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**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>
456 lines
16 KiB
C++
456 lines
16 KiB
C++
// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include <filesystem>
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#include <utility>
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#include "DetectorSetup.h"
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#include "JFJochException.h"
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#include "NetworkAddressConvert.h"
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#define check_max(param, val, max) if ((val) > (max)) throw JFJochException(JFJochExceptionCategory::InputParameterAboveMax, param)
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#define check_min(param, val, min) if ((val) < (min)) throw JFJochException(JFJochExceptionCategory::InputParameterBelowMin, param)
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DetectorSetup::DetectorSetup(const DetectorGeometryFixed &geom, DetectorType detector_type,
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const std::string &description, const std::vector<std::string> &det_modules_hostname)
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: DetectorSetup(std::make_shared<DetectorGeometryFixed>(geom),
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detector_type, description, det_modules_hostname) {
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switch (detector_type) {
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case DetectorType::DECTRIS:
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break;
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default:
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Detector not compatible with fixed geometry");
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}
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}
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DetectorSetup::DetectorSetup(const DetectorGeometryModular &geom, DetectorType detector_type,
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const std::string &description, const std::vector<std::string> &det_modules_hostname)
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: DetectorSetup(std::make_shared<DetectorGeometryModular>(geom),
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detector_type, description, det_modules_hostname) {
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switch (detector_type) {
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case DetectorType::EIGER:
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case DetectorType::JUNGFRAU:
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break;
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default:
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Detector not compatible with modular geometry");
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}
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}
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DetectorSetup::DetectorSetup(std::shared_ptr<DetectorGeometry> in_geometry,
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DetectorType in_detector_type,
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const std::string &in_description,
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const std::vector<std::string> &
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in_det_modules_hostname)
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: description(in_description),
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geometry(std::move(in_geometry)),
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det_modules_hostname(in_det_modules_hostname),
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gain_calibration(std::make_shared<JFGainCalibration>()),
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detector_type(in_detector_type),
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read_out_time(0),
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min_count_time(MIN_COUNT_TIME),
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min_frame_time(std::chrono::milliseconds(1)) {
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if (description.empty())
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Detector description cannot be empty");
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switch (detector_type) {
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case DetectorType::EIGER:
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high_voltage = 150;
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read_out_time = PSI_EIGER_READOUT_TIME;
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if (!det_modules_hostname.empty() && (2 * geometry->GetModulesNum() != det_modules_hostname.size()))
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Mismatch between number of modules in detector geometry and hostname (For EIGER - one module = 2 hostnames)");
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break;
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case DetectorType::JUNGFRAU:
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high_voltage = 120;
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bit_depth_readout = 16;
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read_out_time = PSI_JUNGFRAU_READOUT_TIME;
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if (!det_modules_hostname.empty() && (geometry->GetModulesNum() != det_modules_hostname.size()))
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Mismatch between number of modules in detector geometry and hostname");
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break;
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case DetectorType::DECTRIS:
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high_voltage = 0;
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// bit_depth_readout stays unset: a DECTRIS detector's electronic readout depth is a
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// constant we never need, and what is reported downstream is the image depth (see
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// DiffractionExperiment::FillMessage).
