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leonarski_f 2e296e6bed jfjoch_writer: the live refinement's model, maps and blobs are written beside the master file 
In broker live mode the refined model, its map coefficients and the difference-map blobs stayed in
the broker for the viewer routes and were lost at the next run. They now go to the writer in the END
message as the placed model and maps already do - EndMessage::refined_model (PlacedModelMessage),
refined_map_coefficients (MtzTable) and blobs (DensityBlobsMessage, one vector per field) - and the
writer writes <prefix>_refined_model.cif (+ .pdb), <prefix>_refined_maps.mtz and <prefix>_blobs.json,
the names the CLI gives them. The blobs' JSON is made by one function (DensityBlobsJson) that the CLI
now writes through as well, so the two files are byte-identical. Optional CBOR fields, no version bump.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit c65220d96a96d2b1897f3c6632c94f9379b670a3)
2026-10-26 15:50:40 +01:00
..
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
Refinement: common cofactors and modified RNA nucleotides in the embedded dictionary; heme iron restrained from LINK records
2026-10-26 13:56:29 +01:00
xds
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
xds_durin
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
xds_neggia
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +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
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
AdaptiveThresholdTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
AndersonMixingTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
AnisotropyAnalysisTest.cpp
v1.0.0-rc.177 (#87)
2026-10-19 16:07:31 +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
BackgroundApertureTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BackgroundGainTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BandwidthEstimateTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BeamCenterFFTGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
BeamCenterFFTTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
BeamCenterFromBackgroundTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +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
Beam stop: a reflection whose signal disk reaches the shadow is not integrated; no-data pixels are dead, not shadow
2026-10-25 07:20:21 +01:00
BraggIntegrationEngineGPUTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BraggIntegrationEngineMetalTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BraggStencilTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
BrokerHttpAuthTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +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
Stills prediction: every frame predicts through two rocking widths of the run, measured first and centred on its radial scale
2026-10-26 10:50:52 +01:00
CalibrationTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CBORTest.cpp
NXmx: the unit cell's e.s.d.s are saved as /entry/sample/unit_cell_esd
2026-10-26 15:50:40 +01:00
CCTest.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
CellEsdTest.cpp
CellEsdTest: synthetic cells in place of cells that looked measured
2026-10-26 15:38:58 +01:00
CellPopulationTest.cpp
Stills geometry: fit only the given cell's crystal form; a stray frame is no cell population
2026-10-25 07:20:25 +01:00
CheckImageOutput.h
v1.0.0-rc.36
2025-05-05 19:32:22 +02:00
CMakeLists.txt
rugnux: unit-cell e.s.d.s - ZERR in a new SHELX .ins beside the .hkl, _cell.*_esd in the mmCIF, CELL_ESD_* in the report
2026-10-26 14:33:38 +01:00
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
CrystFELGeometryTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
CudaHandledErrorTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
CUDAMemHelpersTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
DectrisSimplonClientTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
DetectorGeometryTest.cpp
v1.0.0-rc.103 (#8)
2025-11-19 09:40:50 +01:00
DetectorModulesTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
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.176 (#86)
2026-10-19 07:03:28 +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
DirectHostReadGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
enospc_shim.c
SHIM library improvements from the HDF Group
2026-05-08 11:39:51 +02:00
FFBIDXIndexerCPUTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +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.176 (#86)
2026-10-19 07:03:28 +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
HostMemoryTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
HotPixelFinderTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +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.176 (#86)
2026-10-19 07:03:28 +02:00
IndexingUnitTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +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
JFJochImageBufferReaderTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
JFJochReaderTest.cpp
NXmx: the unit cell's e.s.d.s are saved as /entry/sample/unit_cell_esd
2026-10-26 15:50:40 +01:00
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.178 (#88)
2026-10-21 11:20:01 +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
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +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
Tests: the stills rocking width - the window at a reflection's resolution, _process.h5 round trip
2026-10-26 14:09:32 +01:00
ModelDensityGPUTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ModelDensityMetalTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ModelMaskGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
ModelScaleGPUTest.cpp
Refinement GPU: the robust scale fit on the card, the pool back in every trial slot
2026-10-26 01:38:24 +01:00
ModelScalingTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ModelValidationTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
ModuleRefinementTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
ModuleSummationTest.cpp
version 1.0.0-rc.27 minor fixes
2024-12-04 20:58:51 +01:00
MolecularReplacementMetalTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
MolecularReplacementTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +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
MultiReaderTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
nxmx_geometry_dials_test.py
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
PairSortGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
PanelLayoutTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
ParallelForTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +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
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +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
ReceiveRingBufferTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
RefinementTest.cpp
Refinement restraints: contacts with lattice translates are kept, and an atom's own symmetry contact once
2026-10-26 15:38:59 +01:00
RefineOnlyTest.cpp
Refinement: an exception in a trial slot or in RefineModel no longer ends the run
2026-10-26 15:38:58 +01:00
RegressionTest.cpp
1.0.0-rc.89
2025-10-01 22:54:40 +02:00
ReindexAmbiguityTest.cpp
Serial stills with a reference or model: crystals their own cells anchor keep that indexing
2026-10-26 06:49:20 +01:00
ResolutionShellsTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ResultReportTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +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.179 (#90)
2026-10-24 14:52:29 +02:00
ROIMapTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
RotationIndexerTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
RotationIngestGPUTest.cpp
Scaling: the low-resolution limit bounds the scale fit, not the merge
2026-10-25 07:20:21 +01:00
RotationScaleWalkTest.cpp
rugnux: a rotation scale is integrated with pass 1's lattice refit at it, and walked to the refit's fixed point
2026-10-25 07:20:25 +01:00
RugnuxInputKindTest.cpp
rugnux: a model and a reference among the inputs, in any order, told by their contents
2026-10-26 01:38:25 +01:00
RugnuxLargeTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
RugnuxLiveStatusTest.cpp
rugnux live: a score that is not finite is left out of the status, not sent as null
2026-10-26 15:38:58 +01:00
RugnuxResultFilesTest.cpp
jfjoch_writer: the live refinement's model, maps and blobs are written beside the master file
2026-10-26 15:50:40 +01:00
RugnuxStructureTest.cpp
Rugnux live: the uploaded model is refined after placement; refined scores, model, maps and blobs in the status, the viewer and the hero
2026-10-26 01:38:25 +01:00
RugnuxTest.cpp
rugnux: a placed model is refined by default - giving a model is the opt-in
2026-10-26 01:38:24 +01:00
SaturationCeilingTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
SearchSpaceGroupTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
SearchSpaceGroupTwinTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ShadowFinderTest.cpp
Polarization plane: measured on the pooled background, refused beyond what a source can give, logged, and kept across passes
2026-10-25 07:20:25 +01:00
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
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +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
SpotTilesTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +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
StoredImageDecodeGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
StreamWriterTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +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
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +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.179 (#90)
2026-10-24 14:52:29 +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.175 (#85)
2026-10-16 15:34:43 +02:00
UnitCellTest.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
WilsonOutliersTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
WriteReflectionsTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
XDSPluginTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
XFELReaderTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +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.178 (#88)
2026-10-21 11:20:01 +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