/healthcare-dicom-dicomweb-adapter

Adapter which transforms DIMSE requests to DICOMweb requests

Primary LanguageJavaApache License 2.0Apache-2.0

DICOM Adapter

The DICOM adapter is a set of components that translate between traditional DICOM DIMSE protocols (e.g., C-STORE) and the RESTful DICOMweb protocols (e.g., STOW-RS). There are two components, namely import and export adapter.

Table of Contents

Import Adapter

The Import Adapter converts incoming DIMSE requests to corresponding DICOMWeb requests and passes the converted results back to the DIMSE client. The following requests are supported:

  • C-STORE to STOW-RS
  • C-FIND to QIDO-RS
  • C-MOVE uses QIDO-RS to determine which instances to transfer, then for each instance executes a WADO-RS request to fetch the instance and a C-STORE request to transfer it to the C-MOVE destination
  • Storage commitment service to QIDO-RS

Note that any C-FIND query on the ModalitiesInStudy tag will result in 1 QIDO-RS query per modality.

Available AET destinations for the C-MOVE and storage commitment services are configured via an AET dictionary json file, which can be specified either by using the "--aet_dictionary" command line parameter or specifying the "ENV_AETS_JSON" environment variable.

The following configuration needs to be added to the dicom-adapter.yaml file to use CMOVE. Please see the Deployment using Kubernetes section for more information.

env:
- name: ENV_AETS_JSON
  valueFrom:
    configMapKeyRef:
      name: aet-dictionary
      key: AETs.json

Here is an example JSON dictionary:

[
	{
		"name": "DEVICE_A", 
		"host": "localhost", 
		"port": 11113
	},
	{
		"name": "DEVICE_B", 
		"host": "192.168.0.1", 
		"port": 11114
	},
	...
]

And command to create configmap from it:

kubectl create configmap aet-dictionary --from-file=AETs.json

The AET dictionary JSON can also be specified directly via the "--aet_dictionary_inline" parameter.

For the list of command line flags, see here

Export Adapter

The Export Adapter listens to Google Cloud Pub/Sub for new instances, fetches them using WADO-RS, then sends them to the client. This binary can be configured to output either C-STORE or STOW-RS via command line flags.

To use Google Cloud Pub/Sub, you require a Google Cloud project. Furthermore, Cloud Pubsub API must be enabled in your Google project. The binary expects that each Cloud Pub/Sub notification consists of the WADO-RS path for the DICOM instance that is to be exported (e.g. /studies/<STUDY_UID>/series/<SERIES_UID>/instances/<INSTANCE_UID>).

For the list of command line flags, see here

Stackdriver Monitoring

Both the Import and Export adapter include support for Stackdriver Monitoring. It is enabled by specifying the --monitoring_project_id parameter, which must be the same project in which the adapter is running. For the list of events logged to Stackdriver for the Export Adapter, see here. For the list of events logged to Stackdriver for the Import Adapter, see here.

The monitored resource is configured as k8s_container, with values set from a combination of environment variables configured via Downward API (pod name, pod namespace and container name) and GCP Metadata (project id, cluster name and location). Defaults to the global resource, if k8s_container can't be configured.

The following configuration needs to be added to the dicom-adapter.yaml file to configure the stackdriver monitoring resource. Please see the Deployment using Kubernetes section for more information.

env:
- name: ENV_POD_NAME
  valueFrom:
    fieldRef:
      fieldPath: metadata.name
- name: ENV_POD_NAMESPACE
  valueFrom:
    fieldRef:
      fieldPath: metadata.namespace
- name: ENV_CONTAINER_NAME
  value: *containerName # referencing earlier anchor in same yaml

DICOM Redactor

The Import Adapter can be configured to use the DICOM Redactor Library to redact sensitive data contained in DICOM tags during a C-STORE upload. The user can configure which tags to redact/remove in one of 3 ways:

  • redact_keep_list - a list of DICOM tags to keep untouched. Other tags are removed.
  • redact_remove_list - a list of DICOM tags to remove. Other tags are kept untouched.
  • redact_filter_profile - a predefined profile that will keep and remove particular tags.

If enabled via one of the above options, the redactor also always regenerates the following UIDs:

  • StudyInstanceUID
  • SeriesInstanceUID
  • SOPInstanceUID
  • MediaStorageSOPInstanceUID

Deployment using Kubernetes

The adapters can be deployed to Google Cloud Platform using [GKE] (https://cloud.google.com/kubernetes-engine/). We have published prebuilt Docker images for the both adapters to Google Container Registry.

  • Import Adapter: gcr.io/cloud-healthcare-containers/healthcare-api-dicom-dicomweb-adapter-import
  • Export Adapter: gcr.io/cloud-healthcare-containers/healthcare-api-dicom-dicomweb-adapter-export

Requirements

Deploying Docker Images to GKE

Create a local file called dicom_adapter.yaml. This file will contain the configuration specifying the number of adapters to deploy, along with their command line flags.

