leonarski_fandjungfrau
4dc2534dbf
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**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>
49 lines
1.7 KiB
CMake
49 lines
1.7 KiB
CMake
ADD_LIBRARY(JFJochIndexing STATIC
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Indexer.h
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Indexer.cpp
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IndexerFactory.h
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IndexerFactory.cpp
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IndexerThreadPool.cpp
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IndexerThreadPool.h
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AnalyzeIndexing.cpp
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AnalyzeIndexing.h
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FitProfileRadius.cpp
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FitProfileRadius.h
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PostIndexingRefinement.h
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FFTResult.h
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FFTIndexer.cpp
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FFTIndexer.h
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PostIndexingRefinement.cpp
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MultiLatticeSearch.cpp
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MultiLatticeSearch.h)
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TARGET_LINK_LIBRARIES(JFJochIndexing JFJochCommon JFJochLatticeSearch)
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IF (JFJOCH_CUDA_AVAILABLE)
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# GIT_SUBMODULES "" -> do not fetch ffbidx's bundled eigen submodule; it would add_subdirectory
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# a second Eigen3::Eigen target. ffbidx instead resolves Eigen via the project-level Eigen3
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# (the find_package(Eigen3) at the top of image_analysis/CMakeLists.txt).
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FetchContent_Declare(
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fast-indexer
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GIT_REPOSITORY https://github.com/paulscherrerinstitute/fast-feedback-indexer/
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GIT_TAG a94fd4f5c55289e70860feea358182d2072e02b5
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GIT_SUBMODULES ""
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)
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FetchContent_MakeAvailable(fast-indexer)
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TARGET_SOURCES(JFJochIndexing PRIVATE
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CUDAMemHelpers.h
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FFTIndexerGPU.cu FFTIndexerGPU.h
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FFBIDXIndexer.cpp FFBIDXIndexer.h)
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TARGET_LINK_LIBRARIES(JFJochIndexing fast_indexer_static
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CUDA::cufft
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)
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ELSE()
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MESSAGE(WARNING "CUDA is strongly recommended for image analysis." )
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TARGET_LINK_LIBRARIES(JFJochIndexing Eigen3::Eigen)
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ENDIF()
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# FFTW (fftw3f) is always available via FetchContent -> the CPU FFT indexer is always built.
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TARGET_SOURCES(JFJochIndexing PRIVATE FFTIndexerCPU.cpp FFTIndexerCPU.h)
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TARGET_LINK_LIBRARIES(JFJochIndexing fftw3f)
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