Development Environment Installation (Ubuntu)

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Index

[[TOC]]

Acronyms and definitions
Acronym/Definition	Meaning
N/A	N/A

Referenced Documents
Doc No	Doc Title
DOC00001	Radical Imaging Official Documents Template

PURPOSE AND OBJECTIVES

The purpose of this document is to describe the development environment installation of OHIF viewer/Lesion Tracker on Linux Ubuntu.

DEVELOPMENT ENVIRONMENT INSTALLATION

Docker

Docker is an open source software platform to create, deploy and manage virtualized application containers on common operating systems, with several allied tools.

To install Docker, follow the instructions below:

1. Open a terminal, and update the apt package index, by running the following command:

sudo apt-get update

Expected result:

2. Install packages to allow apt to use a repository over HTTPS, by running the following command:

sudo apt-get install apt-transport-https ca-certificates curl software-properties-common

Expected result:

3. Add Docker’s official GPG key, by running the following command:

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -

Expected result:

4. Verify that you now have the key with the fingerprint 9DC8 5822 9FC7 DD38 854A E2D8 8D81 803C 0EBF CD88, by searching for the last 8 characters of the fingerprint after running the following command:

sudo apt-key fingerprint 0EBFCD88

Expected result:

5. Use the following command to set up the stable repository.

sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"

Expected result:

6. Install the latest version of Docker CE, by running the following command:

sudo apt-get install docker-ce

Expected result:

7. Verify that Docker CE is installed correctly by running the hello-world image:

sudo docker run hello-world

Expected result:

Note: Additional information about Docker installation on Linux Ubuntu OS can be foud at https://docs.docker.com/install/linux/docker-ce/ubuntu/.

DCM4CHE

Dcm4che (https://www.dcm4che.org/) is a collection of open source applications and utilities for healthcare.

To install Dcm4che, follow the instructions below:

1. Before start, you need to create the following folders on your *Home *directory:

• DCM4CHEE

• dcm4chee-arc

• db

• ldap

• slapd.d

• storage

• wildfly

2. Create the following files on the DCM4CHEE folder, with the correspondent contents:

docker-compose.env

STORAGE_DIR=/storage/fs1
POSTGRES_DB=pacsdb
POSTGRES_USER=pacs
POSTGRES_PASSWORD=pacs

docker-compose.yml

version: "3"
services:
ldap:
image: dcm4che/slapd-dcm4chee:2.4.44-14.1
logging:
driver: json-file
options:
max-size: "10m"
ports:
- "389:389"
env_file: docker-compose.env
volumes:
- /etc/localtime:/etc/localtime:ro
- /etc/timezone:/etc/timezone:ro
- ~/dcm4chee-arc/ldap:/var/lib/ldap
- ~/dcm4chee-arc/slapd.d:/etc/ldap/slapd.d
db:
image: dcm4che/postgres-dcm4chee:10.4-14
logging:
driver: json-file
options:
max-size: "10m"
ports:
- "5432:5432"
env_file: docker-compose.env
volumes:
- /etc/localtime:/etc/localtime:ro
- /etc/timezone:/etc/timezone:ro
- ~/dcm4chee-arc/db:/var/lib/postgresql/data
arc:
image: dcm4che/dcm4chee-arc-psql:5.14.1
logging:
driver: json-file
options:
max-size: "10m"
ports:
- "8080:8080"
- "8443:8443"
- "9990:9990"
- "11112:11112"
- "2575:2575"
env_file: docker-compose.env
environment:
WILDFLY_CHOWN: /opt/wildfly/standalone /storage
WILDFLY_WAIT_FOR: ldap:389 db:5432
depends_on:
- ldap
- db
volumes:
- /etc/localtime:/etc/localtime:ro
- /etc/timezone:/etc/timezone:ro
- ~/dcm4chee-arc/wildfly:/opt/wildfly/standalone
- ~/dcm4chee-arc/storage:/storage</td>

Files/Folder will become like the image above:

1. Open a terminal inside DCM4CHE folder, and run the following command:

sudo snap install docker

Expected result:

4. Still inside the DCM4CHE folder, run the following command:

sudo docker-compose -p dcm4chee up -d

Expected result:

1. The following commands can be used to control DCM4CHE:

Stop all 3 containers: docker-compose -p dcm4chee stop

Start all 3 containers again: docker-compose -p dcm4chee start

Stop and delete all 3 containers: docker-compose -p dcm4chee down

2. Now it is necessary to import some DICOM studies to DCM4CHE. Before importing these studies, you will need to download them. To do so, access the address http://34.224.187.57:3000/studylist, right click one or more studies, and select the option Export:

3. Confirm the study export on the modal window that will appear:

4. The study(ies) export will begin. You can follow the exporting progress:

5. After the exporting progress, the study(ies) will be downloaded in a file called "studies.zip". Create a folder named “Studies” on your Home folder, and extract this and any other studies you download in this folder:

6. Open the terminal, go to the DCM4CHE folder, and run the following command in order to send the studies to DCM4CHE:

docker run -v ~/Studies/:/tmp --rm --network=dcm4chee_default dcm4che/dcm4che-tools:5.14.0 storescu -cDCM4CHEE@arc:11112 /tmp

Expected result:

7. Now, go to your browser and access the URL http://localhost:8080/dcm4chee-arc/ui2/. Once opened, click on the refresh icon on the most right:

8. The studies received by DCM4CHE will be shown:

9. Open the terminal, go to your Home folder, and run the following command in order to clone viewers repository to your local:

git clone https://github.com/OHIF/Viewers.git

Expected result:

10. Then, enter the Viewers folder, and run the following command in order to make sure that you are in master branch:

git checkout master

Expected result:

11. Now go to OHIFViewer folder and run the following command:

meteor npm install

Expected result:

12. Still on the OHIFViewer folder, run the following command:

./bin/dcm4cheeDICOMWeb.sh

Expected result:

13. Now, go to your browser and access the URL http://localhost:3000. Once opened, change the Study Date filter to start on the year 2000:

14. The imported studies will be show. Double click a study to open it:

Meteor

Meteor is a JavaScript web framework that allows for rapid prototyping and produces cross-platform code.

To install Meteor, follow the instructions below:

Remark: This guide covers the Linux Ubuntu version. Installation instructions can be different on other operating systems.

1. Open a terminal, and run the following command:

curl https://install.meteor.com/ | sh

Expected result:

Starting OHIF Viewer after system restart

These are the steps to run OHIFVIewer after system restart:.

1. Open terminal

2. Access the DCM4CHEE folder, on your Home folder

3. Run the following command in order to start docker containers:

docker-compose -p dcm4chee start

4. Access the Viewers/OHIFViewer folder, on your Home folder

5. Run the following command in order to run OHIF Viewer:

./bin/dcm4cheeDICOMWeb.sh

6. Access the address http://localhost:3000