pyxnat: Xnat in Python

User guide contents:

• Installing pyxnat
• Under the Hood
• Starters Tutorial
• Advanced Tutorial
• Reference documentation

Introduction

pyxnat is a simple python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data. It features:

1. resources browsing capabilities
2. read and write access to resources
3. complex searches
4. disk-caching of requested files and resources

[1]	http://www.xnat.org/

[2]	http://packages.python.org/pyxnat/

---

A short overview

Setup the connection

>>> from pyxnat import Interface
>>> interface = Interface(server='http://central.xnat.org:8080',
                          user='login',
                          password='pass',
                          cachedir=os.path.join(os.path.expanduser('~'),
                                                '.store')
                          )

Browse the resources

>>> interface.select.projects().get()
[u'CENTRAL_OASIS_CS', u'CENTRAL_OASIS_LONG', ...]

Create new resources

>>> interface.select.project('my_project').create()
>>> interface.select.project('my_project').resource('images').file('image.nii').put('/tmp/image.nii')

Make complex searches

>>> table = interface.select('xnat:subjectData', ['xnat:subjectData/PROJECT', 'xnat:subjectData/SUBJECT_ID']
                    ).where([('xnat:subjectData/SUBJECT_ID','LIKE','%'),
                             ('xnat:subjectData/PROJECT', '=', 'my_project'),
                             'AND'
                             ])

Module contents

Interface	Main entry point to access a XNAT server.
Inspector	Database introspection interface.
Select	Data selection interface. Callable object that indicates the data to be returned to the user.
SearchManager	Search interface. Handles operations to save and get back searches on the server.
Users	Database user management interface. It is used to retrieve information on users registered on a server.