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Jungfraujoch/tests/JFJochStateMachineTest.cpp
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leonarski_f 749db470ca
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v1.0.0-rc.164 (#74)
* rugnux now tells you whether a crystal diffracts anisotropically and how far it reaches in each direction, without a second program: a new `9. DIFFRACTION ANISOTROPY` section in `<prefix>_report.txt` and matching `_reflns.pdbx_aniso_B_tensor_*` / `_reflns.jfjoch_aniso_*` items in the merged mmCIF report the anisotropic deltaB, the diffraction limit along each principal direction, and a `NOT DETECTED` / `DETECTED` / `CANNOT DETERMINE` verdict measured against the data set's own systematic error. It is a description only - no intensity is corrected, no reflection is removed, and the merged data do not depend on direction.
* rugnux can hand its integrated observations to another scaling program: `--export-unmerged` writes `<prefix>_unmerged.mtz`, an unmerged MTZ readable by aimless, pointless, careless and `iotbx.merging_statistics`, in `--mode mx` and `--mode scale` alike. Each rotation reflection's partials are summed into one full; `--export-unmerged-partials` writes one row per image instead. Intensities carry the Lorentz-polarization factor and nothing else, since those programs scale the data themselves. Lattice-centring absences are not written; screw and glide absences are.
* rugnux integrates crystals with broad spots better - where it changes anything, per-shell mean I/sigma improves by up to 31% and R_meas by up to 24% - because on rotation data the integration signal radius is now taken from the crystal's own measured spot width instead of a fixed 4 px. `--adaptive-integration-radius=off` restores the fixed radius and an explicit `--integration-radius` still overrides both. The widened radius applies to the final integration pass only, and a pattern too dense for it is re-integrated at 4 px with a note in the log.
* rugnux discards fewer stills reflections for want of a background ring, improving per-shell R_meas over most of the signal-bearing range: the stills background ring now runs to 14 px instead of 12. The gain reverses in shells below a mean I/sigma of about 4.
* rugnux determines the space group with thresholds that mean the same thing on a weak crystal as on a strong one: symmetry operators are scored on resolution-normalised intensities (E squared) instead of raw merged intensities, and a reflection counts as genuinely present on its counting significance instead of on the merged I/sigma, which saturates at the merge's own ISa. The search resolution cut is no longer able to move the answer, and the twin-law H bound moves from 1.70 to 1.85, which stops one class of correct high-symmetry assignment being refused as twinning.
* rugnux says what the space-group search tested and what it could not: the twin-law disagreement H is printed for every operator together with the adopted point group's H ratio and its bound; alternatives that are not on the reported lattice are named with how their cell differs; and a lattice centring the data could not test - the crystal having been integrated on the primitive sub-cell, so the reflections it extinguishes were never measured - is marked `UNTESTED` and warned about where it is adopted, as coming from the lattice metric rather than from the intensities.
* rugnux `--mode scale` re-merges a `_process.h5` in the right symmetry without being told it: the file now records the space group on every run - a two-pass rotation run wrote none before, so re-merging defaulted to P1 - together with the change of basis under `/entry/MX/reindexMatrix` where the lattice was re-seated, and `--mode scale` also reports the Wilson B-factor estimate instead of `WILSON_B= nan`. A file written before this stops with a message naming the two cells and the override to use, instead of failing inside the merge. A third-party reader of a `_process.h5` must apply `reindexMatrix` where it is present.
* rugnux installs on its own, as a package called `rugnux` - `dnf install rugnux` or `apt install rugnux` - instead of arriving inside `jfjoch-viewer`. It pulls in none of the acquisition stack, so a machine that only processes data no longer has to carry the broker, the detector libraries or Qt to get it. Installing it over a `jfjoch-viewer` from rc.163 or earlier, which still owns `/usr/bin/rugnux`, upgrades cleanly rather than failing on the duplicate file.
* rugnux is also a standalone download, built for arm64 as well as x86_64: `rugnux-<version>-linux-{x86_64|aarch64}-cuda<major>.tgz` and `rugnux-<version>-win64-cuda<major>.zip` on the release page, for machines that are not managed by a package manager. The aarch64 build targets GH200 and DGX Spark, and is untested on hardware.
