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Jungfraujoch/common/DatasetSettings.h
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leonarski_fandClaude Opus 5 8a04773d1d api: record the beam size at the sample, and write it where NXmx puts it 
dataset_settings gains beam_size_x_um and beam_size_y_um, the horizontal and
vertical size of the X-ray beam where it meets the sample. They follow the same
route total_flux takes - OpenAPI, DatasetSettings, the CBOR start message, the
HDF5 master, and back out of a stored file - and nothing consumes them; this is
metadata a beamline can state and a downstream program can read.

NXmx puts this in the application definition rather than the base class: not
NXbeam's extent (rank 2, nP x 2, per scan point, always FWHM of a rectangular
aperture) but NXmx's own incident_beam_size, a recommended rank-1 two-element
array in the order x, y. Both are live and neither is deprecated, so the choice
matters; the MX definition wins in an MX file. Written as one array with a
units attribute of "m", like every other length in the master, so the settings
hold micrometres and FillMessage converts once.

The unit table of ReadLength_m becomes LengthUnitFactor so the array read can
share it: a master written elsewhere may state this in millimetres.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
2026-09-02 09:59:34 +02:00

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// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
#include <cstdint>
#include <string>
#include <optional>
#include "UnitCell.h"
#include "Coord.h"
#include "../compression/CompressionAlgorithmEnum.h"
#include "JFJochMessages.h"
#include "XrayFluorescenceSpectrum.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%)
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& 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;
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;
};
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