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Use DICOMweb Standard APIs with Python

  • Artikkeli

This article shows how to work with the DICOMweb service using Python and sample .dcm DICOM® files.

Use these sample files:

  • blue-circle.dcm
  • dicom-metadata.csv
  • green-square.dcm
  • red-triangle.dcm

The filename, studyUID, seriesUID, and instanceUID of the sample DICOM files are:

File StudyUID SeriesUID InstanceUID
green-square.dcm 1.2.826.0.1.3680043.8.498.13230779778012324449356534479549187420 1.2.826.0.1.3680043.8.498.45787841905473114233124723359129632652 1.2.826.0.1.3680043.8.498.12714725698140337137334606354172323212
red-triangle.dcm 1.2.826.0.1.3680043.8.498.13230779778012324449356534479549187420 1.2.826.0.1.3680043.8.498.45787841905473114233124723359129632652 1.2.826.0.1.3680043.8.498.47359123102728459884412887463296905395
blue-circle.dcm 1.2.826.0.1.3680043.8.498.13230779778012324449356534479549187420 1.2.826.0.1.3680043.8.498.77033797676425927098669402985243398207 1.2.826.0.1.3680043.8.498.13273713909719068980354078852867170114

Note

Each of these files represents a single instance and is part of the same study. Also, the green-square and red-triangle are part of the same series, while the blue-circle is in a separate series.

Prerequisites

To use the DICOMweb Standard APIs, you must have an instance of the DICOM service deployed. For more information, see Deploy DICOM service using the Azure portal.

After you deploy an instance of the DICOM service, retrieve the URL for your App service:

  1. Sign in to the Azure portal.
  2. Search Recent resources and select your DICOM service instance.
  3. Copy the Service URL of your DICOM service.
  4. If you don't have a token, see Get access token for the DICOM service using Azure CLI.

For this code, you access a Public Preview Azure service. It's important that you don't upload any private health information (PHI).

Work with the DICOM service

The DICOMweb Standard makes heavy use of multipart/related HTTP requests combined with DICOM specific accept headers. Developers familiar with other REST-based APIs often find working with the DICOMweb standard awkward. However, after it's up and running, it's easy to use. It just takes a little familiarity to get started.

Import the Python libraries

First, import the necessary Python libraries.

We implement this example by using the synchronous requests library. For asynchronous support, consider using httpx or another async library. Additionally, we're importing two supporting functions from urllib3 to support working with multipart/related requests.

Additionally, we're importing DefaultAzureCredential to log into Azure and get a token.

import requests
import pydicom
from pathlib import Path
from urllib3.filepost import encode_multipart_formdata, choose_boundary
from azure.identity import DefaultAzureCredential

Configure user-defined variables

Replace all variable values wrapped in { } with your own values. Additionally, validate that any constructed variables are correct. For instance, base_url is constructed using the Service URL and then appended with the version of the REST API being used. The Service URL of your DICOM service is: https://<workspacename-dicomservicename>.dicom.azurehealthcareapis.com. You can use the Azure portal to navigate to the DICOM service and obtain your Service URL. You can also visit the API Versioning for DICOM service Documentation for more information on versioning. If you're using a custom URL, you need to override that value with your own.

dicom_service_name = "{server-name}"
path_to_dicoms_dir = "{path to the folder that includes green-square.dcm and other dcm files}"

base_url = f"{Service URL}/v{version}"

study_uid = "1.2.826.0.1.3680043.8.498.13230779778012324449356534479549187420"; #StudyInstanceUID for all 3 examples
series_uid = "1.2.826.0.1.3680043.8.498.45787841905473114233124723359129632652"; #SeriesInstanceUID for green-square and red-triangle
instance_uid = "1.2.826.0.1.3680043.8.498.47359123102728459884412887463296905395"; #SOPInstanceUID for red-triangle

Authenticate to Azure and get a token

DefaultAzureCredential allows us to use various ways to get tokens to log into the service. In this example, use the AzureCliCredential to get a token to log into the service. There are other credential providers such as ManagedIdentityCredential and EnvironmentCredential that you may use. To use the AzureCliCredential, you need to sign in to Azure from the CLI before running this code. For more information, see Get access token for the DICOM service using Azure CLI. Alternatively, copy and paste the token retrieved while signing in from the CLI.

