leonarski_fandClaude Opus 5 aa5a31b345 grid scan: an unstated beam is reported as the grid step, not as zero ...

A raster is stepped at about the beam size, so the step is the best proxy there is
when neither --beam-size nor the file's incident_beam_size says anything. Zero is the
worse answer: the reported crystal extents still contain a whole beam, and a zero
tells a consumer deconvolving them that they are already exact.

The substitution is in AnalyzeGridScan, so it holds for the broker and for rugnux
alike. The extents themselves do not move - they are measured either way, and the
test pins that. BEAM_SIZE_SOURCE in the raster report gains GRID_STEP, so a reader
can still tell a measured beam from a stood-in one, which matters because removing an
anisotropic beam is a covariance subtraction and a wrong one rotates the crystal axis.

The comment at the rugnux call site had argued for the old behaviour in as many
words; it now describes what the code does.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N

2026-09-08 09:11:26 +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

AnalysisSettingsTest.cpp

grid scan: a raster reaches the spot engine, and the crystal cap says none rather than zero

2026-09-08 08:22:14 +02:00

AnalyzeGridScanTest.cpp

grid scan: an unstated beam is reported as the grid step, not as zero

2026-09-08 09:11:26 +02:00

AnisotropyAnalysisTest.cpp

rugnux: the per-reflection correction factor is named for what it is, not for what it once held

2026-09-05 13:41:16 +02:00

AutoIncrVectorTest.cpp

v1.0.0-rc.139 (#49)

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

AzimuthalIntegrationTest.cpp

image analysis: the ice score takes the pipeline's own band width, and the ice quantities are named for what kind of number they are

2026-09-08 07:19:03 +02:00

BeamCenterFromBackgroundTest.cpp

v1.0.0-rc.166 (#76)

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

BeamCenterFromSpotsTest.cpp

v1.0.0-rc.166 (#76)

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

BraggIntegrationEngineCompressedImageTest.cpp

rugnux: the per-reflection correction factor is named for what it is, not for what it once held

2026-09-05 13:41:16 +02:00

BraggIntegrationEngineGPUTest.cpp

Revert "integration: the background is fitted over the ring that survives, not averaged over it"

2026-09-07 16:30:22 +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

integration: the flight path between the sample and the detector is corrected for, and named

2026-09-05 17:55:43 +02:00

CalibrationTest.cpp

v1.0.0-rc.166 (#76)

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

CBORTest.cpp

file format: the ice ring ratio is stored and sent under its own name, and the retired one is still read

2026-09-08 07:42:23 +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

Merge branch 'worktree-agent-ae76aa0c66b33a4db' into grid-scan-integration

2026-09-08 07:55:31 +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

DetectionScoreTest.cpp

grid scan: review fixes - the ice channel sees its own spots, and a needle is not mirrored

2026-09-08 09:04:52 +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

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.156 (#66)

2026-07-03 19:18:56 +02:00

FrenchWilsonTest.cpp

v1.0.0-rc.166 (#76)

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

GoniometerAxisTest.cpp

v1.0.0-rc49

2025-06-18 15:19:18 +02:00

GridScanCompositeTest.cpp

grid scan: a test spans the seam between the angle a raster measures and the frame drawn from it

2026-09-08 08:23:43 +02:00

GridScanSettingsTest.cpp

v1.0.0-rc.166 (#76)

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

HDF5WritingTest.cpp

reader: a one-element string array is a scalar

2026-09-03 10:58:38 +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

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: a cell given with -C is matched in any equivalent description

2026-09-06 20:26:38 +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

integration: the flight path between the sample and the detector is corrected for, and named

2026-09-05 17:55:43 +02:00

JFJochReceiverIntegrationTest.cpp

v1.0.0-rc.150 (#60)

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

JFJochReceiverLiteTest.cpp

v1.0.0.rc-162 (#72)

2026-08-25 08:21:39 +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.166 (#76)

2026-09-02 21:17:31 +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

v1.0.0-rc.166 (#76)

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

LePageLatticeTest.cpp

symmetry: a metric two-fold the lattice search refused is asked of the intensities

2026-09-06 07:21:41 +02:00

LoadReferenceMtzFreeFlagsTest.cpp

v1.0.0-rc.159 (#69)

2026-07-13 13:54:03 +02:00

LossyFilterTest.cpp

version 1.0.0-rc.25

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

MergeScaleTest.cpp

rugnux: the per-reflection correction factor is named for what it is, not for what it once held

2026-09-05 13:41:16 +02:00

ModelScalingTest.cpp

model validation: the bulk solvent is searched inside its physical range, not fitted without bounds

2026-09-07 10:34:21 +02:00

ModelValidationTest.cpp

model validation: the placement target carries a bulk solvent that means something

2026-09-07 15:27:30 +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

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

RasterReportTest.cpp

grid scan: a raster reaches the spot engine, and the crystal cap says none rather than zero

2026-09-08 08:22:14 +02:00

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.166 (#76)

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

ResolutionShellsTest.cpp

v1.0.0-rc.166 (#76)

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

ResultReportTest.cpp

model validation: the model says, shell by shell, where the data still carry signal

2026-09-07 13:12:32 +02:00

RfreeFlagsTest.cpp

v1.0.0-rc.166 (#76)

2026-09-02 21:17:31 +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

v1.0.0-rc.166 (#76)

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

RugnuxLargeTest.cpp

analysis: what runs over the images is one stated mode, shared by broker, rugnux and viewer

2026-09-08 00:16:26 +02:00

RugnuxTest.cpp

analysis: what runs over the images is one stated mode, shared by broker, rugnux and viewer

2026-09-08 00:16:26 +02:00

SearchSpaceGroupTest.cpp

tests: the report version pin and the screw-gate section follow the code

2026-09-06 21:12:42 +02:00

SearchSpaceGroupTwinTest.cpp

v1.0.0.rc-161 (#71)

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

ShadowFinderTest.cpp

v1.0.0.rc-162 (#72)

2026-08-25 08:21:39 +02:00

SpindleBlindFractionTest.cpp

spindle: three trigger states, and the threshold is geometry rather than tuning

2026-09-04 10:59:05 +02:00

SpindleCuspLossTest.cpp

rugnux: the mounting's cost is computed exactly from the measured group, not guessed from an angle

2026-09-04 10:59:05 +02:00

SpotExtractorGPUParityTest.cpp

v1.0.0.rc-161 (#71)

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

SpotUtilsTest.cpp

rugnux: a measured spot budget below the input floor degrades the run instead of killing it

2026-09-05 23:33:43 +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

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

diagnostics: a translational pseudo-symmetry is detected and named

2026-09-05 20:08:40 +02:00

TwinningAnalysisTest.cpp

twinning: the L-test partners are chosen so a pseudo-translation cannot silence it

2026-09-05 20:09:00 +02:00

UnitCellTest.cpp

v1.0.0-rc.146 (#56)

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

WriteReflectionsTest.cpp

integration: the flight path between the sample and the detector is corrected for, and named

2026-09-05 17:55:43 +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.129 (#36)

2026-03-05 22:13:12 +01:00

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