Jungfraujoch/image_analysis/indexing/PostIndexingRefinement.h

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

#pragma once

#include <vector>
#include <optional>
#include <algorithm>
#include <cmath>
#include <cstdint>
#include <Eigen/Dense>

#include "../common/CrystalLattice.h"

constexpr float REFINE_CANDIDATE_SPOT_COUNT_RATIO_THRESHOLD = 0.9f;
constexpr float REFINE_CANDIDATE_VOLUME_RATIO_THRESHOLD = 1.05f;
constexpr float REFINE_CANDIDATE_OVERLAP_RATIO_THRESHOLD = 0.4f;
constexpr float REFINE_MIN_VOLUME_EPSILON = 1e-12f;
constexpr float REFINE_MIN_REFERENCE_LENGTH_EPSILON = 1e-6f;
// Max deviation (deg) of a candidate cell angle from the reference cell angle, compared after
// folding both to the acute complement (min(x,180-x)) so the obtuse/acute setting is irrelevant.
constexpr float REFINE_ANGLE_TOLERANCE_VS_REFERENCE_DEG = 10.0f;

struct RefineParameters {
    int64_t viable_cell_min_spots;
    float dist_tolerance_vs_reference;
    bool step_down_to_reference = false;
    std::optional<UnitCell> reference_unit_cell;
    float min_length_A;
    float max_length_A;
    float min_angle_deg;
    float max_angle_deg;
    float indexing_tolerance;
    unsigned refine_threads = 1;
};

bool IntegerRelated(const Eigen::Matrix3f &a, const Eigen::Matrix3f &b);

std::vector<CrystalLattice> Refine(const std::vector<Coord> &in_spots,
                                          size_t nspots,
                                          Eigen::MatrixX3<float> &oCell,
                                          Eigen::VectorX<float> &scores,
                                          RefineParameters &p);