Note

DefaultAzureCredential returns several different Credential objects. We reference the AzureCliCredential as the 5th item in the returned collection. This may not always be the case. If not, uncomment the print(credential.credential) line. This will list all the items. Find the correct index, recalling that Python uses zero-based indexing.

Note

If you have not logged into Azure using the CLI, this will fail. You must be logged into Azure from the CLI for this to work.

from azure.identity import DefaultAzureCredential
credential = DefaultAzureCredential()

#print(credential.credentials) # this can be used to find the index of the AzureCliCredential
token = credential.credentials[4].get_token('https://dicom.healthcareapis.azure.com')
bearer_token = f'Bearer {token.token}'

Create supporting methods to support multipart\related

The Requests libraries (and most Python libraries) don't work with multipart\related in a way that supports DICOMweb. Because of these libraries, we must add a few methods to support working with DICOM files.

encode_multipart_related takes a set of fields (in the DICOM case, these libraries are generally Part 10 dam files) and an optional user-defined boundary. It returns both the full body, along with the content_type, which can be used.

def encode_multipart_related(fields, boundary=None):
    if boundary is None:
        boundary = choose_boundary()

    body, _ = encode_multipart_formdata(fields, boundary)
    content_type = str('multipart/related; boundary=%s' % boundary)

    return body, content_type

Create a requests session

Creates a requests session, called client that is used to communicate with the DICOM service.

client = requests.session()

Verify authentication is configured correctly

Call the changefeed API endpoint, which returns a 200 if authentication is successful.

headers = {"Authorization":bearer_token}
url= f'{base_url}/changefeed'

response = client.get(url,headers=headers)
if (response.status_code != 200):
    print('Error! Likely not authenticated!')

Upload DICOM instances (STOW)

The following examples highlight persisting DICOM files.

Store instances using multipart/related

This example demonstrates how to upload a single DICOM file, and it uses Python to preload the DICOM file into memory as bytes. When an array of files is passed to the fields parameter encode_multipart_related, multiple files can be uploaded in a single POST. It's sometimes used to upload several instances inside a complete series or study.

Details:

  • Path: ../studies

  • Method: POST

  • Headers:

    • Accept: application/dicom+json
    • Content-Type: multipart/related; type="application/dicom"
    • Authorization: Bearer $token"

  • Body:

    • Content-Type: application/dicom for each file uploaded, separated by a boundary value

Some programming languages and tools behave differently. For example, some require you to define your own boundary. For those languages and tools, you might need to use a slightly modified Content-Type header. These languages and tools can be used successfully.

  • Content-Type: multipart/related; type="application/dicom"; boundary=ABCD1234
  • Content-Type: multipart/related; boundary=ABCD1234
  • Content-Type: multipart/related
#upload blue-circle.dcm
filepath = Path(path_to_dicoms_dir).joinpath('blue-circle.dcm')

# Read through file and load bytes into memory 
with open(filepath,'rb') as reader:
    rawfile = reader.read()
files = {'file': ('dicomfile', rawfile, 'application/dicom')}

#encode as multipart_related
body, content_type = encode_multipart_related(fields = files)

headers = {'Accept':'application/dicom+json', "Content-Type":content_type, "Authorization":bearer_token}

url = f'{base_url}/studies'
response = client.post(url, body, headers=headers, verify=False)

Store instances for a specific study

This example demonstrates how to upload multiple DICOM files into the specified study. It uses Python to preload the DICOM file into memory as bytes.

When an array of files is passed to the fields parameter encode_multipart_related, multiple files can be uploaded in a single POST. It's sometimes used to upload a complete series or study.