* Every portable Linux binary is now a single self-contained file: cuFFT is linked statically instead of being shipped beside the executable and found through an rpath, so `rugnux` and `jfjoch_viewer` need nothing but an NVIDIA driver, and only to use the GPU. The `.rpm`/`.deb` continue to take cuFFT from the distribution. The developer utilities `jfjoch_extract_hkl` and `jfjoch_recompress` are no longer packaged anywhere.
* Jungfraujoch needs six fewer shared libraries on the machine - libopenblas and libmetis, and libgfortran, libquadmath, libgomp and libz behind them - because the Ceres LAPACK, METIS and SuiteSparse back-ends are no longer built. Nothing in the code ever selected them, and results are unchanged.
* The PCIe driver DKMS package builds for the kernel it is being installed for instead of the running one, so a module built while a kernel update is being applied loads after the reboot.
* The PCIe driver builds on RHEL 9.5 and later, and on their CentOS Stream, Rocky and AlmaLinux equivalents, where the `vm_flags` kernel interface was backported into the 5.14 kernel.
* A data collection started with `async_start` that fails to start - a writer refusing to overwrite an existing file, for instance - is reported as an error by `/wait_until_running` and `/wait_till_done` instead of as a timeout and a successful collection respectively. The error message is the one the writer gave.
* A calibration that is cancelled or that fails to collect its pedestals is no longer reported as a successful one. The broker goes to `Inactive` with an error message and has to be initialized again, instead of sitting in `Idle` looking ready to measure while holding partial pedestals - data collected in that state was silently mis-converted.
* A failed `/initialize` is reported to `/wait_until_running` and `/wait_till_done` as soon as it happens, instead of when their timeout expires.
* `space_group_number` accepts space groups up to 230 in the API schema, so cubic space groups can be recorded. The broker always accepted them; the generated clients rejected them before the request was sent.
* The results report's `REPORT_VERSION` is 3, two sections having been added. Existing key names and table columns are unchanged.
* The merged statistics table has **9** resolution shells instead of 10, which is what XDS reports. The bins were already XDS's - equal steps in 1/d^2 between the lowest- and the highest-resolution reflection the merge kept - so at the same resolution limits the two tables now have the same shell boundaries and can be read row for row. `--resolution-shells` sets a different count.
* `rugnux --model` now settles the frame the merged reflections are written in, not only the frame the R-factors and the maps are computed in: the `.mtz`/`.cif`/`.hkl` come out in the model's indexing, and where the data were merged in the model's enantiomorph they take the model's hand and space group - which on anomalous data puts I(+) and I(-) the right way round. The indexing choice is logged with the winning R-free and the runner-up, so a decision made within noise is visible.
* `rugnux --model` can resolve the indexing ambiguity of a **serial stills** run, which a model could not do before: structure factors computed from the model become the per-image reference, the same role a reference MTZ plays. It needs the cell and space group up front (`-C` / `-S`). Without one or the other, a merohedral serial run still merges both hands together and says so.
* The rugnux documentation opens with a quick start - the default run, and runs with a reference MTZ, with a model, or with the space group and cell pinned - and explains the indexing ambiguity: what it costs on rotation and on serial data, and which of `-z` / `--model` resolves it in each case. The long reference pages now carry a table of contents.

