Jungfraujoch/common/DatasetSettings.cpp

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

#include <cmath>

#include "DatasetSettings.h"
#include "Definitions.h"
#include "JFJochException.h"
#include "CheckPath.h"

#define check_max(param, val, max) if ((val) > (max)) throw JFJochException(JFJochExceptionCategory::InputParameterAboveMax, param)
#define check_min(param, val, min) if ((val) < (min)) throw JFJochException(JFJochExceptionCategory::InputParameterBelowMin, param)
#define check_finite(param, val) if (!std::isfinite(val)) throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, param)

DatasetSettings::DatasetSettings() {
    photon_energy_keV = WVL_1A_IN_KEV;
    detector_distance_mm = 100;
    beam_x_pxl = 0.0;
    beam_y_pxl = 0.0;
    file_prefix = "test";
    ntrigger = 1;
    images_per_trigger = 1;
    compression = CompressionAlgorithm::BSHUF_LZ4;
    data_reduction_factor_serialmx = 1.0;
    write_nxmx_hdf5_master = true;
    spot_finding_enable = true;

    poni_rot_1_rad = 0.0f;
    poni_rot_2_rad = 0.0f;
    poni_rot_3_rad = 0.0f;

    max_spot_count = std::min(MAX_SPOT_COUNT, 250);

    detect_ice_rings = false;
}

DatasetSettings &DatasetSettings::ImagesPerTrigger(int64_t input) {
    check_max("Total number of images", input, 10*1000*1000);
    check_min("Total number of images", input, 0);
    images_per_trigger = input;
    return *this;
}

DatasetSettings &DatasetSettings::NumTriggers(int64_t input) {
    check_max("Total number of triggers", input, 10*1000*1000);
    check_min("Total number of triggers", input, 1);
    ntrigger = input;
    return *this;
}

DatasetSettings &DatasetSettings::PhotonEnergy_keV(float input) {
    check_finite("Energy (keV)", input);
    check_min("Energy (keV)", input, MIN_ENERGY_KEV);
    check_max("Energy (keV)", input, MAX_ENERGY_KEV);
    photon_energy_keV = input;
    return *this;
}

DatasetSettings &DatasetSettings::BeamX_pxl(float input) {
    check_finite("Beam center x", input);
    beam_x_pxl = input;
    return *this;
}

DatasetSettings &DatasetSettings::BeamY_pxl(float input) {
    check_finite("Beam center y", input);
    beam_y_pxl = input;
    return *this;
}

DatasetSettings &DatasetSettings::DetectorDistance_mm(float input) {
    check_finite("Detector distance (mm)", input);
    check_min("Detector distance (mm)", input, 1);
    detector_distance_mm = input;
    return *this;
}

DatasetSettings &DatasetSettings::FilePrefix(std::string input) {
    CheckPath(input);   // multi-user guard: no absolute path, no '..' traversal
    return FilePrefixTrusted(std::move(input));
}

DatasetSettings &DatasetSettings::FilePrefixTrusted(std::string input) {
    // Offline/local callers (rugnux, the viewer's processing) supply their own output path, so the
    // CheckPath guard applied by FilePrefix() is deliberately skipped here - an absolute path is
    // allowed. Not reachable from the broker/writer remote-input path.
    if ((input.find("_master.h5") == input.length() - 10) && (input.length() > 10))
        file_prefix = input.substr(0, input.length() - 10);
    else
        file_prefix = input;

    return *this;
}

DatasetSettings &DatasetSettings::Compression(CompressionAlgorithm input) {
    switch (input) {
        case CompressionAlgorithm::NO_COMPRESSION:
        case CompressionAlgorithm::BSHUF_LZ4:
        case CompressionAlgorithm::BSHUF_ZSTD:
        case CompressionAlgorithm::BSHUF_ZSTD_RLE:
        case CompressionAlgorithm::BSHUF_ZSTD_RLE_HUFF:
            compression = input;
            break;
        default:
            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                  "Invalid value for compression enum parameter");
    }
    return *this;
}

