Jungfraujoch/common/DatasetSettings.h

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#pragma once

#include <chrono>
#include <cstdint>
#include <string>
#include <optional>

#include "UnitCell.h"
#include "Coord.h"
#include "../compression/CompressionAlgorithmEnum.h"
#include "JFJochMessages.h"
#include "XrayFluorescenceSpectrum.h"
#include "DetectorModules.h"

#include "gemmi/symmetry.hpp"

class DatasetSettings {
    int64_t images_per_trigger;
    int64_t ntrigger;

    float beam_x_pxl;
    float beam_y_pxl;
    float detector_distance_mm;
    float photon_energy_keV;

    std::string file_prefix;
    std::optional<int64_t> images_per_file;

    CompressionAlgorithm compression;

    std::string sample_name;
    std::optional<UnitCell> unit_cell;
    // The whole group, not its number: a number can only name the reference setting, so
    // "P 1 1 2" and "R 3:R" are lost the moment a number is all that is kept.
    std::optional<gemmi::SpaceGroup> space_group;

    std::optional<float> total_flux;
    std::optional<float> attenuator_transmission;
    // Size of the beam where it meets the sample, x then y (NXmx incident_beam_size)
    std::optional<float> beam_size_x_um;
    std::optional<float> beam_size_y_um;
    std::optional<float> ring_current_mA;
    std::optional<GoniometerAxis> goniometer;
    std::optional<GridScanSettings> grid_scan;
    std::optional<float> sample_temperature_K;

    nlohmann::json image_appendix;
    nlohmann::json header_appendix;

    float data_reduction_factor_serialmx;

    std::optional<std::chrono::nanoseconds> image_time;
    std::optional<uint64_t> run_number;
    std::optional<std::string> run_name;
    std::string group;
    std::optional<int64_t> compression_poisson_factor;
    std::optional<int64_t> pixel_value_low_threshold;
    std::optional<int64_t> pixel_value_high_threshold;
    std::optional<bool> save_calibration;

    bool write_nxmx_hdf5_master;

    std::optional<float> polarization_factor;
    std::optional<float> bandwidth_fwhm; // relative X-ray bandwidth, FWHM of dlambda/lambda (e.g. 0.01 for 1%)
    // Where the modules are for this dataset (rugnux's <prefix>_module_placement.json); empty: as the detector
    // assembles them.
    std::vector<::ModulePlacement> module_placement;
    float poni_rot_1_rad;
    float poni_rot_2_rad;
    float poni_rot_3_rad;

    bool spot_finding_enable;
    int64_t max_spot_count;

    bool detect_ice_rings; // Enable special handling of ice rings
    XrayFluorescenceSpectrum fluorescence_spectrum;

    std::optional<SmargonPosition> smargon_position;
public:

    DatasetSettings();

    DatasetSettings& ImagesPerTrigger(int64_t input);
    DatasetSettings& NumTriggers(int64_t triggers);
    DatasetSettings& PhotonEnergy_keV(float input);
    DatasetSettings& BeamX_pxl(float input);
    DatasetSettings& BeamY_pxl(float input);
    DatasetSettings& DetectorDistance_mm(float input);
    DatasetSettings& FilePrefix(std::string input);
    DatasetSettings& FilePrefixTrusted(std::string input);   // offline/local: no CheckPath guard (absolute allowed)
    DatasetSettings& Compression(CompressionAlgorithm input);
    DatasetSettings& SetUnitCell(const std::optional<UnitCell> &cell);
    DatasetSettings& SpaceGroupNumber(std::optional<int64_t> input);
    DatasetSettings& SetSpaceGroup(const std::optional<gemmi::SpaceGroup> &input);
    DatasetSettings& SampleName(std::string input);
    DatasetSettings& AttenuatorTransmission(const std::optional<float> &input);
    DatasetSettings& TotalFlux(const std::optional<float> &input);
    DatasetSettings& BeamSizeX_um(const std::optional<float> &input);
    DatasetSettings& BeamSizeY_um(const std::optional<float> &input);
    DatasetSettings& Goniometer(const std::optional<GoniometerAxis>& input);
    DatasetSettings& GridScan(const std::optional<GridScanSettings>& input);
    DatasetSettings& HeaderAppendix(const nlohmann::json& input);
    DatasetSettings& ImageAppendix(const nlohmann::json& input);
    DatasetSettings& ImagesPerFile(const std::optional<int64_t> &input);
    DatasetSettings& RunNumber(const std::optional<uint64_t> &run_number);
    DatasetSettings& RunName(const std::optional<std::string> &input);
    DatasetSettings& ExperimentGroup(const std::string &group);
    DatasetSettings& ImageTime(const std::optional<std::chrono::nanoseconds> &input);

