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leonarski_fandClaude Opus 4.8 03814b1425 writer: save ROI bitmap and definitions in the master file 
Persist regions of interest so an acquisition's ROI layout can be
recovered from the master (_master.h5 / _process.h5):

- /entry/roi/roi_map: uint16 per-pixel bitmask (bit i == ROI i).
- /entry/roi/<name>: logical definition (type + geometry params, incl.
  azimuthal phi sector) plus bit_index tying it to the bitmap plane.

The bitmap rides along in the StartMessage (CBOR, mirroring az_int_map)
and is filled both online (JFJochReceiver::SendStartMessage) and offline
(jfjoch_process). Definitions come from the already-transmitted rois.
Both are dataset-wide metadata, so they are written by the NXmx master
writer (new NXmx::ROI), not the per-image data-file plugin.

Documented the /entry/roi layout in docs/HDF5.md and the master-vs-data
writer convention in CLAUDE.md; added a CBOR roi_map round-trip test.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
2026-06-19 09:41:26 +02:00
..
ADUHistogram.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
ADUHistogram.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
AutoIncrVector.h
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
AzimuthalIntegrationMapping.cpp
portability: replace M_PI / std::numbers::pi with a host+device-safe PI
2026-06-18 14:54:01 +02:00
AzimuthalIntegrationMapping.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
AzimuthalIntegrationProfile.cpp
common: spell the azimuthal d-spacing unit d_A consistently
2026-06-18 14:25:30 +02:00
AzimuthalIntegrationProfile.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
AzimuthalIntegrationSettings.cpp
v1.0.0-rc.152 (#62)
2026-06-17 20:36:24 +02:00
AzimuthalIntegrationSettings.h
Merge upstream
2026-06-18 18:52:22 +02:00
BraggIntegrationSettings.cpp
PixelRefine: profile multiplier as --profile-multiplier flag; outlier rejection default off
2026-06-15 13:48:11 +02:00
BraggIntegrationSettings.h
PixelRefine: profile multiplier as --profile-multiplier flag; outlier rejection default off
2026-06-15 13:48:11 +02:00
BrokerStatus.h
v1.0.0-rc.129 (#36)
2026-03-05 22:13:12 +01:00
CheckPath.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
CMakeLists.txt
Remove NUMAHWPolicy and the libnuma dependency
2026-06-17 20:25:36 +02:00
ColorScale.cpp
v1.0.0-rc.124 (#31)
2026-02-01 13:29:33 +01:00
ColorScale.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
CompressedImage.cpp
v1.0.0-rc.40
2025-05-28 18:49:27 +02:00
CompressedImage.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
Coord.cpp
portability: replace M_PI / std::numbers::pi with a host+device-safe PI
2026-06-18 14:54:01 +02:00
Coord.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
CorrelationCoefficient.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
CorrelationCoefficient.h
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
CrystalLattice.cpp
portability: replace M_PI / std::numbers::pi with a host+device-safe PI
2026-06-18 14:54:01 +02:00
CrystalLattice.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
CUDAWrapper.cpp
Remove NUMAHWPolicy and the libnuma dependency
2026-06-17 20:25:36 +02:00
CUDAWrapper.cu
Remove NUMAHWPolicy and the libnuma dependency
2026-06-17 20:25:36 +02:00
CUDAWrapper.h
Remove NUMAHWPolicy and the libnuma dependency
2026-06-17 20:25:36 +02:00
DarkMaskSettings.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
DarkMaskSettings.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DatasetSettings.cpp
jfjoch_process: First pixel refine integration
2026-06-08 15:37:27 +02:00
DatasetSettings.h
jfjoch_process: First pixel refine integration
2026-06-08 15:37:27 +02:00
Definitions.h
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
DetectorGeometry.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DetectorGeometryFixed.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
DetectorGeometryFixed.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DetectorGeometryModular.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
DetectorGeometryModular.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DetectorModuleGeometry.cpp
v1.0.0-rc.103 (#8)
2025-11-19 09:40:50 +01:00
DetectorModuleGeometry.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DetectorSettings.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
DetectorSettings.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DetectorSetup.cpp
v1.0.0-rc.143 (#53)
2026-04-30 22:16:50 +02:00
DetectorSetup.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DiffractionExperiment.cpp
jfjoch_writer: Add incident_wavelength_spread
2026-06-08 15:47:12 +02:00
DiffractionExperiment.h
indexing: make the resolved-algorithm invariant explicit in the pool
2026-06-18 14:25:30 +02:00
DiffractionGeometry.cpp
portability: replace M_PI / std::numbers::pi with a host+device-safe PI
2026-06-18 14:54:01 +02:00
DiffractionGeometry.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DiffractionSpot.cpp
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DiffractionSpot.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
FileWriterSettings.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
FileWriterSettings.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
GitInfo.cpp.in
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
GitInfo.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
GoniometerAxis.cpp
portability: replace M_PI / std::numbers::pi with a host+device-safe PI
