell = data_cell;
    }
    st.setup_cell_images();
    const gemmi::UnitCell &ucell = st.cell;

    logger.Info("Model validation: {} atoms, cell a={:.2f} b={:.2f} c={:.2f}, sg {}, to {:.2f} A",
                gemmi::count_atom_sites(st.models[0]), ucell.a, ucell.b, ucell.c, sg->hm, d_min);

    // --- Fcalc (atomic) via electron density on a grid + FFT ---
    gemmi::DensityCalculator<Table, float> dc;
    dc.d_min = d_min;
    dc.rate = 1.5;
    dc.set_grid_cell_and_spacegroup(st);
    dc.set_refmac_compatible_blur(st.models[0]);
    dc.put_model_density_on_grid(st.models[0]);
    gemmi::AsuData<std::complex<float>> fmodel =
        gemmi::transform_map_to_f_phi(dc.grid, true).prepare_asu_data(dc.d_min, dc.blur, false, false, false);

    // --- flat bulk-solvent mask -> Fmask ---
    // Refmac radii give a slightly lower R than the Cctbx set on our test cases, at no cost.
    gemmi::SolventMasker masker(gemmi::AtomicRadiiSet::Refmac);
    gemmi::Grid<float> mask_grid;
    mask_grid.unit_cell = dc.grid.unit_cell;
    mask_grid.spacegroup = dc.grid.spacegroup;
    mask_grid.set_size_from_spacing(dc.requested_grid_spacing(), gemmi::GridSizeRounding::Up);
    masker.put_mask_on_grid(mask_grid, st.models[0]);
    gemmi::AsuData<std::complex<float>> fmask =
        gemmi::transform_map_to_f_phi(mask_grid, true).prepare_asu_data(dc.d_min, 0);

    // --- observed amplitudes into the model ASU, keyed by hkl (also remember free flag) ---
    gemmi::GroupOps gops = sg->operations();
    gemmi::ReciprocalAsu asu(sg);
    gemmi::AsuData<gemmi::ValueSigma<float>> fobs;
    fobs.unit_cell_ = ucell;
    fobs.spacegroup_ = sg;
    std::unordered_map<long, std::pair<double, bool>> obs_by_hkl;  // hkl -> (Fobs, is_free)

    // Observed amplitudes are the French-Wilson |F| already computed at the end of the merge
    // (MergedReflection.F), so the model R-free / maps use exactly the same amplitudes as the
    // written reflection file.
    for (const MergedReflection &r : obs) {
        if (std::isnan(r.F)) continue;
        gemmi::Miller h{{r.h, r.k, r.l}};
        if (!asu.is_in(h)) h = asu.to_asu(h, gops).first;
        fobs.v.push_back({h, {r.F, 1.0f}});
        obs_by_hkl[hkl_key(h)] = {r.F, r.rfree_flag};
    }
    fobs.ensure_asu();
    fobs.ensure_sorted();

    // --- scale Fmodel(+solvent) to Fobs: k_overall, anisotropic B, k_sol, b_sol ---
    gemmi::Scaling<float> scaling(ucell, sg);
    scaling.use_solvent = true;
    scaling.prepare_points(fmodel, fobs, &fmask);
    scaling.fit_isotropic_b_approximately();
    scaling.fit_parameters();
    scaling.scale_data(fmodel, &fmask);   // fmodel now holds the scaled, solvent-corrected Fmodel

