XNATpy Tutorial¶

XNAT REST API¶

The XNAT REST API allows users to work with xnat via scripts. The REST API is an interface that is language independent and is build on top of HTTP. Operations are carried out by HTTP requests with one of the verbs GET, PUT, POST or DELETE. The GET request is generally used for retrieving data, whereas the PUT, POST, and DELETE are used for modifying data.

A simple GET request can be send by simply putting the target url in a web browser and looking at the result. For a sending more complex HTTP requests, you can for example use curl (a command-line tool for linux), postman (an extension for the chrome browser), or the requests package for Python (on top of which this package as well as pyxnat is build)

To get an idea of how the XNAT REST API works it is helpful to visit the following URLs in your browser:

The first URL give you a table with an overview of all projects you can access on XNAT central. The second and third URL give the same information, but in different machine readable formats (XML and JSON respectively). This is extremely useful when creating scripts to automatically retrieve or store data from XNAT.

Installation¶

The easiest way to install xnat is via to python package index via pip:

pip install xnat

However, if you do not have pip or want to install from source just use the setup.py normally:

python setup.py install

Connecting to a server¶

To get started, create a connection:

>>> import xnat
>>> session = xnat.connect('https://central.xnat.org')

To see all options for creating connections see the xnat.connect(). The connection holds your login information, the server information and a session. It will also send a heartbeat every 14 minutes to keep the connection alive.

When working with a session it is always important to disconnect when done:

>>> session.disconnect()

Credentials¶

It is possible to pass your credentials for the session when connecting. This would look like:

>>> session = xnat.connect('http://my.xnat.server', user='admin', password='secret')

This would work and log in fine, but your password might be visible in your source code, command history or just on your screen. If you only give a user, but not a password xnatpy will prompt you for your password. This is fine for interactive use, but for automated scripts this is useless.

To store credentials this xnatpy uses the .netrc file. On linux the file is located in ~/.netrc. This file contains login information and should be accessible ONLY by the user (if not, the module with throw an error to let you know the file is unsafe). For example:

echo "machine images.xnat.org
>     login admin
>     password admin" > ~/.netrc
chmod 600 ~/.netrc

This will create the netrc file with the correct contents and set the permission correct.

Self-closing sessions¶

When in a script where there is a possibility for unforeseen errors it is safest to use a context operator in Python. This can be achieved by using the following:

>>> with xnat.connect('http://my.xnat.server') as session:
...     print session.projects

As soon as the scope of the with exists (even if because of an exception thrown!) the session will be disconnected automatically.

Exploring your xnat server¶

When a session is established, it is fairly easy to explore the data on the XNAT server. The data structure of XNAT is mimicked as Python objects. The connection gives access to a listing of all projects, subjects, and experiments on the server.

>>> import xnat
>>> session = xnat.connect('http://images.xnat.org', user='admin', password='admin')
>>> session.projects
<XNATListing (sandbox, sandbox project): <ProjectData sandbox project (sandbox)>>

The XNATListing is a special type of mapping in which you can access elements by a primary key (usually the ID or Accession #) and a secondary key (e.g. the label for a subject or experiment). Selection can be performed the same as a Python dict:

>>> sandbox_project = session.projects["sandbox"]
>>> sandbox_project.subjects
<XNATListing (XNAT_S00001, test001): <SubjectData test001 (XNAT_S00001)>>

You can browse the following levels on the XNAT server: projects, subjects, experiments, scans, resources, files. Also under experiments you have assessors which again can contain resources and files. This all following the same structure as XNAT.

Warning

Loading all subjects/experiments on a server can take very long if there is a lot of data. Going down through the project level is more efficient.

Looping over data¶

There are situations in which you want to perform an action for each subject or experiment. To do this, you can think of an XNATListing as a Python dict and most things will work naturally. For example:

>>> sandbox_project.subjects.keys()
[u'XNAT_S00001']
>>> sandbox_project.subjects.values()
[<SubjectData test001 (XNAT_S00001)>]
>>> len(sandbox_project.subjects)
1
>>> for subject in sandbox_project.subjects.values():
...     print(subject.label)
test001

Downloading data¶

If you have the following in your XNAT:

>>> experiment.scans['T1']
<MrScanData T1 (1001-MR3)>

In some cases you might want to download an individual scan to inspect/process locally. This is using:

>>> experiment.scans['T1'].download('/home/hachterberg/temp/T1.zip')
Downloading http://127.0.0.1/xnat/data/experiments/demo_E00091/scans/1001-MR3/files?format=zip:
13035 kb
Saved as /home/hachterberg/temp/T1.zip...

As you can see, the scan is downloaded as a zip archive that contains all the DICOM files.

