Documentation updates

docs/JFJOCH_VIEWER.md

@@ -0,0 +1,19 @@
+# jfjoch_viewer
+
+Jungfraujoch diffraction viewer is distributed as a standalone application.
+It uses Qt library version 6, and allows to open HDF5 files generated by [`jfjoch_writer`](JFJOCH_WRITER.md). 
+It as well allows to open NXmx files written by DECTRIS detectors, though testing is very limited.
+It can be downloaded pre-built from Gitea release page, or from Jungfraujoch RPM/APT repositories.
+See [Deployment](DEPLOYMENT.md) section for more information.
+This viewer can be also sync online with [`jfjoch_broker`](JFJOCH_BROKER.md) HTTP interface
+to visualize data during data collection.
+
+# Data processing pipeline
+Viewer contains embedded data processing pipeline, which is the same as the one used
+in Jungfraujoch installation. On systems equipped with GPU, it is preferable to use version
+compiled with CUDA support (proper RPM/APT repositories).
+
+At the moment data processing results are not saved to disk.
+
+# DBus interface
+Viewer can be controlled externally with DBus interface, allowing to open file, open detector via HTTP or load image.

docs/JFJOCH_WRITER.md

@@ -130,19 +130,25 @@ There are custom extension to NXmx format. These will be documented in the futur
 Specifically, if data collection was configured with `header_appendix` having key equal to `hdf5` and value as JSON 
 object with number and string values. These will be added to `/entry/user`.
 
-There are two versions of master file possible.
+There are three versions of master file possible.
 
+#### Legacy version (NXmxLegacy)
 By default, *legacy version* is used. This version is compatible with DECTRIS file writer version 1.0 format. 
 This ensures the file compatibility of Neggia and Durin XDS plugins, as well as DECTRIS Albula viewer version 4.0.
 Distinct feature is that if images are split into data files, there will be multiple links in `/entry/data`, 
 each corresponding to a data file.
 Yet, certain new HDF5 features, like virtual datasets, are not possible in this format since it has to be compatible with HDF5 1.8 features.
 
+#### VDS format (NXmxVDS)
 Therefore, we have enabled format *VDS version*. This will link to all data files via a single virtual dataset `/entry/data/data`.
 The same way spot finding, azimuthal integration and others, will be linked between master and data files.
 This format allows to display processing results in currently developed Jungfraujoch Viewer.
 For the time being it only works with Durin XDS plugin, and require DECTRIS Albula viewer version 4.1+.
 
+#### Integrated format (NXmxIntegrated)
+This is format, where no data files are created, but both images and metadata are stored in the same master file.
+This is generally equivalent to VDS format described above.
+
 ### Data file
 
 Data file has the following structure:

docs/SOFTWARE_INTEGRATION.md

@@ -0,0 +1,24 @@
+# Integration with MX data processing software
+
+## XDS
+Jungfraujoch files are compatible with XDS, but there is a need of a dedicated plugin.
+First we recommend to use Jungfraujoch own XDS plugin. It is available for Linux only and can
+be downloaded from Gitea release directory (compiled on RHEL 8), it is also distributed in [`jfjoch_viewer`](JFJOCH_VIEWER.md) RPM/APT packages. 
+To use the plugin, download the file `libjfjoch_xds_plugin.so.1.0.0` (three numbers at the end represent version of the plugin, and can differ later in time), 
+save it to common directory (e.g., `/opt/xds`) and add the following line in the XDS.INP file:
+```
+LIB="/opt/xds/libjfjoch_xds_plugin.so.1.0.0"
+```
+We are also testing XDS with Durin and Neggia plugins, though they don't have full functionality:
+
+* Neggia plugin doesn't support HDF5 virtual data sets. It can be downloaded from [github.com/dectris/neggia](https://github.com/dectris/neggia/).
+* Durin has known bugs with handling non-DECTRIS files (so with virtual data sets or single format HDF5 file format). 
+We recommend Durin plugin prepared by the Global Phasing consortium: [github.com/CV-GPhL/durin](https://github.com/CV-GPhL/durin), rather than original from the Diamond Light Source.
+
+## DIALS
+Jungfraujoch files are tested regularly with DIALS (currently v. 3.27.0).
+There is one known limitation: files generated with NXmxLegacy format (mimicking DECTRIS filewriter1 format) 
+are not handled properly with DIALS. We recommend VDS based format (NXmxVDS). 
+
+## CrystFEL
+Jungfraujoch files are compatible with CrystFEL.

docs/index.rst

@@ -30,6 +30,7 @@ Jungfraujoch is distributed under the GPLv3 license.
 
    JFJOCH_BROKER
    JFJOCH_WRITER
+   SOFTWARE_INTEGRATION
    TOOLS
 
 .. toctree::