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init: sudah ganti logo, hilangin setting, dan investigational use dialog

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.browserslistrc Normal file
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# Browsers that we support
> 1%
IE 11
not dead
not op_mini all

495
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version: 2.1
orbs:
codecov: codecov/codecov@1.0.5
cypress: cypress-io/cypress@3.4.2
defaults: &defaults
docker:
- image: cimg/node:20.18.1
environment:
TERM: xterm
QUICK_BUILD: true
working_directory: ~/repo
commands:
install_bun:
steps:
- restore_cache:
keys:
- bun-cache-v2-{{ arch }}-latest
- run:
name: Install Bun
command: |
if [ ! -d "$HOME/.bun" ]; then
curl -fsSL https://bun.sh/install | bash
fi
echo 'export BUN_INSTALL="$HOME/.bun"' >> $BASH_ENV
echo 'export PATH="$BUN_INSTALL/bin:$PATH"' >> $BASH_ENV
source $BASH_ENV
- save_cache:
key: bun-cache-v2-{{ arch }}-latest
paths:
- ~/.bun
jobs:
UNIT_TESTS:
<<: *defaults
resource_class: large
steps:
- install_bun
- run: node --version
- checkout
- run:
name: Install Dependencies
command: bun install --no-save
# RUN TESTS
- run:
name: 'JavaScript Test Suite'
command: bun run test:unit:ci
# platform/app
- run:
name: 'VIEWER: Combine report output'
command: |
viewerCov="/home/circleci/repo/platform/app/coverage"
touch "${viewerCov}/reports"
cat "${viewerCov}/clover.xml" >> "${viewerCov}/reports"
echo "\<<\<<\<< EOF" >> "${viewerCov}/reports"
cat "${viewerCov}/lcov.info" >>"${viewerCov}/reports"
echo "\<<\<<\<< EOF" >> "${viewerCov}/reports"
- codecov/upload:
file: '/home/circleci/repo/platform/app/coverage/reports'
flags: 'viewer'
# PLATFORM/CORE
- run:
name: 'CORE: Combine report output'
command: |
coreCov="/home/circleci/repo/platform/core/coverage"
touch "${coreCov}/reports"
cat "${coreCov}/clover.xml" >> "${coreCov}/reports"
echo "\<<\<<\<< EOF" >> "${coreCov}/reports"
cat "${coreCov}/lcov.info" >> "${coreCov}/reports"
echo "\<<\<<\<< EOF" >> "${coreCov}/reports"
- codecov/upload:
file: '/home/circleci/repo/platform/core/coverage/reports'
flags: 'core'
BUILD:
<<: *defaults
resource_class: large
steps:
# Checkout code and ALL Git Tags
- checkout
- install_bun
- run:
name: Install Dependencies
command: bun install --no-save
# Build & Test
- run:
name: 'Perform the versioning before build'
command: bun ./version.mjs
- run:
name: 'Build the OHIF Viewer'
command: bun run build
no_output_timeout: 45m
- run:
name: 'Upload SourceMaps, Send Deploy Notification'
command: |
# export FILE_1=$(find ./build/static/js -type f -name "2.*.js" -exec basename {} \;)
# export FILE_MAIN=$(find ./build/static/js -type f -name "main.*.js" -exec basename {} \;)
# export FILE_RUNTIME_MAIN=$(find ./build/static/js -type f -name "runtime~main.*.js" -exec basename {} \;)
# curl https://api.rollbar.com/api/1/sourcemap -F source_map=@build/static/js/$FILE_1.map -F access_token=$ROLLBAR_TOKEN -F version=$CIRCLE_SHA1 -F minified_url=https://$GOOGLE_STORAGE_BUCKET/static/js/$FILE_1
# curl https://api.rollbar.com/api/1/sourcemap -F source_map=@build/static/js/$FILE_MAIN.map -F access_token=$ROLLBAR_TOKEN -F version=$CIRCLE_SHA1 -F minified_url=https://$GOOGLE_STORAGE_BUCKET/static/js/$FILE_MAIN
# curl https://api.rollbar.com/api/1/sourcemap -F source_map=@build/static/js/$FILE_RUNTIME_MAIN.map -F access_token=$ROLLBAR_TOKEN -F version=$CIRCLE_SHA1 -F minified_url=https://$GOOGLE_STORAGE_BUCKET/static/js/$FILE_RUNTIME_MAIN
curl --request POST https://api.rollbar.com/api/1/deploy/ -F access_token=$ROLLBAR_TOKEN -F environment=$GOOGLE_STORAGE_BUCKET -F revision=$CIRCLE_SHA1 -F local_username=CircleCI
# Persist :+1:
- persist_to_workspace:
root: ~/repo
paths:
- platform/app/dist
- Dockerfile
- version.txt
- commit.txt
- version.json
BUILD_PACKAGES_QUICK:
<<: *defaults
resource_class: large
steps:
- install_bun
# Checkout code and ALL Git Tags
- checkout
- attach_workspace:
at: ~/repo
- run:
name: Install Dependencies
command: bun install --frozen-lockfile
- run:
name: Avoid hosts unknown for github
command: |
rm -rf ~/.ssh
mkdir ~/.ssh/
echo -e "Host github.com\n\tStrictHostKeyChecking no\n" > ~/.ssh/config
git config --global user.email "danny.ri.brown+ohif-bot@gmail.com"
git config --global user.name "ohif-bot"
- run:
name: Authenticate with NPM registry
command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
- run:
name: build half of the packages (to avoid out of memory in circleci)