If you are interested in downloading all data of an entire subject, it is possible to use a helper function that downloads the data and extracts it in the target directory. This will create a data structure similar to that of XNAT on your local disk:

>>> subject = experiment.subject

>>> subject.download_dir('/home/hachterberg/temp/')
Downloading http://120.0.0.1/xnat/data/experiments/demo_E00091/scans/ALL/files?format=zip:
23736 kb
Downloaded image session to /home/hachterberg/temp/ANONYMIZ3
Downloaded subject to /home/hachterberg/temp/ANONYMIZ3

To see what is downloaded, we can use the linux command find from ipython:

$ find /home/hachterberg/temp/ANONYMIZ3
/home/hachterberg/temp/ANONYMIZ3
/home/hachterberg/temp/ANONYMIZ3/ANONYMIZ3
/home/hachterberg/temp/ANONYMIZ3/ANONYMIZ3/scans
/home/hachterberg/temp/ANONYMIZ3/ANONYMIZ3/scans/1001-MR2-FLAIR
/home/hachterberg/temp/ANONYMIZ3/ANONYMIZ3/scans/1001-MR2-FLAIR/resources
/home/hachterberg/temp/ANONYMIZ3/ANONYMIZ3/scans/1001-MR2-FLAIR/resources/DICOM
/home/hachterberg/temp/ANONYMIZ3/ANONYMIZ3/scans/1001-MR2-FLAIR/resources/DICOM/files
/home/hachterberg/temp/ANONYMIZ3/ANONYMIZ3/scans/1001-MR2-FLAIR/resources/DICOM/files/IM2.dcm
/home/hachterberg/temp/ANONYMIZ3/ANONYMIZ3/scans/1001-MR2-FLAIR/resources/DICOM/files/IM32.dcm
/home/hachterberg/temp/ANONYMIZ3/ANONYMIZ3/scans/1001-MR2-FLAIR/resources/DICOM/files/IM11.dcm
...

The REST API allows for downloading of data from XNAT. The xnatpy package includes helper functions to make the downloading of data easier. For example, to download all experiments belonging to a subject:

>>> subject = sandbox_project.subjects['test001']
>>> subject.download_dir('./Downloads/test001')

This will download all the relevant experiments and unpack them in the target folder. This is available for projects, subjects, experiments, scans, and resources.

Experiments, scans and resources can also be downloaded in a zip bundle using the download method for experiments, scans, and resources.

Custom variables¶

The custom variables are exposed as a dict-like object in xnatpy. They are located in the field attribute under the objects that can have custom variables:

In [18]: experiment = project.subjects['ANONYMIZ'].experiments['ANONYMIZ']

In [19]: experiment.fields
Out[19]: <VariableMap {u'brain_volume': u'0'}>

In [20]: experiment.fields['brain_volume']
Out[20]: u'0'

In [21]: experiment.fields['brain_volume'] = 42.0

In [22]: experiment.fields
Out[22]: <VariableMap {u'brain_volume': u'42.0'}>

In [27]: experiment.fields['brain_volume']
Out[27]: u'42.0'

Getting external urls of an object¶

Sometimes you want to know the full external URL of a resource in XNAT, for this all XNAT objects have a function to retrieve this:

>>> experiment_01.external_uri()
'https://xnat.server.com/data/archive/projects/project/subjects/XNAT_S09618/experiments/XNAT_E36346'

You can change the query string or scheme used with extra arguments:

>>> experiment_01.external_uri(scheme='test', query={'hello': 'world'})
'test://xnat.server.com/data/archive/projects/project/subjects/XNAT_S09618/experiments/XNAT_E36346?hello=world'

Importing data into XNAT¶

To add new data into XNAT it is possible to use the REST import service. It allows you to upload a zip file containing an experiment and XNAT will automatically try to store it in the correct place:

>>> session.services.import_('/path/to/archive.zip', project='sandbox', subject='test002')

Will upload the DICOM files in archive.zip and add them as scans under the subject test002 in project sandbox. For more information on importing data see import_

As it is dangerous to add data straight into the archive due to lack of reviewing, it is possible to also upload the data to the prearchive first. This can be achieved by adding the destination argument as follows:

# Import via prearchive:
>>> prearchive_session = session.services.import_('/home/hachterberg/temp/ANONYMIZ.zip', project='brainimages', destination='/prearchive')
>>> print(prearchive_session)
<PrearchiveSession brainimages/20161107_114859342/ANONYMIZ>

Once the data is uploaded (either via xnatpy or other means) it is possible to query the prearchive and process the scans in it. To get a list of sessions waiting for archiving use the following:

>>> session.prearchive.sessions()
[<PrearchiveSession brainimages/20161107_114859342/ANONYMIZ>]

Once the data in the prearchive is located it can be archived as follows:

>>> prearchive_session = session.prearchive.sessions()[0]
>>> experiment = prearchive_session.archive(subject='ANONYMIZ3', experiment='ANONYMIZ3')
>>> print(experiment)
<MrSessionData ANONYMIZ3 (demo_E00092)>

Note

It is worth noting that it is possible to inspect the scan before archiving: one can look at the status, move it between projects, list the scans and files contained in the scans.

