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v1.0.0.rc-162 (#72)
**Files written by Jungfraujoch now import correctly in DIALS, XDS and pyFAI.** A tilted detector, a grid scan, a still recorded at a goniometer position, and saturated or unreadable pixels were each described in a way that a third-party program acted on wrongly. If you process Jungfraujoch data outside Jungfraujoch, prefer this release to any earlier one.

* HDF5: the detector tilt (`rot1`/`rot2`/`rot3`) is exported correctly in the NXmx transformation chain; untilted geometries are unaffected.
* HDF5: a still recorded at a goniometer position is no longer read back as a single image, and a grid scan records a stationary spindle so a program that requires a rotation axis can open it.
* HDF5: the sample transformation chain is written in mounting order, with a Smargon head position told apart from the spindle, one entry per image, `module_offset` as a float unit vector, and `offset_units` on every offset.
* HDF5: saturated, underloaded and unreadable pixels are described so a downstream program masks them - `saturation_value`, `underload_value`, `error_value` and `bit_depth_readout` are written correctly, and a data file missing next to a VDS master reads as the error marker rather than as zero counts.
* HDF5: the rotation axis is read back under whatever name it carries, and `mirror_y` records whether the assembled image is mirrored in Y relative to the detector's raw readout.
* A grid scan and a goniometer axis can both be set; they are no longer alternatives.
* `images_per_file` is chosen from the acquisition when it is not given: a rotation sweep of at most 20000 images goes into a single data file, a grid scan splits on whole fast-axis rows, and stills and serial keep 1000.
* The writer refuses a stream whose start message declares a different pixel format than its images carry, and a DECTRIS detector sending signed images is no longer declared unsigned.
* The image stream can carry the sample transformation chain (`transformations`, in the END message); a producer that does not send it gets the same chain built by the writer.
* rugnux: fixing the space group with `-S` no longer prevents the lattice from being found - a lattice indexed in a different setting is reindexed into that group's own setting, and a run whose crystal does not have that group's lattice stops and names the cell it indexed as, rather than reporting statistics that cannot describe it.
* rugnux: the per-image resolution estimate now predicts the resolution the merged data reach rather than the highest-resolution spot found, and is reported as `SPOT_RESOLUTION_ESTIMATE`.
* rugnux: two runs of the same command on the same images produce the same merged intensities; the azimuthal profile written alongside them is not yet reproducible in the same way.
* rugnux: the offline lattice refinement is bounded by iterations rather than by a wall clock, so a loaded machine can no longer refine to a different lattice; a live acquisition keeps its real-time bound.
* rugnux: the detector-frame modulation correction is fitted on a grid spanning the detector, so whether it is applied no longer depends on how far integration reached.
* rugnux: the geometry pre-pass no longer writes `<prefix>_01.mtz`, `_01.cif`, `_01.hkl` and `_01_image.dat`; the refined second pass writes those files under `<prefix>`, and that is the result to use.
* rugnux: `_process.h5` describes the pixel format of the images it links to, and is written on a thread of its own.
* rugnux: the detector geometry is also logged in XDS's convention (`ORGX`/`ORGY`, detector axis vectors, rotation axis), so it can be compared with an XDS refinement.
* rugnux: an image integrated in pyFAI through the `.poni` file written by `--mode calibration` comes out with the correct azimuth, and the file declares pyFAI's `orientation`, which needs pyFAI 2024.01 or newer. Radial integration is unchanged.
* rugnux: a rotation run is substantially faster throughout - beam-stop detection, first-pass indexing, geometry refinement, integration, scaling and merging - and observations outside the scaling resolution range are dropped as they are ingested. The refined geometry, the space group chosen and the merged statistics are unchanged.
* Faster spot finding and indexing, on the broker as well as in rugnux; the spots found and the lattices indexed are unchanged.
* A run reserves substantially less GPU memory: nothing is allocated for buffers that are never read, and a worker builds only the engines it uses.
* rugnux: with `-N` left at its default the per-image loop of `--mode mx` uses at most 16 workers per GPU, rather than one per hardware thread; an explicit `-N` is obeyed as given.
* CUDA 12 builds now contain device code for Volta, so the RHEL 8 packages and the portable Linux `.tgz` run on a V100; the CUDA 13 artefacts (RHEL 9, Ubuntu, Windows) remain Turing and newer.
* The build resolves a single Eigen for the whole project, and refuses to configure if Ceres picks up a different one; a build that mixed two Eigen versions was undefined behaviour and crashed at -O2.
* Documentation: a security page, and the supported GPU generations and minimum NVIDIA driver version of every released artefact.

**Breaking change to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.162, `frontend/src/client`):
* `dataset_settings.images_per_file` is no longer `default: 1000` and no longer accepts `0`; it is optional, and its minimum is 1. A client sending `0` (previously "one file for the whole run") is now rejected - omit the field instead, which for a rotation sweep gives the same single file.
* `file_writer_format` now defaults to `NXmxVDS`, matching the server's own default and the layout recommended for DIALS, XDS and CrystFEL. A generated client that fills in schema defaults and does not set the format explicitly will write VDS masters where it previously wrote legacy ones; set `NXmxLegacy` explicitly to keep them.

---------

Co-authored-by: jungfrau <jungfrau@mx-aare-test.psi.ch>
Reviewed-on: #72
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-08-25 08:21:39 +02:00

156 lines
4.9 KiB
CMake

# git header
# the commit's SHA1, and whether the building workspace was dirty or not
FIND_PACKAGE(Git)
EXECUTE_PROCESS(COMMAND
"${GIT_EXECUTABLE}" describe --match=NeVeRmAtCh --always --abbrev=8
WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
OUTPUT_VARIABLE GIT_SHA1
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
# the date of the commit
EXECUTE_PROCESS(COMMAND
"${GIT_EXECUTABLE}" log -1 --format=%ad --date=local
WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
OUTPUT_VARIABLE GIT_DATE
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
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: ${JFJOCH_VERSION}")
CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/GitInfo.cpp.in" "${CMAKE_CURRENT_BINARY_DIR}/GitInfo.cpp" @ONLY)
ADD_LIBRARY(JFJochVersion STATIC
${CMAKE_CURRENT_BINARY_DIR}/GitInfo.cpp GitInfo.h)
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)
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
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
DetectorGeometryFixed.cpp
DetectorGeometryFixed.h
GridScanSettings.cpp
GridScanSettings.h
JFJochMessages.h
GoniometerAxis.cpp
GoniometerAxis.h
DetectorTransformation.cpp
DetectorTransformation.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
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()