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v1.0.0-rc.157 (#67)
This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.

* rugnux: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`.
* rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling.
* rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics.
* rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1.
* rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group.
* rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix.
* jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation.
* jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning.
* jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint.
* jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed).
* jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types.
* jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails.
* jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak.
* Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation.
* CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-07-11 07:19:11 +02:00

95 lines
3.2 KiB
CMake

ADD_EXECUTABLE(jfjoch_test
DiffractionExperimentTest.cpp
RawToConvertedGeometryTest.cpp
../common/RawToConvertedGeometry.h
../common/DiffractionExperiment.h
CheckImageOutput.h
FPGAIntegrationTest.cpp
StrongPixelSetTest.cpp
ZSTDCompressorTest.cpp
FrameTransformationTest.cpp
HDF5WritingTest.cpp PedestalCalcTest.cpp
ZMQImagePusherTest.cpp StreamWriterTest.cpp
CoordTest.cpp JFJochStateMachineTest.cpp
JFJochReceiverIntegrationTest.cpp
AcquisitionCountersTest.cpp
IndexingUnitTest.cpp
ThreadSafeFIFOSetTest.cpp
FPGANetworkTest.cpp
JFPedestalTest.cpp
JFCalibrationTest.cpp
AzimuthalIntegrationTest.cpp
StatusVectorTest.cpp
CBORTest.cpp
DetectorGeometryTest.cpp DetectorSetupTest.cpp DiffractionGeometryTest.cpp
FPGASpotFindingUnitTest.cpp
PreviewCounterTest.cpp
FPGAFrameGeneratorTest.cpp
FPGAHostWriterTest.cpp
DiffractionSpotTest.cpp
TIFFTest.cpp
JFJochReceiverProcessingTest.cpp
JPEGTest.cpp
HistogramTest.cpp
ROIMapTest.cpp
ROIIntegrationCPUTest.cpp
ROIIntegrationGPUTest.cpp
BraggIntegrationEngineGPUTest.cpp
BraggIntegrationEngineCompressedImageTest.cpp
LossyFilterTest.cpp
ImageBufferTest.cpp
PixelMaskTest.cpp
RegressionTest.cpp
FPGAHLSModulesTest.cpp
ZMQPreviewSocketTest.cpp
DetectorSettingsTest.cpp
AutoIncrVectorTest.cpp
ModuleSummationTest.cpp
ZMQMetadataSocketTest.cpp
JFJochReaderTest.cpp
RugnuxTest.cpp
RugnuxLargeTest.cpp
TestData.h
MovingAverageTest.cpp
ImageMetadataTest.cpp
JFJochReceiverLiteTest.cpp
GridScanSettingsTest.cpp
JFJochReceiverPlotsTest.cpp
GoniometerAxisTest.cpp
DetGeomCalibTest.cpp
XtalOptimizerTest.cpp
CrystalLatticeTest.cpp
FPGAPTPTest.cpp
ResolutionShellsTest.cpp
ImageSpotFinderCPUTest.cpp
ImageSpotFinderGPUTest.cpp
CalcBraggPredictionTest.cpp
SpotUtilsTest.cpp
LatticeSearchTest.cpp
TimeTest.cpp
RotationIndexerTest.cpp
TopPixelsTest.cpp
HKLKeyTest.cpp
TCPImagePusherTest.cpp
SearchSpaceGroupTest.cpp
XDSPluginTest.cpp
MergeScaleTest.cpp
UnitCellTest.cpp
CCTest.cpp
MultiLatticeSearchTest.cpp
LatticeReductionTest.cpp
)
target_link_libraries(jfjoch_test Catch2WithMain JFJochBroker JFJochReceiver JFJochReader JFJochStreamWriter
Rugnux JFJochImageAnalysis JFJochCommon JFJochHLSSimulation JFJochPreview
jfjoch_xds_plugin)
target_include_directories(jfjoch_test PRIVATE .)
find_package(Threads REQUIRED)
add_library(enospc_shim MODULE enospc_shim.c)
target_link_libraries(enospc_shim PRIVATE Threads::Threads dl)
set_target_properties(enospc_shim PROPERTIES PREFIX "" POSITION_INDEPENDENT_CODE ON) # remove "lib"
ADD_EXECUTABLE(jfjoch_hdf5_enospc_test jfjoch_hdf5_enospc_test.cpp)
target_link_libraries(jfjoch_hdf5_enospc_test Catch2WithMain JFJochWriter)