leonarski_fandClaude Opus 5.5 fcbe92042b Merge branch 'af-mr3' into rc175: --af-model searches several copies per asymmetric unit (Matthews probability, sequential translation function, fixed-copy rigid body, tNCS) ...

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

2026-10-12 01:36:26 +02:00

..

crystfel

v1.0.0.rc-161 (#71)

2026-08-13 17:03:10 +02:00

data

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

test_data

v1.0.0-rc.160 (#70)

2026-07-19 09:39:28 +02:00

xds

XDS plugin 1.1.0: mask module/chip edges, pass saturation through; recommend Durin

2026-10-08 10:56:34 +02:00

xds_durin

XDS plugin 1.1.0: mask module/chip edges, pass saturation through; recommend Durin

2026-10-08 10:56:34 +02:00

xds_neggia

XDS plugin 1.1.0: mask module/chip edges, pass saturation through; recommend Durin

2026-10-08 10:56:34 +02:00

AcquisitionCountersTest.cpp

v1.0.0-rc.36

2025-05-05 19:32:22 +02:00

AdaptiveSpotFinderCPUTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

AdaptiveSpotFinderGPUTest.cpp

GPU azimuthal profile: sum the corrected values in fixed point

2026-10-08 12:33:34 +02:00

AdaptiveThresholdTest.cpp

v1.0.0-rc.166 (#76)

2026-09-02 21:17:31 +02:00

AnisotropyAnalysisTest.cpp

Anisotropy verdict: the directional limits are a second hypothesis beside the tensor

2026-10-11 02:21:32 +02:00

AutoIncrVectorTest.cpp

v1.0.0-rc.139 (#49)

2026-04-29 09:50:50 +02:00

AzimuthalIntegrationTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

BackgroundGainTest.cpp

rugnux: background clip scaled by the CCD gain measured in the pre-scan

2026-10-09 21:18:12 +02:00

BandwidthEstimateTest.cpp

Move SpotWidth to bragg_integration/, SpindleCuspLoss and LeftoverLattices to indexing/

2026-10-07 14:05:37 +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

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +02:00

BearerTokensTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

BraggIntegrationEngineCompressedImageTest.cpp

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +02:00

BraggIntegrationEngineCPUTest.cpp

rugnux two-pass: the integration radius decided on the pre-pass frames, before the canonical pass

2026-10-11 13:01:23 +02:00

BraggIntegrationEngineGPUTest.cpp

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +02:00

BraggStencilTest.cpp

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +02:00

BrokerHttpAuthTest.cpp

Broker: a collection can be followed from /start, its start message comes in the event stream

2026-10-08 17:03:09 +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

BraggPredictionRot: walk only the l of each column that can pass the phi test

2026-10-08 06:46:28 +02:00

CalibrationTest.cpp

v1.0.0-rc.166 (#76)

2026-09-02 21:17:31 +02:00

CBORTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +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 --af-model (experimental): single-copy molecular replacement of a predicted model

2026-10-11 13:35:05 +02:00

CoordTest.cpp

v1.0.0-rc.41

2025-06-10 18:14:04 +02:00

CorrectionSurfaceGPUTest.cpp

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +02:00

CrystalLatticeTest.cpp

v1.0.0-rc.166 (#76)

2026-09-02 21:17:31 +02:00

CrystalSettingTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

CudaHandledErrorTest.cpp

Indexer failures are thrown, not read as "no lattice"; GPU memory errors say what to do

2026-10-10 18:56:00 +02:00

CUDAMemHelpersTest.cpp

tests: FFT-indexer admission test fills every card, right before each Run

2026-10-11 16:39:43 +02:00

DectrisSimplonClientTest.cpp

DectrisSimplonClient: separate connections for commands and status reads

2026-10-08 22:53:01 +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

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +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

HotPixelFinder: mask dead pixels, and run on CCD sweeps too

2026-10-08 06:53:40 +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.173 (#83)

2026-09-29 15:57:32 +02:00

ImageSpotFinderGPUTest.cpp

v1.0.0.rc-161 (#71)

2026-08-13 17:03:10 +02:00

IndexingUnitTest.cpp

rugnux: doubled-cell hypothesis - the supercell probe reads its class to the limit, and a class that stands clear is merged in the doubled cell as well

2026-10-10 10:47:55 +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

HDF5 reader: read variable-length string attributes and datasets

2026-10-09 21:15:01 +02:00

JFJochReceiverIntegrationTest.cpp

v1.0.0-rc.150 (#60)

2026-06-15 20:24:15 +02:00

JFJochReceiverLiteTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +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.173 (#83)

2026-09-29 15:57:32 +02:00

LatticeReductionTest.cpp

v1.0.0-rc.153 (#63)

2026-06-23 20:29:49 +02:00

LatticeSearchTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

LePageLatticeTest.cpp

v1.0.0-rc.167 (#77)

2026-09-09 07:25:13 +02:00

LiveCollectionTest.cpp

Broker: a collection can be followed from /start, its start message comes in the event stream

