LinkedDicom

This repository provides a basic version of the LinkedDicom package and project. You can use this LinkedDicom package as an API to include in your project, or as a command-line utility. Mind this repository is work-in-progress and has not been finalised yet.

The following content is available:

• The ontology used is available in the folder ./ontology.
• The main contents of the python package are available in ./package
• An example for using the package (as a python API, and for example SPARQL queries) is available in ./examples
• The use as command-line utility is below

Installation instructions

Currently, the tool has been tested with Python version 3.8.10. You can find the installation instructions for python here.

Afterwards, you can run the following command to install the package from PyPI:

pip install LinkedDicom

Use as command-line utility

At the moment, there are two command line utilities:

• Parsing folders locally using ldcm-parse
• A DICOM SCP service using ldcm-scp

Parsing folders locally

This tool can be usefull if you have a (limited) folder of DICOM files and want to create a local turtle file. A full description of the command is given when executing ldcm-parse --help.

A copy of this help is presented below:

Usage: ldcm-parse [OPTIONS] DICOM_INPUT_FOLDER

  Search the DICOM_INPUT_FOLDER for dicom files, and process these files. The
  resulting turtle file will be stored in linkeddicom.ttl within this folder

Options:
  -o, --ontology-file TEXT  Location of ontology file to use for override.
  -fp, --file-persistent    Store file path while parsing metadata.
  --help                    Show this message and exit.

The output is saved in linkeddicom.ttl in the DICOM_INPUT_FOLDER. This data can be used by importing it into an RDF endpoint (such as Apache Jena or GraphDB). If you want to use the files afterwards to calculate DVH parameters, you need to include the -fp option.

Calculating DVH curves locally

Based on the previous parsing (ldcm-parse) you can calculate DVH curve results and store them in a JSON-LD file (per RTSTRUCT-RTDOSE combination). Currently, the combination is being calculated following the references in the DICOM file:

• RTDOSE references to RTPlan
• RTPlan references to RTStruct

A copy of this help is presented below:

Usage: ldcm-calc-dvh [OPTIONS] LDCM_RDF_LOCATION OUTPUT_LOCATION

Options:
  --help  Show this message and exit.

DICOM SCP service

This tool can be used if you want to start a DICOM SCP service which supports C-STORE commands. A full description of the command is given when executing ldcm-scp --help.

A copy of this help is presented below:

Usage: ldcm-scp [OPTIONS] PORT

  Create a DICOM SCP which can accept C-STORE commands. For every association,
  an analysis is triggered on association close. For every association close,
  the analysis is triggered in a separate thread.

Options:
  -o, --ontology-file TEXT       Location of ontology file to use for
                                 override.
  -s, --sparql-endpoint TEXT     SPARQL endpoint URL to post the resulting
                                 triples towards
  -dvh, --dose-volume-histogram  Compute and store DVH for all available structures.
  --help                         Show this message and exit.

By default, the UUID for the DICOM association is used as filename for the created local turtle file. If someone uses the optional -s tag, users can send data to a specific SPARQL endpoint (e.g. GraphDB or other SPARQL endpoints). An example URL is given below. Mind that there is a named graph (http://ldcm.local/) specified. This is optional and depends on the REST-API possibilities.

ldcm-scp -s "https://graphdb.jvsoest.eu/repositories/public_dump/statements?context\=%3Chttp://ldcm.local/%3E" 104

Afterwards, you can send data using DICOM protocol to this service using e.g. DCMTK. For example using the command below:

storescu +r +sd localhost 104 ./