dicom-client-python 0.3.1

A small dicom client in python

Dicom Client V1

Build Status

(Currently Private Build Badges)

Main:

Dev:

API Introduction

There are four core methods that make up DICOM-Client. An interface has been defined to simplify interaction with DicomClient(). The purpose of these methods is to upload, download, and delete DCM files from DICOM Server:

class DicomClientInterface(ABC):
    @abstractmethod
    def __init__(self, base_url, token_cache):
        pass
    @abstractmethod
    def upload_dicom_folder(self, folder_name):
        pass
    @abstractmethod
    def upload_dicom_file(self, file_name):
        pass
    @abstractmethod
    def delete_dicom(self, study_id, series_id=None, instance_id=None):
        pass
    @abstractmethod
    def download_dicom(self, output_folder, study_id, series_id=None, instance_id=None):
        pass
    @abstractmethod
    def get_patient_study_ids(self, patient_id):
        pass

To use:

$ pip install dicom_client
$ export AUTH_CONNECTION_INFO="{'authority': 'https://login.microsoftonline.com/72f988bf-86f1-41af-91ab-2d7cd011db47', 'client_id': '9cfb139d-d05d-4f5c-a10c-54e0ec338f53', 'client_secret': 'D.oD1q9SHc77syVRD-8vKi8UhbDXYoi~n~', 'oauth_resource': 'api://9cfb139d-d05d-4f5c-a10c-54e0ec338f53'}"

import ast 
import os 
from dicom_client import (
    DicomClient,
    TokenCache,
    make_get_token_func,
)

base_url = "https://tonydicom.azurewebsites.net"

auth = ast.literal_eval(os.environ["AUTH_CONNECTION_INFO"])

token_cache = TokenCache(make_get_token_func(auth))
dicom_client = DicomClient(base_url, token_cache)

dicom_client.upload_dicom_folder("folder_name")
dicom_client.upload_dicom_file("file_name")
dicom_client.delete_dicom("study_id", "series_id", "instance_id")
dicom_client.download_dicom("output_folder", "study_id", "series_id", "instance_id")
dicom_client.get_patient_study_ids("patient_id")

This script can be used to validate your DICOM server deployment.

See Microsoft Dicom Server here: https://github.com/microsoft/dicom-server

For contributors:

Pre-reqs

• Provision a dicom server
• Get credentials for dicom server string values
• Export them as environment variables for your debugging environment.

Our .vscode/settings.json point to a .env file:

"python.envFile": "${workspaceFolder}/.vscode/dev.env",

Our dev.env file needs these values in this format:

AUTH_CONNECTION_INFO="{'authority': 'https://login.microsoftonline.com/72f988bf-86f1-41af-91ab-2d7cd011db47', 'client_id': '5bef631a-c4cd-4feb-aaf2-78ff5f7d7347', 'client_secret': 'REPLACE_WITH_YOUR_SECRET_mrpc.lgXK~C0.g146Gu3PcDG.W6Eg0d0I', 'oauth_resource': 'api://REPLACE_WITH_YOUR_RESOURCE_ID5bef631a-c4cd-4feb-aaf2-78ff5f7d7347'}"

Running Tests

Complete the pre-reqs and set the AUTH_CONNECTION_INFO environment variable, then:

$ git clone our_git_url
$ python3 -m venv .venv
$ pip install -r requirements.txt 
$ pytest tests

Make sure you've followed the prerequisites for running the tests locally and validated your dicom server host and exported the correct credentials. See README.md for more details or raise an issue for DICOM server support.

Unit tests

To run most of the unit tests (optionally with code coverage reporting), simply run:

$ pytest tests/unit [--cov=handler --cov-report=html:htmlcov]

Please see conftest.py for more information on these test parameters as they can be found with environment variables instead of arguments for development environments.

Pylint

Pylint provides static code analysis for python and uses our ./.pylintrc file for managing the configuration of the linter. We run pylint in our integration tests to ensure python coding standards. See more info about pylint here.

To run pylint locally:

pylint handler --output-format=colorized --rcfile=".pylintrc"

Formatting with Black

Black is an auto-formatting tool and checker for python that provides further code analysis, it to is run in our integration tests and is helpful to run locally to maintain code clarity and conform to team standards. More info can be found here.

To run black locally:

black --check --line-length 100 .
black --line-length 100 .