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bit_depth_image = 16; // placeholder, replaced from the stream2 image_dtype when armed
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read_out_time = std::chrono::microseconds(0);
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if (!det_modules_hostname.empty() && ( det_modules_hostname.size() != 1))
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Just one address need to be provided for DECTRIS detector");
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break;
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default:
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Detector not supported");
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}
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}
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DetectorSetup &DetectorSetup::Description(const std::string &input) {
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if (input.empty())
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Detector description cannot be empty");
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description = input;
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return *this;
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}
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const DetectorGeometry &DetectorSetup::GetGeometry() const {
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return *geometry;
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}
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const std::vector<std::string> &DetectorSetup::GetDetectorModuleHostname() const {
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return det_modules_hostname;
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}
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uint64_t DetectorSetup::GetModulesNum() const {
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return geometry->GetModulesNum();
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}
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std::string DetectorSetup::GetDescription() const {
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return description;
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}
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float DetectorSetup::GetPixelSize_mm() const {
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return pixel_size_um / 1000.0f;
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}
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std::string DetectorSetup::GetSensorMaterial() const {
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return sensor_material;
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}
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float DetectorSetup::GetSensorThickness_um() const {
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return sensor_thickness_um;
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}
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void DetectorSetup::LoadGain(const std::vector<std::string> &filenames) {
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if (filenames.size() != GetModulesNum())
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Mismatch in number of gain calibration files");
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gain_file_names = filenames;
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gain_calibration->LoadGain(filenames);
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}
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DetectorSetup &DetectorSetup::UDPInterfaceCount(int64_t input) {
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if ((input != 1) && (input != 2))
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Only 1 and 2 are supported as UDP interface count");
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udp_interface_count = input;
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return *this;
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}
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const std::vector<JFModuleGainCalibration> &DetectorSetup::GetGainCalibration() const {
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return gain_calibration->GetCalibration();
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}
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int64_t DetectorSetup::GetUDPInterfaceCount() const {
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if (detector_type == DetectorType::EIGER)
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return 2;
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return udp_interface_count;
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}
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DetectorSetup &DetectorSetup::SensorMaterial(const std::string &input) {
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sensor_material = input;
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return *this;
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}
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DetectorSetup &DetectorSetup::SensorThickness_um(float input) {
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sensor_thickness_um = input;
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return *this;
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}
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DetectorSetup &DetectorSetup::PixelSize_um(float input) {
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pixel_size_um = input;
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return *this;
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}
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DetectorSetup &DetectorSetup::Geometry(const DetectorGeometryFixed &input) {
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if (detector_type != DetectorType::DECTRIS)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"PSI detector geometry cannot be updated during operation");
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geometry = std::make_shared<DetectorGeometryFixed>(input);
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return *this;
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}
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DetectorSetup &DetectorSetup::TxDelay(const std::vector<int64_t> &v) {
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if (!v.empty() && (v.size() != GetModulesNum()))
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Mismatch between size of TX delay vector and modules number");
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for (const auto &i: v) {
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if ((i < 0) || (i > 31))
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "TX delay must be in range 0-31");
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}
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tx_delay = v;
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return *this;
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}
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const std::vector<int64_t> &DetectorSetup::GetTxDelay() const {
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return tx_delay;
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}
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const std::vector<std::string> &DetectorSetup::GetGainFileNames() const {