command: |
bun run build:package-all
- run:
name: build the other half of the packages
command: |
bun run build:package-all-1
NPM_PUBLISH:
<<: *defaults
resource_class: large
steps:
- install_bun
# Checkout code and ALL Git Tags
- checkout
- attach_workspace:
at: ~/repo
- run:
name: Install Dependencies
command: bun install --no-save
- run:
name: Avoid hosts unknown for github
command: |
rm -rf ~/.ssh
mkdir ~/.ssh/
echo -e "Host github.com\n\tStrictHostKeyChecking no\n" > ~/.ssh/config
git config --global user.email "danny.ri.brown+ohif-bot@gmail.com"
git config --global user.name "ohif-bot"
- run:
name: Authenticate with NPM registry
command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
- run:
name: build half of the packages (to avoid out of memory in circleci)
command: |
bun run build:package-all
- run:
name: build the other half of the packages
command: |
bun run build:package-all-1
- run:
name: increase min time out
command: |
npm config set fetch-retry-mintimeout 20000
- run:
name: increase max time out
command: |
npm config set fetch-retry-maxtimeout 120000
- run:
name: publish package versions
command: |
bun ./publish-version.mjs
- run:
name: Again set the NPM registry (was deleted in the version script)
command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
- run:
name: publish package dist
command: |
bun ./publish-package.mjs
- persist_to_workspace:
root: ~/repo
paths:
- .
DOCKER_RELEASE_PUBLISH:
<<: *defaults
resource_class: large
steps:
- attach_workspace:
at: ~/repo
- setup_remote_docker:
docker_layer_caching: false
- run:
name: Build Docker image for amd64
command: |
# This file will exist if a new version was published by
# our command in the previous job.
if [[ ! -e version.txt ]]; then
exit 0
else
# Remove npm config
rm -f ./.npmrc
# Set our version number using vars
export IMAGE_VERSION=$(cat version.txt)
export IMAGE_VERSION_FULL=v$IMAGE_VERSION
echo $IMAGE_VERSION
echo $IMAGE_VERSION_FULL
# Build our amd64 image, auth, and push
docker build --platform linux/amd64 --tag ohif/app:$IMAGE_VERSION_FULL-amd64 --tag ohif/app:latest-amd64 .
echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
docker push ohif/app:$IMAGE_VERSION_FULL-amd64
docker push ohif/app:latest-amd64
fi
- persist_to_workspace:
root: ~/repo
paths:
- .
DOCKER_RELEASE_PUBLISH_ARM:
<<: *defaults
resource_class: arm.large
steps:
- attach_workspace:
at: ~/repo
- setup_remote_docker:
docker_layer_caching: false
- run:
name: Build Docker image for arm64
command: |
# This file will exist if a new version was published by
# our command in the previous job.
if [[ ! -e version.txt ]]; then
exit 0
else
# Remove npm config
rm -f ./.npmrc
# Set our version number using vars
export IMAGE_VERSION=$(cat version.txt)
export IMAGE_VERSION_FULL=v$IMAGE_VERSION
echo $IMAGE_VERSION
echo $IMAGE_VERSION_FULL
# Build our arm64 image, auth, and push
docker build --platform linux/arm64 --tag ohif/app:$IMAGE_VERSION_FULL-arm64 --tag ohif/app:latest-arm64 .
echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
docker push ohif/app:$IMAGE_VERSION_FULL-arm64
docker push ohif/app:latest-arm64
fi
- persist_to_workspace:
root: ~/repo
paths:
- .
DOCKER_BETA_PUBLISH:
<<: *defaults
resource_class: large
steps:
- attach_workspace:
at: ~/repo
- setup_remote_docker:
docker_layer_caching: false
- run:
name: Build Docker image for amd64 (Beta)
command: |
echo $(ls -l)
# This file will exist if a new version was published by
# our command in the previous job.
if [[ ! -e version.txt ]]; then
echo "don't have version txt"
exit 0
else
echo "Building and pushing Docker image from the master branch (beta releases)"
rm -f ./.npmrc
# Set our version number using vars
export IMAGE_VERSION=$(cat version.txt)
export IMAGE_VERSION_FULL=v$IMAGE_VERSION
echo $IMAGE_VERSION
echo $IMAGE_VERSION_FULL
# Build our amd64 image, auth, and push
docker build --platform linux/amd64 --tag ohif/app:$IMAGE_VERSION_FULL-amd64 --tag ohif/app:latest-beta-amd64 .
echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
docker push ohif/app:$IMAGE_VERSION_FULL-amd64
docker push ohif/app:latest-beta-amd64
fi
DOCKER_BETA_PUBLISH_ARM:
<<: *defaults
resource_class: arm.large
steps:
- attach_workspace:
at: ~/repo
- setup_remote_docker:
docker_layer_caching: false
- run:
name: Build Docker image for arm64 (Beta)
command: |
echo $(ls -l)
# This file will exist if a new version was published by
# our command in the previous job.
if [[ ! -e version.txt ]]; then
