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leonarski_fandClaude Opus 4.8 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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jfjoch_viewer

jfjoch_viewer is the interactive desktop application of Jungfraujoch. It opens diffraction datasets, displays each image together with the analysis overlay (spots, predictions, azimuthal integration, per-image statistics), and can follow a live data collection by syncing with a running jfjoch_broker over its HTTP interface.

It is a standalone Qt 6 application, distributed pre-built on the Gitea release page and in the Jungfraujoch RPM/APT repositories (see Deployment).

Where it fits among the three analysis tools

Tool	Mode	Driven by	Output
`jfjoch_broker`	Online, real-time streaming analysis on FPGA + GPU	HTTP/REST + ZeroMQ	Live results and statistics, images streamed to `jfjoch_writer`
`jfjoch_viewer`	Interactive, on-screen exploration	Qt desktop application	Displayed on screen (results not saved to disk)
`jfjoch_process`	Offline batch processing of a stored dataset	Command-line interface	`_process.h5`, and `.mtz`/`.cif`/`.hkl` when merging

Functionality

Opens HDF5 files written by jfjoch_writer (*_master.h5) and the *_process.h5 files produced by jfjoch_process. It also opens NXmx files written by DECTRIS detectors, though that path has had only limited testing.
Runs an embedded data-processing pipeline — the same analysis code as the rest of Jungfraujoch — performing spot finding, indexing and integration on the displayed images. Results are shown on screen but are not saved to disk.
Auxiliary windows and panels: image list, image metadata, spot list, reflection list, per-region-of-interest statistics, the azimuthal-integration profile, and dataset-info charts.
User-mask editing: build a user mask interactively, clear it, save it as TIFF, or upload it to a connected server.

Hardware

As with the rest of Jungfraujoch, serious performance requires an NVIDIA GPU. On systems with a GPU, use the CUDA build (provided as separate RPM/APT repositories) for the embedded indexing and integration; the non-CUDA build runs the same pipeline on the CPU at much lower throughput.

Opening data

File ▸ Open (Ctrl+O) — open a local HDF5 file.
File ▸ Open HTTP (Ctrl+H) — connect to a jfjoch_broker HTTP endpoint to follow a live collection. The dialog defaults to host localhost and port 8080; these defaults can be overridden with the environment variables JUNGFRAUJOCH_HTTP_HOST and JUNGFRAUJOCH_HTTP_PORT.
Command line — jfjoch_viewer <file.h5> opens a file (or an http://host:port URL) on start-up. --dbus <true|false> (-d) enables or disables the D-Bus interface (default: enabled); --help and --version behave as usual.

D-Bus interface

When enabled, the viewer registers the D-Bus interface ch.psi.jfjoch_viewer, so other processes can drive it:

LoadFile(filename, image_number=0, summation=1) — open a file (or an http://host:port URL) and display the given image.
LoadImage(image_number, summation=1) — navigate to an image in the already-open dataset.

summation sums that many consecutive images before display.

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