# 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.