echo "don't have version txt"
exit 0
else
echo "Building and pushing ARM64 Docker image from the master branch (beta releases)"
rm -f ./.npmrc
# Set our version number using vars
export IMAGE_VERSION=$(cat version.txt)
export IMAGE_VERSION_FULL=v$IMAGE_VERSION
echo $IMAGE_VERSION
echo $IMAGE_VERSION_FULL
# Build our arm64 image, auth, and push
docker build --platform linux/arm64 --tag ohif/app:$IMAGE_VERSION_FULL-arm64 --tag ohif/app:latest-beta-arm64 .
echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
docker push ohif/app:$IMAGE_VERSION_FULL-arm64
docker push ohif/app:latest-beta-arm64
fi
CYPRESS:
<<: *defaults
resource_class: large
parallelism: 8
steps:
- install_bun
- run:
name: Install System Dependencies
command: |
sudo apt-get update
sudo apt-get install -y xvfb libgtk2.0-0 libgtk-3-0 libgbm-dev libnotify-dev libgconf-2-4 libnss3 libxss1 libasound2 libxtst6
- run:
name: Start Xvfb
command: Xvfb :99 -screen 0 1920x1080x24 &
background: true
- run:
name: Export Display Variable
command: export DISPLAY=:99
- cypress/install:
install-command: bun install --no-save
package-manager: yarn
- cypress/run-tests:
cypress-command: |
npx wait-on@latest http://localhost:3000 && cd platform/app && npx cypress run --record --parallel
start-command: bun run test:data && bun run test:e2e:serve
DOCKER_MULTIARCH_MANIFEST:
<<: *defaults
resource_class: large
steps:
- attach_workspace:
at: ~/repo
- setup_remote_docker:
docker_layer_caching: false
- run:
name: Create and push multi-architecture manifest
command: |
# This file will exist if a new version was published by
# our command in the previous job.
if [[ ! -e version.txt ]]; then
exit 0
else
echo "Building and pushing multi-architecture manifest from the master branch (release releases)"
rm -f ./.npmrc
# Set our version number using vars
export IMAGE_VERSION=$(cat version.txt)
export IMAGE_VERSION_FULL=v$IMAGE_VERSION
echo $IMAGE_VERSION
echo $IMAGE_VERSION_FULL
echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
# Create and push manifest for specific version
docker manifest create ohif/app:$IMAGE_VERSION_FULL \
--amend ohif/app:$IMAGE_VERSION_FULL-amd64 \
--amend ohif/app:$IMAGE_VERSION_FULL-arm64
docker manifest push ohif/app:$IMAGE_VERSION_FULL
# Create and push manifest for "latest" tag
docker manifest create ohif/app:latest \
--amend ohif/app:latest-amd64 \
--amend ohif/app:latest-arm64
docker manifest push ohif/app:latest
fi
DOCKER_BETA_MULTIARCH_MANIFEST:
<<: *defaults
resource_class: large
steps:
- attach_workspace:
at: ~/repo
- setup_remote_docker:
docker_layer_caching: false
- run:
name: Create and push multi-architecture manifest (Beta)
command: |
echo $(ls -l)
# This file will exist if a new version was published by
# our command in the previous job.
if [[ ! -e version.txt ]]; then
exit 0
else
echo "Building and pushing multi-architecture manifest from the master branch (beta releases)"
rm -f ./.npmrc
# Set our version number using vars
export IMAGE_VERSION=$(cat version.txt)
export IMAGE_VERSION_FULL=v$IMAGE_VERSION
echo $IMAGE_VERSION
echo $IMAGE_VERSION_FULL
echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
# Create and push manifest for specific beta version
docker manifest create ohif/app:$IMAGE_VERSION_FULL \
--amend ohif/app:$IMAGE_VERSION_FULL-amd64 \
--amend ohif/app:$IMAGE_VERSION_FULL-arm64
docker manifest push ohif/app:$IMAGE_VERSION_FULL
# Create and push manifest for "latest-beta" tag
docker manifest create ohif/app:latest-beta \
--amend ohif/app:latest-beta-amd64 \
--amend ohif/app:latest-beta-arm64
docker manifest push ohif/app:latest-beta
fi
workflows:
PR_CHECKS:
jobs:
- BUILD_PACKAGES_QUICK:
filters:
branches:
ignore: master
- UNIT_TESTS
- CYPRESS:
name: 'Cypress Tests'
context: cypress
# viewer-dev.ohif.org
DEPLOY_MASTER:
jobs:
- BUILD:
filters:
branches:
only: master
- NPM_PUBLISH:
requires:
- BUILD
- DOCKER_BETA_PUBLISH:
requires:
- NPM_PUBLISH
- DOCKER_BETA_PUBLISH_ARM:
requires:
- DOCKER_BETA_PUBLISH
- DOCKER_BETA_MULTIARCH_MANIFEST:
requires:
- DOCKER_BETA_PUBLISH_ARM
# viewer.ohif.org
DEPLOY_RELEASE:
jobs:
- BUILD:
filters:
branches:
only: /^release\/.*/
- HOLD_FOR_APPROVAL:
type: approval
requires:
- BUILD
- NPM_PUBLISH:
requires:
- HOLD_FOR_APPROVAL
- DOCKER_RELEASE_PUBLISH:
requires:
- NPM_PUBLISH
- DOCKER_RELEASE_PUBLISH_ARM:
requires:
- DOCKER_RELEASE_PUBLISH
- DOCKER_MULTIARCH_MANIFEST:
requires:
- DOCKER_RELEASE_PUBLISH_ARM

