leonarski_fandFilip Leonarski
19b135186d
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* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`). * Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection. * Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS). * Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead. * Rugnux: On macOS, Bragg integration runs on the Apple GPU. * Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand. * Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`. * Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit. * Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed. * Rugnux: The beam-stop shadow is found correctly on tilted detectors. * Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement. * jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps. * jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection. * jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images. * Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges. --------- Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home> Reviewed-on: #85 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
66 lines
3.3 KiB
CMake
66 lines
3.3 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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# jfjoch_extract_hkl and jfjoch_recompress are developer utilities: still built, deliberately not
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# installed into any package. They used to ride inside the viewer tarball, which is part of what
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# made that artifact confusing.
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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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# 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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# 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_PORTABLE_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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# Not installed: replays a stored dataset as a DECTRIS detector's image stream, to run the broker
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# without a detector (demonstrations and tests).
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ADD_EXECUTABLE(jfjoch_stream2_replay jfjoch_stream2_replay.cpp)
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TARGET_LINK_LIBRARIES(jfjoch_stream2_replay JFJochReader JFJochZMQ CBORStream2FrameSerialize JFJochCommon)
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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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