This tutorial is intended as an introduction on how to work with
pyxnat. Reading the XNAT documentation, especially on the pages on the REST
Web Services, can be a huge help to deeper understand
XNAT and consequently
pyxnat design decisions.
>>> import pyxnat
This tutorial also assumes that you have access to an XNAT instance. You may also use XNAT Central, which is a public instance managed by the XNAT team and updated on a regular basis.
Setting up a connection¶
The first step when working with
pyxnat is to connect to an XNAT
Interface. For this, you will need valid
credentials. Make sure you have them or request them through the web interface
of the targeted host.
>>> from pyxnat import Interface >>> central = Interface(server="https://central.xnat.org", ... user='my_login', ... password='my_pass')
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. You might end up with something like: http://server_ip:port/xnat
If at least one of server, user and password arguments is 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
The first one is used with the config parameter.
>>> central = Interface(config='central.cfg')
The easiest way to create this configuration file is to use the
save_config() method on an existing interface.
The second one is the XNAT format config file, which is placed at a
default location (i.e. ~/.xnatPass in Linux). 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
+loginone@http://central.xnat.org=password -logintwo@http://central.xnat.org=password -logintwo@http://localhost=password
>>> central = Interface()
Interface is used without any parameter
and any configuration file at default location,
user will be prompted for server, user and password.
You may prefer not to have your password either displayed onscreen or embedded in your programs. Two alternatives for interactive sessions and scripts: if you omit any of these three required parameters, the call to Interface(.) will prompt for the missing ones, and will not display the password as you enter it from the keyboard. Alternately, you can prompt for the password in the same way by using Python’s getpass.getpass(.) method, some variations of which are demonstrated in examples below.
You can save an entire configuration to a file and then load it later. Note that the configuration file contains the password, so be sure only to save this file in an access-protected location.
Traversing the database¶
Traversing the database requires basic knowledge of XNAT data model.
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
sub-interface allows for data selection and basic filtering through
Python objects or
paths, more akin to native REST calls.
>>> central.select.projects().get() [..., 'CENTRAL_OASIS_CS', 'CENTRAL_OASIS_LONG', ...] >>> central.select('/projects').get() [..., 'CENTRAL_OASIS_CS', 'CENTRAL_OASIS_LONG', ...]
>>> 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']
>>> central.select.projects('*OASIS_CS*').get() >>> central.select('/projects/*OASIS_CS*').get() ['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 which means it can handle files.
Files resources in
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')