Details:

  • Path: ../studies/{study}
  • Method: POST
  • Headers:
    • Accept: application/dicom+json
    • Content-Type: multipart/related; type="application/dicom"
    • Authorization: Bearer $token"
  • Body:
    • Content-Type: application/dicom for each file uploaded, separated by a boundary value

filepath_red = Path(path_to_dicoms_dir).joinpath('red-triangle.dcm')
filepath_green = Path(path_to_dicoms_dir).joinpath('green-square.dcm')

# Open up and read through file and load bytes into memory 
with open(filepath_red,'rb') as reader:
    rawfile_red = reader.read()
with open(filepath_green,'rb') as reader:
    rawfile_green = reader.read()  
       
files = {'file_red': ('dicomfile', rawfile_red, 'application/dicom'),
         'file_green': ('dicomfile', rawfile_green, 'application/dicom')}

#encode as multipart_related
body, content_type = encode_multipart_related(fields = files)

headers = {'Accept':'application/dicom+json', "Content-Type":content_type, "Authorization":bearer_token}

url = f'{base_url}/studies'
response = client.post(url, body, headers=headers, verify=False)

Store single instance (nonstandard)

The following code example demonstrates how to upload a single DICOM file. It's a nonstandard API endpoint that simplifies uploading a single file as binary bytes sent in the body of a request

Details:

  • Path: ../studies
  • Method: POST
  • Headers:
    • Accept: application/dicom+json
    • Content-Type: application/dicom
    • Authorization: Bearer $token"
  • Body:
    • Contains a single DICOM file as binary bytes.
#upload blue-circle.dcm
filepath = Path(path_to_dicoms_dir).joinpath('blue-circle.dcm')

# Open up and read through file and load bytes into memory 
with open(filepath,'rb') as reader:
    body = reader.read()

headers = {'Accept':'application/dicom+json', 'Content-Type':'application/dicom', "Authorization":bearer_token}

url = f'{base_url}/studies'
response = client.post(url, body, headers=headers, verify=False)
response  # response should be a 409 Conflict if the file was already uploaded in the above request

Retrieve DICOM instances (WADO)

The following examples highlight retrieving DICOM instances.

Retrieve all instances within a study

This example retrieves all instances within a single study.

Details:

  • Path: ../studies/{study}
  • Method: GET
  • Headers:
    • Accept: multipart/related; type="application/dicom"; transfer-syntax=*
    • Authorization: Bearer $token"

All three of the dcm files that uploaded previously are part of the same study, so the response should return all three instances. Validate that the response has a status code of OK and that all three instances are returned.

url = f'{base_url}/studies/{study_uid}'
headers = {'Accept':'multipart/related; type="application/dicom"; transfer-syntax=*', "Authorization":bearer_token}

response = client.get(url, headers=headers) #, verify=False)

Use the retrieved instances

The instances are retrieved as binary bytes. You can loop through the returned items and convert the bytes into a file that pydicom can read as follows.

import requests_toolbelt as tb
from io import BytesIO

mpd = tb.MultipartDecoder.from_response(response)
for part in mpd.parts:
    # Note that the headers are returned as binary!
    print(part.headers[b'content-type'])
    
    # You can convert the binary body (of each part) into a pydicom DataSet
    #   And get direct access to the various underlying fields
    dcm = pydicom.dcmread(BytesIO(part.content))
    print(dcm.PatientName)
    print(dcm.SOPInstanceUID)

Retrieve metadata of all instances in study

This request retrieves the metadata for all instances within a single study.

Details:

  • Path: ../studies/{study}/metadata
  • Method: GET
  • Headers:
    • Accept: application/dicom+json
    • Authorization: Bearer $token"

All three of the .dcm files that we uploaded previously are part of the same study so the response should return the metadata for all three instances. Validate that the response has a status code of OK and that all the metadata is returned.

url = f'{base_url}/studies/{study_uid}/metadata'
headers = {'Accept':'application/dicom+json', "Authorization":bearer_token}

response = client.get(url, headers=headers) #, verify=False)

Retrieve all instances within a series

This request retrieves all instances within a single series.

Details:

  • Path: ../studies/{study}/series/{series}
  • Method: GET
  • Headers:
    • Accept: multipart/related; type="application/dicom"; transfer-syntax=*
    • Authorization: Bearer $token"

This series has two instances (green-square and red-triangle), so the response should return both instances. Validate that the response has a status code of OK and that both instances are returned.

url = f'{base_url}/studies/{study_uid}/series/{series_uid}'
headers = {'Accept':'multipart/related; type="application/dicom"; transfer-syntax=*', "Authorization":bearer_token}

response = client.get(url, headers=headers) #, verify=False)

Retrieve metadata of all instances in series

This request retrieves the metadata for all instances within a single series.

