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.

Download the Reference Pipeline

Please refer to Setup section for downloading this Pipeline.

Run Reference Pipelines by Sending DICOM Instances Over Network

Many reference pipelines are triggered by Clara DICOM Adaptor after it has received DICOM instances from external sender to one of its mapped AE Titles. This section explains the process with an example Series Selection Pipeline.

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 external DICOM sender and DICOM receiver functionality.

Install DCMTK

Install DCMTK utilities by issuing the following command:

sudo apt-get install dcmtk

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 set up 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.

Setup an External DICOM Sender

You can use the storescu utility from DCMTK as a DICOM sender.

Create the Pipeline

Please refer to Setup section to create this Pipeline.

Note: Note down the pipeline ID as it would be used in a later section to define a new pipeline mapping in the DICOM adapter.

Configure the Clara DICOM Adapter

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.

Please refer to Clara DICOM Adapter for setup instructions.

Trigger Pipeline

A pipeline is triggered when DICOM instances are 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 pipeline, a sample test dataset in dicom format is available within the package in <unzipped input>/dcm.

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 "SeriesSelect" AA.BB.CC.DD 104 ./

Replace "AA.BB.CC.DD" with the IP of your local machine.

When the above step is completed, you should see the following result in the terminal

I: Received Store Response (Success) <br>
I: Releasing Association

Verify the Pipeline Execution in Management Console

Go to the Clara Management Console using a web browser: The URL is: <IP of the machine>:32002
Go to the JOBS view. You should see a job with a name that includes the name of the job you specified (e.g. series-selection)
You can inspect the status of each operator inside that job

Please check Clara Management Console to see the web application in detail.

Download and Verify the Outputs

Once the job has completed successfully, download the output payload by using clara download command.