    // --- per-resolution-shell scaling on top of the overall scaling ---
    // Fit a smooth scale K(1/d^2) least-squares per shell (sum(Fo*Fc)/sum(Fc^2)) and apply it to
    // every reflection. This mops up the residual radial Fobs/Fmodel mismatch that a single overall
    // B leaves behind. The shells are fit on the work set only, so R-free stays untouched by the fit.
    int n_shells = 0;
    {
        struct ShellPoint { double s2, fo, fc; };
        std::vector<ShellPoint> pts;
        pts.reserve(fmodel.v.size());
        for (const auto &hv : fmodel.v) {
            auto it = obs_by_hkl.find(hkl_key(hv.hkl));
            if (it == obs_by_hkl.end() || it->second.second) continue;   // skip missing + free set
            if (it->second.first <= 0) continue;
            pts.push_back({ucell.calculate_1_d2(hv.hkl), it->second.first, std::abs(hv.value)});
        }
        std::sort(pts.begin(), pts.end(), [](const ShellPoint &a, const ShellPoint &b) { return a.s2 < b.s2; });
        int nb = std::max(6, std::min(40, static_cast<int>(pts.size() / 300)));   // ~300 refl/shell
        std::vector<double> shell_s2, shell_k;
        for (int b = 0; b < nb; ++b) {
            size_t i0 = pts.size() * b / nb, i1 = pts.size() * (b + 1) / nb;
            double sum_fofc = 0, sum_fc2 = 0, sum_s2 = 0;
            int n = 0;
            for (size_t i = i0; i < i1; ++i) {
                sum_fofc += pts[i].fo * pts[i].fc;
                sum_fc2 += pts[i].fc * pts[i].fc;
                sum_s2 += pts[i].s2;
                ++n;
            }
            if (sum_fc2 > 0 && n > 0) { shell_s2.push_back(sum_s2 / n); shell_k.push_back(sum_fofc / sum_fc2); }
        }
        auto scale_at = [&](double s2) -> double {
            if (shell_s2.empty()) return 1.0;
            if (s2 <= shell_s2.front()) return shell_k.front();
            if (s2 >= shell_s2.back()) return shell_k.back();
            for (size_t i = 1; i < shell_s2.size(); ++i)
                if (s2 <= shell_s2[i]) {
                    double t = (s2 - shell_s2[i - 1]) / (shell_s2[i] - shell_s2[i - 1]);
                    return shell_k[i - 1] * (1 - t) + shell_k[i] * t;
                }
            return shell_k.back();
        };
        for (auto &hv : fmodel.v)
            hv.value *= static_cast<float>(scale_at(ucell.calculate_1_d2(hv.hkl)));
        n_shells = static_cast<int>(shell_k.size());
    }

    // --- R-work / R-free and map coefficients (2Fo-Fc and Fo-Fc, model phases) ---
    gemmi::AsuData<std::complex<float>> map2fofc, mapfofc;
    map2fofc.unit_cell_ = ucell; map2fofc.spacegroup_ = sg;
    mapfofc.unit_cell_ = ucell;  mapfofc.spacegroup_ = sg;
    double num_w = 0, den_w = 0, num_f = 0, den_f = 0;
    int n_w = 0, n_f = 0;
    for (const auto &hv : fmodel.v) {
        auto it = obs_by_hkl.find(hkl_key(hv.hkl));
        if (it == obs_by_hkl.end()) continue;
        double Fo = it->second.first;
        double Fc = std::abs(hv.value);
        double phi = std::arg(hv.value);
        if (it->second.second) { num_f += std::fabs(Fo - Fc); den_f += Fo; ++n_f; }
        else                   { num_w += std::fabs(Fo - Fc); den_w += Fo; ++n_w; }
        std::complex<float> ph = std::polar(1.0f, static_cast<float>(phi));
        map2fofc.v.push_back({hv.hkl, static_cast<float>(2 * Fo - Fc) * ph});
        mapfofc.v.push_back({hv.hkl, static_cast<float>(Fo - Fc) * ph});
    }

    result.r_work = den_w > 0 ? num_w / den_w : 0;
    result.r_free = den_f > 0 ? num_f / den_f : 0;
    result.n_work = n_w;
    result.n_free = n_f;
    result.k_sol = scaling.k_sol;
    result.b_sol = scaling.b_sol;
    result.k_overall = scaling.k_overall;