DatasetSettings &DatasetSettings::SetUnitCell(const std::optional<UnitCell> &cell) {
    // If one or more cell parameters are zero - assume cell is not provided
    // But if all parameters non-zero - throw exception for non-sense values
    if (cell && (cell->a != 0) && (cell->b != 0) && (cell->c != 0)
        && (cell->alpha != 0) && (cell->beta != 0) && (cell->gamma != 0)) {
        check_min("Unit cell a", cell->a, 0.1);
        check_min("Unit cell b", cell->b, 0.1);
        check_min("Unit cell c", cell->c, 0.1);
        check_min("Angle alpha", cell->alpha, 5.0);
        check_min("Angle beta", cell->beta, 5.0);
        check_min("Angle gamma", cell->gamma, 5.0);
        check_max("Angle alpha", cell->alpha, 355.0);
        check_max("Angle beta", cell->beta, 355.0);
        check_max("Angle gamma", cell->gamma, 360);
        unit_cell = cell;
    } else
        unit_cell.reset();
    return *this;
}

DatasetSettings &DatasetSettings::SpaceGroupNumber(std::optional<int64_t> input) {
    if (input) {
        check_min("Space group number", input, 1);
        check_max("Space group number", input, 230);
    }
    // A bare number can only name the reference setting.
    if (input)
        space_group = *gemmi::find_spacegroup_by_number(static_cast<int>(*input));
    else
        space_group.reset();
    return *this;
}

DatasetSettings &DatasetSettings::SetSpaceGroup(const std::optional<gemmi::SpaceGroup> &input) {
    space_group = input;
    return *this;
}

DatasetSettings &DatasetSettings::SampleName(std::string input) {
    sample_name = input;
    return *this;
}

DatasetSettings &DatasetSettings::AttenuatorTransmission(const std::optional<float> &input) {
    if (input) {
        check_finite("Attenuator transmission", input.value());
        check_max("Attenuator transmission", input.value(), 1.0);
        check_min("Attenuator transmission", input.value(), 0.0);
    }
    attenuator_transmission = input;
    return *this;
}

DatasetSettings &DatasetSettings::TotalFlux(const std::optional<float> &input) {
    if (input) {
        check_finite("Total flux", input.value());
        check_min("Total flux", input.value(), 0.0);
    }
    total_flux = input;
    return *this;
}

DatasetSettings &DatasetSettings::BeamSizeX_um(const std::optional<float> &input) {
    if (input) {
        check_finite("Beam size X", input.value());
        check_min("Beam size X", input.value(), 0.0);
    }
    beam_size_x_um = input;
    return *this;
}

DatasetSettings &DatasetSettings::BeamSizeY_um(const std::optional<float> &input) {
    if (input) {
        check_finite("Beam size Y", input.value());
        check_min("Beam size Y", input.value(), 0.0);
    }
    beam_size_y_um = input;
    return *this;
}

DatasetSettings &DatasetSettings::Goniometer(const std::optional<GoniometerAxis> &input) {
    goniometer = input;
    return *this;
}

DatasetSettings &DatasetSettings::HeaderAppendix(const nlohmann::json &input) {
    header_appendix = input;
    return *this;
}

DatasetSettings &DatasetSettings::ImageAppendix(const nlohmann::json &input) {
    image_appendix = input;
    return *this;
}

std::optional<float> DatasetSettings::GetAttenuatorTransmission() const {
    return attenuator_transmission;
}

std::optional<float> DatasetSettings::GetTotalFlux() const {
    return total_flux;
}

std::optional<float> DatasetSettings::GetBeamSizeX_um() const {
    return beam_size_x_um;
}

std::optional<float> DatasetSettings::GetBeamSizeY_um() const {
    return beam_size_y_um;
}

const std::optional<GoniometerAxis> &DatasetSettings::GetGoniometer() const {
    return goniometer;
}

std::optional<GoniometerAxis> &DatasetSettings::Goniometer() {
    return goniometer;
}

const nlohmann::json& DatasetSettings::GetHeaderAppendix() const {
    return header_appendix;
}

const nlohmann::json& DatasetSettings::GetImageAppendix() const {
    return image_appendix;
}

std::optional<UnitCell> DatasetSettings::GetUnitCell() const {
    return unit_cell;
}

std::optional<int64_t> DatasetSettings::GetSpaceGroupNumber() const {
    if (!space_group)
        return std::nullopt;
    return space_group->number;
}

const std::optional<gemmi::SpaceGroup> &DatasetSettings::GetSpaceGroup() const {
    return space_group;
}

std::string DatasetSettings::GetSampleName() const {
    return sample_name;
}

float DatasetSettings::GetPhotonEnergy_keV() const {
    return photon_energy_keV;
}

float DatasetSettings::GetBeamX_pxl() const {
    return beam_x_pxl;
}

float DatasetSettings::GetBeamY_pxl() const {
    return beam_y_pxl;
}

float DatasetSettings::GetDetectorDistance_mm() const {
    return detector_distance_mm;
}

