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Jungfraujoch/tests/CMakeLists.txt
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leonarski_fandClaude Opus 5 6468dd13be
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rugnux: --mode, and detector calibration from powder rings
--azint-only and --scale are replaced by --mode mx|azint|scale|calibration, with
mx the default. The old flags are removed rather than aliased.

Calibration mode fits the detector geometry - PONI x/y, the two tilts and the
distance - to a calibrant's powder rings and writes a pyFAI .poni alongside a
report of how far each parameter moved from the header. Bragg data constrain the
beam centre worst, because it is gauge-coupled to the crystal orientation; a
powder ring has no orientation to couple to.

--calibrant takes lab6, agbh, ceo2, si or ice. A calibrant is a list of ring
positions rather than a unit cell, because hexagonal ice is P6_3/mmc: rings
enumerated from its cell would include systematically absent ones. So the
crystalline standards generate their rings from a cell and ice carries the
measured list, and RingsFromAzimuthalProfile, GuessGeometry and OptimizeGeometry
all take ring q. The calibrant table is shared with the viewer's powder panel,
which previously carried its own copy.

--calibration picks how the rings are measured: rings (default) sums the
(q x azimuth) profile over every processed image and fits the arcs in it; spots
pools the found spots and fits those. Both use the whole run, with -s/-e/-t
selecting images. rings defaults --azim-phi-bins to 32, since a profile with one
azimuthal bin has averaged the ring over every direction and cannot locate it.

Two fixes this exposed:

The extraction window is capped at half the gap to the neighbouring ring. The
background under a peak is taken from the ends of its window, so a window wider
than half that gap measures the next ring's flank as this ring's background -
and hexagonal ice has three rings within 0.06 1/A. Ice calibration was 3.5 px
out before this and 0.29 px after; LaB6 is unaffected.

RingOptimizer holds rot1/rot2 fixed when only one ring is present. A tilt and a
centre offset both move a ring as cos(phi) and are separated only by the tilt's
amplitude growing as the ring radius squared, so on a single ring they are
exactly degenerate.

Measured. LaB6 at five distances: the fitted direct beam is within 0.36 px of an
independent implementation out to 300 mm, and D = -0.046 + 1.000788 dtz with an
rms of 0.011 mm. At 500 mm one ring is fully on the detector and a second only
clips the corners, which is not enough to constrain a tilt - restricting the q
range to the resolved ring recovers 0.06 px. Ice: 5.53 -> 0.29 px on one crystal
and 4.71 -> 0.80 px on another, against XDS's refined direct beam. On an ice-free
crystal the fit is worse than the header, which is the correct outcome.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-08-07 10:00:03 +02:00

110 lines
3.7 KiB
CMake

ADD_EXECUTABLE(jfjoch_test
DiffractionExperimentTest.cpp
RawToConvertedGeometryTest.cpp
../common/RawToConvertedGeometry.h
../common/DiffractionExperiment.h
CheckImageOutput.h
FPGAIntegrationTest.cpp
StrongPixelSetTest.cpp
AdaptiveThresholdTest.cpp
AdaptiveSpotFinderCPUTest.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
RingsFromProfileTest.cpp
CalibrationTest.cpp
XtalOptimizerTest.cpp
CrystalLatticeTest.cpp
FPGAPTPTest.cpp
ResolutionShellsTest.cpp
ImageSpotFinderCPUTest.cpp
ImageSpotFinderGPUTest.cpp
BSLZ4DecoderGPUTest.cpp
BSLZ4DecoderGPUFuzzTest.cpp
ImagePreprocessorGPUFusedTest.cpp
AdaptiveSpotFinderGPUTest.cpp
SpotExtractorGPUParityTest.cpp
CalcBraggPredictionTest.cpp
SpotUtilsTest.cpp
LatticeSearchTest.cpp
TimeTest.cpp
RotationIndexerTest.cpp
TopPixelsTest.cpp
HKLKeyTest.cpp
TCPImagePusherTest.cpp
SearchSpaceGroupTest.cpp
SearchSpaceGroupTwinTest.cpp
SyntheticMergedReflections.h
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)