Details:

  • Path: ../studies/{study}/series/{series}/metadata
  • Method: GET
  • Headers:
    • Accept: application/dicom+json
    • Authorization: Bearer $token"

This series has two instances (green-square and red-triangle), so the response should return for both instances. Validate that the response has a status code of OK and that the metadata of both instances are returned.

url = f'{base_url}/studies/{study_uid}/series/{series_uid}/metadata'
headers = {'Accept':'application/dicom+json', "Authorization":bearer_token}

response = client.get(url, headers=headers) #, verify=False)

Retrieve a single instance within a series of a study

This request retrieves a single instance.

Details:

  • Path: ../studies/{study}/series{series}/instances/{instance}
  • Method: GET
  • Headers:
    • Accept: application/dicom; transfer-syntax=*
    • Authorization: Bearer $token"

This code example should only return the instance red-triangle. Validate that the response has a status code of OK and that the instance is returned.

url = f'{base_url}/studies/{study_uid}/series/{series_uid}/instances/{instance_uid}'
headers = {'Accept':'application/dicom; transfer-syntax=*', "Authorization":bearer_token}

response = client.get(url, headers=headers) #, verify=False)

Retrieve metadata of a single instance within a series of a study

This request retrieves the metadata for a single instance within a single study and series.

Details:

  • Path: ../studies/{study}/series/{series}/instances/{instance}/metadata
  • Method: GET
  • Headers:
    • Accept: application/dicom+json
    • Authorization: Bearer $token"

This code example should only return the metadata for the instance red-triangle. Validate that the response has a status code of OK and that the metadata is returned.

url = f'{base_url}/studies/{study_uid}/series/{series_uid}/instances/{instance_uid}/metadata'
headers = {'Accept':'application/dicom+json', "Authorization":bearer_token}

response = client.get(url, headers=headers) #, verify=False)

Retrieve one or more frames from a single instance

This request retrieves one or more frames from a single instance.

Details:

  • Path: ../studies/{study}/series{series}/instances/{instance}/frames/1,2,3
  • Method: GET
  • Headers:
    • Authorization: Bearer $token"
    • Accept: multipart/related; type="application/octet-stream"; transfer-syntax=1.2.840.10008.1.2.1 (Default) or
    • Accept: multipart/related; type="application/octet-stream"; transfer-syntax=* or
    • Accept: multipart/related; type="application/octet-stream";

This code example should return the only frame from the red-triangle. Validate that the response has a status code of OK and that the frame is returned.

url = f'{base_url}/studies/{study_uid}/series/{series_uid}/instances/{instance_uid}/frames/1'
headers = {'Accept':'multipart/related; type="application/octet-stream"; transfer-syntax=*', "Authorization":bearer_token}

response = client.get(url, headers=headers) #, verify=False)

Query DICOM (QIDO)

In the following examples, we search for items using their unique identifiers. You can also search for other attributes, such as PatientName.

Refer to the DICOM Conformance Statement for supported DICOM attributes.

Search for studies

This request searches for one or more studies by DICOM attributes.

Details:

  • Path: ../studies?StudyInstanceUID={study}
  • Method: GET
  • Headers:
    • Accept: application/dicom+json
    • Authorization: Bearer $token"

Validate that the response includes one study and that the response code is OK.

url = f'{base_url}/studies'
headers = {'Accept':'application/dicom+json', "Authorization":bearer_token}
params = {'StudyInstanceUID':study_uid}

response = client.get(url, headers=headers, params=params) #, verify=False)

Search for series

This request searches for one or more series by DICOM attributes.

Details:

  • Path: ../series?SeriesInstanceUID={series}
  • Method: GET
  • Headers:
    • Accept: application/dicom+json
    • Authorization: Bearer $token"

Validate that the response includes one series and that the response code is OK.

url = f'{base_url}/series'
headers = {'Accept':'application/dicom+json', "Authorization":bearer_token}
params = {'SeriesInstanceUID':series_uid}

response = client.get(url, headers=headers, params=params) #, verify=False)

Search for series within a study

This request searches for one or more series within a single study by DICOM attributes.

