leonarski_fandClaude Fable 5
01e4f81e44
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Fold jfjoch_azint and rugnux_scale into the single rugnux CLI, and flip scaling/merging from opt-in to on-by-default. - rugnux --azint-only replaces jfjoch_azint (reuses ProcessMode:: AzimuthalIntegration; adds the correction toggles and geometry overrides the old tool carried). - rugnux --scale replaces rugnux_scale (re-scale/merge stored reflections, same simpler scale/merge as before: no space-group search or rot3d defaults). Its workflow is folded into the CLI verbatim. - Merging is now on by default for rotation and stills; --no-merge disables it, replacing -M/--scale-merge. Also fix the batch ReadReflections reader so it works on rugnux's own NXmxIntegrated _process.h5: read per-image reflections/mosaicity/lattice from the master (global index) first, falling back to the source-data locator for legacy/VDS datasets. Without this, both --scale and the former rugnux_scale read zero reflections from an integrated snapshot. RugnuxCommandLine now emits `rugnux --azint-only` and `--no-merge`; docs and tests updated to match. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
67 lines
2.7 KiB
Markdown
67 lines
2.7 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). Two extra modes
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narrow the work: `--azint-only` runs only azimuthal integration (no spot finding/indexing), and
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`--scale` re-scales/merges the already-integrated reflections in a `_process.h5` without
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re-integrating. See [rugnux](RUGNUX.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.
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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. |