Difference between revisions of "Connectathon Tool Installation"

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(Central Archive Software)
(Central Archive Data Files)
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==Central Archive Data Files==
 
==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.
 +
 +
:<code> git clone https://github.com/IHE-Tools/dicom-connectathon.git</code>
 +
:<code> cd data-sets/scripts</code>
 +
:<code> ./get_NA2020.sh [folder]</code>
 +
 +
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:
 +
:<code> ./store_NA2020.sh [folder]</code>
 +
 +
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.

Revision as of 15:35, 14 February 2020

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.git
cd 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.git
cd 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.