2026-06-18 14:54:01 +02:00
GoniometerAxis.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
GridScanSettings.cpp
v1.0.0-rc.104 (#9)
2025-11-19 17:28:10 +01:00
GridScanSettings.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
Histogram.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
hkl_key.h
v1.0.0-rc.124 (#31)
2026-02-01 13:29:33 +01:00
ImageBuffer.cpp
ImageBuffer: replace NUMA interleave with parallel first-touch
2026-06-17 17:03:13 +02:00
ImageBuffer.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ImageFormatSettings.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
ImageFormatSettings.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
IndexingSettings.cpp
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
IndexingSettings.h
jfjoch_process: First pixel refine integration
2026-06-08 15:37:27 +02:00
InstrumentMetadata.cpp
version 1.0.0-rc.27
2024-12-02 21:17:14 +01:00
InstrumentMetadata.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
JFJochException.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
JFJochMath.h
portability: replace M_PI / std::numbers::pi with a host+device-safe PI
2026-06-18 14:54:01 +02:00
JFJochMessages.h
writer: save ROI bitmap and definitions in the master file
2026-06-19 09:41:26 +02:00
JfjochTCP.h
v1.0.0-rc.129 (#36)
2026-03-05 22:13:12 +01:00
Logger.cpp
v1.0.0-rc.82
2025-09-22 19:49:39 +02:00
Logger.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ModuleSummation.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
ModuleSummation.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
MovingAverage.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
MovingAverage.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
MultiLinePlot.cpp
v1.0.0-rc.40
2025-05-28 18:49:27 +02:00
MultiLinePlot.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
NetworkAddressConvert.cpp
build: portability groundwork toward a Windows/MSVC viewer
2026-06-17 08:37:21 +02:00
NetworkAddressConvert.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
PixelMask.cpp
mask: accept any-bit-depth TIFF for user mask upload
2026-06-18 16:05:04 +02:00
PixelMask.h
mask: accept any-bit-depth TIFF for user mask upload
2026-06-18 16:05:04 +02:00
Plot.h
common: spell the azimuthal d-spacing unit d_A consistently
2026-06-18 14:25:30 +02:00
print_license.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
RawToConvertedGeometry.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
RawToConvertedGeometryCore.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
Reflection.h
PixelRefine: Some improvements
2026-06-11 21:25:05 +02:00
ResolutionShells.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
ResolutionShells.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ROIAzimuthal.cpp
common: add azimuthal-angle (phi) sectors to ROIAzimuthal
2026-06-19 09:21:39 +02:00
ROIAzimuthal.h
common: add azimuthal-angle (phi) sectors to ROIAzimuthal
2026-06-19 09:21:39 +02:00
ROIBox.cpp
common: add azimuthal-angle (phi) sectors to ROIAzimuthal
2026-06-19 09:21:39 +02:00
ROIBox.h
common: add azimuthal-angle (phi) sectors to ROIAzimuthal
2026-06-19 09:21:39 +02:00
ROICircle.cpp
common: add azimuthal-angle (phi) sectors to ROIAzimuthal
2026-06-19 09:21:39 +02:00
ROICircle.h
common: add azimuthal-angle (phi) sectors to ROIAzimuthal
2026-06-19 09:21:39 +02:00
ROIDefinition.cpp
version 1.0.0-rc.29
2024-12-08 13:26:13 +01:00
ROIDefinition.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ROIElement.cpp
common: add azimuthal-angle (phi) sectors to ROIAzimuthal
2026-06-19 09:21:39 +02:00
ROIElement.h
common: add azimuthal-angle (phi) sectors to ROIAzimuthal
2026-06-19 09:21:39 +02:00
ROIMap.cpp
common: add azimuthal-angle (phi) sectors to ROIAzimuthal
2026-06-19 09:21:39 +02:00
ROIMap.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ScalingSettings.cpp
Merge: make outlier rejection a ScalingSettings parameter + CLI flag, default 6
2026-06-15 12:42:25 +02:00
ScalingSettings.h
PixelRefine: profile multiplier as --profile-multiplier flag; outlier rejection default off
2026-06-15 13:48:11 +02:00
ScanResult.cpp
v1.0.0-rc.44
2025-06-15 17:46:46 +02:00
ScanResult.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ScanResultGenerator.cpp
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ScanResultGenerator.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
SpotToSave.cpp
v1.0.0-rc.72
2025-09-08 20:28:59 +02:00
SpotToSave.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
StatusVector.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
StatusVector.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ThreadSafeFIFO.h
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
time_utc.h
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
TopPixels.cpp
v1.0.0-rc.121 (#28)
2025-12-12 21:24:20 +01:00
TopPixels.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
UnitCell.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
UnitCell.h
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
XrayFluorescenceSpectrum.cpp
v1.0.0-rc.81
2025-09-21 19:27:51 +02:00
XrayFluorescenceSpectrum.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ZeroCopyReturnValue.cpp
v1.0.0-rc.128 (#35)
2026-03-03 22:24:44 +01:00
ZeroCopyReturnValue.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ZMQWrappers.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
ZMQWrappers.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00