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Jungfraujoch/common/DetectorSetup.h
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v1.0.0.rc-162 (#72)
**Files written by Jungfraujoch now import correctly in DIALS, XDS and pyFAI.** A tilted detector, a grid scan, a still recorded at a goniometer position, and saturated or unreadable pixels were each described in a way that a third-party program acted on wrongly. If you process Jungfraujoch data outside Jungfraujoch, prefer this release to any earlier one.

* HDF5: the detector tilt (`rot1`/`rot2`/`rot3`) is exported correctly in the NXmx transformation chain; untilted geometries are unaffected.
* HDF5: a still recorded at a goniometer position is no longer read back as a single image, and a grid scan records a stationary spindle so a program that requires a rotation axis can open it.
* HDF5: the sample transformation chain is written in mounting order, with a Smargon head position told apart from the spindle, one entry per image, `module_offset` as a float unit vector, and `offset_units` on every offset.
* HDF5: saturated, underloaded and unreadable pixels are described so a downstream program masks them - `saturation_value`, `underload_value`, `error_value` and `bit_depth_readout` are written correctly, and a data file missing next to a VDS master reads as the error marker rather than as zero counts.
* HDF5: the rotation axis is read back under whatever name it carries, and `mirror_y` records whether the assembled image is mirrored in Y relative to the detector's raw readout.
* A grid scan and a goniometer axis can both be set; they are no longer alternatives.
* `images_per_file` is chosen from the acquisition when it is not given: a rotation sweep of at most 20000 images goes into a single data file, a grid scan splits on whole fast-axis rows, and stills and serial keep 1000.
* The writer refuses a stream whose start message declares a different pixel format than its images carry, and a DECTRIS detector sending signed images is no longer declared unsigned.
* The image stream can carry the sample transformation chain (`transformations`, in the END message); a producer that does not send it gets the same chain built by the writer.
* rugnux: fixing the space group with `-S` no longer prevents the lattice from being found - a lattice indexed in a different setting is reindexed into that group's own setting, and a run whose crystal does not have that group's lattice stops and names the cell it indexed as, rather than reporting statistics that cannot describe it.
* rugnux: the per-image resolution estimate now predicts the resolution the merged data reach rather than the highest-resolution spot found, and is reported as `SPOT_RESOLUTION_ESTIMATE`.
* rugnux: two runs of the same command on the same images produce the same merged intensities; the azimuthal profile written alongside them is not yet reproducible in the same way.
* rugnux: the offline lattice refinement is bounded by iterations rather than by a wall clock, so a loaded machine can no longer refine to a different lattice; a live acquisition keeps its real-time bound.
* rugnux: the detector-frame modulation correction is fitted on a grid spanning the detector, so whether it is applied no longer depends on how far integration reached.
* rugnux: the geometry pre-pass no longer writes `<prefix>_01.mtz`, `_01.cif`, `_01.hkl` and `_01_image.dat`; the refined second pass writes those files under `<prefix>`, and that is the result to use.
* rugnux: `_process.h5` describes the pixel format of the images it links to, and is written on a thread of its own.
* rugnux: the detector geometry is also logged in XDS's convention (`ORGX`/`ORGY`, detector axis vectors, rotation axis), so it can be compared with an XDS refinement.
* rugnux: an image integrated in pyFAI through the `.poni` file written by `--mode calibration` comes out with the correct azimuth, and the file declares pyFAI's `orientation`, which needs pyFAI 2024.01 or newer. Radial integration is unchanged.
* rugnux: a rotation run is substantially faster throughout - beam-stop detection, first-pass indexing, geometry refinement, integration, scaling and merging - and observations outside the scaling resolution range are dropped as they are ingested. The refined geometry, the space group chosen and the merged statistics are unchanged.
* Faster spot finding and indexing, on the broker as well as in rugnux; the spots found and the lattices indexed are unchanged.
* A run reserves substantially less GPU memory: nothing is allocated for buffers that are never read, and a worker builds only the engines it uses.
* rugnux: with `-N` left at its default the per-image loop of `--mode mx` uses at most 16 workers per GPU, rather than one per hardware thread; an explicit `-N` is obeyed as given.
* CUDA 12 builds now contain device code for Volta, so the RHEL 8 packages and the portable Linux `.tgz` run on a V100; the CUDA 13 artefacts (RHEL 9, Ubuntu, Windows) remain Turing and newer.
* The build resolves a single Eigen for the whole project, and refuses to configure if Ceres picks up a different one; a build that mixed two Eigen versions was undefined behaviour and crashed at -O2.
* Documentation: a security page, and the supported GPU generations and minimum NVIDIA driver version of every released artefact.

