Connectathon Tool Installation
Introduction
The sections below do not repeat the use of the tools. They assume the reader understands why the tool is needed for a Connectathon.
Central Archive
Central Archive Software
We use the DCM4CHEE Archive 5 that is described here: https://www.dcm4che.org. For January 2020, we installed and configured using the Docker version:
git clone https://github.com/IHE-Tools/dicom-connectathon.gitcd dicom-connectathon/dcm4chee/scripts
Review the file master_run.sh. It has a ROOT variable that points to a folder that should exist and will be used to hold files.
- Change that value to match your installation
- You might have to tell docker about that folder to provide access.
./master_run.sh
You now have this version of dcm4chee running:
- dcm4che/dcm4chee-arc-psql:5.10.5
You could certainly modify the dcm4chee_run.sh script to use a different version. Note that we did not use Docker compose. The files in the docker-compose folder were not tested to completion.
Central Archive Data Files
The section Central Archive Software gave you a pointer to a git repository to pull configuration files. That same repository has scripts to retrieve DICOM files and place them on the Central Archive.
git clone https://github.com/IHE-Tools/dicom-connectathon.gitcd data-sets/scripts./get_NA2020.sh [folder]
The last script retrieves a number of data sets (complete list below) and places them in the folder you specify. If you omit <folder>, the files are stored in /opt/connectathon-2020/data-sets.
Some of the data sets contain non-DICOM images. The get_NA2020.sh script removes those files in a hard coded way. If you extend the script, you will have to take this into consideration.
To store the images to the Central Archive:
./store_NA2020.sh [folder]
This script walks through all of the files stored in <folder> and sends them to the Central Archive using DICOM C-Store. If <folder> is not specified, the default value /opt/connectathon-2020/data-sets is used.
- This script is hard coded to send to a PACS with these parameters: DCM4CHEE:localhost:11112. That is easy to change in one place.
- The script assumes that all files under <folder> are DICOM files. It will abort if it runs into non-DICOM files.
- This script assumes that the dcm4che command line tools are installed and are on the PATH of the current user. You can use a different command line tool by modifying store.sh.
Images Retrieved by the NA 2020 Scripts
| Data Set | Location |
|---|---|
| (3) GE Synocrystal Images | ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/MAMMO_Samples/2019-EU-Samples/GE%20Senocrystal%20Images/STORE/51346117/70288881 |
| (4) IMSGIOTTO Images | ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/MAMMO_Samples/2018_EU_Samples/IMSGIOTTO_MOD_RAFFAELLO |
| (5) GE DBT samples | ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/DBT_samples/2017-EU-Samples/GEHC/ |
| (6) IMSGIOTTO Images | ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/DBT_samples/2018-EU-Samples/ |
| (7) Siemens images | ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/DBT_samples/2017-EU-Samples/Siemens/ |
| (8) GE samples | ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/REM-NM_samples/GE_NM_830 |
| (9) Toshiba samples | ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/REM-NM_samples/MOD_TOSHIBA_1 |
FHIR Read-Write Server (HAPI FHIR Server)
- Clone a copy of the HAPI-FHIR server
- Checkout the appropriate branch or version. For NA 2020, we used v4.1.0. Your event may use a more recent version.
cd hapi-fhirgit checkout v4.1.0
- Modify source code
There are small changes necessary to configure the software. These are completed directly in the source code and not in a configuration file. Please see HAPI FHIR Software for IHE Connectathons
- Build the war file
Use the mvn command to build the war file. You want to use the flag -DskipTests unless you want to wait a long time for the unit tests to complete.
mvn -DskipTests install
Structure Sets and Other Test Data
XDS-I Software
Mitre Canary
The Mitre Canary software used during the NA 2020 Connectahon was managed using docker:
docker run --rm -p 18080:80 adammitre/canary:2.12.0
This provided a URL of the form: http://host:18080
Notes for NA 2020
- The original suggestion was to run the latest version of the software. The authors discovered something and asked us to run the specific version listed above (2.12.0).
- It will certainly be worth revisiting the versioning information in future years.