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leonarski_fandClaude Opus 5.5 a42b73ccfb Rugnux: fit the beam centre without the transmitting beam-stop pieces 
a1816e905 adds the partly transmitting holder-arm pieces to the beam-stop mask, and the
background beam-centre fit read that mask too. A thin arm running into the beam, masked, takes
cells out of the rings it crosses; which radial bins stay above the sector-coverage gate then
changes as the trial centre moves, and a walk seeded beside the arm (the FFT capture sat 48 px off)
limit-cycled on that edge and stopped 44 px short (sigma 0.34 -> 2.27 px). On an open-arm set whose
header centre is 171 px out, the measured centre no longer indexed (60/60 -> 0/60), the run kept the
file's centre and merged P1 at CC1/2 0.004 instead of P212121 at 0.995.

The arm's dimming is multiplicative in azimuth, which the fit's per-sector amplitude already
absorbs, so the fit now uses the mask without those pieces (ShadowFinder marks them TRANSMITTING);
integration still masks them. The fitted centre is back to its a0518abe6 value on every set checked
(the failing one plus four arm sets); the failing set merges P212121, CC1/2 0.995, ISa 22.6.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
2026-09-27 08:34:36 +02:00
..
crystfel
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
data
v1.0.0-rc.160 (#70)
2026-07-19 09:39:28 +02:00
test_data
v1.0.0-rc.160 (#70)
2026-07-19 09:39:28 +02:00
xds
v1.0.0-rc.134 (#43)
2026-04-09 13:30:47 +02:00
xds_durin
version 1.0.0-rc.13
2024-10-05 13:14:49 +02:00
xds_neggia
version 1.0.0-rc.13
2024-10-05 13:14:49 +02:00
AcquisitionCountersTest.cpp
v1.0.0-rc.36
2025-05-05 19:32:22 +02:00
AdaptiveSpotFinderCPUTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
AdaptiveSpotFinderGPUTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
AdaptiveThresholdTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
AnisotropyAnalysisTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
AutoIncrVectorTest.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
AzimuthalIntegrationTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
BandwidthEstimateTest.cpp
rugnux: measure the X-ray bandwidth from the pre-scan's spot shapes (reported only)
2026-09-23 20:42:46 +02:00
BeamCenterFFTGPUTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
BeamCenterFFTTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
BeamCenterFromBackgroundTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
BeamCenterFromSpotsTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
BraggIntegrationEngineCompressedImageTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
BraggIntegrationEngineGPUTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
BraggStencilTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
BSLZ4DecoderGPUFuzzTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
BSLZ4DecoderGPUTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
CalcBraggPredictionTest.cpp
Rotation prediction: place each partial at its slice of the rocking curve
2026-09-24 14:06:24 +02:00
CalibrationTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CBORTest.cpp
Record the corrections a DECTRIS detector applied; read multichannel NXmx
2026-09-23 21:04:16 +02:00
CCTest.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
CheckImageOutput.h
v1.0.0-rc.36
2025-05-05 19:32:22 +02:00
CMakeLists.txt
Rugnux: spherical-harmonic crystal-frame absorption as a candidate surface
2026-09-26 13:43:59 +02:00
CoordTest.cpp
v1.0.0-rc.41
2025-06-10 18:14:04 +02:00
CrystalLatticeTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CrystalSettingTest.cpp
Rugnux: write the standard setting, or the user's; match a reference MTZ on its own axes
2026-09-25 20:16:42 +02:00
CudaHandledErrorTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
CUDAMemHelpersTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
DetectorGeometryTest.cpp
v1.0.0-rc.103 (#8)
2025-11-19 09:40:50 +01:00
DetectorSettingsTest.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
DetectorSetupTest.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
DetGeomCalibTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DiagnosticOutputTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
DiffractionExperimentTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DiffractionGeometryTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DiffractionSpotTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
enospc_shim.c
SHIM library improvements from the HDF Group
2026-05-08 11:39:51 +02:00
FPGAFrameGeneratorTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
FPGAHLSModulesTest.cpp
v1.0.0-rc.91
2025-10-20 20:43:44 +02:00
FPGAHostWriterTest.cpp
v1.0.0-rc.34
2025-04-14 11:52:06 +02:00
FPGAIntegrationTest.cpp
v1.0.0-rc.97
2025-11-09 12:42:27 +01:00
FPGANetworkTest.cpp
v1.0.0-rc.72
2025-09-08 20:28:59 +02:00
FPGAPTPTest.cpp
v1.0.0-rc.72
2025-09-08 20:28:59 +02:00
FPGASpotFindingUnitTest.cpp
v.1.0.0-rc.32
2025-03-24 12:16:33 +01:00
FrameTransformationTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
FrenchWilsonTest.cpp
Rugnux: French-Wilson amplitudes as ctruncate gives them
2026-09-26 13:43:59 +02:00
GoniometerAxisTest.cpp
v1.0.0-rc49
2025-06-18 15:19:18 +02:00
GridScanSettingsTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
HDF5WritingTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
HistogramTest.cpp
v1.0.0-rc.121 (#28)
2025-12-12 21:24:20 +01:00
HKLKeyTest.cpp
v1.0.0-rc.124 (#31)
2026-02-01 13:29:33 +01:00
HotPixelFinderTest.cpp
rugnux: mask defective pixels measured on the pre-scan's own frames
2026-09-23 20:42:46 +02:00
ImageBufferTest.cpp
v1.0.0-rc.128 (#35)
2026-03-03 22:24:44 +01:00
ImageMetadataTest.cpp
v1.0.0-rc.103 (#8)
2025-11-19 09:40:50 +01:00
ImagePreprocessorGPUFusedTest.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
ImageSpotFinderCPUTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
ImageSpotFinderGPUTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
IndexingUnitTest.cpp
