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   sphinx-quickstart on Fri Oct  5 10:31:38 2018.
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YAXIL: yet another XNAT interface library
=========================================

-----------------------------------------

Yaxil is an XNAT interface library that started a long time ago in a galaxy far, 
far away. It works with Python 2 and 3 and XNAT 1.4 through 1.7. This 
documentation covers all of the functions and classes in YAXIL and examples 
to help you get going.

Here is a very basic example of YAXIL in action

.. code-block:: python

  import os
  import yaxil

  auth = yaxil.XnatAuth(url='https://xnatastic.org', username='you', password='*****')

  with yaxil.session(auth) as sess:
    # get all subjects for given project
    for subject in sess.subjects(project='PROJECT'):
      # get all MRIs for the given subject
      for experiment in sess.experiments(subject=subject):
        # get all scans for the given experiment
        for scan in sess.scans(experiment=experiment):
          # download scans with note 'REST1', 'REST2', or 'ANAT1'
          if scan['note'] in ('REST1', 'REST2', 'ANAT1'):
            sid = scan['id']
            outdir = os.path.join(subject.label, experiment.label, sid)
            sess.download(experiment.label, [sid], out_dir=outdir)

Huzzah! There are many more functions for accessing your scan metadata, 
experiment metadata, subject metadata, and more. Head over to the API 
documentation for more examples.

The API Documentation / Guide
-----------------------------

If you are looking for information on a specific function, read this

.. toctree::
   :maxdepth: 2

   api

ArcGet.py Guide
---------------

If you're looking for information about ``ArcGet.py`` look no further

.. toctree::
   :maxdepth: 2

   arcget

xnat_auth
---------------

Command line tool that helps to set up ~/.xnat_auth file used by ``ArcGet.py``

.. toctree::
   :maxdepth: 2

   xnat_auth