To deploy an Import Adapter, add the following to dicom_adapter.yaml. Modify the flags for your use case.

apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: dicom-adapter
spec:
  replicas: 1
  template:
    metadata:
      labels:
        app: dicom-adapter
    spec:
      containers:
        - name: dicom-import-adapter
          image: gcr.io/cloud-healthcare-containers/healthcare-api-dicom-dicomweb-adapter-import:0.2.29
          ports:
            - containerPort: 2575
              protocol: TCP
              name: "port"
          args:
            - "--dimse_aet=IMPORTADAPTER"
            - "--dimse_port=2575"
            - "--dicomweb_address=https://healthcare.googleapis.com/v1/projects/myproject/locations/us-central1/datasets/mydataset/dicomStores/mydicomstore/dicomWeb"

The yaml configuration has changed slightly from version 0.1 to 0.2. Please see the upgrade guide for instructions on how to upgrade your configuration.

The dicomweb_addr and dicomweb_stow_path parameters have been deprecated, please use the dicomweb_address parameter instead as shown above. The old address parameters will not work with C-FIND, C-MOVE, and storage commitment.

If needed, to additionally include an Export Adapter, you can add the to the containers in dicom_adapter.yaml. Modify the flags for your use case.

        - name: dicom-export-adapter
          image: gcr.io/cloud-healthcare-containers/healthcare-api-dicom-dicomweb-adapter-export:0.2.29
          args:
            - "--peer_dimse_aet=PEERAET"
            - "--peer_dimse_ip=localhost"
            - "--peer_dimse_port=104"
            - "--project_id=myproject"
            - "--subscription_id=mysub"
            - "--dicomweb_addr=https://healthcare.googleapis.com/v1"
            - "--oauth_scopes=https://www.googleapis.com/auth/pubsub"

The peer_dicomweb_addr and peer_dicomweb_stow_path parameters have been deprecated, please use the peer_dicomweb_address parameter instead.

To deploy the configuration to GKE cluster, execute the following:

gcloud container clusters create dicom-adapter --zone=us-central1-a --scopes https://www.googleapis.com/auth/cloud-healthcare,https://www.googleapis.com/auth/pubsub
kubectl create -f dicom_adapter.yaml

If you are deploying an Import Adapter, you can expose the DIMSE port internally (e.g. 2575 here). This can be done through a load balancer. Create a dicom_adapter_load_balancer.yaml, and add the following:

apiVersion: v1
kind: Service
metadata:
  name: dicom-adapter-load-balancer
  # The "Internal" annotation will result in an load balancer that can only
  # be accessed from within the VPC the Kubernetes cluster is in.
  # You can remove this annotation to get an externally accessible load balancer.
  annotations:
    cloud.google.com/load-balancer-type: "Internal"
spec:
  ports:
  - port: 2575
    targetPort: 2575
    protocol: TCP
    name: port
  selector:
    app: dicom-adapter
  type: LoadBalancer

To deploy the load balancer, execute the following:

kubectl create -f dicom_adapter_load_balancer.yaml

The status and IP address of load balancer can be seen by executing:

kubectl get service dicom-adapter-load-balancer

Local Deployment

Instructions on how to run the Import Adapter Docker image locally are available on the wiki.

Deployment using Data Protection Toolkit

The adapters can be deployed as a gke_workload using the data protection toolkit. Sample configuration may be found in this folder.

Building from source

As an alternative to using the prebuilt Docker images, you can build the adapters from source code. Both adapters exist as separate binaries and are built using Gradle. Please refer to these instructions to build Gradle for your system.

For example, to build Import Adapter:

cd import
gradle build

For example, to additionally execute Import Adapter locally:

gradle run -Dexec.args="--dimse_aet=IMPORTADAPTER --dimse_port=4008 --dicomweb_address=http://localhost:80"

Building and publishing Docker Images

To build and upload Import Adapter Docker images:

cd import
PROJECT=<Your Google Cloud Project>
TAG=gcr.io/${PROJECT}/dicom-import-adapter
gradle dockerBuildImage -Pdocker_tag=${TAG}
docker push ${TAG}

To build and upload Export Adapter Docker images:

cd export
PROJECT=<Your Google Cloud Project>
TAG=gcr.io/${PROJECT}/dicom-export-adapter
gradle dockerBuildImage -Pdocker_tag=${TAG}
docker push ${TAG}

Wiki

For addition documentation please see the Wiki. The wiki includes information on advanced features such as:

Troubleshooting

Both the Import and Export adapter output server logs that can be used to diagnose issues. When running on GKE, these server logs show up in Cloud Logging. You can view these logs by navigating to https://console.cloud.google.com/kubernetes/workload, clicking on dicom-adapter deployment and following the link titled "Container logs". Alternatively you can view the logs via kubectl logs <pod-name> where <pod-name> can be found by running kubectl get pods.