Reviewed-on: #74
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-08-26 22:47:00 +02:00

358 lines
16 KiB
C++

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <catch2/catch_all.hpp>
#include "../broker/JFJochStateMachine.h"
#include "../acquisition_device/HLSSimulatedDevice.h"
#include "../receiver/JFJochReceiverService.h"
using namespace std::literals::chrono_literals;
TEST_CASE("JFJochStateMachine_States") {
Logger logger("JFJochStateMachine_States");
JFJochServices services(logger);
DiffractionExperiment experiment;
JFJochStateMachine state_machine(experiment, services, logger);
state_machine.AddDetectorSetup(DetJF4M());
DatasetSettings setup;
REQUIRE(state_machine.GetStatus().state == JFJochState::Inactive);
REQUIRE_THROWS(state_machine.Start(setup));
REQUIRE_THROWS(state_machine.Pedestal());
REQUIRE_NOTHROW(state_machine.Initialize());
REQUIRE_NOTHROW(state_machine.WaitTillMeasurementDone());
REQUIRE(state_machine.GetStatus().state == JFJochState::Idle);
REQUIRE_NOTHROW(state_machine.Deactivate());
REQUIRE(state_machine.GetStatus().state == JFJochState::Inactive);
}
TEST_CASE("JFJochStateMachine_State_Pedestal") {
Logger logger("JFJochStateMachine_State_Pedestal");
JFJochServices services(logger);
DiffractionExperiment experiment;
JFJochStateMachine state_machine(experiment, services, logger);
state_machine.AddDetectorSetup(DetJF4M());
DatasetSettings setup;
state_machine.DebugOnly_SetState(JFJochState::Calibration);
REQUIRE(state_machine.GetStatus().state == JFJochState::Calibration);
REQUIRE_THROWS(state_machine.Start(setup));
REQUIRE_THROWS(state_machine.Pedestal());
REQUIRE_THROWS(state_machine.Initialize());
REQUIRE(state_machine.WaitTillMeasurementDone(std::chrono::milliseconds(1)).state == JFJochState::Calibration);
}
TEST_CASE("JFJochStateMachine_State_Measure") {
Logger logger("JFJochStateMachine_State_Measure");
JFJochServices services(logger);
DiffractionExperiment experiment;
JFJochStateMachine state_machine(experiment, services, logger);
state_machine.AddDetectorSetup(DetJF4M());
DatasetSettings setup;
state_machine.DebugOnly_SetState(JFJochState::Measuring);
REQUIRE(state_machine.GetStatus().state == JFJochState::Measuring);
REQUIRE_THROWS(state_machine.Start(setup));
REQUIRE_THROWS(state_machine.Pedestal());
REQUIRE_THROWS(state_machine.Initialize());
REQUIRE(state_machine.WaitTillMeasurementDone(std::chrono::milliseconds(1)).state == JFJochState::Measuring);
DetectorSettings settings{};
REQUIRE_THROWS(state_machine.LoadDetectorSettings(settings));
}
TEST_CASE("JFJochStateMachine_State_Error") {
Logger logger("JFJochStateMachine_State_Error");
JFJochServices services(logger);
DiffractionExperiment experiment;
JFJochStateMachine state_machine(experiment, services, logger);
state_machine.AddDetectorSetup(DetJF4M());
DatasetSettings setup;
state_machine.DebugOnly_SetState(JFJochState::Error,
"msg1234",
BrokerStatus::MessageSeverity::Error);
REQUIRE(state_machine.GetStatus().state == JFJochState::Error);
REQUIRE(state_machine.GetStatus().message.has_value());
REQUIRE(state_machine.GetStatus().message == "msg1234");
REQUIRE(state_machine.GetStatus().message_severity == BrokerStatus::MessageSeverity::Error);
state_machine.DebugOnly_SetState(JFJochState::Inactive, "msg3456", BrokerStatus::MessageSeverity::Info);
REQUIRE(state_machine.GetStatus().state == JFJochState::Inactive);
REQUIRE(state_machine.GetStatus().message.has_value());
REQUIRE(state_machine.GetStatus().message == "msg3456");
REQUIRE(state_machine.GetStatus().message_severity == BrokerStatus::MessageSeverity::Info);
state_machine.DebugOnly_SetState(JFJochState::Error);
REQUIRE(state_machine.GetStatus().state == JFJochState::Error);
REQUIRE(!state_machine.GetStatus().message.has_value());
REQUIRE_THROWS(state_machine.Start(setup));
REQUIRE_THROWS(state_machine.Pedestal());
REQUIRE(state_machine.WaitTillMeasurementDone(std::chrono::milliseconds(1)).state == JFJochState::Error);
DetectorSettings settings;
REQUIRE_NOTHROW(state_machine.LoadDetectorSettings(settings));
REQUIRE_NOTHROW(state_machine.Initialize());
