Orthanc REST API python wrapper with additional utilities
Project description
PyOrthanc
PyOrthanc is a python client for the Orthanc REST API, which fully wraps all the methods of the REST API. Additionally, it provides many utility functions to interact with an Orthanc instance.
See the full documentation here https://gacou54.github.io/pyorthanc
Install PyOrthanc using pip:
pip install pyorthanc
Then use the client. If Orthanc is running locally, the default URL is http://localhost:8042
.
import pyorthanc
client = pyorthanc.Orthanc('http://localhost:8042', username='orthanc', password='orthanc')
patient_ids = client.get_patients()
Interact with connected modalities
import pyorthanc
modality = pyorthanc.Modality(client, 'MY_MODALITY')
assert modality.echo()
# C-Find on modality
response = modality.query({'Level': 'Study', 'Query': {'PatientID': '*'}})
# C-Move to target modality
modality.move(response['ID'], {'TargetAet': 'target_modality'})
Find patients
patients = pyorthanc.find_patients(client, {'PatientID': '*P001'})
for patient in patients:
patient.labels
patient.is_stable
patient.name
...
for study in patient.studies:
study.labels
study.date
...
for series in study.series:
...
for instance in series.instances:
pydicom_ds = instance.get_pydicom()
Resources (Patient
, Study
, Series
, Instance
) can be easily anonymized.
import pyorthanc
orthanc_patient_id = client.get_patients()[0]
patient = pyorthanc.Patient(orthanc_patient_id, client)
Waiting the for the anonymization process:
new_patient = patient.anonymize()
new_patient_with_given_patient_id = patient.anonymize(
keep=['PatientName'],
replace={'PatientID': 'TheNewPatientID'},
force=True # Needed when changing PatientID/StudyInstanceUID/SeriesInstanceUID/SOPInstanceUID
)
For long-running job (i.e. large patient) or to submit many anonymization jobs at the same time, use
job = patient.anonymize_as_job()
job.state # You can follow the job state
job.wait_until_completion() # Or just wait on its completion
new_patient = pyorthanc.Patient(job.content['ID'], client)
Notes on versioning
PyOrthanc has been rewritten almost entirely from 0.*.*
.
The new Orthanc
client is now automatically generated from https://api.orthanc-server.com/
.
The version *.*.
of PyOrthanc will follow Orthanc version
(e.g. pyorthanc 1.11.*
is generated from the API specification of Orthanc 1.11.*
).
You can still use the old client with
from pyorthanc.deprecated.client import Orthanc
from pyorthanc.deprecated.client_1_11_3 import Orthanc
Note that due to automatic generation some method names may be less clear. However, the automatic generation allows PyOrthanc to cover all the routes of the API of Orthanc.
Citation
If you publish using PyOrthanc, we kindly ask that you credit us. PyOrthanc can be found on Zenodo : https://zenodo.org/record/7086219 .
Contributing
You can contribute to this project with the following steps:
- First, fork the project on Github
- Clone the project
git clone https://github.com/<your-github-username>/pyorthanc cd pyorthanc
- Create a poetry environment
(this project use the poetry for dependency management)
peotry install
- Make a new git branch where you will apply the changes
git checkout -b your-branch-name
Now you can make your changes - Once done,
git add
,git commit
andgit push
the changes. - Make a Pull Request from your branch to the https://github.com/gacou54/pyorthanc.
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