Files
Jungfraujoch/common/CMakeLists.txt
T
leonarski_fandClaude Opus 5.5 0a515bb086 rc179: everything on rc178 after its merge into main (#88), except the CHANGELOG
The rc178 branch continued after #88 was squash-merged; this is its content from b9ada7914 (the tree
#88 squashed) to 094eee31a, as one change on main. The individual commits stay on the rc178 branch:

- still battery: --cold evicts each set's input from the page cache; Alvra pixel masks; manifest fixes
- AGIPD: converter to one rigid panel per module, int16 photons, mask folded in; still battery reads the converted sets
- DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked
- tests: [PanelLayout] equivalence harness, stacked vs assembled panel layout
- Dense per-pixel maps through the panel table (panel layout stage 1)
- Panel id on spots and the panel table in the start message
- Viewer and preview show a panel detector as it lies on the detector plane
- Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster
- Panel layout stage 2: prediction and Bragg integration through the panel table
- XTC reader: frames handed up as stored, streams indexed in parallel
- XFEL reader: integer frames stay integer, one gain, placement by panel
- EXTERNAL_TEST_DATA_STILLS.md: images used vs the entry for every set; drop "Not in the battery"
- still battery: EuXFEL sets read the depositors' Cheetah CXI files directly; AGIPD converter removed
- float32_to_int16.py: a non-finite pixel becomes -32768, the int16 error marker, not a zero count
- CrystFEL geometry: read the pixel masks and bad regions instead of ignoring them
- Panel layout stage 5: the XFEL reader hands up the stored frame and its panel table
- Panel table persisted in NXmx; modulation grid and pre-scan memo key on the plane
- still battery: Alvra sets take their pixel mask from the CrystFEL geometry, not --mask-good
- still battery: take the deposited model as mmCIF where the RCSB has no PDB-format file
- still battery: dimple gets PDB-format coordinates converted from an mmCIF-only deposition
- stills fixed cost: geometry refinement and pre-scan do the same work in less wall time
- stills geometry sample and trial spot finding run as many workers as the image pass
- Stills integration: background ring reach measured on empty apertures, radial curvature from the whole frame
- StillsPartialityRefine: the partiality width is the run's, measured on the crystals, not the prediction window's
- MergeOnTheFly: capture term and multiplicative outlier band for the stills merge (both opt-in)
- Stills given a cell: the written cell is the mean over the frames that are merged
- Stills: the radial curvature correction decided per run on the same empty apertures
- StillsPartialityRefine: measure the run width only on shells with signal
- Stills pre-scan: report the paired z of the radial-correction comparison
- module placement: the five concurrent fits each keep every thread
- still battery: score R-free against the deposited data through the same dimple protocol
- still battery: the R-free target is the lower of the deposition's dimple and published values
- Stills: background clip follows the radial curve; signal disk from the lattice spacing
- Stills keep an overloaded observation as a lower bound instead of dropping it
- Stills: drop the lattice-spacing signal disk; the correction decision back on the plain clip
- battery: R-free against the deposition without refinement only, one protocol for rotation and stills
- still battery: EuXFEL sets run on a 2,000-image subset for now
- stills geometry refinement: fit the detector distance and the cell together
- stills geometry refinement: a distance given with --detector-distance is held in the joint fit
- Metal integration engine: back to its panel-s5 kernels; Mac stills keep the old clip, no saturation count
- Metal integration test: the CPU comparison runs on a rotation experiment
- Stills: kept overloads go back to the drop where they are not concentrated at low resolution
- stills distance search: an absolute 30-3000 mm scan, a sample found without d-limits, the fit iterated
- battery results: XFEL still battery 20261022-1358 on rc178 0cf62452c - 12 sets, cold, R_free unrefined
- battery results: still summary gains the resolution of our merge and of the deposition
- Pre-scan masks a pixel at the saturation limit on most frames, as one holding the error value
- Stills keep an overload as a lower bound only where it has pixels at the limit; run-level gate removed
- XFEL reader: a per-frame mask is read the way the frames are, its chunk inflated outside the HDF5 lock
- stills distance search: every centre scanned with a wider acceptance, a larger sample where nothing indexes
