//The contents of this file are covered by the Mozilla Public License v2, a copy of which is included in include/LICENSE_MOZILLAv2.txt
// Copyright 2020 Global Phasing Ltd.
//
// Anisotropic scaling of data (includes scaling of bulk solvent parameters)

#ifndef GEMMI_SCALING_HPP_
#define GEMMI_SCALING_HPP_

#include "asudata.hpp"
#include "levmar.hpp"

namespace gemmi {

template<typename Real>
struct Scaling {
  struct Point {
    Miller hkl;
    double stol2;
    std::complex<Real> fcmol, fmask;
    Real fobs, sigma;

    Miller get_x() const { return hkl; }
    double get_y() const { return fobs; }
    double get_weight() const { return 1.0 / sigma; }
  };

  UnitCell cell;
  // SpaceGroup is not stored, but we have special handling of monoclinic
  // groups (to handle settings with either angle alpha or gamma being != 90),
  // and trigonal space groups in hexagonal settings are regarded (for the
  // purpose of scaling constraints) to be hexagonal.
  CrystalSystem crystal_system = CrystalSystem::Triclinic;
  signed char monoclinic_angle_idx;
  double SMat33<double>::*monoclinic_angle;
  // model parameters
  double k_overall = 1.;
  // b_star = F B_cart F^T, where F - fractionalization matrix
  SMat33<double> b_star{0, 0, 0, 0, 0, 0};
  bool use_solvent = false;
  bool fix_k_sol = false;
  bool fix_b_sol = false;
  // initialize with average values (Fokine & Urzhumtsev, 2002)
  double k_sol = 0.35;
  double b_sol = 46.0;
  std::vector<Point> points;

  // pre: calc and obs are sorted
  Scaling(const UnitCell& cell_, const SpaceGroup* sg)
      : cell(cell_) {
    if (sg) {
      crystal_system = sg->crystal_system();
      if (crystal_system == CrystalSystem::Monoclinic) {
        // take first letter in "c" or "c1", but second in "-c1"
        char letter = sg->qualifier[sg->qualifier[0] == '-'];
        if (letter == 'a') {
          monoclinic_angle_idx = 5;
          monoclinic_angle = &SMat33<double>::u23;
        } else if (letter == 'c') {
          monoclinic_angle_idx = 3;
          monoclinic_angle = &SMat33<double>::u12;
        } else {
          monoclinic_angle_idx = 4;
          monoclinic_angle = &SMat33<double>::u13;
        }
      } else if (crystal_system == CrystalSystem::Trigonal) {
        if (sg->ext != 'R')
          crystal_system = CrystalSystem::Hexagonal;
      }
    }
  }

  // B_{overall} is stored as B* not B_{cartesian}.
  // Use getter and setter to convert from/to B_{cartesian}.
  void set_b_overall(const SMat33<double>& b_overall) {
    b_star = b_overall.transformed_by(cell.frac.mat);
  }
  SMat33<double> get_b_overall() const {
    return b_star.transformed_by(cell.orth.mat);
  }

  // Scale data, optionally adding bulk solvent correction.
  void scale_data(AsuData<std::complex<Real>>& asu_data,
                  const AsuData<std::complex<Real>>& mask_data) const {
    if (use_solvent && mask_data.size() != asu_data.size())
      fail("scale_data(): mask data not prepared");
    bool use_scaling = (k_overall != 1 || !b_star.all_zero());
    for (size_t i = 0; i != asu_data.v.size(); ++i) {
      HklValue<std::complex<Real>>& hv = asu_data.v[i];
      if (use_solvent) {
        if (hv.hkl != mask_data.v[i].hkl)
          fail("scale_data(): data arrays don't match");
        double stol2 = cell.calculate_stol_sq(hv.hkl);
        hv.value += (Real)get_solvent_scale(stol2) * mask_data.v[i].value;
      }
      if (use_scaling)
        hv.value *= (Real) get_overall_scale_factor(hv.hkl);
    }
  }

  std::complex<Real> scale_value(const Miller& hkl, std::complex<Real> f_value,
                                 std::complex<Real> mask_value) {
    if (use_solvent) {
      double stol2 = cell.calculate_stol_sq(hkl);
      f_value += (Real)get_solvent_scale(stol2) * mask_value;
    }
    return f_value * (Real) get_overall_scale_factor(hkl);
  }