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return gain_file_names;
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}
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DetectorType DetectorSetup::GetDetectorType() const {
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return detector_type;
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}
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DetectorSetup &DetectorSetup::HighVoltage(int32_t input) {
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high_voltage = input;
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return *this;
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}
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int32_t DetectorSetup::GetHighVoltage() const {
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return high_voltage;
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}
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void DetectorSetup::SetTrimFiles(const std::vector<std::string> &filenames) {
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if (detector_type != DetectorType::EIGER)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Trim bits make sense only for EIGER");
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if ((filenames.size() == 1)
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&& std::filesystem::is_directory(filenames[0])) {
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trim_file_directory = filenames[0];
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trim_file_names.clear();
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} else {
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if (filenames.size() != 2 * GetModulesNum())
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Mismatch in number of trim bit calibration files");
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trim_file_directory = "";
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trim_file_names = filenames;
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}
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}
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const std::vector<std::string> &DetectorSetup::GetTrimFileNames() const {
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return trim_file_names;
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}
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std::string DetectorSetup::GetTrimFileDirectory() const {
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return trim_file_directory;
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}
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std::string DetectorSetup::GetSerialNumber() const {
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return serial_number;
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}
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DetectorSetup &DetectorSetup::SerialNumber(const std::string &input) {
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serial_number = input;
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return *this;
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}
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DetectorSetup &DetectorSetup::BaseIPv4Addr(const std::string &input) {
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ipv4_base_addr = IPv4AddressFromStr(input);
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return *this;
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}
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uint32_t DetectorSetup::GetSrcIPv4Addr(uint32_t half_module) const {
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if (half_module >= GetUDPInterfaceCount() * GetModulesNum())
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throw JFJochException(JFJochExceptionCategory::ArrayOutOfBounds, "Non existing module");
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return ipv4_base_addr + (half_module << 24);
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}
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std::string DetectorSetup::GetBaseIPv4Addr() const {
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return IPv4AddressToStr(ipv4_base_addr);
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}
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bool DetectorSetup::IsModuleSync() const {
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if (GetModulesNum() == 1)
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return false;
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else
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return module_sync;
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}
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DetectorSetup &DetectorSetup::ModuleSync(bool input) {
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module_sync = input;
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return *this;
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}
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DetectorSetup &DetectorSetup::MirrorY(bool input) {
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mirror_y = input;
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return *this;
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}
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bool DetectorSetup::IsMirrorY() const {
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return mirror_y;
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}
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DetectorSetup & DetectorSetup::ReadOutTime(std::chrono::nanoseconds input) {
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if (input.count() < 0)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Read out time has to be non-negative");
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read_out_time = input;
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return *this;
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}
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std::chrono::nanoseconds DetectorSetup::GetReadOutTime() const {
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return read_out_time;
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}
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std::chrono::nanoseconds DetectorSetup::GetMinFrameTime() const {
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switch (GetDetectorType()) {
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case DetectorType::EIGER:
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return MIN_FRAME_TIME_EIGER;
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case DetectorType::JUNGFRAU:
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if (GetUDPInterfaceCount() == 1)
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return MIN_FRAME_TIME_JUNGFRAU_HALF_SPEED;
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return MIN_FRAME_TIME_JUNGFRAU_FULL_SPEED;
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case DetectorType::DECTRIS:
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return min_frame_time;
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default:
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Detector not supported");
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}
