Jungfraujoch/common/BraggIntegrationSettings.h

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

#pragma once

#include <optional>

// Spot-intensity extraction method used by the Bragg integration engine. ProfileGaussian (default)
// profile-fits with a measured-width Gaussian (Kabsch-style) - more accurate intensities than the
// classical uniform BoxSum; validated on anomalous data (stronger S/Cl peaks vs box-sum). BoxSum is
// the simpler, faster fallback. ProfileEmpirical learns the profile per resolution shell from strong
// spots - see docs/CPU_DATA_ANALYSIS.md (Bragg integration).
enum class IntegratorMode { BoxSum, ProfileGaussian, ProfileEmpirical };

class BraggIntegrationSettings {
    IntegratorMode integrator_mode = IntegratorMode::ProfileGaussian;
    float r_1 = 4;
    float r_2 = 6;
    float r_3 = 10;
    float d_min_limit_A = 1.0;
    std::optional<float> fixed_profile_radius;
    float minimum_sigma_in_regards_to_i = 0.02;
    bool still_partiality = false;   // experimental stills excitation-error partiality (rugnux --still-partiality)
    // Symmetric trimmed-mean fraction for the r2..r3 background ring: drop the lowest and highest this
    // fraction of ring pixels before averaging. Resists the high-side contamination (neighbour-spot
    // wings, tails, zingers) that biases the plain ring mean up and makes it over-subtract weak
    // high-angle reflections. Applied to monochromatic (rotation) data; the integration engine keeps
    // the tuned high-side sigma-clip for stills instead. 0 = plain ring mean (rugnux --background-trim).
    float bkg_trim_fraction = 0.10f;

public:
    BraggIntegrationSettings& R1(float input);
    BraggIntegrationSettings& R2(float input);
    BraggIntegrationSettings& R3(float input);
    BraggIntegrationSettings& DMinLimit_A(float input);
    BraggIntegrationSettings& FixedProfileRadius_recipA(std::optional<float> input);
    BraggIntegrationSettings& Integrator(IntegratorMode input);
    BraggIntegrationSettings& StillPartiality(bool input);
    BraggIntegrationSettings& BackgroundTrimFraction(float input);


    [[nodiscard]] IntegratorMode GetIntegrator() const;
    [[nodiscard]] float GetR1() const;
    [[nodiscard]] float GetR2() const;
    [[nodiscard]] float GetR3() const;
    [[nodiscard]] std::optional<float> GetFixedProfileRadius_recipA() const;
    [[nodiscard]] float GetDMinLimit_A() const;

    [[nodiscard]] float GetMinimumSigmaInRegardsToI() const;
    [[nodiscard]] bool GetStillPartiality() const;
    [[nodiscard]] float GetBackgroundTrimFraction() const;
};