leonarski_f
451310f43d
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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation. * jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window. * rugnux: Accept an absolute `-o` output prefix in offline processing. * Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed). * Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
60 lines
2.8 KiB
CMake
60 lines
2.8 KiB
CMake
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# Offline analysis CLI tools. These link only the portable libraries (reader,
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# image_analysis, writer, common), so they build in viewer-only / Windows packages too
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# and install into the "viewer" component.
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ADD_EXECUTABLE(jfjoch_extract_hkl jfjoch_extract_hkl.cpp
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XdsIntegrateParser.cpp
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XdsIntegrateParser.h)
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TARGET_LINK_LIBRARIES(jfjoch_extract_hkl JFJochReader)
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INSTALL(TARGETS jfjoch_extract_hkl RUNTIME COMPONENT viewer)
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# rugnux, the single offline analysis CLI, lives in rugnux/ next to its library.
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# In-place re-compress /entry/data/data of a _data file from bitshuffle/LZ4 to bitshuffle/zstd.
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ADD_EXECUTABLE(jfjoch_recompress jfjoch_recompress.cpp)
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TARGET_LINK_LIBRARIES(jfjoch_recompress JFJochHDF5Wrappers)
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INSTALL(TARGETS jfjoch_recompress RUNTIME COMPONENT viewer)
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# On Windows these CLIs get getopt/getopt_long from the vendored wingetopt shim (libc has none).
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IF (WIN32)
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TARGET_LINK_LIBRARIES(jfjoch_extract_hkl wingetopt)
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ENDIF()
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# Online / hardware tools (broker, FPGA, receiver, detector). They link the non-portable
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# libraries and are Linux-only, so they are skipped in a viewer-only build.
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IF(NOT JFJOCH_VIEWER_ONLY)
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ADD_EXECUTABLE(jfjoch_udp_simulator jfjoch_udp_simulator.cpp UDPSimulator.cpp UDPSimulator.h)
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TARGET_LINK_LIBRARIES(jfjoch_udp_simulator JFJochCommon)
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INSTALL(TARGETS jfjoch_udp_simulator RUNTIME COMPONENT jfjoch)
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ADD_EXECUTABLE(jfjoch_hdf5_test jfjoch_hdf5_test.cpp)
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TARGET_LINK_LIBRARIES(jfjoch_hdf5_test JFJochWriter JFJochReceiver JFJochCommon)
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INSTALL(TARGETS jfjoch_hdf5_test RUNTIME COMPONENT jfjoch)
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ADD_EXECUTABLE(jfjoch_pcie_status jfjoch_pcie_status.cpp)
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TARGET_LINK_LIBRARIES(jfjoch_pcie_status JFJochDevice JFJochCommon)
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INSTALL(TARGETS jfjoch_pcie_status RUNTIME COMPONENT jfjoch)
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ADD_EXECUTABLE(jfjoch_pcie_net_cfg jfjoch_pcie_net_cfg.cpp)
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TARGET_LINK_LIBRARIES(jfjoch_pcie_net_cfg JFJochDevice JFJochCommon)
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INSTALL(TARGETS jfjoch_pcie_net_cfg RUNTIME COMPONENT jfjoch)
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ADD_EXECUTABLE(jfjoch_pcie_clear_net_counters jfjoch_pcie_clear_net_counters.cpp)
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TARGET_LINK_LIBRARIES(jfjoch_pcie_clear_net_counters JFJochDevice JFJochCommon)
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INSTALL(TARGETS jfjoch_pcie_clear_net_counters RUNTIME COMPONENT jfjoch)
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ADD_EXECUTABLE(jfjoch_fpga_test jfjoch_fpga_test.cpp)
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TARGET_LINK_LIBRARIES(jfjoch_fpga_test JFJochReceiver)
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INSTALL(TARGETS jfjoch_fpga_test RUNTIME COMPONENT jfjoch)
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ADD_EXECUTABLE(jfjoch_simplon_test jfjoch_simplon_test.cpp)
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TARGET_LINK_LIBRARIES(jfjoch_simplon_test JFJochDetector JFJochPreview)
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INSTALL(TARGETS jfjoch_simplon_test RUNTIME COMPONENT jfjoch)
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ADD_EXECUTABLE(jfjoch_lite_perf_test jfjoch_lite_perf_test.cpp)
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TARGET_LINK_LIBRARIES(jfjoch_lite_perf_test JFJochReceiver JFJochWriter)
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INSTALL(TARGETS jfjoch_lite_perf_test RUNTIME COMPONENT jfjoch)
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ADD_SUBDIRECTORY(xbflash.qspi)
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ENDIF()
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