leonarski_f
680c36c20d
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* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands. * `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion. * Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants. * `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing. * A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed. * `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing. * Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences. * The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to. * The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after. * The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution. * `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have. * Twinning is no longer reported when the L-test contradicts it. * The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's. * `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots. * The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area. Reviewed-on: #76 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
72 lines
3.0 KiB
Markdown
72 lines
3.0 KiB
Markdown
# Tools
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Besides the main services ([`jfjoch_broker`](JFJOCH_BROKER.md),
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[`jfjoch_writer`](JFJOCH_WRITER.md), [`jfjoch_viewer`](JFJOCH_VIEWER.md)), the repository ships a
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number of command-line tools. Each prints its own usage when run with `-h` or without arguments.
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## Data analysis
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### rugnux
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Offline CLI tool that runs the full crystallographic analysis pipeline (spot finding, indexing,
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integration, scaling/merging) on a stored HDF5 dataset, producing a `_process.h5` file and, when
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merging, reflection files. Merging is on by default (`--no-merge` disables it). `--mode` picks what a
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run does: `mx` (the above, the default), `azint` (only azimuthal integration, no spot
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finding/indexing), `scale` (re-scale/merge the already-integrated reflections in a `_process.h5`
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without re-integrating) or `calibration` (detector geometry from a calibrant's powder rings, written
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as `<prefix>.poni` and `<prefix>.json`). See [rugnux](RUGNUX.md).
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`rugnux` installs on its own, as the `rugnux` package or as a standalone archive — see
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[Installing rugnux](RUGNUX_INSTALL.md).
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### jfjoch_extract_hkl
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Extracts reflections (HKL list) from a Jungfraujoch master file; can sum the same HKL across
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neighbouring images and compare against an XDS `INTEGRATE.HKL` reference. A developer utility: it is
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built from source but, like `jfjoch_recompress`, is not installed into any package.
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## FPGA / PCIe card management
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### jfjoch_pcie_status
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Prints detailed status information about the card. Safe to run during data collection:
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```
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./jfjoch_pcie_status /dev/jfjoch0
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```
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### jfjoch_pcie_net_cfg
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Reads and modifies the network configuration of the card's interfaces:
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```
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jfjoch_pcie_net_cfg <device name>
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Read configuration for all network interfaces of a device
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jfjoch_pcie_net_cfg <device name> <if number>|fgen
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Read configuration for a particular network interface / internal frame generator
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jfjoch_pcie_net_cfg <device name> <if number>|fgen ipv4 <IPv4 address>
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Set IPv4 address for a particular network interface / internal frame generator
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jfjoch_pcie_net_cfg <device name> <if number>|fgen direct 0|1
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Set direct mode for a particular network interface / internal frame generator
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jfjoch_pcie_net_cfg <device name> <if number>|fgen clear
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Clear Ethernet counters for a particular network interface / internal frame generator
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```
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### jfjoch_pcie_clear_net_counters
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Resets the card's Ethernet, UDP and ICMP packet counters (which otherwise run from power-on):
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```
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./jfjoch_pcie_clear_net_counters /dev/jfjoch0
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```
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## Testing, benchmarking and simulation
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### jfjoch_udp_simulator
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UDP packet simulator used to test the Jungfraujoch FPGA receiver.
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### jfjoch_fpga_test
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Exercises and benchmarks the FPGA data path and receiver. With `-H` it runs the high-level
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synthesis C model on the CPU, so no FPGA device is required.
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### jfjoch_lite_perf_test
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Performance test of the lite (CPU/GPU) analysis path — indexing, integration and optional file
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writing.
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### jfjoch_hdf5_test
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Tests single-threaded HDF5 writer performance.
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### jfjoch_simplon_test
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Minimal test client for a DECTRIS SIMPLON detector API. |