Tutorial¶
This tutorial is intented as an introduction to working with XNAT and pyxnat. Reading the XNAT documentation, especially on the pages on the REST Web Services, can be a huge help to have a deeper understanding of XNAT mechanisms and consequently pyxnat design decisions.
Prerequisites¶
Before we start, make sure that you have the pyxnat distribution installed. In the Python shell, the following should run without raising an exception:
>>> import pyxnat
This tutorial also assumes that a you have access to an XNAT instance. If you don’t have an XNAT server running you can use XNAT Central, which is a public instance managed by the XNAT team and updated on a regular basis.
Making a Connection¶
The first step when working with pyxnat is to connect to an XNAT
instance with Interface
. For this, you will need valid
credentials that have to be requested through the web interface of the
targeted server.
>>> from pyxnat import Interface
>>> central = Interface(server="https://central.xnat.org",
... user='my_login',
... password='my_pass',
... cachedir='/tmp')
A local disk-based cache is maintained to avoid unnecessary data transfer. The optional cachedir argument enables a custom location for the cache, a default one being chosen otherwise. The default location uses the temporary directory of the machine (which may vary between OS and configurations), and is flushed at reboot.
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
Alternative Connections¶
If a least one of server, user and password arguments are missing, the user will be prompted for it(them). In this mode, a connection to the server will be attempted at the object creation and will raise an exception if something is wrong.
>>> central = Interface(server="https://central.xnat.org")
User:my_login
Password:
There are two types of configuration files that pyxnat uses. The first one is used with the config parameter.
>>> central = Interface(config='central.cfg')
The best way to create this kind of configuration file is to use the
save_config()
method on an existing interface.
>>> central.save_config('central.cfg')
The second one is the XNAT format config file, which is placed at a
default location (on linux in ~/.xnatPass). It is used without passing
any argument to the Interface
object. It is formatted
as follows and supports multiple accounts and servers, the active one
being the one selected by a +
sign:
+loginone@http://central.xnat.org=password
-logintwo@http://central.xnat.org=password
-logintwo@http://localhost=password
>>> central = Interface()
Note
If you don’t pass any parameter to Interface
and don’t have any configuration file at the default location, the
user will be prompted for server, user and password arguments.
Traversing the Database¶
Traversing the database requires basic knowledge of XNAT structure.
This information is available in the
structure()
method of the
inspect
sub-interface, which prints the
hierarchical organization of the data and helps constructing valid
paths
for accessing the data. The select
sub-interface allows for data selection and basic filtering through
Python objects or paths
, more akin to native REST calls.
Simple requests:
>>> central.select.projects().get()
[..., u'CENTRAL_OASIS_CS', u'CENTRAL_OASIS_LONG', ...]
>>> central.select('/projects').get()
[..., u'CENTRAL_OASIS_CS', u'CENTRAL_OASIS_LONG', ...]
Nested requests:
>>> central.select.projects().subjects().get()
>>> central.select('/projects/*/subjects').get()
>>> central.select('/projects/subjects').get()
>>> central.select('//subjects').get()
['IMAGEN_000000001274', 'IMAGEN_000000075717', ...,'IMAGEN_000099954902']
Filtered requests:
>>> central.select.projects('*OASIS_CS*').get()
>>> central.select('/projects/*OASIS_CS*').get()
[u'CENTRAL_OASIS_CS']
>>> central.select.project('IMAGEN').subjects('*55*42*').get()
>>> central.select('/projects/IMAGEN/subjects/*55*42*').get()
['IMAGEN_000055203542', 'IMAGEN_000055982442', 'IMAGEN_000097555742']
Operating the database¶
Python resource Objects that are retrieved from the
select
interface support a range of
operations to interact and insert data in XNAT.
EObject
objects support operations for creation, deletion
and existence checking.
>>> subject.insert()
>>> subject.exists()
True
>>> subject.delete()
>>> subject.exists()
False
Working with Files¶
XNAT was built to store images in addition of related data,
which means it can handle files. Files resources in pynxat
are just EObject
objects with a few additional
methods to upload and download the data.
>>> file.get()
'<cachedir>/hash_of_file_uri.extension'
>>> file.get('/tmp/image.nii')
'/tmp/image.nii'
>>> file.put('/tmp/modified_image.nii')