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Orthanc REST API python wrapper with additional utilities

Project description

PyOrthanc

Python library that wrap the Orthanc REST API and facilitate the manipulation of data.

Link to Orthanc web site: https://www.orthanc-server.com/

Notes: Please note that this is an early version of the wrapper (version < 1.0), therefore some methods description (and maybe name) may change because they don't describe adequately the behavior of the corresponding Orthanc REST API route. Also note that this librairy is still under development. If the description of an Orthanc method does not correspond to the planned behavior, please do an issue.

However, 'PyOrthanc' contains objects and functions that may be useful for anyone writing python script to interact with Orthanc.

Also note that tests (python setup.py test) might only work on a linux machine.

Installation

$ pip install pyorthanc

Or from the repository:

pip install git+https://gitlab.physmed.chudequebec.ca/gacou54/pyorthanc.git

Or, if you do not have git installed, clone the repository:

pip install -e pyorthanc.zip

Specific version

If you are looking for a specific version, lookout the version with the desired tag ar https://gitlab.physmed.chudequebec.ca/gacou54/pyorthanc/tags.

Example of usage

Be sure that Orthanc is running. The default URL (if running locally) is http://localhost:8042.

With Orthanc server:

from pyorthanc import Orthanc


orthanc = Orthanc('http://localhost:8042')
orthanc.setup_credentials('username', 'password')  # If needed

# To get patients identifier and main information
patients_identifiers = orthanc.get_patients()

for patient_identifier in patients_identifiers:
    patient_information = orthanc.get_patient_information(patient_identifier)


# To get patient's studies identifier and main information
a_patient_identifier = patients_identifiers[0]
studies_identifiers = orthanc.get_studies(a_patient_identifier)

for study_identifier in studies_identifiers:
    study_information = orthanc.get_studies_information(study_identifier)

Upload DICOM files to Orthanc:

from pyorthanc import Orthanc


orthanc = Orthanc('http://localhost:8042')
orthanc.setup_credentials('username', 'password')  # If needed

with open('A_DICOM_INSTANCE_PATH.dcm', 'rb') as file_handler:
    orthanc.post_instances(file_handler.read())

Getting list of remote modalities:

from pyorthanc import Orthanc


orthanc = Orthanc('http://localhost:8042')
orthanc.setup_credentials('username', 'password')  # If needed

orthanc.get_modalities()

Query (C-Find) and Retrieve (C-Move) from remote modality:

from pyorthanc import RemoteModality, Orthanc


remote_modality = RemoteModality(Orthanc('http://localhost:8042'), 'modality')
remote_modality.setup_credentials('username', 'password')  # If needed

# Query (C-Find) on modality
data = {'Level': 'Study', 'Query': {'PatientID': '*'}}
query_response = remote_modality.query(data=data)

# Retrieve (C-Move) results of query on a target modality (AET)
remote_modality.move(query_response['QUERY_ID'], 'target_modality')

Build a patient tree structure of all patients in Orthanc instance:

Each patient is a tree. Layers in each tree are Patient -> Study -> Series -> Instance.

from pyorthanc import Orthanc, datastructure


patient_forest = datastructure.build_patient_forest(
    Orthanc('http://localhost:8042/')
)    

for patient in patient_forest:
    patient_info = patient.get_main_information()

    for study in patient.get_studies():
        ...

Anonymize patient and get file:

from pyorthanc import Orthanc


orthanc = Orthanc('http://localhost:8042')
orthanc.setup_credentials('username', 'password')  # If needed

A_PATIENT_IDENTIFIER = orthanc.get_patients()[0]

orthanc.anonymize_patient(A_PATIENT_IDENTIFIER)

# result is: (you can retrieve DICOM file from ID)
# {'ID': 'dd41f2f1-24838e1e-f01746fc-9715072f-189eb0a2',
#  'Path': '/patients/dd41f2f1-24838e1e-f01746fc-9715072f-189eb0a2',
#  'PatientID': 'dd41f2f1-24838e1e-f01746fc-9715072f-189eb0a2',
#  'Type': 'Patient'}

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