- rugnux usage: --beam-center-check describes the absolute 30-3000 mm stills distance scan, not the old 60-160 % grid
- stills: detector tilt refined in the geometry pre-pass, kept where held-out frames agree
- CLAUDE.md: the changelog is written once, just before the merge into main - condensed one-liners of what users get
- broker: serve the placed model and its maps of the last rugnux live run (/rugnux/model.cif, /rugnux/map.ccp4)
- frontend: Mol* viewer of the placed model and its density on the Rugnux live page
- writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does
- rugnux live maps: one unit cell centred on the model; the viewer opens on all of it
- Anomalous difference map: ANOM/PHANOM in _maps.mtz, /rugnux/map.ccp4?type=anom, a magenta mesh in the viewer
- Mol* viewer: open with the maps drawn within 10 A of the centre of view
- Mol* viewer: aaredb's structure-viewer setup, on a black stage
- rugnux: the gain of a stills file that states none is read off its single-photon peak where the background resolves photons
- Mol* viewer: in line with AareDB's StructureView at its current head (8ece2c2)
- ACKNOWLEDGEMENT: the web frontend's Mol* viewer follows AareDB's setup (G. Gotthard, PSI)
- stills tilt decision: the modules stay where the run placed them
- still battery: no distance pins and no per-set tuning flags; gain from the data except where a file's baseline hides it
- battery results: rc178 6f6f69 - full still battery and full rotation battery with REFMAC
- Bragg integration: a CCD rotation sweep's sigmas at the measured gain, intensities in photons
- BackgroundGain: the gain of a frame that resolves photons is the spacing of its photon peaks, so a baseline left in the frame no longer hides it
- ShadowFinder: measure the background's azimuthal modulation instead of predicting it from the polarization
- BackgroundGain: one gain estimate for rotation and stills; the still battery no longer gives EuXFEL 152 its gain
- ShadowFinder: measure the modulation robustly under a wide one-sided shadow
- ShadowFinderTest: a one-sided shadow is not fitted as part of the background's modulation
- ShadowFinder: back to the predicted polarization factor, in the plane the background shows
- MXAnalysisAfterFPGA: the Bragg engine's edge mask in the image's layout, so raw / untransformed FPGA runs start again
- battery results: still battery on rc178 e54f55 replaces the earlier rc178 still tables
- XFELReader: per-frame mask and photon conversion without a library call or a branch per pixel
- stills geometry trial: the hypotheses a search asks are indexed side by side
- stills tilt decision: the fits start beside the pre-scan and the geometry trial
- XFELReader: a deflated frame is inflated and converted a piece at a time, while it is in the cache
- XFELReader: a byte-shuffled frame is unshuffled a piece at a time, a whole pixel per step
- GeometryRefiner: residuals carry only the blocks a fit moves; beam and distance one block
- GeometryRefiner: a spot's residual differentiates its observed and predicted halves apart
- docs: EXTERNAL_TEST_DATA lists every open-arm battery set, with corrected values and counts
- battery: doc_check.py cross-checks the manifests against the dataset pages
- stills module placement: the placement fit gets half the threads, each held-out fit an eighth
- still battery: the EuXFEL sets run on all their frames, as the published still runs did
- battery results: still battery on rc178 a0ce6c, cold on a quiet machine, replaces the earlier rc178 table
- macOS build: explicit size_t in the XFEL reader's row bounds; parentheses in the CPU preprocessor's select

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
2026-10-23 17:56:42 +02:00

202 lines
7.2 KiB
CMake

# git header
# the commit's SHA1, and whether the building workspace was dirty or not
FIND_PACKAGE(Git)
SET(GITINFO_SOURCE_DIR "${CMAKE_SOURCE_DIR}")
SET(GITINFO_TEMPLATE "${CMAKE_CURRENT_SOURCE_DIR}/GitInfo.cpp.in")
SET(GITINFO_OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/GitInfo.cpp")
SET(JFJOCH_BUILD_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
# The compiler, and the CUDA toolkit where the build uses one, for the line each program logs at start.
SET(JFJOCH_BUILD_COMPILER "${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILER_VERSION}")
IF (JFJOCH_CUDA_AVAILABLE)
SET(JFJOCH_BUILD_CUDA "${CMAKE_CUDA_COMPILER_VERSION}")
ELSE()
SET(JFJOCH_BUILD_CUDA "")
ENDIF()
INCLUDE("${CMAKE_CURRENT_SOURCE_DIR}/GitInfoStamp.cmake")
set (THREADS_PREFER_PTHREAD_FLAG ON)
find_package (Threads REQUIRED)
MESSAGE(STATUS "Jungfraujoch git SHA1: ${GIT_SHA1}")
MESSAGE(STATUS "Jungfraujoch git date: ${GIT_DATE}")
MESSAGE(STATUS "Jungfraujoch version: ${JFJOCH_VERSION}")
