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leonarski_fandClaude Opus 5 d4f280047f grid scan: a raster reaches the spot engine, and the crystal cap says none rather than zero 
Two defects the merge created and one the API carried.

Rugnux gated the per-image spot engine on AnalysisModeIsMX, so AnalysisMode::Grid
fell through to the azimuthal-integration-only path: a raster ran, scored nothing,
and reported no crystals. The gate now asks the stages table whether the mode does
spot finding, which is the actual question - three modes need that engine for three
different reasons, and a fourth would otherwise have to be remembered here too.

max_crystals was a required integer defaulting to 10, with 0 meaning "all". Zero
reads as "report no crystals", the opposite of what it did. It is now optional, and
absent means no cap; a crystal found and then dropped is information the caller
cannot get back. grow_score_threshold was missing from the schema entirely.

Measured over the labelled corpus after these fixes: 34 of 34 confirmed-protein
rasters yield a crystal, 0 of 8 water, 0 of 6 ice, 19 of 19 heldout.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
2026-09-08 08:22:14 +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: one cell is a crystal when that cell is decisive, and the list can be capped
2026-09-08 07:15:30 +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
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
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
viewer: a grid scan shows protein and ice over the shape of the loop, with a frame around each crystal
2026-09-07 23:59:56 +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