REQUIRE_NOTHROW(state_machine.WaitTillMeasurementDone());
REQUIRE(state_machine.GetStatus().state == JFJochState::Idle);
}
TEST_CASE("JFJochStateMachine_NoDetectorSetup") {
Logger logger("JFJochStateMachine_NoDetectorSetup");
JFJochServices services(logger);
DiffractionExperiment experiment;
JFJochStateMachine state_machine(experiment, services, logger);
REQUIRE_THROWS(state_machine.Initialize());
REQUIRE_NOTHROW(state_machine.WaitTillMeasurementDone());
}
TEST_CASE("JFJochStateMachine_AddDetectorSetup") {
Logger logger("JFJochStateMachine_AddDetectorSetup");
JFJochServices services(logger);
DiffractionExperiment experiment;
JFJochStateMachine state_machine(experiment, services, logger);
DetectorSetup setup = DetJF4M();
state_machine.AddDetectorSetup(setup);
REQUIRE_NOTHROW(state_machine.Initialize());
REQUIRE_NOTHROW(state_machine.WaitTillMeasurementDone());
}
TEST_CASE("JFJochStateMachine_AddDetectorSetup_Gain") {
Logger logger("JFJochStateMachine_AddDetectorSetup_Gain");
JFJochServices services(logger);
DiffractionExperiment experiment;
JFJochStateMachine state_machine(experiment, services, logger);
DetectorSetup setup = DetJF(4);
setup.LoadGain({"../../tests/test_data/gainMaps_M049.bin",
"../../tests/test_data/gainMaps_M049.bin",
"../../tests/test_data/gainMaps_M049.bin",
"../../tests/test_data/gainMaps_M049.bin"});
state_machine.AddDetectorSetup(setup);
REQUIRE_NOTHROW(state_machine.Initialize());
REQUIRE_NOTHROW(state_machine.WaitTillMeasurementDone());
}
TEST_CASE("JFJochStateMachine_AddDetectorSetup_Multiple") {
Logger logger("JFJochStateMachine_AddDetectorSetup_Multiple");
JFJochServices services(logger);
DiffractionExperiment experiment;
JFJochStateMachine state_machine(experiment, services, logger);
REQUIRE_NOTHROW(state_machine.AddDetectorSetup(DetJF(4, 1, 0,0,false,"Det1", {"mx1", "mx2", "mx3", "mx4"})));
REQUIRE_NOTHROW(state_machine.AddDetectorSetup(DetEIGER(2, 1, 0, 0, false, "Det2", {"mx1", "mx2", "mx3", "mx4"})));
REQUIRE_NOTHROW(state_machine.AddDetectorSetup(DetDECTRIS(23,45, "Det3", {"mx5"})));
auto dl = state_machine.GetDetectorsList();
REQUIRE(dl.detector.size() == 3);
REQUIRE(dl.detector[0].description == "Det1");
REQUIRE(dl.detector[0].nmodules == 4);
REQUIRE(dl.detector[0].detector_type == DetectorType::JUNGFRAU);
REQUIRE(dl.detector[1].description == "Det2");
REQUIRE(dl.detector[1].nmodules == 2);
REQUIRE(dl.detector[1].detector_type == DetectorType::EIGER);
REQUIRE(dl.detector[2].description == "Det3");
REQUIRE(dl.detector[2].nmodules == 1);
REQUIRE(dl.detector[2].detector_type == DetectorType::DECTRIS);
REQUIRE_NOTHROW(state_machine.Initialize());
REQUIRE_NOTHROW(state_machine.WaitTillMeasurementDone());
REQUIRE(state_machine.Experiment().GetModulesNum() == 4);
REQUIRE(state_machine.GetStatus().state == JFJochState::Idle);
REQUIRE_THROWS(state_machine.SelectDetector(7));
REQUIRE(state_machine.GetStatus().state == JFJochState::Idle);
REQUIRE_NOTHROW(state_machine.SelectDetector(2));
REQUIRE(state_machine.Experiment().GetModulesNum() == 1);
REQUIRE(state_machine.Experiment().GetDetectorDescription() == "Det3");
REQUIRE(state_machine.GetStatus().state == JFJochState::Inactive);
}
TEST_CASE("JFJochStateMachine_LoadDetectorSettings_Error") {
Logger logger("JFJochStateMachine_LoadDetectorSettings_Error");
JFJochServices services(logger);
DiffractionExperiment experiment;
JFJochStateMachine state_machine(experiment, services, logger);
state_machine.AddDetectorSetup(DetJF4M());
DatasetSettings setup;
state_machine.DebugOnly_SetState(JFJochState::Idle);
DetectorSettings settings;
settings.FrameTime(std::chrono::microseconds(1));
REQUIRE_THROWS(state_machine.LoadDetectorSettings(settings));
REQUIRE(state_machine.GetStatus().state == JFJochState::Idle);
}
namespace {
// Stands in for a writer that refuses to start the run - e.g. the output file exists and cannot be
// overwritten. The refusal reaches the broker as an ordinary exception thrown while the start
// message is being sent, which is what separates it from a critical detector fault.
