leonarski_fandClaude Opus 4.8
58910274bf
MXAnalysisWithoutFPGA never filled DataMessage.roi, so ROI integrals were only available on the FPGA path. Add a software ROI engine that mirrors the FPGA roi_calc kernel: per-ROI sum, sum of squares, good-pixel count, max and intensity-weighted centre of mass, with each pixel carrying a 16-bit mask so it can contribute to any subset of up to 16 ROIs. New image_analysis/roi/ library (JFJochROIIntegration), structured like azint: a base that precomputes the per-pixel mask and names, a templated CPU engine (generic over pixel type for a future 16-bit path), and a GPU kernel using per-block shared-memory atomics for the STXM case (half-detector ROIs). Masked pixels are excluded entirely; saturated pixels are excluded from the sums but still count towards the max, matching roi_calc exactly. The engine is only constructed when at least one ROI is defined. Downstream CBOR/HDF5 already consume message.roi, so no further changes are needed. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
57 lines
1.8 KiB
CMake
57 lines
1.8 KiB
CMake
SET(MINIGLOG ON)
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SET(PROVIDE_UNINSTALL_TARGET OFF)
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SET(USE_CUDA OFF)
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SET(EIGENSPARSE ON)
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# Prevent MKL from being found (guarantees no MKL)
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SET(CMAKE_DISABLE_FIND_PACKAGE_MKL TRUE)
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SET(CERES_THREADING_MODEL "CXX_THREADS")
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FetchContent_Declare(
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ceres
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GIT_REPOSITORY https://github.com/ceres-solver/ceres-solver
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GIT_TAG 0c70ed3
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EXCLUDE_FROM_ALL
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)
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FetchContent_MakeAvailable(ceres)
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ADD_LIBRARY(JFJochImageAnalysis STATIC
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MXAnalysisWithoutFPGA.cpp
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MXAnalysisWithoutFPGA.h
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MXAnalysisAfterFPGA.h
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MXAnalysisAfterFPGA.cpp
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IndexAndRefine.cpp
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IndexAndRefine.h
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dark_mask_analysis/DarkMaskAnalysis.cpp
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dark_mask_analysis/DarkMaskAnalysis.h
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rotation_indexer/RotationIndexer.cpp
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rotation_indexer/RotationIndexer.h
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RotationParameters.cpp
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RotationParameters.h
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WriteReflections.cpp
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WriteReflections.h
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LoadFCalcFromMtz.cpp
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LoadFCalcFromMtz.h
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UpdateReflectionResolution.cpp
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UpdateReflectionResolution.h
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IntegrationOutcome.h
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rotation_indexer/RotationIndexerCounter.cpp
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rotation_indexer/RotationIndexerCounter.h)
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FIND_PACKAGE(Eigen3 3.4 REQUIRED NO_MODULE) # provides Eigen3::Eigen
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ADD_SUBDIRECTORY(spot_finding)
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ADD_SUBDIRECTORY(bragg_integration)
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ADD_SUBDIRECTORY(bragg_prediction)
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ADD_SUBDIRECTORY(indexing)
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ADD_SUBDIRECTORY(geom_refinement)
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ADD_SUBDIRECTORY(lattice_search)
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ADD_SUBDIRECTORY(scale_merge)
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ADD_SUBDIRECTORY(image_preprocessing)
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ADD_SUBDIRECTORY(azint)
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ADD_SUBDIRECTORY(roi)
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ADD_SUBDIRECTORY(pixel_refinement)
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TARGET_LINK_LIBRARIES(JFJochImageAnalysis JFJochAzIntEngine JFJochROIIntegration JFJochImagePreprocessing JFJochBraggPrediction JFJochBraggIntegration JFJochLatticeSearch JFJochIndexing JFJochSpotFinding JFJochCommon JFJochGeomRefinement JFJochScaleMerge JFJochPixelRefine gemmi)
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