rugnux: report-only supercell probe - the eight parity classes of the doubled cell
2026-09-25 06:02:50 +02:00
JFCalibrationTest.cpp
v1.0.0-rc.36
2025-05-05 19:32:22 +02:00
JFConversionTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
jfjoch_hdf5_enospc_test.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
JFJochReaderTest.cpp
Record the corrections a DECTRIS detector applied; read multichannel NXmx
2026-09-23 21:04:16 +02:00
JFJochReceiverIntegrationTest.cpp
v1.0.0-rc.150 (#60)
2026-06-15 20:24:15 +02:00
JFJochReceiverLiteTest.cpp
pixel_mask_applied is false on the DECTRIS broker path
2026-09-23 21:17:42 +02:00
JFJochReceiverPlotsTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
JFJochReceiverProcessingTest.cpp
v1.0.0-rc.160 (#70)
2026-07-19 09:39:28 +02:00
JFJochStateMachineTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
JFPedestalTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
JPEGTest.cpp
v1.0.0-rc.40
2025-05-28 18:49:27 +02:00
LatticeReductionTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
LatticeSearchTest.cpp
Rugnux: test angle promotions of the metric symmetry; score model frames at the data's best indexing
2026-09-26 13:43:58 +02:00
LePageLatticeTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
LoadReferenceMtzFreeFlagsTest.cpp
v1.0.0-rc.159 (#69)
2026-07-13 13:54:03 +02:00
LoadReferenceSfCifTest.cpp
rugnux: accept a PDB structure-factor mmCIF as the -z reference
2026-09-25 20:17:03 +02:00
LossyFilterTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
MergeScaleTest.cpp
Merge statistics: R_meas weighted as the merge weights each observation
2026-09-25 04:52:24 +02:00
ModelScalingTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
ModelValidationTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
ModuleSummationTest.cpp
version 1.0.0-rc.27 minor fixes
2024-12-04 20:58:51 +01:00
MovingAverageTest.cpp
v1.0.0-rc.31
2025-03-02 13:15:28 +01:00
MultiLatticeSearchTest.cpp
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
nxmx_geometry_dials_test.py
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
ParallelForTest.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
PedestalCalcTest.cpp
v1.0.0-rc.97
2025-11-09 12:42:27 +01:00
PixelMaskTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
PostRefineTest.cpp
Rugnux: report the oscillation the run integrated at; test the rotation-scale fit on a simulated sweep
2026-09-24 11:37:38 +02:00
PreflightTest.cpp
v1.0.0-rc.165 (#75)
2026-08-27 22:16:54 +02:00
PreviewCounterTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
RawToConvertedGeometryTest.cpp
v1.0.0-rc.97
2025-11-09 12:42:27 +01:00
RegressionTest.cpp
1.0.0-rc.89
2025-10-01 22:54:40 +02:00
ReindexAmbiguityTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
ResolutionShellsTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ResultReportTest.cpp
Rugnux report: low warning thresholds, worded as prompts to check; ice apart from powder
2026-09-26 14:02:05 +02:00
RfreeFlagsTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
RingsFromProfileTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ROIIntegrationCPUTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIIntegrationGPUTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIMapTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
RotationIndexerTest.cpp
Make a first-pass detector tilt no mounting can have prove itself on the spots
2026-09-23 19:01:08 +02:00
RotationScaleWalkTest.cpp
Rugnux: walk the goniometer rotation scale to its fixed point, decided on the whole sweep
2026-09-24 11:34:06 +02:00
RugnuxLargeTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
RugnuxTest.cpp
Beam-centre check: carry both centres when only lean first passes index, decide on the merge
2026-09-24 13:44:52 +02:00
SearchSpaceGroupTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
SearchSpaceGroupTwinTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
ShadowFinderTest.cpp
Rugnux: fit the beam centre without the transmitting beam-stop pieces
2026-09-27 08:34:36 +02:00
SphericalHarmonicSurfaceTest.cpp
Rugnux: spherical-harmonic crystal-frame absorption as a candidate surface
2026-09-26 13:43:59 +02:00
SpindleBlindFractionTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
SpindleCuspLossTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
SpotExtractorGPUParityTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
SpotUtilsTest.cpp
Rugnux report: low warning thresholds, worded as prompts to check; ice apart from powder
2026-09-26 14:02:05 +02:00
StatusVectorTest.cpp
v1.0.0-rc.127 (#34)
2026-03-02 15:57:12 +01:00
StreamWriterTest.cpp
v1.0.0-rc.97
2025-11-09 12:42:27 +01:00
StrongPixelSetTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
SweepLayoutTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
SyntheticMergedReflections.h
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
TCPImagePusherTest.cpp
v1.0.0-rc.157 (#67)
2026-07-11 07:19:11 +02:00
TestData.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ThreadSafeFIFOSetTest.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
TIFFTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
TimeTest.cpp
v1.0.0-rc.96 (#1)
2025-11-02 13:45:57 +01:00
TopPixelsTest.cpp
v1.0.0-rc.121 (#28)
2025-12-12 21:24:20 +01:00
TranslationalNCSTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
TwinningAnalysisTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
UnitCellTest.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
WilsonOutliersTest.cpp
Merge: a clipped observation is no witness in the Wilson test
2026-09-24 07:26:42 +02:00
WriteReflectionsTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
XDSPluginTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
XtalOptimizerTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ZMQImagePusherTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
ZMQMetadataSocketTest.cpp
v1.0.0-rc.133
2026-03-26 20:50:33 +01:00
ZMQPreviewSocketTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
ZSTDCompressorTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00