class RefusingImagePusher : public ImagePusher {
public:
bool refuse = true;
void StartDataCollection(StartMessage &) override {
if (refuse)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "writer_refused_1234");
}
bool EndDataCollection(const EndMessage &) override { return true; }
bool SendImage(const uint8_t *, size_t, int64_t) override { return true; }
bool SendCalibration(const CompressedImage &) override { return true; }
std::string PrintSetup() const override { return "RefusingImagePusher"; }
ImagePusherType GetType() const override { return ImagePusherType::Test; }
};
}
// An asynchronous start returns before the measurement thread runs, so a failure there has to be
// reported to whoever asks next. Without this the state is a plain Idle, indistinguishable from a
// timeout, and the writer's message is lost.
TEST_CASE("JFJochStateMachine_AsyncStartFailure") {
Logger logger("JFJochStateMachine_AsyncStartFailure");
DiffractionExperiment experiment(DetJF(2));
experiment.Conversion().PedestalG0Frames(0).NumTriggers(1).UseInternalPacketGenerator(true)
.ImagesPerTrigger(4).IncidentEnergy_keV(12.4);
AcquisitionDeviceGroup aq_devices;
for (int i = 0; i < experiment.GetDataStreamsNum(); i++)
aq_devices.Add(std::make_unique<HLSSimulatedDevice>(i, 64));
RefusingImagePusher pusher;
JFJochReceiverService receiver_service(aq_devices, logger, pusher);
JFJochServices services(logger);
services.Receiver(&receiver_service);
JFJochStateMachine state_machine(experiment, services, logger);
state_machine.AddDetectorSetup(DetJF(2));
state_machine.DebugOnly_SetState(JFJochState::Idle);
DatasetSettings setup;
setup.ImagesPerTrigger(4).NumTriggers(1);
// The asynchronous start itself succeeds - it only launches the measurement thread.
REQUIRE_NOTHROW(state_machine.Start(setup, true));
// Both wait functions report the failure, and repeatedly: the exception_ptr is not consumed.
REQUIRE_THROWS_WITH(state_machine.WaitTillNotBusy(std::chrono::seconds(10)),
Catch::Matchers::ContainsSubstring("writer_refused_1234"));
REQUIRE_THROWS_WITH(state_machine.WaitTillNotBusy(std::chrono::seconds(10)),
Catch::Matchers::ContainsSubstring("writer_refused_1234"));
REQUIRE_THROWS_WITH(state_machine.WaitTillMeasurementDone(std::chrono::seconds(10)),
Catch::Matchers::ContainsSubstring("writer_refused_1234"));
// An ordinary failure leaves the detector usable, so the run can be retried from Idle. The
// status keeps the writer's message, and nothing is left of the run that never happened - a
// progress figure in particular would show up in the frontend as a stalled acquisition.
auto status = state_machine.GetStatus();
REQUIRE(status.state == JFJochState::Idle);
REQUIRE(status.message_severity == BrokerStatus::MessageSeverity::Error);
REQUIRE_THAT(status.message.value_or(""), Catch::Matchers::ContainsSubstring("writer_refused_1234"));
REQUIRE_FALSE(status.progress.has_value());
auto statistics = state_machine.GetMeasurementStatistics();
REQUIRE(statistics.has_value());
REQUIRE(statistics->images_collected == 0);
REQUIRE(statistics->images_sent == 0);
REQUIRE_FALSE(statistics->collection_efficiency.has_value());
// A synchronous start reports the same failure directly, and leaves it visible to the wait
// functions afterwards.
REQUIRE_THROWS_WITH(state_machine.Start(setup),
Catch::Matchers::ContainsSubstring("writer_refused_1234"));
REQUIRE_THROWS_WITH(state_machine.WaitTillNotBusy(std::chrono::seconds(10)),
Catch::Matchers::ContainsSubstring("writer_refused_1234"));
// A start rejected before the measurement thread is launched must not leave the previous
// failure behind for the next wait call to report.
