YAXIL API¶

Functions¶

yaxil.auth(alias=None, url=None, cfg='~/.xnat_auth')¶

Read connection details from an xnat_auth XML file

Example:

>>> import yaxil
>>> auth = yaxil.auth('xnatastic')
>>> auth.url, auth.username, auth.password
('https://www.xnatastic.org/', 'username', '********')

Parameters:	alias (str) – XNAT alias url (str) – XNAT URL cfg (str) – Configuration file
Returns:	Named tuple of (url, username, password)
Return type:	`yaxil.XnatAuth`

yaxil.session(*args, **kwds)¶

Create a session context to avoid explicitly passing authentication to every function.

Example:

import yaxil

auth = yaxil.XnatAuth(url='...', username='...', password='...')

with yaxil.session(auth) as sess:
    aid = sess.accession('AB1234C')
    experiment = sess.experiment('AB1234C')
    sess.download('AB1234C', [1,3,14], out_dir='./dicomz')

Parameters:	auth (`yaxil.XnatAuth`) – XNAT authentication
Returns:	YAXIL session object
Return type:	`yaxil.session.Session`

yaxil.subjects(auth, label=None, project=None)¶

Retrieve Subject tuples for subjects returned by this function.

Example:

>>> import yaxil
>>> auth = yaxil.XnatAuth(url='...', username='...', password='...')
>>> yaxil.subjects(auth, 'AB1234C')
Subject(uri=u'/data/experiments/XNAT_S0001', label=u'AB1234C', id=u'XNAT_S0001',
    project=u'MyProject')

Parameters:	auth (`yaxil.XnatAuth`) – XNAT authentication label (str) – XNAT Subject label project (str) – XNAT Subject Project
Returns:	Subject objects
Return type:	`yaxil.Subject`

yaxil.experiments(auth, label=None, project=None, subject=None)¶

Retrieve Experiment tuples for experiments returned by this function.

Example:

>>> import yaxil
>>> auth = yaxil.XnatAuth(url='...', username='...', password='...')
>>> yaxil.experiment(auth, 'AB1234C')
Experiment(uri=u'/data/experiments/XNAT_E0001', label=u'AB1234C', id=u'XNAT_E0001',
    project=u'MyProject', subject_id=u'XNAT_S0001', subject_label='ABC')

Parameters:	auth (`yaxil.XnatAuth`) – XNAT authentication label (str) – XNAT Experiment label project (str) – XNAT Experiment Project subject (`yaxil.Subject`) – YAXIL Subject
Returns:	Experiment object
Return type:	`yaxil.Experiment`

yaxil.accession(*args)¶

Get the Accession ID for any Experiment label.

Example:

>>> import yaxil
>>> auth = yaxil.XnatAuth(url='...', username='...', password='...')
>>> yaxil.accession(auth, 'AB1234C')
u'XNAT_E00001'

Parameters:	auth (`yaxil.XnatAuth`) – XNAT authentication label (str) – XNAT Experiment label project (str) – XNAT Experiment Project
Returns:	Accession ID
Return type:	str

yaxil.extendedboldqc(auth, label, scan_ids=None, project=None, aid=None)¶

Get ExtendedBOLDQC data as a sequence of dictionaries.

Example:

>>> import yaxil
>>> import json
>>> auth = yaxil.XnatAuth(url='...', username='...', password='...')
>>> for eqc in yaxil.extendedboldqc2(auth, 'AB1234C')
...     print(json.dumps(eqc, indent=2))

Parameters:	auth (`yaxil.XnatAuth`) – XNAT authentication object label (str) – XNAT MR Session label scan_ids (list) – Scan numbers to return project (str) – XNAT MR Session project aid (str) – XNAT Accession ID
Returns:	Generator of scan data dictionaries
Return type:	`dict`

yaxil.scans(auth, label=None, scan_ids=None, project=None, experiment=None)¶

Get scan information for a MR Session as a sequence of dictionaries.

Example:

>>> import yaxil
>>> import json
>>> auth = yaxil.XnatAuth(url='...', username='...', password='...')
>>> for scan in yaxil.scans2(auth, 'AB1234C'):
...     print(json.dumps(scan, indent=2))

Parameters:	auth (`yaxil.XnatAuth`) – XNAT authentication object label (str) – XNAT MR Session label scan_ids (list) – Scan numbers to return project (str) – XNAT MR Session project experiment (`yaxil.Experiment`) – YAXIL Experiment
Returns:	Generator of scan data dictionaries
Return type:	dict

yaxil.scansearch(auth, label, filt, project=None, aid=None)¶

Search for scans by supplying a set of SQL-based conditionals.

Example:

>>> import yaxil
>>> auth = yaxil.XnatAuth(url='...', username='...', password='...')
>>> query = {
...   'eor1': "note LIKE %EOR1%",
...   'eor2': "note LIKE %EOR2%",
...   'mpr':  "series_description='T1_MEMPRAGE RMS' OR note LIKE %ANAT%"
... }
>>> yaxil.scansearch(auth, 'AB1234C', query)
{"mpr": [4], "eor1": [13], "eor2": [14]}

Parameters:	auth (`yaxil.XnatAuth`) – XNAT authentication object label (str) – XNAT MR Session label filt (dict) – Scan search filter/query project (str) – XNAT MR Session project aid (str) – XNAT Accession ID
Returns:	Same dictionary that was passed in, but values are now matching scans
Return type:	dict

yaxil.download(auth, label, scan_ids=None, project=None, aid=None, out_dir='.', in_mem=True, progress=False, attempts=1, out_format='flat')¶

Download scan data from XNAT.

Example:

>>> import yaxil
>>> auth = yaxil.XnatAuth(url='...', username='...', password='...')
>>> yaxil.download(auth, 'AB1234C', ['1', '2'], out_dir='./data')

Parameters:

auth (yaxil.XnatAuth) – XNAT authentication object
label (str) – XNAT MR Session label
scan_ids (list) – Scan numbers to return; use None for all
project (str) – XNAT MR Session project
aid (str) – XNAT Accession ID
out_dir (str) – Output directory
out_format – Extract all files or leave native structure
in_mem (bool) – Keep download content in memory; faster but uses more memory
progress (int) – Show download progress every N bytes
attempts (int) – Number of download attempts

yaxil.has(auth, xsitype, project=None)¶

Test if a project contains any items of a particular xsi:type.

Example:

>>> import yaxil
>>> auth = yaxil.XnatAuth(url='...', username='...', password='...')
>>> yaxil.has(auth, 'neuroinfo:extendedboldqc', project='MyProject')

Parameters:	auth (`yaxil.XnatAuth`) – XNAT authentication xsitype – XNAT xsi:type xsitype – str project (str) – XNAT Project
Returns:	True or False
Return type:	bool

Classes¶

class yaxil.XnatAuth(url, username, password)¶: Container to hold XNAT authentication information. Fields include the url, username, and password.

class yaxil.Experiment(uri, label, id, project, subject_id, subject_label, archived_date)¶: Container to hold XNAT Experiment information. Fields include the Experiment URI (uri), Accession ID (id), Project (project), Label (label), Subject Accession ID (subject_id), Subject label (subject_label), and archived date (archived_date).

class yaxil.Subject(uri, label, id, project)¶: Container to hold XNAT Subject information. Fields include the Subject URI (uri), Accession ID (id), Project (project), and Label (label).

YAXIL API¶

Functions¶

Classes¶

yaxil

Navigation

Related Topics