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v1.0.0-rc.159 (#69)
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: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell.
* rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged.
* rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set.
* rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme.
* rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free.
* rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry.
* Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md.
* Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-07-13 13:54:03 +02:00

99 lines
3.3 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
RfreeFlagsTest.cpp
FrenchWilsonTest.cpp
ReindexAmbiguityTest.cpp
LoadReferenceMtzFreeFlagsTest.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)