# Re-stamped on every build, so RUGNUX_GIT in the rugnux report (and every other consumer of
# jfjoch_git_sha1) names the commit that was actually compiled.
ADD_CUSTOM_TARGET(JFJochGitInfo
COMMAND "${CMAKE_COMMAND}"
"-DGIT_EXECUTABLE=${GIT_EXECUTABLE}"
"-DGITINFO_SOURCE_DIR=${CMAKE_SOURCE_DIR}"
"-DGITINFO_TEMPLATE=${CMAKE_CURRENT_SOURCE_DIR}/GitInfo.cpp.in"
"-DGITINFO_OUTPUT=${CMAKE_CURRENT_BINARY_DIR}/GitInfo.cpp"
"-DJFJOCH_VERSION=${JFJOCH_VERSION}"
"-DJFJOCH_BUILD_CXX_FLAGS=${CMAKE_CXX_FLAGS}"
"-DJFJOCH_BUILD_COMPILER=${JFJOCH_BUILD_COMPILER}"
"-DJFJOCH_BUILD_CUDA=${JFJOCH_BUILD_CUDA}"
-P "${CMAKE_CURRENT_SOURCE_DIR}/GitInfoStamp.cmake"
BYPRODUCTS "${CMAKE_CURRENT_BINARY_DIR}/GitInfo.cpp"
COMMENT "Stamping GitInfo.cpp from git HEAD"
VERBATIM)
ADD_LIBRARY(JFJochVersion STATIC
${CMAKE_CURRENT_BINARY_DIR}/GitInfo.cpp GitInfo.h)
ADD_DEPENDENCIES(JFJochVersion JFJochGitInfo)
set_target_properties(JFJochVersion PROPERTIES
POSITION_INDEPENDENT_CODE ON
)
ADD_LIBRARY(JFJochLogger STATIC
Logger.cpp Logger.h
)
TARGET_LINK_LIBRARIES(JFJochLogger PUBLIC spdlog::spdlog JFJochVersion)
# NVTX v3 is header-only and architecture-neutral. CUDA::nvtx3 is no help here: it only points at
# CUDAToolkit_INCLUDE_DIRS, which in a cross build is the target tree (targets/sbsa-linux/include),
# and NVIDIA's cross-sbsa packages do not put nvtx3 there. So look in the target tree first and then
# in the toolkit's own include dir next to nvcc; where neither has it, the ranges compile out.
IF (JFJOCH_CUDA_AVAILABLE)
FIND_PATH(JFJOCH_NVTX3_INCLUDE_DIR nvtx3/nvToolsExt.h
HINTS ${CUDAToolkit_INCLUDE_DIRS} "${CUDAToolkit_BIN_DIR}/../include"
NO_DEFAULT_PATH NO_CMAKE_FIND_ROOT_PATH)
IF (JFJOCH_NVTX3_INCLUDE_DIR)
TARGET_INCLUDE_DIRECTORIES(JFJochLogger SYSTEM PRIVATE "${JFJOCH_NVTX3_INCLUDE_DIR}")
TARGET_LINK_LIBRARIES(JFJochLogger PRIVATE ${CMAKE_DL_LIBS}) # NVTX loads its injection library with dlopen
TARGET_COMPILE_DEFINITIONS(JFJochLogger PRIVATE JFJOCH_USE_NVTX)
ELSE()
MESSAGE(STATUS "NVTX3 headers not found - NVTX ranges compiled out")
ENDIF()
ENDIF()
ADD_LIBRARY(JFJochZMQ STATIC ZMQWrappers.cpp ZMQWrappers.h)
ADD_LIBRARY(JFJochCommon STATIC
Coord.cpp Coord.h
DiffractionExperiment.cpp DiffractionExperiment.h
RawToConvertedGeometry.h
JFJochException.h
Definitions.h
ThreadSafeFIFO.h
DiffractionSpot.cpp DiffractionSpot.h
StatusVector.cpp StatusVector.h
SpotToSave.h
NetworkAddressConvert.h NetworkAddressConvert.cpp
DetectorGeometry.h
DetectorModuleGeometry.cpp DetectorModuleGeometry.h
DetectorSetup.h DetectorSetup.cpp ZeroCopyReturnValue.h Histogram.h DiffractionGeometry.h
CUDAWrapper.cpp CUDAWrapper.h
CudaJitCache.cpp CudaJitCache.h
