leonarski_fandClaude Opus 5.5
ebce906025
Combines the stills reader and module work (stills-readers, stills-modgeom, stills-euxfel) onto rc178 with the owner's decisions for this release: - Inputs are files, never a directory; several files of one format are one dataset (the multi-input CLI of the previous commit), so every reader takes an explicit list: JFJochXFELReader::ReadFiles, ReadCXI, ReadPanelTable and JFJochXTCReader::ReadFiles take std::vector<std::string>; ListFiles and xtc::CollectStreams are gone, CanRead* accept a regular file only. - One HDF5 frame reader (JFJochCrystFELReader -> JFJochXFELReader) parameterised by what the file holds: per-shot groups or a 3D stack, a /metadata panel table (posx/posy/angle, pixel size, nominal camera length, pixel mask: as SACLA writes), a Cheetah CXI single panel (square frame; a tiled slab is refused with a message). At most 8 files open; every file checked against the first. Signed 32-bit decode, per-frame 3D masks, panels at their own coffset (from the EuXFEL work). - Frames stored one chunk each are read the way the NXmx reader reads its images: only the chunk's place is asked of HDF5 under its lock (H5Dget_chunk_info_by_coord), the bytes are read through HDF5ImageSource::RawFile (positional, no lock) and decoded outside it - deflate(+shuffle) by zlib, bitshuffle/LZ4 (and zstd, plain LZ4) by CompressedImage's decoders. Bitshuffle/LZ4 used to go through HDF5's filter under the global lock, one frame at a time. - LCLS-I XTC (Rayonix): wavelength from the beam record, pixel size from the Rayonix model and binning, only --detector-distance needed; damaged/compressed frames skipped, a truncated last event dropped; std::ifstream, no POSIX calls: builds with MSVC. No DIALS .expt support at all. - CrystFEL .geom: module geometry only (panel ranges, fs/ss, corners, pixel size, coffset, data path) and optionally the camera length; everything else is ignored with a note in the log. - --mask-good / --mask-bad <file>:<dataset>: a mask array in another HDF5 file, in the frames' stored layout (what a .geom's mask_file used to give). - Gain measured on the background for panel-table and CXI input that states none (--gain overrides). - Detector modules from explicit geometry only (DetectorModules: the reader's panels, an NXmx file with one NXdetector_module per module, or --module-geometry); never from the image. Spots and predictions are mapped through the modules, the image is not re-assembled. - Module refinement in the stills bundle adjustment (Ceres; per-module shift and in-plane turn, gauge on mean shift/turn/scale and on the two tilt-like patterns when the tilt is refined; adopted only where it predicts held-out frames better). Applied for a foreign multi-panel detector (panel table, .geom panels); for a JUNGFRAU measured and reported only. Written to <prefix>_modules.h5 (NXmx NXdetector_module groups), read back with --module-geometry. - A panel-table file's camera length is nominal: with a reference cell it is refined from the cell. - Broker and writer output unchanged: masters keep the single NXdetector_module group, the start message carries no module list. Tests: [CrystFELGeometry], JFJochXFELReader_*, JFJochXTCReader, [JFJochMultiReader], [CellPopulation], SaturationCeiling_*, [DetectorModules], RefineGlobalGeometry_ModulePlacement, [reindex], Sublattice. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
57 lines
1.8 KiB
CMake
57 lines
1.8 KiB
CMake
ADD_LIBRARY(JFJochReader STATIC
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JFJochReader.cpp JFJochReader.h
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JFJochHDF5Reader.cpp
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JFJochHDF5Reader.h
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JFJochMultiReader.cpp
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JFJochMultiReader.h
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SweepLayout.cpp
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SweepLayout.h
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MiniCBF.cpp
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MiniCBF.h
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JFJochCBFReader.cpp
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JFJochCBFReader.h
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MarCCD.cpp
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MarCCD.h
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JFJochMarCCDReader.cpp
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JFJochMarCCDReader.h
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CrystFELGeometry.cpp
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CrystFELGeometry.h
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JFJochXFELReader.cpp
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JFJochXFELReader.h
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DetectorLayout.h
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SMV.cpp
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SMV.h
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JFJochSMVReader.cpp
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JFJochSMVReader.h
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XTC.cpp
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XTC.h
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JFJochXTCReader.cpp
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JFJochXTCReader.h
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NXmxModules.cpp
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NXmxModules.h
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HDF5ImageLocator.cpp
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JFJochStartMessageReader.cpp
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JFJochStartMessageReader.h
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JFJochImageBufferReader.cpp
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JFJochImageBufferReader.h
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HDF5ImageLocator.h
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HDF5ImageSource.cpp
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HDF5ImageSource.h
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HDF5MetadataSource.cpp
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HDF5MetadataSource.h
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JFJochReaderImage.cpp
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JFJochReaderImage.h
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JFJochReaderDataset.cpp
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JFJochReaderDataset.h
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JFJochReaderSpots.h
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)
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# NB: JFJochHttpReader (the viewer's live-broker HTTP client) lives in viewer/ and links Mbed TLS;
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# it is deliberately NOT part of this always-built library, so the broker/writer never pull in a
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# TLS stack.
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# tiff: the marCCD reader's files are ordinary uncompressed TIFFs, so libtiff - which the build
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# already fetches for JFJochPreview in every mode - reads the pixels and there is no new dependency.
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TARGET_LINK_LIBRARIES(JFJochReader JFJochImageAnalysis JFJochAPI JFJochCommon JFJochZMQ JFJochLogger
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JFJochHDF5Wrappers CBORStream2FrameSerialize tiff ZLIB::ZLIB
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${CMAKE_DL_LIBS})
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