    DatasetSettings& LossyCompressionSerialMX(float input);
    DatasetSettings& LossyCompressionPoisson(std::optional<int64_t> input);
    DatasetSettings& WriteNXmxHDF5Master(bool input);
    DatasetSettings& SaveCalibration(std::optional<bool> input);
    DatasetSettings& PixelValueLowThreshold(const std::optional<int64_t> &input);
    DatasetSettings& PixelValueHighThreshold(const std::optional<int64_t> &input);
    DatasetSettings& PolarizationFactor(const std::optional<float> &input);
    DatasetSettings& BandwidthFWHM(const std::optional<float> &input);
    DatasetSettings& ModulePlacement(const std::vector<::ModulePlacement> &input);
    DatasetSettings& PoniRot1_rad(float input);
    DatasetSettings& PoniRot2_rad(float input);
    DatasetSettings& PoniRot3_rad(float input);
    DatasetSettings& RingCurrent_mA(const std::optional<float> &input);
    DatasetSettings& SampleTemperature_K(const std::optional<float> &input);
    DatasetSettings& SpotFindingEnable(bool input);
    DatasetSettings& MaxSpotCount(int64_t input);
    DatasetSettings& DetectIceRings(bool input);
    DatasetSettings& FluorescenceSpectrum(const XrayFluorescenceSpectrum& input);
    DatasetSettings& Smargon(const std::optional<SmargonPosition>& input);

    std::optional<float> GetAttenuatorTransmission() const;
    std::optional<float> GetTotalFlux() const;
    std::optional<float> GetBeamSizeX_um() const;
    std::optional<float> GetBeamSizeY_um() const;

    std::optional<GoniometerAxis> &Goniometer();
    std::optional<GridScanSettings> &GridScan();
    const std::optional<GoniometerAxis> &GetGoniometer() const;
    const std::optional<GridScanSettings> &GetGridScan() const;

    const nlohmann::json& GetHeaderAppendix() const;
    const nlohmann::json& GetImageAppendix() const;
    std::optional<UnitCell> GetUnitCell() const;
    std::optional<int64_t> GetSpaceGroupNumber() const;
    const std::optional<gemmi::SpaceGroup> &GetSpaceGroup() const;
    std::string GetSampleName() const;
    float GetPhotonEnergy_keV() const;
    float GetBeamX_pxl() const;
    float GetBeamY_pxl() const;
    float GetDetectorDistance_mm() const;

    Coord GetScatteringVector() const;

    std::string GetFilePrefix() const;

    CompressionAlgorithm GetCompressionAlgorithm() const;
    int64_t GetNumTriggers() const;
    int64_t GetImageNumPerTrigger() const;
    std::optional<int64_t> GetImagesPerFile() const;

    std::optional<uint64_t> GetRunNumber() const;
    std::optional<std::string> GetRunName() const;
    std::string GetExperimentGroup() const;
    std::optional<std::chrono::nanoseconds> GetImageTime() const;
    
    float GetLossyCompressionSerialMX() const;
    std::optional<int64_t> GetLossyCompressionPoisson() const;

    std::optional<int64_t> GetPixelValueLowThreshold() const;
    std::optional<int64_t> GetPixelValueHighThreshold() const;
    bool IsWriteNXmxHDF5Master() const;
    std::optional<bool> IsSaveCalibration() const;

    std::optional<float> GetPolarizationFactor() const;
    std::optional<float> GetBandwidthFWHM() const;
    const std::vector<::ModulePlacement> &GetModulePlacement() const;
    float GetPoniRot1_rad() const;
    float GetPoniRot2_rad() const;
    float GetPoniRot3_rad() const;

    std::optional<float> GetRingCurrent_mA() const;
    std::optional<float> GetSampleTemperature_K() const;

    bool IsSpotFindingEnabled() const;
    int64_t GetMaxSpotCount() const;

    bool IsDetectIceRings() const;
    const XrayFluorescenceSpectrum &GetFluorescenceSpectrum() const;
    std::optional<SmargonPosition> GetSmargonPosition() const;
};