HostMemory.cpp HostMemory.h
ThreadAffinity.cpp ThreadAffinity.h
ADUHistogram.cpp ADUHistogram.h
RawToConvertedGeometryCore.h
Plot.h
../fpga/pcie_driver/jfjoch_fpga.h
DatasetSettings.cpp DatasetSettings.h
ROIMap.cpp ROIMap.h
ROIElement.cpp ROIElement.h
ROICircle.cpp ROICircle.h
ROIBox.cpp ROIBox.h
ImageBuffer.cpp ImageBuffer.h
time_utc.h
PixelMask.cpp PixelMask.h
InstrumentMetadata.cpp InstrumentMetadata.h
ImageFormatSettings.cpp
ImageFormatSettings.h
DetectorSettings.cpp
DetectorSettings.h
AzimuthalIntegrationSettings.cpp
AzimuthalIntegrationSettings.h
AzimuthalIntegrationProfile.h
AzimuthalIntegrationProfile.cpp
AzimuthalIntegrationMapping.h
AzimuthalIntegrationMapping.cpp
CheckPath.h
AutoIncrVector.h
ModuleSummation.cpp
ModuleSummation.h
ROIDefinition.cpp
ROIDefinition.h
ZeroCopyReturnValue.cpp
ColorScale.cpp ColorScale.h
FileWriterSettings.cpp
FileWriterSettings.h
MovingAverage.cpp
MovingAverage.h
DiffractionGeometry.cpp
ROIAzimuthal.cpp
ROIAzimuthal.h
print_license.h
DetectorGeometryModular.cpp
DetectorGeometryModular.h
DetectorModules.cpp
DetectorModules.h
PanelRows.h
PanelBoxes.cpp
PanelBoxes.h
AssembleToPlane.cpp
AssembleToPlane.h
ModuleShift.h
DetectorGeometryFixed.cpp
DetectorGeometryFixed.h
GridScanSettings.cpp
GridScanSettings.h
JFJochMessages.h
GoniometerAxis.cpp
GoniometerAxis.h
DetectorTransformation.cpp
DetectorTransformation.h
DetectorOrientation.cpp
DetectorOrientation.h
CompressedImage.cpp
CompressedImage.h
Reflection.h
MultiLinePlot.cpp
MultiLinePlot.h
IndexingSettings.cpp
IndexingSettings.h
CrystalLattice.cpp
CrystalLattice.h
ScanResult.cpp
ScanResult.h
ScanResultGenerator.cpp
ScanResultGenerator.h
BraggIntegrationSettings.cpp
BraggIntegrationSettings.h
SpotToSave.cpp
XrayFluorescenceSpectrum.cpp
XrayFluorescenceSpectrum.h
ResolutionShells.cpp
ResolutionShells.h
DarkMaskSettings.cpp
DarkMaskSettings.h
TopPixels.cpp
TopPixels.h
hkl_key.h
JfjochTCP.h
BrokerStatus.h
ScalingSettings.cpp
ScalingSettings.h
UnitCell.cpp
UnitCell.h
MtzTable.h
CorrelationCoefficient.cpp
CorrelationCoefficient.h
JFJochReceiverPlots.cpp
JFJochReceiverPlots.h
)
# librt is Linux/glibc-only (older glibc keeps clock_gettime/timer_*/sem_* there, and some
# distros are picky about it for pthreads); it does not exist on macOS/Windows.
TARGET_LINK_LIBRARIES(JFJochCommon JFJochLogger Compression JFCalibration gemmi Threads::Threads
$<$<PLATFORM_ID:Linux>:rt>)
TARGET_LINK_LIBRARIES(JFJochZMQ "$<BUILD_INTERFACE:libzmq-static>")
IF (JFJOCH_CUDA_AVAILABLE)
TARGET_SOURCES(JFJochCommon PRIVATE CUDAWrapper.cu )
TARGET_LINK_LIBRARIES(JFJochCommon CUDA::cudart_static
${CMAKE_DL_LIBS} $<$<PLATFORM_ID:Linux>:rt>)
ENDIF()