beren 0.7.1

Description:

beren 0.7.1

beren

beren provides a REST client for Orthanc, an open-source DICOM server.
Built using the excellent apiron library.
Install
Use pip:
pip install beren

How to use
Import the client and provide the server details
from beren import Orthanc
orthanc = Orthanc('https://example-orthanc-server.com')

# Patient endpoints
orthanc.get_patients()
orthanc.get_patient(id)
...and so on

# Study endpoints
orthanc.get_studies()
orthanc.get_study(id)
...and so on

# Series endpoints
orthanc.get_series()
orthanc.get_one_series(id)
...and so on

# Instance endpoints
orthanc.get_instances()
orthanc.get_instance(id)
...and so on

# Get changes
orthanc.get_changes()

# Find objects by query
query = {'PatientName': 'Jon*'}
orthanc.find(query, level='Patient', expand=False, limit=2)

# Get previous queries
orthanc.get_queries()

There are many other preconfigured endpoints.
Authentication
Many servers require authentication to utilize their API. Simply provide a valid authentication object when defining the client:
from requests.auth import HTTPBasicAuth
auth = HTTPBasicAuth('orthanc', 'orthanc')
orthanc = Orthanc('https://test.server.com', auth=auth)

To override the default authentication, provide a new authentication object when calling the endpoint:
new_auth = HTTPBasicAuth('new_user', 'new_password')
orthanc.get_patients(auth=auth)

Advanced Configuration
Timeouts
Some servers are slow (and some methods can be slow). For example, asking for all instances from a server can cause a timeout before the server responds. To
modify the timeout settings, use apiron's Timeout class:
from apiron import Timeout
t = Timeout(read_timeout=6, connection_timeout=1) # Modify the timeout

from beren import Orthanc
orthanc = Orthanc('https://example-orthanc-server.com')
orthanc.get_instances(timeout_spec=t) # Use new timeout

Increase the read timeout if the endpoint is slow. Increase the connection timeout for slow servers.
Disable Certificate Checks
To disable TLS certificate checking, use sessions:
import requests
session = requests.sessions.Session() # New session
session.verify = False # Disable certificate checking

from beren import Orthanc
orthanc = Orthanc('https://example-orthanc-server.com')
orthanc.get_patients(session=session) # Use session

Non-HTTPS endpoints
The client will warn when using HTTP endpoints. Medical data is particularly sensitive, consequently, strongly consider using HTTPS.
You can disable the warning using the warn_insecure argument:
from beren import Orthanc
orthanc = Orthanc('http://insecure.endpoint.com', warn_insecure=False)

Examples
To save an instance file to the local directory:
from beren import Orthanc
orthanc = Orthanc('https://example-orthanc-server.com')

with open('test_file.dcm', 'wb') as dcm:
for chunk in orthanc.get_instance_file(<instance_id>):
dcm.write(chunk)

To get an archive of a series (DCM files in a zip file):
from beren import Orthanc
orthanc = Orthanc('https://example-orthanc-server.com')

with open('test.zip', 'wb') as z:
for chunk in orthanc.get_series_archive(<instance_id>):
z.write(chunk)

Further help

apiron
Orthanc documentation
Orthanc OpenAPI
Orthanc REST API spreadsheet

Future goals

Asynchronous requests
Document every function
Better test coverage