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[codespell]
skip = .git,*.pdf,*.svg,yarn.lock,*.min.js,locales
# ignore words ending with … and some camelcased variables and names
ignore-regex = \b\S+…\S*|\b(doubleClick|afterAll|PostgresSQL)\b|\bWee, L\.|.*te.*Telugu.*
# some odd variables
ignore-words-list = datea,ser,childrens

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# Docker compose files
This folder contains docker-compose files used to spin up OHIF-Viewer with
different options such as locally or with any PAS you desire to
## Public Server
## Local Orthanc
### Build
`$ docker-compose -f docker-compose-orthanc.yml build`
### Run
Starts containers and leaves them running in the background.
`$ docker-compose -f docker-compose-orthanc.yml up -d`
then, access the application at [http://localhost](http://localhost)
**remember that you have to access orthanc application and include your studies
there**
## Local Dcm4chee
#### build
`$ docker-compose -f docker-compose-dcm4chee.yml build`
#### run
`$ docker-compose -f docker-compose-dcm4chee.yml up -d`
then, access the application at [http://localhost](http://localhost)
**remember that you have to access dcm4chee application and include your studies
there** You can use the following command to import your studies into dcm4che
`$ docker run -v {YOUR_STUDY_FOLDER}:/tmp --rm --network=docker_dcm4che_default dcm4che/dcm4che-tools:5.14.0 storescu -cDCM4CHEE@arc:11112 /tmp`
**make sure that your Docker network name is docker_dcm4chee_default or change
it to the right one**

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server {
gzip_static always;
gzip_proxied expired no-cache no-store private auth;
gunzip on;
listen ${PORT} default_server;
listen [::]:${PORT} default_server;
location / {
root /usr/share/nginx/html;
index index.html index.htm;
try_files $uri $uri/ /index.html;
add_header Cross-Origin-Resource-Policy same-origin;
proxy_set_header Host $host;
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Proto $http_x_forwarded_proto;
}
error_page 500 502 503 504 /50x.html;
location = /50x.html {
root /usr/share/nginx/html;
}
}

