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leonarski_f c69b5297d5 docs: add jfjoch_process page, refresh viewer/tools docs, unify CLI naming

- 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>

2026-06-17 07:38:36 +02:00

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Tools

Besides the main services (jfjoch_broker, jfjoch_writer, jfjoch_viewer), 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_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_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.

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