Quick start

This is a short tutorial going through the main features of this API. Depending on the policy of the XNAT server you are using, and your user level, you can have read and write access to a specific set of resources. During this tutorial, we will use a fake standard user account on the XNAT Central repository, where you will have limited access to a number of projects and full access to the projects you own.

Note

XNAT Central is a public XNAT repository managed by the XNAT team and updated regularly with the latest improvements of the development branch.


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

Connect to the server

Connecting to a XNAT server requires valid credentials so you might want to start by requesting those on the Web interface of your server.

>>> from pyxnat import Interface
>>> interface = Interface(server='http://central.xnat.org:8080',
                          user='my_login',
                          password='my_pass',
                          datastore=os.path.join( os.path.expanduser('~'),
                                                  'XnatStore'
                                                )
                         )

The datastore argument specifies where the local disk-cache will be stored. Every query and every downloaded file will be stored here so choose a location with sufficient free space. If the datastore argument if not given, a temporary location is picked automatically but it may be flushed at every reboot of the machine. Here the datastore argument is set to a XnatSore directory in the user’s home directory in a cross platform manner.

Warning

Depending on the server configuration, you may have to include the port in the server url, as well as the name of the XNAT tomcat application. So you might end up with something like: http://server_ip:port/xnat

Browse the resources

Now that we have an Interface object, we can start browsing the server:

>>> interface.projects()
[..., u'CENTRAL_OASIS_CS', u'CENTRAL_OASIS_LONG', ...]
>>> # with an optional filter argument
>>> interface.projects('*OASIS_CS*')
[u'CENTRAL_OASIS_CS']
>>> oasis_cs = interface.project('OASIS_CS')
>>> oasis_cs.exists()
True
>>> oasis_cs.subjects()
[..., u'OAS1_0307', u'OAS1_0308', u'OAS1_0309', u'OAS1_0310', ...]
>>> oasis_cs.subject('OAS1_0307').experiments()
[u'OAS1_0307_CLIN_1', u'OAS1_0307_MR1']

Resources operations

Several operations are accessible for every resource level. The most importants are responsible for creating new resources, deleting existing one and testing whether a given resource exists or not:

>>> my_project = interface.project('my_project')
>>> my_project.exists()
False
>>> my_project.create()
>>> my_project.exists()
True
>>> subject_1 = my_project.subject('first_subject')
>>> subject_1.create()
>>> subject_1.delete()
>>> subject_1.exists()
False

For some levels, it is possible to give a xnat_type argument to the create method, so that the resource is created accordingly:

>>> subject1.create()
>>> subject1.experiment('pet_session').create('xnat:petSessionData')

Other common operations are available such as:

>>> experiment = oasis_cs.subject('OAS1_0307').experiment('OAS1_0307_MR1')
>>> experiment.xsi_type()
'xnat:mrSessionData'
>>> experiment.level()
'experiment'
>>> experiment.id()
'OAS1_0307_MR1'
>>> experiment.label()
'OAS1_0307_MR1'

See the ResourceObject class reference documentation for further details.

File support

It is possible to upload and then download files at every resource level. When grouping files makes sense, it is possible to use a level called resources:

>>> my_project.files()
[]
>>> my_project.file('image.nii').put('/tmp/image.nii')
>>> # you can add any of the following arguments to give additional information
      on the file you are uploading
>>> my_project.file('image.nii').put( '/tmp/image.nii',
                                      content='T1',
                                      format='NIFTI'
                                      tags='image test'
                                    )
>>> my_project.file('image.nii').size()
98098
>>> my_project.file('image.nii').content()
'T1'
>>> my_project.file('image.nii').format()
'NIFTI'
>>> my_project.file('image.nii').tags()
'image test'
>>> my_project.file('image.nii').get()
<open file '<fdopen>', mode 'r' at 0x9602750>
>>> my_project.file('image.nii').get_copy()
'~/XnatStore/REST/projects/my_project/resources/123150742/files/image.nii'
>>> my_project.file('image.nii').get_copy('/tmp')
'/tmp/image.nii'
>>> # grouping files
>>> my_project.resource('ANALYZE').file('image.hdr').put('/tmp/image.hdr')
>>> my_project.resource('ANALYZE').file('image.img').put('/tmp/image.img')
>>> my_project.resources()
['123150742', 'ANALYZE']
>>> my_project.resource('ANALYZE').files()
['image.hdr', 'image.img']
>>> my_project.resource('ANALYZE').file('image.hdr').get()
'~/XnatStore/REST/projects/my_project/resources/ANALYZE/files/image.hdr'
>>> my_project.resource('ANALYZE').file('image.img').get()
'~/XnatStore/REST/projects/my_project/resources/ANALYZE/files/image.img'

Note

For the image.nii, the resources level is implicit and an ID for that level is generated automatically.

Metadata support

Each resource level also has a set of metadata fields that can be informed. This set of fields depends on the resource level and on its type in the XNAT schema:

>>> my_project.attrib.keys()
['note','alias','secondary_ID','name','pi_lastname',
 'label','keywords','pi_firstname','ID','description']
>>> my_project.attrib.set('note', 'a note')
>>> my_project.attrib.get('note')
'a note'
>>> my_project.attrib.update({'pi_lastname':'doe', 'pi_firstname':'john'})
>>> my_project.attrib['description'] = 'a description here'
>>> my_project.attrib.set('description', 'a description here')

Warning

Write access is currently broken.

See the Attrib class reference documentation for further details.

Note

The list of fields is actually generated from a config file so one can set a convenient shortcut on the XNAT schema.

e.g. Choose your shortcut by editing the configuration file:
  • description = xnat:projectData/description
  • desc = xnat:projectData/description

The configuration file is called xnat_shortcuts.cfg and is located in $HOME/.pyxnat under Unix and in $HOME/pyxnat under Windows.

Warning

The list of fields is not generated knowing the type of the resource in the XNAT schema.

It means that an experiment will have both:
  • tracer_isotope = xnat:petSessionData/tracer/isotope/half-life
  • coil = xnat:mrSessionData/coil

But if the experiment it a mrSessionData, it will not be able to set tracer_isotope and tracer_isotope value will always be None.


[2]http://nrg.wikispaces.com/XNAT+REST+XML+Path+Shortcuts

Make complex searches

The XNAT search engine can be queried via the REST model. The following query finds all the subjects that are within my_project or that have an age superior to 14:

>>> search = interface.search( 'my_search',
                               [ ('xnat:subjectData/SUBJECT_ID','LIKE','%'),
                                 ('xnat:subjectData/PROJECT', '=', 'my_project'),
                                 'OR',
                                 [ ('xnat:subjectData/AGE','>','14'),
                                   'AND'
                                 ]
                               ]
                             )
>>> search.get_subjects()

See the Search and SeachManager classes reference documentation for further details.

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