  std::vector<double> get_parameters() const {
    std::vector<double> ret;
    ret.push_back(k_overall);
    if (use_solvent) {
      if (!fix_k_sol)
        ret.push_back(k_sol);
      if (!fix_b_sol)
        ret.push_back(b_sol);
    }
    switch (crystal_system) {
      case CrystalSystem::Triclinic:
        ret.insert(ret.end(), {b_star.u11, b_star.u22, b_star.u33,
                               b_star.u12, b_star.u13, b_star.u23});
        break;
      case CrystalSystem::Monoclinic:
        ret.insert(ret.end(), {b_star.u11, b_star.u22, b_star.u33,
                               b_star.*monoclinic_angle});
        break;
      case CrystalSystem::Orthorhombic:
        ret.insert(ret.end(), {b_star.u11, b_star.u22, b_star.u33});
        break;
      case CrystalSystem::Tetragonal:
        ret.insert(ret.end(), {b_star.u11, b_star.u33});
        break;
      case CrystalSystem::Trigonal:
        ret.insert(ret.end(), {b_star.u11, b_star.u12});
        break;
      case CrystalSystem::Hexagonal:
        ret.insert(ret.end(), {b_star.u11, b_star.u33});
        break;
      case CrystalSystem::Cubic:
        ret.push_back(b_star.u11);
        break;
    }
    return ret;
  }

  void set_parameters(const std::vector<double>& p) {
    k_overall = p[0];
    int n = 0;
    if (use_solvent) {
      if (!fix_k_sol)
        k_sol = p[++n];
      if (!fix_b_sol)
        b_sol = p[++n];
    }
    switch (crystal_system) {
      case CrystalSystem::Triclinic:
        b_star = {p[n+1], p[n+2], p[n+3], p[n+4], p[n+5], p[n+6]}; break;
      case CrystalSystem::Monoclinic:
        b_star = {p[n+1], p[n+2], p[n+3], 0, 0, 0};
        b_star.*monoclinic_angle = p[n+4];
        break;
      case CrystalSystem::Orthorhombic:
        b_star = {p[n+1], p[n+2], p[n+3], 0., 0., 0.}; break;
      case CrystalSystem::Tetragonal:
        b_star = {p[n+1], p[n+1], p[n+2], 0., 0., 0.}; break;
      case CrystalSystem::Trigonal:
        b_star = {p[n+1], p[n+1], p[n+1], p[n+2], p[n+2], p[n+2]}; break;
      case CrystalSystem::Hexagonal:
        b_star = {p[n+1], p[n+1], p[n+2], 0.5*p[n+1], 0., 0.}; break;
      case CrystalSystem::Cubic:
        b_star = {p[n+1], p[n+1], p[n+1], 0., 0., 0.}; break;
    }
  }

  void prepare_points(const AsuData<std::complex<Real>>& calc,
                      const AsuData<ValueSigma<Real>>& obs,
                      const AsuData<std::complex<Real>>& mask_data) {
    if (use_solvent && mask_data.size() != calc.size())
      fail("prepare_points(): mask data not prepared");
    std::complex<Real> fmask;
    points.reserve(std::min(calc.size(), obs.size()));
    auto c = calc.v.begin();
    for (const HklValue<ValueSigma<Real>>& o : obs.v) {
      if (c->hkl != o.hkl) {
        while (*c < o.hkl) {
          ++c;
          if (c == calc.v.end())
            return;
        }
        if (c->hkl != o.hkl)
          continue;
      }
      if (use_solvent) {
        const HklValue<std::complex<Real>>& m = mask_data.v[c - calc.v.begin()];
        if (m.hkl != c->hkl)
          fail("prepare_points(): unexpected data");
        fmask = m.value;
      }
      double stol2 = cell.calculate_stol_sq(o.hkl);
      points.push_back({o.hkl, stol2, c->value, fmask, o.value.value, o.value.sigma});
      ++c;
      if (c == calc.v.end())
        break;
    }
  }


  double get_solvent_scale(double stol2) const {
    return k_sol * std::exp(-b_sol * stol2);
  }

  double get_overall_isotropic_scale_factor(const Miller& hkl) const {
    return k_overall * std::exp(-b_star.u11 * Vec3(hkl).length_sq());
  }

  double get_overall_scale_factor(const Miller& hkl) const {
    return k_overall * std::exp(-0.25 * b_star.r_u_r(hkl));
  }