2026-10-08 17:03:09 +02:00

LoadReferenceMtzFreeFlagsTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

LoadReferenceSfCifTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

LossyFilterTest.cpp

version 1.0.0-rc.25

2024-11-22 21:25:20 +01:00

MergeScaleTest.cpp

Global Wilson B: minimum fit window, no upper cap

2026-10-11 02:21:32 +02:00

ModelMaskGPUTest.cpp

ModelMaskGPU: gemmi's shrink step, so fine rigid-body zones stay on the GPU

2026-10-09 12:38:37 +02:00

ModelScaleGPUTest.cpp

Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/

2026-10-07 14:05:37 +02:00

ModelScalingTest.cpp

--model: the bulk-solvent b_sol ceiling follows the model's atomic B

2026-10-10 20:47:04 +02:00

ModelValidationTest.cpp

rugnux --model: a wrong model confirms no shell, fits no hand, and fits the GPU reserve

2026-10-11 21:30:34 +02:00

ModuleSummationTest.cpp

version 1.0.0-rc.27 minor fixes

2024-12-04 20:58:51 +01:00

MolecularReplacementTest.cpp

rugnux --af-model: several copies in the asymmetric unit, tNCS, a search-matched null, faster

2026-10-12 00:27:17 +02:00

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

PairSortGPUTest.cpp

RotationScaleMerge: sort the outlier band's log-spread pairs on the device

2026-10-08 07:27:25 +02:00

ParallelForTest.cpp

rugnux: on a machine of several sockets, keep to the sockets the GPUs are on

2026-10-11 09:27:32 +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

PortableTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

PostRefineTest.cpp

rugnux hypothesis arms read their residual on the pre-pass frames

2026-10-11 07:12:05 +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

Model validation expands strict NCS; the written cell follows the model's indexing

2026-10-10 13:35:49 +02:00

ResolutionShellsTest.cpp

v1.0.0-rc.166 (#76)

2026-09-02 21:17:31 +02:00

ResultReportTest.cpp

rugnux --model: a wrong model confirms no shell, fits no hand, and fits the GPU reserve

2026-10-11 21:30:34 +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

Indexer failures are thrown, not read as "no lattice"; GPU memory errors say what to do

2026-10-10 18:56:00 +02:00

RotationScaleWalkTest.cpp

rugnux: the no-crystal near-tie line prints the exact log10 tail against log10 significance

2026-10-10 09:33:34 +02:00

RugnuxLargeTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

RugnuxTest.cpp

Merge branch 'doubled-cell' into rc175: a doubled-cell hypothesis for a half-translation pseudo-symmetry that breaks down with resolution

2026-10-10 15:18:14 +02:00

SearchSpaceGroupTest.cpp

SearchSpaceGroup: offer every monoclinic setting the holohedry holds; break sibling ties on axial screw evidence

2026-10-09 21:42:33 +02:00

SearchSpaceGroupTwinTest.cpp

v1.0.0-rc.169 (#79)

2026-09-15 17:09:31 +02:00

ShadowFinderTest.cpp

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +02:00

SphericalHarmonicSurfaceTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

SpindleBlindFractionTest.cpp

v1.0.0-rc.167 (#77)

2026-09-09 07:25:13 +02:00

SpindleCuspLossTest.cpp

Move SpotWidth to bragg_integration/, SpindleCuspLoss and LeftoverLattices to indexing/

2026-10-07 14:05:37 +02:00

SpotExtractorGPUParityTest.cpp

v1.0.0.rc-161 (#71)

2026-08-13 17:03:10 +02:00

SpotFootprintTest.cpp

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +02:00

SpotUtilsTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

StatusVectorTest.cpp

v1.0.0-rc.127 (#34)

2026-03-02 15:57:12 +01:00

StreamWriterTest.cpp

Writer and broker: the master file appears only after every data file it links to

2026-10-08 14:55:56 +02:00

StrongPixelSetTest.cpp

v1.0.0-rc.166 (#76)

2026-09-02 21:17:31 +02:00

SweepLayoutTest.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

SyntheticMergedReflections.h

v1.0.0.rc-161 (#71)

2026-08-13 17:03:10 +02:00

TCPImagePusherTest.cpp

TCP pusher: never block the receiver thread; queue bounded by image-buffer slots

2026-10-10 21:11:09 +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

rugnux: write the twin hypothesis beside the answer as <prefix>_twin_<SG>.mtz/.cif

2026-10-09 19:40:22 +02:00

UnitCellTest.cpp

v1.0.0-rc.146 (#56)

2026-05-28 18:48:35 +02:00

WilsonOutliersTest.cpp

RotationScaleMerge: the Wilson outlier test on the device in the GPU build

2026-10-08 07:07:32 +02:00

WriteReflectionsTest.cpp

Merged mmCIF: drop the scaled unmerged block

2026-10-09 18:51:56 +02:00

XDSPluginTest.cpp

XDSPluginTest: expect a signed image's INTx_MAX to pass through as saturated

2026-10-08 12:36:40 +02:00

XtalOptimizerTest.cpp

v1.0.0-rc.166 (#76)

2026-09-02 21:17:31 +02:00

XtalRefineCeres.h

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +02:00

XtalRefineTest.cpp

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +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.173 (#83)

2026-09-29 15:57:32 +02:00