Prearchive¶

When scans are send to the XNAT they often end up in the prearchive pending review before adding them to the main archive. It is possible to view the prearchive via xnatpy:

>>> session.prearchive.sessions()
[]

This gives a list of PrearchiveSessions in the archive. It is possible to archive, rebuild, move, or delete the session using simple methods. For more information see PrearchiveSession

Object creation¶

It is possible to create object on the XNAT server (such as a new subject, experiment, etc). This is achieved by creating such an object in python and xnatpy will create a version of the server. For example you can create a subject:

>>> import xnat
>>> connection = xnat.connect('https://xnat.example.com')
>>> project = connection.projects['myproject']
>>> subject = connection.classes.SubjectData(parent=project, label='new_subject_label')
>>> subject
<SubjectData new_subject_label>

Note

the parent need to be the correct parent for the type, so an MRSessionData would need a SubjectData to be the parent.

In the connection.classes are all classes known the XNAT, also MRSessionData, CTSessionData. To get a complete list you can do:

>>> dir(connection.classes)

Note

the valid parent for a project (ProjectData) would be the connection object itself

Accessing XNAT files as local files (partial read)¶

There is a helper added in xnatpy that allows you to open a remote file (FileData object) similarly as a local file. Note that it will read the file from the start and until it is done, seeking will download until the seek point.

For example:

>>> import xnat
>>> connection = xnat.connect('https://xnat.server.com')
>>> file_obj = connection.projects['project'].subjects['S'].experiments['EXP'].scans['T1'].resources['DICOM'].files[0]
<FileData 1.3.6.1...-18s1eb2.dcm (1.3.6.1...-18s1eb2.dcm)>
>>> with file_obj.open() as fin:
        data = fin.read(3000)
>>> print(len(data))
3000

You can also use this to read the headers of a dicom file using pydicom:

>>> import pydicom
>>> with file_obj.open() as fin:
        data = pydicom.dcmread(fin, stop_before_pixels=True)

This should read the header and stop downloading once the entire header is read.

Note

The file is read in chucks so there might be a bit too much data downloaded

Note

If you open the file and not close it, the memory buffer might not be cleaned properly

Accessing DICOM headers of scan¶

Sometimes it is desired to read DICOM headers without downloading the entire scan. XNAT has a dicomdump service which can be used:

>>> connection.service.dicom_dump(scan_uri)

For more details see import_. As a helper we added a dicom_dump method to ScanData:

>>> scan.dicom_dump()

See ScanData.dicom_dump for the details.

A limitation of the dicomdump of XNAT is that field values are truncated under 64 characters. If you want to access the entire dicom header, a convenience method is added that reads the header via pydicom:

>>> scan.read_dicom()

This reads only the header and not the pixel data and will only download part of the file. To read the pixel data use:

>>> scan.read_dicom(read_pixel_data=True)

For the details see ScanData.dicom_dump

Note

Only one file is loaded, so the pixel data will only contain a single slice unless it is a DICOM Enhanced file

Example scripts¶

There is a number of example scripts located in the examples folder in the source code. The following code is a small command-line tool that prints all files for a given scan in the XNAT archive:

#!/usr/bin/env python

import xnat
import argparse
import re


def get_files(connection, project, subject, session, scan):
    xnat_project = connection.projects[project]
    xnat_subject = xnat_project.subjects[subject]
    xnat_experiment = xnat_subject.experiments[session]
    xnat_scan = xnat_experiment.scans[scan]
    files = xnat_scan.files.values()
    return files


def filter_files(xnat_files, regex):
    filtered_files = []
    regex = re.compile(regex)
    for file in xnat_files:
        found = regex.match(file.name)
        if found:
            filtered_files.append(file)
    return filtered_files


def main():
    parser = argparse.ArgumentParser(description='Prints all files from a certain scan.')
    parser.add_argument('--xnathost', type=unicode, required=True, help='xnat host name')
    parser.add_argument('--project', type=unicode, required=True, help='Project id')
    parser.add_argument('--subject', type=unicode, required=True, help='subject')
    parser.add_argument('--session', type=unicode, required=True, help='session')
    parser.add_argument('--scan', type=unicode, required=True, help='scan')
    parser.add_argument('--filter', type=unicode, required=False, default='.*', help='regex filter for file names')
    args = parser.parse_args()

    with xnat.connect(args.xnathost) as connection:
        xnat_files = get_files(connection, args.project, args.subject, args.session, args.scan)
        xnat_files = filter_files(xnat_files, args.filter)
        for file in xnat_files:
            print('{}'.format(file.name))


if __name__ == '__main__':
    main()