DatasetSettings rejected_setup;
rejected_setup.ImagesPerTrigger(4).NumTriggers(1)
.ImageTime(state_machine.Experiment().GetFrameTime() + std::chrono::nanoseconds(1));
REQUIRE_THROWS(state_machine.Start(rejected_setup, true));
REQUIRE_NOTHROW(state_machine.WaitTillNotBusy(std::chrono::seconds(10)));
// Any other operation started from Idle supersedes the pending failure - it must not be
// attributed to the pedestal, which is allowed from Idle and has nothing to do with it.
REQUIRE_THROWS_WITH(state_machine.Start(setup),
Catch::Matchers::ContainsSubstring("writer_refused_1234"));
REQUIRE_NOTHROW(state_machine.Pedestal());
REQUIRE_NOTHROW(state_machine.WaitTillMeasurementDone());
// Nothing is left half-started: once the writer accepts the run, the next start goes through
// and completes without any intervening re-initialisation.
pusher.refuse = false;
REQUIRE_NOTHROW(state_machine.Start(setup));
REQUIRE(state_machine.GetStatus().state == JFJochState::Measuring);
REQUIRE_NOTHROW(state_machine.WaitTillMeasurementDone());
REQUIRE(state_machine.GetStatus().state == JFJochState::Idle);
REQUIRE(state_machine.GetMeasurementStatistics()->images_sent == 4);
// Re-initialising discards a pending failure too, so a detector brought back up does not report
// the failure of the run before it.
pusher.refuse = true;
REQUIRE_THROWS_WITH(state_machine.Start(setup),
Catch::Matchers::ContainsSubstring("writer_refused_1234"));
services.Receiver(nullptr);
REQUIRE_NOTHROW(state_machine.Initialize());
REQUIRE_NOTHROW(state_machine.WaitTillMeasurementDone());
REQUIRE(state_machine.GetStatus().state == JFJochState::Idle);
}
// A calibration that does not complete must not be reported as a good one. Every step signals
// failure by calling SetState and returning normally, so nothing threw and the sequence used to
// finish with an unconditional "Calibration sequence done"/Success on top of it - leaving the
// broker Idle and apparently ready while holding partial pedestals.
TEST_CASE("JFJochStateMachine_CalibrationFailure") {
Logger logger("JFJochStateMachine_CalibrationFailure");
JFJochServices services(logger);
DiffractionExperiment experiment;
JFJochStateMachine state_machine(experiment, services, logger);
state_machine.AddDetectorSetup(DetJF4M());
// Ask for a G0 pedestal. There is no receiver, so no frames come back and the import fails -
// the same outcome as a pedestal that collected nothing on real hardware.
DetectorSettings settings = state_machine.GetDetectorSettings();
settings.PedestalG0Frames(100);
REQUIRE_NOTHROW(state_machine.LoadDetectorSettings(settings));
REQUIRE_NOTHROW(state_machine.Initialize());
REQUIRE_NOTHROW(state_machine.WaitTillMeasurementDone());
// Inactive, not Idle and not Error: the calibration is undefined, so the detector has to be
// initialized again rather than looking ready to measure.
auto status = state_machine.GetStatus();
REQUIRE(status.state == JFJochState::Inactive);
REQUIRE(status.message_severity == BrokerStatus::MessageSeverity::Error);
REQUIRE(status.message == "Pedestal not collected properly");
// ... and a data collection is refused on it, instead of producing mis-converted images.
DatasetSettings setup;
REQUIRE_THROWS(state_machine.Start(setup));
// The success path is unchanged - with no pedestal to take, the sequence still reports success.
JFJochStateMachine calibrated(experiment, services, logger);
calibrated.AddDetectorSetup(DetJF4M());
REQUIRE_NOTHROW(calibrated.Initialize());
REQUIRE_NOTHROW(calibrated.WaitTillMeasurementDone());
REQUIRE(calibrated.GetStatus().state == JFJochState::Idle);
REQUIRE(calibrated.GetStatus().message_severity == BrokerStatus::MessageSeverity::Success);
}