pyxnat 0.4.1a.dev

Xnat in Python

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',
                          datastore=os.path.join( os.path.expanduser('~'),
                                                  'XnatStore'
                                                )
                         )

Browse the resources

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

Create new resources

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

Metadata support

>>> proj = interface.project('my_project')
>>> proj.attrib.keys()
['note','alias','secondary_ID','name','pi_lastname',
 'label','keywords','pi_firstname','ID','description']
>>> proj.attrib.set('note', 'a note')
>>> proj.attrib.get('note')
'a note'

Make complex searches

>>> search = interface.search( 'my_search',
                               [ ('xnat:subjectData/SUBJECT_ID','LIKE','%'),
                                 ('xnat:subjectData/PROJECT', '=', 'my_project'),
                                 'AND'
                               ]
                             )
>>> search.get_subjects()