**Breaking change to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.162, `frontend/src/client`):
* `dataset_settings.images_per_file` is no longer `default: 1000` and no longer accepts `0`; it is optional, and its minimum is 1. A client sending `0` (previously "one file for the whole run") is now rejected - omit the field instead, which for a rotation sweep gives the same single file.
* `file_writer_format` now defaults to `NXmxVDS`, matching the server's own default and the layout recommended for DIALS, XDS and CrystFEL. A generated client that fills in schema defaults and does not set the format explicitly will write VDS masters where it previously wrote legacy ones; set `NXmxLegacy` explicitly to keep them.

---------

Co-authored-by: jungfrau <jungfrau@mx-aare-test.psi.ch>
Reviewed-on: #72
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-08-25 08:21:39 +02:00

159 lines
7.5 KiB
C++

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
#include <memory>
#include <chrono>
#include <optional>
#include "DetectorGeometry.h"
#include "../jungfrau/JFModuleGainCalibration.h"
#include "DetectorGeometryFixed.h"
#include "DetectorGeometryModular.h"
#include "DetectorSettings.h"
constexpr uint16_t SimplonStream2Port = 31001;
enum class DetectorType {EIGER, JUNGFRAU, DECTRIS};
class DetectorSetup {
std::string description;
std::string serial_number;
std::shared_ptr<DetectorGeometry> geometry;
std::vector<std::string> det_modules_hostname;
std::vector<std::string> gain_file_names;
std::vector<std::string> trim_file_names;
std::string trim_file_directory;
std::vector<int> trim_energy_eV_values;
std::shared_ptr<JFGainCalibration> gain_calibration;
int64_t udp_interface_count = 2;
float pixel_size_um = 75.0f;
std::string sensor_material = "Si";
float sensor_thickness_um = 320.0f;
std::vector<int64_t> tx_delay;
DetectorType detector_type;
int32_t high_voltage = 120.0;
uint32_t ipv4_base_addr = 0x010a0a0a;
bool module_sync = true;
// Whether the assembled image is mirrored in Y relative to the detector's raw readout order.
// A property of the configuration, not something derivable from the assembled image: it says
// how the modules were laid out to reach the MX convention of row 0 at the top.
bool mirror_y = true;
std::chrono::nanoseconds read_out_time;
std::chrono::nanoseconds min_count_time;
std::chrono::nanoseconds min_frame_time;
float min_energy_threshold_keV = 2.7f;
int32_t temperature_thresold_degC = 55;
std::string dectris_roi;
std::optional<int64_t> bit_depth_image;
std::optional<int64_t> bit_depth_readout;
std::optional<int64_t> saturation_limit;
std::optional<DetectorSettings> settings;
DetectorSetup(std::shared_ptr<DetectorGeometry> geom,
DetectorType detector_type,
const std::string &description = "Detector",
const std::vector<std::string> &det_modules_hostname = {});
public:
DetectorSetup(const DetectorGeometryFixed& geom,
DetectorType detector_type,
const std::string &description = "Detector",
const std::vector<std::string> &det_modules_hostname = {});
DetectorSetup(const DetectorGeometryModular& geom,
DetectorType detector_type,
const std::string &description = "Detector",
const std::vector<std::string> &det_modules_hostname = {});
void LoadGain(const std::vector<std::string> &filenames);
void SetTrimFiles(const std::vector<std::string> &filenames);
DetectorSetup& TxDelay(const std::vector<int64_t> &v);
DetectorSetup& UDPInterfaceCount(int64_t input);
DetectorSetup& SensorMaterial(const std::string &input);
DetectorSetup& SensorThickness_um(float input);
DetectorSetup& PixelSize_um(float input);
DetectorSetup& HighVoltage(int32_t input);
DetectorSetup& SerialNumber(const std::string &input);
DetectorSetup& BaseIPv4Addr(const std::string &input);
DetectorSetup& ModuleSync(bool input);
