5. How to run a Reference Pipeline¶
Clara Deploy SDK comes bundled with a set of reference pipelines. This section provides general guidelines on how to execute them on your local development machine. For information specific to a reference pipeline, please view the documentation of that pipeline.
5.1. Select a Reference Pipeline¶
Create a directory called “my-pipelines” in your development machine where you will store your pipelines.
Clara Reference Pipelines and associated artifacts are available at:
ReconPipelineunder the directory mentioned above and copy the yaml file
my-pipelinesdirectory. The yaml file provides the definition of the reference pipeline.
5.2. External DICOM Sender and DICOM Receiver¶
You need an external DICOM Service Class User (SCU) application to send images to the Clara DICOM Adapter (acting as a DICOM SCP). Similarly when your pipeline finishes executing, you may want to send the output to an external DICOM receiver.
For this example we will use the open-source DICOM toolkit DCMTK to provide the DICOM sender and DICOM receiver functionality.
5.2.1. Install DCMTK¶
Install DCMTK utilities by issuing the following command:
sudo apt-get install dcmtk
5.2.2. Setup an External DICOM Receiver¶
You can use the storescp utility as an external DICOM receiver. Open a terminal and run the following command to setup a DICOM Receiver. Create a directory in your machine where DICOM images produced by Clara Deploy SDK will be stored. We will refer to that directory as “dicom-destination-directory”
mkdir dicom-destination-directory cd dicom-destination-directory sudo storescp -v --fork -aet MYPACS 1004
MYPACS is the Application Entity (AE) title of the external DICOM Receiver.
1004 is the port number where
storescp would be listening for any incoming DICOM traffic. Please note that the IP address will be the same as the local system.
5.2.3. Setup an External DICOM Sender¶
You can use the storescu utility from DCMTK as a DICOM sender.
5.3. Publish the Pipeline¶
Publishing a pipeline registers it with the platform. Once a pipeline is registered, it is represented with an ID. Follow the steps below:
Open a terminal and navigate to the directory
my-pipelineswhich contains the reference pipeline
Publish the pipeline by issuing the following command
clara create pipelines -p ct-recon.yaml
Clara CLI should successfully submit the pipeline and in return should print a pipeline ID.
Note down this pipeline ID as it would be used in a later section to define a new pipeline mapping in the DICOM adapter.
Verify that the pipeline is correctly stored by issuing the following command
kubectl get pipeline
In the list of pipeline IDs, you should see the pipeline ID created in the previous step.
5.4. Configure the Clara DICOM Destination¶
When you send images to the Clara Deploy SDK, the DICOM Adapter component acts as the internal DICOM Service Class Provider or a receiving agent.
Open the file
In the dicom->scp->sources section, ensure sender host-ip and ae-titles are correct. Alternatively, set reject-unknown-sources to false, which will allow any DICOM sender to create an association.
dicom: scp: reject-unknown-sources: false sources: - host-ip: 172.22.8.156 ae-title: DCM4CHEE
In the dicom->scp->ae-titles section, add a new ae-title with the name “CTRecon”
dicom: scp: ae-titles: - ae-title: CTRecon
Per the DICOM standard, the length of AE-Title should not exceed 16 characters.
In the pipeline-mappings section, define a new mapping with: “my-ct-recon-pipeline” as the name and
clara-ae-title, and use the pipeline-id that was created before.
pipeline-mappings: - name: my-ct-recon-pipeline clara-ae-title: CTRecon pipeline-id: [your-pipeline-id-from-above]
Update the IP address of the destination with the name
MYPACSby updating the field host-ip with the IP of your local development machine.
dicom: scu: destinations: - name: MYPACS host-ip: [IP-address-of-remote-PACS] port: 1004 ae-title: MYPACS
Restart the DICOM server by issuing the following commands:
# Stop DICOM Adapter by running the following command: clara dicom stop # Run the following command to check whether the DICOM adapter pod is still running: kubectl get pods | grep clara-dicom-adapter # Once the DICOM adapter pod is fully stopped and no pod is returned with the above command, the DICOM adapter can be started by running the following command: clara dicom start
Verify that the DICOM Adapter is correctly started:
helm ls | grep dicom-adapter kubectl get pods | grep dicom-adapter
5.5. Trigger Pipeline¶
A pipeline is triggered when a DICOM series is sent to the specific AE title of the Clara DICOM Adapter which is associated with that pipeline. To trigger this pipeline, you will need to have a set of relevant DICOM images that can be used as source input data.
For this created pipeline, a sample lung dataset in dicom format is available within the SDK in
/path-to-clara-deploy-installer/test-data/nvrtk_sample_d1_dicom_raw_0.0.1.zip. It can be extracted in the test-data folder using unzip.
cd /path-to-clara-deploy-installer/test-data unzip nvrtk_sample_d1_dicom_raw_0.0.1.zip
Open a terminal and go to the directory which contains all your DICOM images.
Trigger the pipeline (push DICOM data to the proper ae title)
storescu -v +sd +r -xb -aet "DCM4CHEE" -aec "CTRecon" AA.BBB.CC.DD 104 ./
Replace “AA.BBB.CC.DD” with the IP of your local machine.
When the above step is successfully completed, you should see the following result in the terminal
I: Received Store Response (Success) <br> I: Releasing Association
5.6. Verify the Pipeline Execution in Dashboard¶
Go to the Clara dashboard UI using a web browser: The URL is:
<IP of the machine>:8000
You should see a job with a name that includes the name of the pipeline you created
You can inspect the status of each operator inside that job
5.7. Verify That the External DICOM Receiver Received Your Images¶
If your pipeline outputs DICOM images and sends them to an external DICOM
receiver, you may want to verify that the images were indeed received. If you
storescp utility from DCMTK as mentioned earlier, please use a terminal
to navigate to the “dicom-destination-directory” and verify whether the expected
images are stored there. In addition, you may want to use a third party DICOM
viewer to view those images.