diff --git a/docs/OHIF-Viewer/environment-installations.md b/docs/OHIF-Viewer/environment-installations.md new file mode 100644 index 000000000..ba5c0ca6a --- /dev/null +++ b/docs/OHIF-Viewer/environment-installations.md @@ -0,0 +1,395 @@ +**Development Environment Installation (Ubuntu)** + +**CONFIDENTIAL DOCUMENT** + +This is a confidential document and property of Radical Imaging LLC. It shall not be transmitted, copied or sent to anyone without prior authorization. + +**Index** + +[[TOC]] + + + + + + + + + + + + + + +
Acronyms and definitions
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Referenced Documents
Doc NoDoc Title
DOC00001Radical 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: + +![image alt text](image_0.png) + +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: + +![image alt text](image_1.png) + +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: + +![image alt text](image_2.png) + +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: + +![image alt text](image_3.png) + +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: + +![image alt text](image_4.png) + +6. Install the latest version of Docker CE, by running the following command: + +sudo apt-get install docker-ce + +Expected result: + +![image alt text](image_5.png) + +7. Verify that Docker CE is installed correctly by running the hello-world image: + +sudo docker run hello-world + +Expected result: + +![image alt text](image_6.png) + +**Note**: Additional information about Docker installation on Linux Ubuntu OS can be foud at [https://docs.docker.com/install/linux/docker-ce/ubuntu/](https://docs.docker.com/install/linux/docker-ce/ubuntu/). + +## DCM4CHE + +Dcm4che ([https://www.dcm4che.org/](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
+ + +Files/Folder will become like the image above: + +![image alt text](image_7.png) + +3. Open a terminal inside DCM4CHE folder, and run the following command: + +sudo snap install docker + +Expected result: + +![image alt text](image_8.png) + +4. Still inside the DCM4CHE folder, run the following command: + +sudo docker-compose -p dcm4chee up -d + +Expected result: + +![image alt text](image_9.png) + +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](http://34.224.187.57:3000/studylist), right click one or more studies, and select the option Export: + +![image alt text](image_10.png) + +3. Confirm the study export on the modal window that will appear: + +![image alt text](image_11.png) + +4. The study(ies) export will begin. You can follow the exporting progress: + +![image alt text](image_12.png) + +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: + +![image alt text](image_13.png) + +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: + +![image alt text](image_14.png) + +7. Now, go to your browser and access the URL [http://localhost:8080/dcm4chee-arc/ui2/](http://localhost:8080/dcm4chee-arc/ui2/). Once opened, click on the refresh icon on the most right: + +![image alt text](image_15.png) + +8. The studies received by DCM4CHE will be shown: + +![image alt text](image_16.png) + +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: + +![image alt text](image_17.png) + +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: + +![image alt text](image_18.png) + +11. Now go to OHIFViewer folder and run the following command: + +meteor npm install + +Expected result: + +![image alt text](image_19.png) + +12. Still on the OHIFViewer folder, run the following command: + +./bin/dcm4cheeDICOMWeb.sh + +Expected result: + +![image alt text](image_20.png) + +13. Now, go to your browser and access the URL [http://localhost:3000](http://localhost:3000). Once opened, change the Study Date filter to start on the year 2000: + +![image alt text](image_21.png) + +14. The imported studies will be show. Double click a study to open it: + +![image alt text](image_22.png) + +## 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: + +![image alt text](image_23.png) + +## 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](http://localhost:3000) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +