leonarski_fandClaude Opus 4.8
c69b5297d5
- Add docs/JFJOCH_PROCESS.md describing the offline analysis tool, its options, output files, and the broker/viewer/process distinction; mention jfjoch_scale for re-scaling/merging. - Rewrite docs/JFJOCH_VIEWER.md for consistency: functionality, HTTP env vars (JUNGFRAUJOCH_HTTP_HOST/PORT), command line, and the real D-Bus API. - Refresh docs/TOOLS.md to the current set of tools; add both pages to index.rst. - jfjoch_process: fix stale self-name (jfjoch_analysis -> jfjoch_process) in usage/license/logger. - jfjoch_scale: unify --scaling-high-resolution with jfjoch_process (drop -D short flag, make it long-only) and remove dead p/q/i short options. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
76 lines
2.9 KiB
Markdown
76 lines
2.9 KiB
Markdown
# Tools
|
|
|
|
Besides the main services ([`jfjoch_broker`](JFJOCH_BROKER.md),
|
|
[`jfjoch_writer`](JFJOCH_WRITER.md), [`jfjoch_viewer`](JFJOCH_VIEWER.md)), the repository ships a
|
|
number of command-line tools. Each prints its own usage when run with `-h` or without arguments.
|
|
|
|
## Data analysis
|
|
|
|
### jfjoch_process
|
|
Offline CLI tool that runs the full crystallographic analysis pipeline (spot finding, indexing,
|
|
integration, scaling/merging) on a stored HDF5 dataset, producing a `_process.h5` file and, when
|
|
merging, reflection files. See [jfjoch_process](JFJOCH_PROCESS.md).
|
|
|
|
### jfjoch_scale
|
|
Re-scales and merges the already-integrated reflections from one or more `_process.h5` files
|
|
(no re-integration). Useful to re-merge with a different space group, partiality, resolution limit
|
|
or reference MTZ, or to combine several runs. See [jfjoch_process](JFJOCH_PROCESS.md).
|
|
|
|
### jfjoch_extract_hkl
|
|
Extracts reflections (HKL list) from a Jungfraujoch master file; can sum the same HKL across
|
|
neighbouring images and compare against an XDS `INTEGRATE.HKL` reference.
|
|
|
|
## FPGA / PCIe card management
|
|
|
|
### jfjoch_pcie_status
|
|
Prints detailed status information about the card. Safe to run during data collection:
|
|
```
|
|
./jfjoch_pcie_status /dev/jfjoch0
|
|
```
|
|
|
|
### jfjoch_pcie_net_cfg
|
|
Reads and modifies the network configuration of the card's interfaces:
|
|
```
|
|
jfjoch_pcie_net_cfg <device name>
|
|
Read configuration for all network interfaces of a device
|
|
jfjoch_pcie_net_cfg <device name> <if number>|fgen
|
|
Read configuration for a particular network interface / internal frame generator
|
|
jfjoch_pcie_net_cfg <device name> <if number>|fgen ipv4 <IPv4 address>
|
|
Set IPv4 address for a particular network interface / internal frame generator
|
|
jfjoch_pcie_net_cfg <device name> <if number>|fgen direct 0|1
|
|
Set direct mode for a particular network interface / internal frame generator
|
|
jfjoch_pcie_net_cfg <device name> <if number>|fgen clear
|
|
Clear Ethernet counters for a particular network interface / internal frame generator
|
|
```
|
|
|
|
### jfjoch_pcie_clear_net_counters
|
|
Resets the card's Ethernet, UDP and ICMP packet counters (which otherwise run from power-on):
|
|
```
|
|
./jfjoch_pcie_clear_net_counters /dev/jfjoch0
|
|
```
|
|
|
|
### jfjoch_pcie_read_register
|
|
Reads raw Jungfraujoch FPGA registers.
|
|
|
|
## Testing, benchmarking and simulation
|
|
|
|
### jfjoch_udp_simulator
|
|
UDP packet simulator used to test the Jungfraujoch FPGA receiver.
|
|
|
|
### jfjoch_fpga_test
|
|
Exercises and benchmarks the FPGA data path and receiver. With `-H` it runs the high-level
|
|
synthesis C model on the CPU, so no FPGA device is required.
|
|
|
|
### jfjoch_lite_perf_test
|
|
Performance test of the lite (CPU/GPU) analysis path — indexing, integration and optional file
|
|
writing.
|
|
|
|
### jfjoch_hdf5_test
|
|
Tests single-threaded HDF5 writer performance.
|
|
|
|
### jfjoch_azint_test
|
|
Tests the azimuthal integration code on synthetic data.
|
|
|
|
### jfjoch_simplon_test
|
|
Minimal test client for a DECTRIS SIMPLON detector API.
|