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server {
listen ${SSL_PORT} ssl http2 default_server;
listen [::]:${SSL_PORT} ssl http2 default_server;
ssl_certificate /etc/ssl/certs/ssl-certificate.crt;
ssl_certificate_key /etc/ssl/private/ssl-private-key.key;
location / {
root /usr/share/nginx/html;
index index.html index.htm;
try_files $uri $uri/ /index.html;
add_header Cross-Origin-Resource-Policy same-origin;
proxy_set_header Host $host;
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Proto $http_x_forwarded_proto;
}
error_page 500 502 503 504 /50x.html;
location = /50x.html {
root /usr/share/nginx/html;
}
}

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#!/bin/sh
if [ -n "$SSL_PORT" ]
then
envsubst '${SSL_PORT}:${PORT}' < /usr/src/default.ssl.conf.template > /etc/nginx/conf.d/default.conf
else
envsubst '${PORT}' < /usr/src/default.conf.template > /etc/nginx/conf.d/default.conf
fi
if [ -n "$APP_CONFIG" ]; then
echo "$APP_CONFIG" > /usr/share/nginx/html${PUBLIC_URL}app-config.js
echo "Using custom APP_CONFIG environment variable"
else
echo "Not using custom APP_CONFIG"
fi
if [ -f /usr/share/nginx/html${PUBLIC_URL}app-config.js ]; then
if [ -s /usr/share/nginx/html${PUBLIC_URL}app-config.js ]; then
echo "Detected non-empty app-config.js. Ensuring .gz file is updated..."
rm -f /usr/share/nginx/html${PUBLIC_URL}app-config.js.gz
gzip /usr/share/nginx/html${PUBLIC_URL}app-config.js
touch /usr/share/nginx/html${PUBLIC_URL}app-config.js
echo "Compressed app-config.js to app-config.js.gz"
else
echo "app-config.js is empty. Skipping compression."
fi
else
echo "No app-config.js file found. Skipping compression."
fi
if [ -n "$CLIENT_ID" ] || [ -n "$HEALTHCARE_API_ENDPOINT" ]
then
# If CLIENT_ID is specified, use the google.js configuration with the modified ID
if [ -n "$CLIENT_ID" ]
then
echo "Google Cloud Healthcare \$CLIENT_ID has been provided: "
echo "$CLIENT_ID"
echo "Updating config..."
# - Use SED to replace the CLIENT_ID that is currently in google.js
sed -i -e "s/YOURCLIENTID.apps.googleusercontent.com/$CLIENT_ID/g" /usr/share/nginx/html/google.js
fi
# If HEALTHCARE_API_ENDPOINT is specified, use the google.js configuration with the modified endpoint
if [ -n "$HEALTHCARE_API_ENDPOINT" ]
then
echo "Google Cloud Healthcare \$HEALTHCARE_API_ENDPOINT has been provided: "
echo "$HEALTHCARE_API_ENDPOINT"
echo "Updating config..."
# - Use SED to replace the HEALTHCARE_API_ENDPOINT that is currently in google.js
sed -i -e "s+https://healthcare.googleapis.com/v1+$HEALTHCARE_API_ENDPOINT+g" /usr/share/nginx/html/google.js
fi
# - Copy google.js to overwrite app-config.js
cp /usr/share/nginx/html/google.js /usr/share/nginx/html/app-config.js
fi
echo "Starting Nginx to serve the OHIF Viewer on ${PUBLIC_URL}"
exec "$@"

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find platform/app/dist -name "*.js" -exec gzip -9 "{}" \; -exec touch "{}" \;
find platform/app/dist -name "*.map" -exec gzip -9 "{}" \; -exec touch "{}" \;
find platform/app/dist -name "*.css" -exec gzip -9 "{}" \; -exec touch "{}" \;
find platform/app/dist -name "*.svg" -exec gzip -9 "{}" \; -exec touch "{}" \;

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# Reduces size of context and hides
# files from Docker (can't COPY or ADD these)
# Note that typically the Docker context for various OHIF containers is the
# directory of this file (i.e. the root of the source). As such, this is
# the .dockerignore file for ALL Docker containers that are built. For example,
# the Docker containers built from the recipes in ./platform/app/.recipes will
# have this file as their .dockerignore.
# Output
**/dist/
**/build/
# Dependencies
**/node_modules/
# Root
README.md
Dockerfile
dockerfile
# Misc. Config
.git
.DS_Store
.gitignore
.vscode
.circleci
# Unnecessary things to pull into container
.circleci/
.github/
.netlify/
.scripts/
.vscode/
coverage/
platform/docs/
testdata/

