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

#pragma once

#include "../gemmi_gph/gemmi/math.hpp"
#include "../gemmi_gph/gemmi/symmetry.hpp"

#include <vector>
#include <array>
#include "Coord.h"
#include "UnitCell.h"

// Below this a basis counts as coplanar. 0.02 is 1.1 deg off flat: an order of magnitude below the
// flattest basis a real indexing candidate has been seen to reach, and three orders above the point
// where float cell angles stop carrying even the SIGN of the metric determinant.
constexpr float MIN_BASIS_VOLUME_FRACTION = 0.02f;

class CrystalLattice {
    Coord vec[3];
    void FixHandedness();
    // Throws if the basis is too flat to have a reciprocal cell. Everything that builds a lattice
    // rejects one this flat, so reaching it means a degenerate basis got through somewhere.
    void CheckHasReciprocal() const;
public:
    void ReorderABEqual();
    void ReorderMonoclinic();
    CrystalLattice() = default;
    explicit CrystalLattice(const UnitCell &cell);
    explicit CrystalLattice(const std::vector<float>& input);
    CrystalLattice(float a, float b, float c, float alpha, float beta, float gamma);
    CrystalLattice(const Coord &a, const Coord &b, const Coord &c);
    [[nodiscard]] float CalcVolume() const;
    // |V| / (|a| |b| |c|) - the cell volume made scale-free: 1 for an orthogonal basis, 0 for three
    // coplanar rows. This is the test for a degenerate basis, not CalcVolume(): three nearly-coplanar
    // 300 A rows still enclose hundreds of A^3, so an absolute volume cannot see them, and a basis
    // that flat has no usable reciprocal cell (1/V blows up) whatever its size.
    [[nodiscard]] float VolumeFraction() const;
    [[nodiscard]] const Coord &Vec0() const;
    [[nodiscard]] const Coord &Vec1() const;
    [[nodiscard]] const Coord &Vec2() const;
    [[nodiscard]] Coord Astar() const;
    [[nodiscard]] Coord Bstar() const;
    [[nodiscard]] Coord Cstar() const;
    [[nodiscard]] UnitCell GetUnitCell() const;
    [[nodiscard]] std::vector<float> GetVector() const;
    CrystalLattice FromPrimitive(char centering) const;
    CrystalLattice ToPrimitive(char centering) const;
    CrystalLattice Multiply(const RotMatrix &input) const;
    CrystalLattice Multiply(const gemmi::Mat33 &input) const;
    void Sort();
    void Regularize(const gemmi::CrystalSystem &input);
    [[nodiscard]] std::vector<float> GetUBMatrix() const;
    CrystalLattice NiggliReduce() const;
    void FlipSign(size_t i1);
};

inline std::ostream &operator<<( std::ostream &output, const CrystalLattice &in ) {
    output << in.Vec0() << std::endl << in.Vec1() << std::endl << in.Vec2() << std::endl;
    return output;
}