    // --- write the maps and score the 2Fo-Fc map at atom centres (a real map peaks there) ---
    const std::string p2 = output_prefix + "_2fofc.ccp4";
    const std::string pd = output_prefix + "_fofc.ccp4";
    double rms2 = write_ccp4(map2fofc, p2);
    write_ccp4(mapfofc, pd);

    // Recompute the 2Fo-Fc real-space grid once more to sample it at atom positions.
    {
        map2fofc.ensure_sorted();
        std::array<int, 3> size = gemmi::get_size_for_hkl(map2fofc, {{0, 0, 0}}, 3.0);
        gemmi::Grid<float> grid =
            gemmi::transform_f_phi_grid_to_map(gemmi::get_f_phi_on_grid<float>(map2fofc, size, true));
        double s = 0; int n = 0;
        for (gemmi::Model &m : st.models)
            for (gemmi::Chain &ch : m.chains)
                for (gemmi::Residue &r : ch.residues)
                    for (gemmi::Atom &a : r.atoms) { s += grid.interpolate_value(a.pos); ++n; }
        result.mean_atom_density_sigma = (n > 0 && rms2 > 0) ? (s / n) / rms2 : 0;
    }

    // --- MTZ of map coefficients so the maps can be re-opened / rebuilt in Coot etc. ---
    try {
        gemmi::Mtz mtz(true);
        mtz.spacegroup = sg;
        mtz.set_cell_for_all(ucell);
        mtz.add_dataset("model_validation");
        mtz.add_column("FP", 'F', -1, -1, false);
        mtz.add_column("FC", 'F', -1, -1, false);
        mtz.add_column("PHIC", 'P', -1, -1, false);
        mtz.add_column("FWT", 'F', -1, -1, false);
        mtz.add_column("PHWT", 'P', -1, -1, false);
        mtz.add_column("DELFWT", 'F', -1, -1, false);
        mtz.add_column("PHDELWT", 'P', -1, -1, false);
        mtz.add_column("FREE", 'I', -1, -1, false);
        std::vector<float> data;
        int nref = 0;
        for (const auto &hv : fmodel.v) {
            auto it = obs_by_hkl.find(hkl_key(hv.hkl));
            if (it == obs_by_hkl.end()) continue;
            double Fo = it->second.first;
            double Fc = std::abs(hv.value);
            double phi_deg = gemmi::phase_in_angles(hv.value);
            data.insert(data.end(), {static_cast<float>(hv.hkl[0]), static_cast<float>(hv.hkl[1]),
                                     static_cast<float>(hv.hkl[2]),
                                     static_cast<float>(Fo), static_cast<float>(Fc),
                                     static_cast<float>(phi_deg),
                                     static_cast<float>(2 * Fo - Fc), static_cast<float>(phi_deg),
                                     static_cast<float>(Fo - Fc), static_cast<float>(phi_deg),
                                     it->second.second ? 0.0f : 1.0f});
            ++nref;
        }
        mtz.nreflections = nref;
        mtz.data = std::move(data);
        mtz.write_to_file(output_prefix + "_maps.mtz");
    } catch (const std::exception &e) {
        logger.Warning("Model validation: could not write map MTZ: {}", e.what());
    }

    result.ok = true;
    result.maps_prefix = output_prefix;
    logger.Info("Model validation: R-work={:.4f} ({} refl)  R-free={:.4f} ({} refl)  [overall + {}-shell scaling]",
                result.r_work, result.n_work, result.r_free, result.n_free, n_shells);
    logger.Info("Model validation: bulk solvent k_sol={:.3f} b_sol={:.1f}, k_overall={:.3f}",
                result.k_sol, result.b_sol, result.k_overall);
    logger.Info("Model validation: mean 2Fo-Fc density at atom centres = {:.2f} sigma", result.mean_atom_density_sigma);
    logger.Info("Model validation: wrote {}_2fofc.ccp4, {}_fofc.ccp4, {}_maps.mtz",
                output_prefix, output_prefix, output_prefix);
    return result;
}