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config/**
docs/**
img/**
node_modules

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{
"plugins": ["@typescript-eslint", "import", "eslint-plugin-tsdoc", "prettier"],
"extends": [
"react-app",
"eslint:recommended",
"plugin:react/recommended",
"plugin:@typescript-eslint/recommended",
"plugin:prettier/recommended"
],
"parser": "@typescript-eslint/parser",
"env": {
"jest": true
},
"settings": {
"react": {
"version": "detect"
}
},
"rules": {
// Enforce consistent brace style for all control statements for readability
"curly": "error",
"import/no-anonymous-default-export": "off"
},
"globals": {
"cy": true,
"before": true,
"context": true,
"Cypress": true,
"assert": true
}
}

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# Set the default behavior,
# in case people don't have core.autocrlf set.
* text=auto
# Declares that files will always have CRLF line ends
*.sh text eol=lf

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custom: https://giving.massgeneral.org/ohif

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name: 'Bug report'
description: Create a report to help us improve
title: '[Bug] '
labels: ['Community: Report :bug:', 'Awaiting Reproduction']
body:
- type: markdown
attributes:
value: |
👋 Hello, and thank you for contributing to our project! Your support is greatly appreciated.
🔍 Before proceeding, please make sure to read our [Rules of Conduct](https://github.com/OHIF/Viewers/blob/master/CODE_OF_CONDUCT.md) and familiarize yourself with our [development process](https:/docs.ohif.org/development/our-process).
❓ If you're here to seek general support or ask a question, we encourage you to visit our [community discussion board](https://community.ohif.org/)
🐞 For bug reports, please complete the following template in as much detail as possible. This will help us reproduce and address the issue efficiently.
🧪 Finally, ensure that you're using the latest version of the software and check if your issue has already been reported to avoid duplicates.
- type: textarea
id: bug_description
attributes:
label: Describe the Bug
description: 'A clear and concise description of what the bug is.'
validations:
required: true
- type: textarea
id: reproduction_steps
attributes:
label: Steps to Reproduce
description: 'Please describe the steps to reproduce the issue.'
placeholder: "1. First step\n2. Second step\n3. ..."
validations:
required: true
- type: textarea
id: current_behavior
attributes:
label: The current behavior
description:
'A clear and concise description of what happens instead of the expected behavior.'
validations:
required: true
- type: textarea
id: expected_behavior
attributes:
label: The expected behavior
description: 'A clear and concise description of what you expected to happen.'
validations:
required: true
- type: input
id: os
attributes:
label: 'OS'
description: 'Your operating system.'
placeholder: 'e.g., Windows 10, macOS 10.15.4'
validations:
required: true
- type: input
id: node-version
attributes:
label: 'Node version'
description: 'Your Node.js version.'
placeholder: 'e.g., 20.18.1'
validations:
required: true
- type: input
id: browser
attributes:
label: 'Browser'
description: 'Your browser.'
placeholder: 'e.g., Chrome 83.0.4103.116, Firefox 77.0.1, Safari 13.1.1'
validations:
required: true
- type: markdown
attributes:
value: >
> :warning: Reports we cannot reproduce are at risk of being marked stale and > closed. The
more information you can provide, the more likely we are to look > into and address your
issue.

5
.github/ISSUE_TEMPLATE/config.yml vendored Normal file
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blank_issues_enabled: false
contact_links:
- name: 🤗 Support Question
url: https://community.ohif.org/
about: Please use our forum if you have questions or need help.

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.github/ISSUE_TEMPLATE/feature-request.yml vendored Normal file
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name: Feature request
description: Create a feature request
labels: ['Community: Request :hand:']
title: '[Feature Request] '
body:
- type: markdown
attributes:
value: |
👋 Hello and thank you for your interest in our project!
🔍 Before you proceed, please read our [Rules of Conduct](https://github.com/OHIF/Viewers/blob/master/CODE_OF_CONDUCT.md).
🚀 If your request is specific to your needs, consider contributing it yourself! Read our [contributing guides](https://docs.ohif.org/development/contributing) to get started.
🖊️ Please provide as much detail as possible for your feature request. Mock-up screenshots, workflow or logic flow diagrams are very helpful. Discuss how your requested feature would interact with existing features.
⏱️ Lastly, tell us why we should prioritize your feature. What impact would it have?
- type: textarea
attributes:
label: 'What feature or change would you like to see made?'
description:
'Please include as much detail as possible including possibly mock up screen shots, workflow
or logic flow diagrams etc.'
placeholder: '...'
validations:
required: true
- type: textarea
attributes:
label: 'Why should we prioritize this feature?'
description: 'Discuss if and how the requested feature interacts with existing features.'
placeholder: '...'
validations:
required: true

