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

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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