Details:

  • Path: ../studies/{study}/series?SeriesInstanceUID={series}
  • Method: GET
  • Headers:
    • Accept: application/dicom+json
    • Authorization: Bearer $token"

Validate that the response includes one series and that the response code is OK.

url = f'{base_url}/studies/{study_uid}/series'
headers = {'Accept':'application/dicom+json', "Authorization":bearer_token}
params = {'SeriesInstanceUID':series_uid}

response = client.get(url, headers=headers, params=params) #, verify=False)

Search for instances

This request searches for one or more instances by DICOM attributes.

Details:

  • Path: ../instances?SOPInstanceUID={instance}
  • Method: GET
  • Headers:
    • Accept: application/dicom+json
    • Authorization: Bearer $token"

Validate that the response includes one instance and that the response code is OK.

url = f'{base_url}/instances'
headers = {'Accept':'application/dicom+json', "Authorization":bearer_token}
params = {'SOPInstanceUID':instance_uid}

response = client.get(url, headers=headers, params=params) #, verify=False)

Search for instances within a study

This request searches for one or more instances within a single study by DICOM attributes.

Details:

  • Path: ../studies/{study}/instances?SOPInstanceUID={instance}
  • Method: GET
  • Headers:
    • Accept: application/dicom+json
    • Authorization: Bearer $token"

Validate that the response includes one instance and that the response code is OK.

url = f'{base_url}/studies/{study_uid}/instances'
headers = {'Accept':'application/dicom+json', "Authorization":bearer_token}
params = {'SOPInstanceUID':instance_uid}

response = client.get(url, headers=headers, params=params) #, verify=False)

Search for instances within a study and series

This request searches for one or more instances within a single study and single series by DICOM attributes.

Details:

  • Path: ../studies/{study}/series/{series}/instances?SOPInstanceUID={instance}
  • Method: GET
  • Headers:
    • Accept: application/dicom+json
    • Authorization: Bearer $token"

Validate that the response includes one instance and that the response code is OK.

url = f'{base_url}/studies/{study_uid}/series/{series_uid}/instances'
headers = {'Accept':'application/dicom+json'}
params = {'SOPInstanceUID':instance_uid}

response = client.get(url, headers=headers, params=params) #, verify=False)

Delete DICOM

Note

Delete is not part of the DICOM standard, but it has been added for convenience.

A 204 response code is returned when the deletion is successful. A 404 response code is returned if the items never existed or are already deleted.

Delete a specific instance within a study and series

This request deletes a single instance within a single study and single series.

Details:

  • Path: ../studies/{study}/series/{series}/instances/{instance}
  • Method: DELETE
  • Headers:
    • Authorization: Bearer $token

This request deletes the red-triangle instance from the server. If successful, the response status code contains no content.

headers = {"Authorization":bearer_token}
url = f'{base_url}/studies/{study_uid}/series/{series_uid}/instances/{instance_uid}'
response = client.delete(url, headers=headers)

Delete a specific series within a study

This request deletes a single series (and all child instances) within a single study.

Details:

  • Path: ../studies/{study}/series/{series}
  • Method: DELETE
  • Headers:
    • Authorization: Bearer $token

This code example deletes the green-square instance from the server (it's the only element left in the series). If successful, the response status code doesn't delete content.

headers = {"Authorization":bearer_token}
url = f'{base_url}/studies/{study_uid}/series/{series_uid}'
response = client.delete(url, headers=headers)

Delete a specific study

This request deletes a single study (and all child series and instances).

Details:

  • Path: ../studies/{study}
  • Method: DELETE
  • Headers:
    • Authorization: Bearer $token
headers = {"Authorization":bearer_token}
url = f'{base_url}/studies/{study_uid}'
response = client.delete(url, headers=headers)

Note

DICOM® is the registered trademark of the National Electrical Manufacturers Association for its Standards publications relating to digital communications of medical information.