Jungfraujoch/docs/documentation.rst

Documentation
=============

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   <p class="jfj-lead">The manuals and reference of Jungfraujoch and Rugnux, open-source software
   from the <a href="https://www.psi.ch">Paul Scherrer Institute</a> for X-ray diffraction data.
   The <a href="index.html">front page</a> has the overview and the downloads; this page is the
   map of the documentation.</p>

   <div class="jfj-cards">

   <div class="jfj-card">
   <p class="jfj-card__kicker">Data processing</p>
   <h2 class="jfj-card__title">Rugnux</h2>
   <p class="jfj-card__text">Processes a stored macromolecular diffraction dataset, a rotation
   sweep or serial stills, from the images to merged data: spot finding, indexing, integration,
   scaling and merging, with the space group, cell and resolution decided from the data and a
   report that says on what evidence. Given an atomic model it goes on to a refined structure and
   maps: the model is placed (rigid body or molecular replacement) and refined against the merge.
   One command, no parameters.</p>
   <pre class="jfj-card__run"><code>rugnux &lt;diffraction image file&gt;
   rugnux &lt;diffraction image file&gt; &lt;CIF/PDB model file&gt;</code></pre>
   <p class="jfj-platforms">Linux &middot; macOS &middot; Windows &middot; fast on an NVIDIA GPU,
   works without one</p>
   <p class="jfj-card__links"><a href="RUGNUX.html">Get started</a>
   <a href="RUGNUX_DOWNLOAD.html">Download</a>
   <a href="RUGNUX_OVERVIEW.html">What it does</a>
   <a href="RUGNUX_TUTORIAL.html">Manual</a></p>
   </div>

   <div class="jfj-card">
   <p class="jfj-card__kicker">Desktop application</p>
   <h2 class="jfj-card__title">Jungfraujoch Viewer</h2>
   <p class="jfj-card__text">Shows what is in a diffraction dataset: every image with its spots,
   predictions and resolution rings, per-image statistics over the sweep, grid-scan maps, and
   the same processing pipeline as Rugnux, run from a settings panel on the open file. Follows a
   live collection from a running Jungfraujoch broker.</p>
   <p class="jfj-platforms">Linux &middot; macOS &middot; Windows &middot; Qt 6</p>
   <p class="jfj-card__links"><a href="JFJOCH_VIEWER.html">Get started</a>
   <a href="VIEWER_DOWNLOAD.html">Download</a>
   <a href="JFJOCH_VIEWER.html#a-guided-tour">Guided tour</a></p>
   </div>

   <div class="jfj-card">
   <p class="jfj-card__kicker">Data acquisition</p>
   <h2 class="jfj-card__title">Jungfraujoch</h2>
   <p class="jfj-card__text">The data-acquisition and real-time analysis system for the PSI
   JUNGFRAU and EIGER detectors, and for DECTRIS detectors through their control unit: an FPGA
   and GPU pipeline that takes the detector's frames at full rate, analyses them on the fly,
   streams them to the NXmx HDF5 writer and serves a web interface and REST API to the
   beamline.</p>
   <p class="jfj-platforms">Linux servers &middot; AMD Alveo U55C FPGA &middot; NVIDIA GPUs</p>
   <p class="jfj-card__links"><a href="JUNGFRAUJOCH.html">Get started</a>
   <a href="DEPLOYMENT.html">Install</a>
   <a href="JFJOCH_BROKER.html">Broker</a>
   <a href="JFJOCH_WRITER.html">Writer</a></p>
   </div>

   </div>

**Licence.** Rugnux, the viewer and the Jungfraujoch services are free software under the
:doc:`GNU General Public License v3 <LICENSE>`; the FPGA design is released under the
:doc:`CERN Open Hardware Licence v2, strongly reciprocal <FPGA_LICENSE>`. Both let anyone, in
academia or industry, use, study and modify the software and the hardware design at no charge,
commercial use included; what they ask is that a modified version which is passed on is shared
under the same terms. The released binaries bundle third-party components under GPL-compatible
licences, and the CUDA builds the NVIDIA CUDA runtime under NVIDIA's own EULA: see the
:doc:`third-party notices <THIRD_PARTY_NOTICES>`.

All pages
---------

Everything a user of Rugnux or the viewer needs comes first; the :doc:`technical reference <TECHNICAL>`
holds the algorithms, the file formats and streams, the interfaces and the FPGA design. The names
are explained in :doc:`Naming <NAMING>`, the releases in the :doc:`changelog <CHANGELOG>`, and how to
cite the software in :doc:`Publications <PUBLICATIONS>`.

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.. toctree::
   :maxdepth: 1
   :caption: Rugnux

   Getting started <RUGNUX>
   Download <RUGNUX_DOWNLOAD>
   RUGNUX_OVERVIEW
   RUGNUX_INSTALL
   RUGNUX_FORMATS
   RUGNUX_TUTORIAL
   RUGNUX_CLI
   RUGNUX_REPORT
   RUGNUX_INTEGRATION
   RUGNUX_ADVANCED
   RUGNUX_MODEL_AND_REFERENCE
   Detector calibration <RUGNUX_CALIBRATION>

.. toctree::
   :maxdepth: 1
   :caption: Jungfraujoch Viewer

   Using the viewer <JFJOCH_VIEWER>
   Download <VIEWER_DOWNLOAD>

.. toctree::
   :maxdepth: 1
   :caption: Jungfraujoch

   Overview <JUNGFRAUJOCH>
   DEPLOYMENT
   REPOSITORIES
   RELEASE_CONTENTS
   JFJOCH_BROKER
   JFJOCH_WRITER
   WEB_FRONTEND
   MX software integration <SOFTWARE_INTEGRATION>
   TOOLS
   Python client <PYTHON_CLIENT>

.. toctree::
   :maxdepth: 1
   :caption: Reference

   TECHNICAL

.. toctree::
   :maxdepth: 1
   :caption: Project

   PUBLICATIONS
   ACKNOWLEDGEMENT
   LICENSE
   THIRD_PARTY_NOTICES
   NAMING
   CHANGELOG

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