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}
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std::chrono::nanoseconds DetectorSetup::GetMinCountTime() const {
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return min_count_time;
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}
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DetectorSetup &DetectorSetup::MinCountTime(std::chrono::nanoseconds input) {
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min_count_time = input;
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return *this;
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}
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DetectorSetup &DetectorSetup::MinFrameTime(std::chrono::nanoseconds input) {
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min_frame_time = input;
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return *this;
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}
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DetectorSetup &DetectorSetup::BitDepthImage(int64_t input) {
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if (GetDetectorType() != DetectorType::DECTRIS)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Bit depth image can be only changed for DECTRIS detector");
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switch (input) {
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case 8:
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case 16:
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case 32:
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bit_depth_image = input;
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return *this;
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default:
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Bit depth image can be only 8, 16 or 32");
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}
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}
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std::optional<int64_t> DetectorSetup::GetBitDepthReadout() const {
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return bit_depth_readout;
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}
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std::optional<int64_t> DetectorSetup::GetBitDepthImage() const {
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return bit_depth_image;
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}
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std::string DetectorSetup::GetDECTRISStream2Addr() const {
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if (GetDetectorType() != DetectorType::DECTRIS)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Stream2 only possible for DECTRIS systems");
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if (det_modules_hostname.size() != 1)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Stream2 address not defined");
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return "tcp://" + det_modules_hostname[0] + ":" + std::to_string(SimplonStream2Port);
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}
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float DetectorSetup::GetMinThreshold_keV() const {
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return min_energy_threshold_keV;
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}
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DetectorSetup &DetectorSetup::MinThreshold_keV(float input) {
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if (input <= 0.0f)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Min threshold must be positive number");
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min_energy_threshold_keV = input;
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return *this;
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}
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DetectorSetup &DetectorSetup::SaturationLimit(std::optional<int64_t> input) {
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if (input && input <= 0)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"Saturation limit must be positive number");
|
|
saturation_limit = input;
|
|
return *this;
|
|
}
|
|
|
|
std::optional<int64_t> DetectorSetup::GetSaturationLimit() const {
|
|
return saturation_limit;
|
|
}
|
|
|
|
DetectorSetup &DetectorSetup::DECTRISROI(const std::string &input) {
|
|
dectris_roi = input;
|
|
return *this;
|
|
}
|
|
|
|
std::string DetectorSetup::GetDECTRISROI() const {
|
|
if (dectris_roi.empty())
|
|
return "disabled";
|
|
return dectris_roi;
|
|
}
|
|
|
|
std::optional<DetectorSettings> DetectorSetup::GetDefaultSettings() const {
|
|
return settings;
|
|
}
|
|
|
|
DetectorSetup &DetectorSetup::DefaultSettings(const std::optional<DetectorSettings> &input) {
|
|
settings = input;
|
|
return *this;
|
|
}
|
|
|
|
DetectorSetup DetJF4M(const std::string &description, const std::vector<std::string> &det_modules_hostname) {
|
|
return DetJF(8, 2, 8, 36, true, description, det_modules_hostname);
|
|
}
|
|
|
|
DetectorSetup DetJF9M(const std::string &description, const std::vector<std::string> &det_modules_hostname) {
|
|
return DetJF(18, 3, 8, 36, true, description, det_modules_hostname);
|
|
}
|
|
|
|
DetectorSetup DetJF(int32_t nmodules, int32_t horizontal_stacking, int32_t gap_x, int32_t gap_y, bool mirror_y,
|
|
const std::string &description, const std::vector<std::string> &det_modules_hostname) {
|
|
return DetJF(DetectorGeometryModular(nmodules, horizontal_stacking, gap_x, gap_y, mirror_y),
|
|
description, det_modules_hostname);
|
|
}
|
|
|
|
DetectorSetup DetJF(const DetectorGeometryModular &geom, const std::string &description,
|
|
const std::vector<std::string> &det_modules_hostname) {
|
|
return {geom, DetectorType::JUNGFRAU, description, det_modules_hostname};
|
|
}
|
|
|
|
DetectorSetup DetEIGER(int32_t nmodules, int32_t horizontal_stacking, int32_t gap_x, int32_t gap_y, bool mirror_y,
|
|
const std::string &description, const std::vector<std::string> &det_modules_hostname) {
|
|
return DetEIGER(DetectorGeometryModular(nmodules, horizontal_stacking, gap_x, gap_y, mirror_y),
|
|
description, det_modules_hostname);
|
|
}
|
|
|
|
DetectorSetup DetEIGER(const DetectorGeometryModular &geom, const std::string &description,
|
|
const std::vector<std::string> &det_modules_hostname) {
|
|
return {geom, DetectorType::EIGER, description, det_modules_hostname};
|
|
}
|
|
|
|
DetectorSetup DetDECTRIS(int64_t width, int64_t height, const std::string &description, const std::string &addr) {
|
|
if (addr.empty())
|
|
return {DetectorGeometryFixed(width, height), DetectorType::DECTRIS, description, {}};
|
|
else
|
|
return {DetectorGeometryFixed(width, height), DetectorType::DECTRIS, description, {addr}};
|
|
}
|
|
|
|
int32_t DetectorSetup::GetTempThreshold_degC() const {
|
|
return temperature_thresold_degC;
|
|
}
|
|
|
|
DetectorSetup &DetectorSetup::TempThreshold_degC(int64_t input) {
|
|
check_min("Temperature threshold (degC)", input, 40);
|
|
check_max("Temperature threshold (degC)", input, 70);
|
|
temperature_thresold_degC = static_cast<int32_t>(input);
|
|
return *this;
|
|
}
|
|
|
|
DetectorSetup &DetectorSetup::TrimEnergies_eV(std::vector<int> input) {
|
|
trim_energy_eV_values = std::move(input);
|
|
return *this;
|
|
}
|
|
|
|
std::vector<int> DetectorSetup::GetTrimEnergies_eV() const {
|
|
return trim_energy_eV_values;
|
|
}
|