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.github/pull_request_template.md vendored Normal file
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<!-- Do Not Delete This! pr_template -->
<!-- Please read our Rules of Conduct: https://github.com/OHIF/Viewers/blob/master/CODE_OF_CONDUCT.md -->
<!-- 🕮 Read our guide about our Contributing Guide here https://docs.ohif.org/development/contributing -->
<!-- :hand: Thank you for starting this amazing contribution! -->
<!--
⚠️⚠️ Please make sure the checklist section below is complete before submitting your PR.
To complete the checklist, add an 'x' to each item: [] -> [x]
(PRs that do not have all the checkboxes marked will not be approved)
-->
### Context
<!--
Provide a clear explanation of the reasoning behind this change, such as:
- A link to the issue being addressed, using the format "Fixes #ISSUE_NUMBER"
- An image showing the issue or problem being addressed (if not already in the issue)
- Error logs or callStacks to help with the understanding of the problem (if not already in the issue)
-->
### Changes & Results
<!--
List all the changes that have been done, such as:
- Add new components
- Remove old components
- Update dependencies
What are the effects of this change?
- Before vs After
- Screenshots / GIFs / Videos
-->
### Testing
<!--
Describe how we can test your changes.
- open a URL
- visit a page
- click on a button
- etc.
-->
### Checklist
#### PR
<!--
https://semantic-release.gitbook.io/semantic-release/#how-does-it-work
Examples:
Please note the letter casing in the provided examples (upper or lower).
- feat(MeasurementService): add ...
- fix(Toolbar): fix ...
- docs(Readme): update ...
- style(Whitespace): fix ...
- refactor(ExtensionManager): ...
- test(HangingProtocol): Add test ...
- chore(git): update ...
- perf(VolumeLoader): ...
You don't need to have each commit within the Pull Request follow the rule,
but the PR title must comply with it, as it will be used as the commit message
after the commits are squashed.
-->
- [] My Pull Request title is descriptive, accurate and follows the
semantic-release format and guidelines.
#### Code
- [] My code has been well-documented (function documentation, inline comments,
etc.)
#### Public Documentation Updates
<!-- https://docs.ohif.org/ -->
- [] The documentation page has been updated as necessary for any public API
additions or removals.
#### Tested Environment
- [] OS: <!--[e.g. Windows 10, macOS 10.15.4]-->
- [] Node version: <!--[e.g. 18.16.1]-->
- [] Browser:
<!--[e.g. Chrome 83.0.4103.116, Firefox 77.0.1, Safari 13.1.1]-->
<!-- prettier-ignore-start -->
[blog]: https://circleci.com/blog/triggering-trusted-ci-jobs-on-untrusted-forks/
[script]: https://github.com/jklukas/git-push-fork-to-upstream-branch
<!-- prettier-ignore-end -->

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.github/stale.yml vendored Normal file
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# GitHub App: Stale
# https://github.com/apps/stale
#
# Number of days of inactivity before an issue becomes stale
daysUntilStale: 180
# Number of days of inactivity before a stale issue is closed
daysUntilClose: 60
# Issues with these labels will never be considered stale
exemptLabels:
- 'Bug: Verified :bug:'
- 'PR: Awaiting Review 👀'
- 'Announcement 🎉'
- 'IDC:priority'
- 'IDC:candidate'
- 'IDC:collaboration'
- 'Community: Request :hand:'
- 'Community: Report :bug:'
# Label to use when marking an issue as stale
staleLabel: 'Stale :baguette_bread:'
# Comment to post when marking an issue as stale. Set to `false` to disable
markComment: >
This issue has been automatically marked as stale because it has not had recent activity. It will
be closed if no further activity occurs. Thank you for your contributions.
# Comment to post when closing a stale issue. Set to `false` to disable
closeComment: false