Coord DatasetSettings::GetScatteringVector() const {
    return {0, 0, photon_energy_keV / WVL_1A_IN_KEV};
}

std::string DatasetSettings::GetFilePrefix() const {
    return file_prefix;
}

CompressionAlgorithm DatasetSettings::GetCompressionAlgorithm() const {
    return compression;
}

int64_t DatasetSettings::GetNumTriggers() const {
    return ntrigger;
}

int64_t DatasetSettings::GetImageNumPerTrigger() const {
    return images_per_trigger;
}

DatasetSettings &DatasetSettings::ImagesPerFile(const std::optional<int64_t> &input) {
    if (input.has_value())
        check_min("Images per file", input.value(), 1);
    images_per_file = input;
    return *this;
}

std::optional<int64_t> DatasetSettings::GetImagesPerFile() const {
    return images_per_file;
}

DatasetSettings &DatasetSettings::LossyCompressionSerialMX(float input) {
    check_min("Data reduction factor for serial MX", input, 0.0);
    check_max("Data reduction factor for serial MX", input, 1.0);
    data_reduction_factor_serialmx = input;
    return *this;
}

float DatasetSettings::GetLossyCompressionSerialMX() const {
    return data_reduction_factor_serialmx;
}

DatasetSettings &DatasetSettings::RunNumber(const std::optional<uint64_t> &input) {
    if (input) {
        check_min("Run number", input, 0);
        check_max("Run number", input, INT64_MAX);
    }
    run_number = input;
    return *this;
}

DatasetSettings & DatasetSettings::RunName(const std::optional<std::string> &input) {
    if (input && input.value().empty())
        run_name = {};
    else
        run_name = input;
    return *this;
}

DatasetSettings &DatasetSettings::ExperimentGroup(const std::string &input) {
    group = input;
    return *this;
}

std::optional<uint64_t> DatasetSettings::GetRunNumber() const {
    return run_number;
}

std::optional<std::string> DatasetSettings::GetRunName() const {
    return run_name;
}

std::string DatasetSettings::GetExperimentGroup() const {
    return group;
}

std::optional<std::chrono::nanoseconds> DatasetSettings::GetImageTime() const {
    return image_time;
}

DatasetSettings &DatasetSettings::ImageTime(const std::optional<std::chrono::nanoseconds> &input) {
    if (input && (input.value().count() == 0))
        image_time = {};
    else
        image_time = input;
    return *this;
}

DatasetSettings &DatasetSettings::LossyCompressionPoisson(std::optional<int64_t> input) {
    if (!input || (input == 0))
        compression_poisson_factor = {};
    else {
        check_min("Poisson compression factor", input.value(), 1);
        check_max("Poisson compression factor", input.value(), 16);
        compression_poisson_factor = input;
    }
    return *this;
}

std::optional<int64_t> DatasetSettings::GetLossyCompressionPoisson() const {
    return compression_poisson_factor;
}

DatasetSettings &DatasetSettings::PixelValueLowThreshold(const std::optional<int64_t> &input) {
    if (!input || (input == 0))
        pixel_value_low_threshold = {};
    else {
        check_min("Pixel value low threshold", input.value(), 0);
        check_max("Pixel value low threshold", input.value(), INT24_MAX - 1);
        pixel_value_low_threshold = input;
    }
    return *this;
}

DatasetSettings &DatasetSettings::PixelValueHighThreshold(const std::optional<int64_t> &input) {
    if (!input || (input == 0))
        pixel_value_high_threshold = {};
    else {
        check_min("Pixel value high threshold", input.value(), 1);
        check_max("Pixel value high threshold", input.value(), INT32_MAX);
        pixel_value_high_threshold = input;
    }
    return *this;
}

std::optional<int64_t> DatasetSettings::GetPixelValueLowThreshold() const {
    return pixel_value_low_threshold;
}

std::optional<int64_t> DatasetSettings::GetPixelValueHighThreshold() const {
    return pixel_value_high_threshold;
}

bool DatasetSettings::IsWriteNXmxHDF5Master() const {
    return write_nxmx_hdf5_master;
}

DatasetSettings &DatasetSettings::WriteNXmxHDF5Master(bool input) {
    write_nxmx_hdf5_master = input;
    return *this;
}

std::optional<bool> DatasetSettings::IsSaveCalibration() const {
    return save_calibration;
}

DatasetSettings &DatasetSettings::SaveCalibration(std::optional<bool> input) {
    save_calibration = input;
    return *this;
}

DatasetSettings &DatasetSettings::GridScan(const std::optional<GridScanSettings> &input) {
    grid_scan = input;
    return *this;
}

std::optional<GridScanSettings> &DatasetSettings::GridScan() {
    return grid_scan;
}

const std::optional<GridScanSettings> &DatasetSettings::GetGridScan() const {
    return grid_scan;
}

std::optional<float> DatasetSettings::GetPolarizationFactor() const {
    return polarization_factor;
}

DatasetSettings &DatasetSettings::BandwidthFWHM(const std::optional<float> &input) {
    bandwidth_fwhm = input;
    return *this;
}

std::optional<float> DatasetSettings::GetBandwidthFWHM() const {
    return bandwidth_fwhm;
}

DatasetSettings &DatasetSettings::ModulePlacement(const std::vector<::ModulePlacement> &input) {
    module_placement = input;
    return *this;
}

const std::vector<::ModulePlacement> &DatasetSettings::GetModulePlacement() const {
    return module_placement;
}

float DatasetSettings::GetPoniRot3_rad() const {
    return poni_rot_3_rad;
}

float DatasetSettings::GetPoniRot2_rad() const {
    return poni_rot_2_rad;
}

float DatasetSettings::GetPoniRot1_rad() const {
    return poni_rot_1_rad;
}

DatasetSettings &DatasetSettings::PoniRot1_rad(float input) {
    check_finite("PONI rotation 1 (radians)", input);
    poni_rot_1_rad = input;
    return *this;
}

DatasetSettings &DatasetSettings::PoniRot2_rad(float input) {
    check_finite("PONI rotation 2 (radians)", input);
    poni_rot_2_rad = input;
    return *this;
}

DatasetSettings &DatasetSettings::PoniRot3_rad(float input) {
    check_finite("PONI rotation 3 (radians)", input);
    poni_rot_3_rad = input;
    return *this;
}

DatasetSettings &DatasetSettings::PolarizationFactor(const std::optional<float> &input) {
    if (input.has_value()) {
        check_finite("Polarization factor", input.value());
        check_min("Polarization factor", input.value(), -1.0);
        check_max("Polarization factor", input.value(), 1.0);
    }
    polarization_factor = input;
    return *this;
}

std::optional<float> DatasetSettings::GetRingCurrent_mA() const {
    return ring_current_mA;
}

DatasetSettings &DatasetSettings::RingCurrent_mA(const std::optional<float> &input) {
    if (input.has_value()) {
        check_min("Ring current (mA)", input, 0.0);
    }
    ring_current_mA = input;
    return *this;
}

std::optional<float> DatasetSettings::GetSampleTemperature_K() const {
    return sample_temperature_K;
}

DatasetSettings &DatasetSettings::SampleTemperature_K(const std::optional<float> &input) {
    if (input.has_value()) {
        check_min("Sample temperature (K)", input, 0.0);
        check_max("Sample temperature (K)", input, 1000.0);
    }
    sample_temperature_K = input;
    return *this;
}

DatasetSettings &DatasetSettings::SpotFindingEnable(bool input) {
    spot_finding_enable = input;
    return *this;
}

bool DatasetSettings::IsSpotFindingEnabled() const {
    return spot_finding_enable;
}

DatasetSettings &DatasetSettings::MaxSpotCount(int64_t input) {
    check_min("Max spot count", input, MIN_SPOT_COUNT);
    check_max("Max spot count", input, MAX_SPOT_COUNT);
    max_spot_count = input;
    return *this;
}

DatasetSettings & DatasetSettings::DetectIceRings(bool input) {
    detect_ice_rings = input;
    return *this;
}

bool DatasetSettings::IsDetectIceRings() const {
    return detect_ice_rings;
}

DatasetSettings &DatasetSettings::FluorescenceSpectrum(const XrayFluorescenceSpectrum &input) {
    fluorescence_spectrum = input;
    return *this;
}

const XrayFluorescenceSpectrum & DatasetSettings::GetFluorescenceSpectrum() const {
    return fluorescence_spectrum;
}

int64_t DatasetSettings::GetMaxSpotCount() const {
    return max_spot_count;
}

std::optional<SmargonPosition> DatasetSettings::GetSmargonPosition() const {
    return smargon_position;
}

DatasetSettings &DatasetSettings::Smargon(const std::optional<SmargonPosition> &input) {
    smargon_position = input;
    return *this;
}