  // quick linear fit (ignoring sigma) to get initial parameters
  void fit_isotropic_b_approximately() {
    double sx = 0, sy = 0, sxx = 0, sxy = 0;
    for (const Point& p : points) {
      if (p.fobs < 1 || p.fobs < p.sigma)  // skip weak reflections
        continue;
      double x = p.stol2;
      double fcalc = std::abs(use_solvent ? p.fcmol + (Real)get_solvent_scale(x) * p.fmask
                                          : p.fcmol);
      double y = std::log(static_cast<float>(p.fobs / fcalc));
      sx += x;
      sy += y;
      sxx += x * x;
      sxy += x * y;
    }
    if (points.size() <= 5)  // this is not expected to happen
      return;
    double n = (double) points.size();
    double slope = (n * sxy - sx * sy) / (n * sxx - sx * sx);
    double intercept = (sy - slope * sx) / n;
    double b_iso = -slope;
    k_overall = exp(intercept);
    set_b_overall({b_iso, b_iso, b_iso, 0, 0, 0});
  }

  void fit_parameters() {
    LevMar levmar;
    levmar.fit(*this);
  }


  // interface for fitting
  std::vector<double> compute_values() const {
    std::vector<double> values;
    values.reserve(points.size());
    for (const Point& p : points) {
      double fcalc = std::abs(p.fcmol + (Real)get_solvent_scale(p.stol2) * p.fmask);
      values.push_back(fcalc * (Real) get_overall_scale_factor(p.hkl));
    }
    return values;
  }

  // the tile_* parameters allow tiling: computing derivatives from a span
  // of points at one time, which limits memory usage.
  void compute_values_and_derivatives(size_t tile_start, size_t tile_size,
                                      std::vector<double>& yy,
                                      std::vector<double>& dy_da) const {
    assert(tile_size == yy.size());
    size_t npar = dy_da.size() / tile_size;
    assert(dy_da.size() == npar * tile_size);
    int n = 1;
    if (use_solvent)
      n += int(!fix_k_sol) + int(!fix_b_sol);
    for (size_t i = 0; i != tile_size; ++i) {
      const Point& pt = points[tile_start+i];
      Vec3 h(pt.hkl);
      double kaniso = std::exp(-0.25 * b_star.r_u_r(h));
      double fcalc_abs;
      if (use_solvent) {
        double solv_b = std::exp(-b_sol * pt.stol2);
        double solv_scale = k_sol * solv_b;
        auto fcalc = pt.fcmol + (Real)solv_scale * pt.fmask;
        fcalc_abs = std::abs(fcalc);
        size_t offset = i * npar + 1;
        double dy_dsol = (fcalc.real() * pt.fmask.real() +
                          fcalc.imag() * pt.fmask.imag()) / fcalc_abs * k_overall * kaniso;
        if (!fix_k_sol)
          dy_da[offset++] = solv_b * dy_dsol;
        if (!fix_b_sol)
          dy_da[offset] = -pt.stol2 * solv_scale * dy_dsol;
      } else {
        fcalc_abs = std::abs(pt.fcmol);
      }
      double fe = fcalc_abs * kaniso;
      yy[i] = k_overall * fe;
      dy_da[i * npar + 0] = fe; // dy/d k_overall
      double du[6] = {
        -0.25 * yy[i] * (h.x * h.x),
        -0.25 * yy[i] * (h.y * h.y),
        -0.25 * yy[i] * (h.z * h.z),
        -0.5 * yy[i] * (h.x * h.y),
        -0.5 * yy[i] * (h.x * h.z),
        -0.5 * yy[i] * (h.y * h.z),
      };
      double* dy_db = &dy_da[i * npar + n];
      switch (crystal_system) {
        case CrystalSystem::Triclinic:
          for (int j = 0; j < 6; ++j)
            dy_db[j] = du[j];
          break;
        case CrystalSystem::Monoclinic:
          for (int j = 0; j < 3; ++j)
            dy_db[j] = du[j];
          dy_db[3] = du[monoclinic_angle_idx];
          break;
        case CrystalSystem::Orthorhombic:
          for (int j = 0; j < 3; ++j)
            dy_db[j] = du[j];
          break;
        case CrystalSystem::Tetragonal:
          dy_db[0] = du[0] + du[1];
          dy_db[1] = du[2];
          break;
        case CrystalSystem::Trigonal:
          dy_db[0] = du[0] + du[1] + du[2];
          dy_db[1] = du[3] + du[4] + du[5];
          break;
        case CrystalSystem::Hexagonal:
          dy_db[0] = du[0] + du[1] + 0.5 * du[3];
          dy_db[1] = du[2];
          break;
        case CrystalSystem::Cubic:
          dy_db[0] = du[0] + du[1] + du[2];
          break;
      }
    }
  }
};

} // namespace gemmi
#endif