DetectorSetup& MirrorY(bool input);
DetectorSetup& ReadOutTime(std::chrono::nanoseconds input);
DetectorSetup& Geometry(const DetectorGeometryFixed& input);
DetectorSetup& BitDepthImage(int64_t input);
DetectorSetup& MinFrameTime(std::chrono::nanoseconds input);
DetectorSetup& MinCountTime(std::chrono::nanoseconds input);
DetectorSetup& MinThreshold_keV(float input);
DetectorSetup& SaturationLimit(std::optional<int64_t> input);
DetectorSetup& Description(const std::string &input);
DetectorSetup& DECTRISROI(const std::string &input);
DetectorSetup& DefaultSettings(const std::optional<DetectorSettings> &input);
DetectorSetup& TempThreshold_degC(int64_t input);
DetectorSetup& TrimEnergies_eV(std::vector<int> input);
[[nodiscard]] DetectorType GetDetectorType() const;
[[nodiscard]] const DetectorGeometry& GetGeometry() const;
[[nodiscard]] const std::vector<std::string>& GetDetectorModuleHostname() const;
[[nodiscard]] uint64_t GetModulesNum() const;
[[nodiscard]] std::string GetDescription() const;
[[nodiscard]] float GetPixelSize_mm() const;
[[nodiscard]] float GetSensorThickness_um() const;
[[nodiscard]] std::string GetSensorMaterial() const;
[[nodiscard]] const std::vector<JFModuleGainCalibration> &GetGainCalibration() const;
[[nodiscard]] int64_t GetUDPInterfaceCount() const;
[[nodiscard]] const std::vector<int64_t> &GetTxDelay() const; // can be empty for default
[[nodiscard]] const std::vector<std::string> &GetGainFileNames() const;
[[nodiscard]] const std::vector<std::string> &GetTrimFileNames() const;
[[nodiscard]] std::string GetTrimFileDirectory() const;
[[nodiscard]] int32_t GetHighVoltage() const;
[[nodiscard]] std::string GetSerialNumber() const;
[[nodiscard]] uint32_t GetSrcIPv4Addr(uint32_t half_module) const;
[[nodiscard]] std::string GetBaseIPv4Addr() const;
[[nodiscard]] bool IsModuleSync() const;
[[nodiscard]] bool IsMirrorY() const;
[[nodiscard]] std::chrono::nanoseconds GetReadOutTime() const;
[[nodiscard]] std::chrono::nanoseconds GetMinFrameTime() const;
[[nodiscard]] std::chrono::nanoseconds GetMinCountTime() const;
[[nodiscard]] std::optional<int64_t> GetBitDepthReadout() const;
[[nodiscard]] std::optional<int64_t> GetBitDepthImage() const;
[[nodiscard]] std::string GetDECTRISStream2Addr() const;
[[nodiscard]] float GetMinThreshold_keV() const;
[[nodiscard]] std::optional<int64_t> GetSaturationLimit() const;
[[nodiscard]] std::string GetDECTRISROI() const;
[[nodiscard]] std::optional<DetectorSettings> GetDefaultSettings() const;
[[nodiscard]] int32_t GetTempThreshold_degC() const;
[[nodiscard]] std::vector<int> GetTrimEnergies_eV() const;
};
DetectorSetup DetJF4M(const std::string &description = "Detector",
const std::vector<std::string> &det_modules_hostname = {});
DetectorSetup DetJF9M(const std::string &description = "Detector",
const std::vector<std::string> &det_modules_hostname = {});
DetectorSetup DetJF(int32_t nmodules,
int32_t horizontal_stacking = 1,
int32_t gap_x = 0,
int32_t gap_y = 0,
bool mirror_y = true,
const std::string &description = "Detector",
const std::vector<std::string> &det_modules_hostname = {});
DetectorSetup DetJF(const DetectorGeometryModular &geom,
const std::string &description = "Detector",
const std::vector<std::string> &det_modules_hostname = {});
DetectorSetup DetEIGER(int32_t nmodules,
int32_t horizontal_stacking = 1,
int32_t gap_x = 0,
int32_t gap_y = 0,
bool mirror_y = true,
const std::string &description = "Detector",
const std::vector<std::string> &det_modules_hostname = {});
DetectorSetup DetEIGER(const DetectorGeometryModular &geom,
const std::string &description = "Detector",
const std::vector<std::string> &det_modules_hostname = {});
DetectorSetup DetDECTRIS(int64_t width, int64_t height,
const std::string &description,
const std::string &addr);