Welcome to DAX's documentation!
===============================

DAX is Distributed Automation for `XNAT <http://xnat.org/>`_

DAX allows you to:

- store analyzed imaging data on XNAT (datatypes)
- extract information from XNAT via scripts (Xnat_tools)
- run pipelines on your data in XNAT via a cluster (processors)

Quick Install
-------------------------
Create a `python3 virtual environment <https://docs.python.org/3/library/venv.html>`_ with dax and all dependencies.

::

  python3 -m venv daxvenv
  source daxvenv/bin/activate
  pip install dax


Configure an environment variable named XNAT_HOST set to the full url of your xnat server. This can 
be incuded in your .bashrc/.bash_profile file.
::

  export XNAT_HOST=https://central.xnat.org

Configure your credentials in a file named ".netrc" in your home directory.
::

  machine <SERVER>
  login <USER>
  password <PASSWORD>

Here SERVER is the server name only. For example, central.xnat.org, not https://xnat.website.com/xnat.


Versions and Installation
-------------------------

Our currently running versions of dax are:

- Dax 2 - 2.2.1 - As of July 8, 2021
  
  - Used for most purposes

- LDAX latest - 0.7.10 - As of October 7, 2020

  - Legacy Dax - Please use DAX 2
  
These can be verified with

::

  dax version
  # or 
  pip freeze | grep dax
  # or
  python3 -m pip freeze | grep dax

To install please reference our `Install Page <https://dax.readthedocs.io/en/latest/installing_dax_in_a_virtual_environment.html>`_

Contents:

.. toctree::
   :maxdepth: 3
   
   installing_dax_in_a_virtual_environment
   dax_xnat_dataypes_install
   dax
   dax_manager
   contributors
   how_to_contribute
   faq
   processors
   processors_v3
   assessors_in_vuiis_xnat
   dax_command_line_tools
   dax_executables
   manage_a_project
   BIDS_walkthrough