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.github/workflows/playwright.yml vendored Normal file
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name: Playwright Tests
on:
push:
branches: [main, master]
pull_request:
branches: [main, master]
jobs:
playwright-tests:
timeout-minutes: 60
runs-on: ubuntu-latest
container:
image: mcr.microsoft.com/playwright:v1.50.0-noble
strategy:
fail-fast: false
matrix:
shardIndex: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
shardTotal: [10]
steps:
- uses: actions/checkout@v4
- name: Install unzip
run: apt-get update && apt-get install -y unzip
- uses: oven-sh/setup-bun@v2
- uses: actions/setup-node@v4
with:
node-version: 20
- name: Install dependencies
run: bun install --frozen-lockfile
- name: Set up Git safe directory
run: git config --global --add safe.directory /__w/Viewers/Viewers
- name: Run Playwright tests
run:
export NODE_OPTIONS="--max_old_space_size=8192" && bun x playwright test --shard=${{
matrix.shardIndex }}/${{ matrix.shardTotal }}
- name: Upload blob report to GitHub Actions Artifacts
if: ${{ !cancelled() }}
uses: actions/upload-artifact@v4
with:
name: blob-report-${{ matrix.shardIndex }}
path: blob-report
retention-days: 1
merge-reports:
if: ${{ !cancelled() }}
needs: [playwright-tests]
runs-on: ubuntu-latest
container:
image: mcr.microsoft.com/playwright:v1.48.1-focal
steps:
- name: Install unzip
run: apt-get update && apt-get install -y unzip
- uses: oven-sh/setup-bun@v2
- uses: actions/checkout@v4
- uses: actions/setup-node@v4
with:
node-version: 20
- name: Install dependencies
run: bun install --frozen-lockfile
- name: Set up Git safe directory
run: git config --global --add safe.directory /__w/Viewers/Viewers
- name: Download blob reports from GitHub Actions Artifacts
uses: actions/download-artifact@v4
with:
path: all-blob-reports
pattern: blob-report-*
merge-multiple: true
- name: Merge into HTML Report
run: bun x playwright merge-reports --reporter html ./all-blob-reports
- name: Upload HTML report
uses: actions/upload-artifact@v4
with:
name: html-report--attempt-${{ github.run_attempt }}
path: playwright-report
retention-days: 14

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.gitignore vendored Normal file
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# Packages
node_modules
# Output
build
dist
docs/_book
src/version.js
junit.xml
coverage/
.docz/
.yarn/
.nx/
addOns/yarn.lock
# YALC (for Erik)
.yalc
yalc.lock
*.dcm
# Logging, System files, misc.
.idea/
.npm
npm-debug.log
package-lock.json
yarn-error.log
.DS_Store
.env
*.code-workspace
.directory
# Common Example Data Directories
sampledata/
example/deps/
docker/dcm4che/dcm4che-arc
# Cypress test results
videos/
# Locize settings
.locize
# autogenerated files
platform/app/src/pluginImports.js
/Viewers.iml
platform/app/.recipes/Nginx-Dcm4Chee/logs/*
platform/app/.recipes/OpenResty-Orthanc/logs/*
.vercel
.vs
# PlayWright
node_modules/
tests/test-results/
tests/playwright-report/
/blob-report/
/playwright/.cache/

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.gitmodules vendored Normal file
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[submodule "testdata"]
path = testdata
url = https://github.com/OHIF/viewer-testdata-dicomweb.git
branch = main

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.netlify/build-deploy-preview.sh Executable file
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#!/bin/bash
# Set directory to location of this script
# https://stackoverflow.com/a/3355423/1867984
cd "$(dirname "$0")"
cd .. # Up to project root
# Helpful to verify which versions we're using
echo 'My yarn version is... '
yarn -v
node -v
# Build && Move PWA Output
yarn run build:ci
mkdir -p ./.netlify/www/pwa
mv platform/app/dist/* .netlify/www/pwa -v
echo 'Web application built and copied'
# Build && Move Docusaurus Output (for the docs themselves)
cd platform/docs
yarn install
yarn run build
cd ../..
mkdir -p ./.netlify/www/docs
mv platform/docs/build/* .netlify/www/docs -v
echo 'Docs built (docusaurus) and copied'
# Cache all of the node_module dependencies in
# extensions, modules, and platform packages
yarn run lerna:cache
echo 'Nothing left to see here. Go home, folks.'

5
.netlify/deploy-workflow/_redirects Normal file
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# Specific to our non-deploy-preview deploys
# Confgure redirects using netlify.toml
# PWA Redirect
/* /index.html 200

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{
"name": "root",
"private": true,
"engines": {
"node": ">=14",
"npm": ">=6",
"yarn": ">=1.16.0"
},
"scripts": {
"deploy": "netlify deploy --prod --dir ./../platform/app/dist"
},
"devDependencies": {
"netlify-cli": "^2.21.0"
}
}

10
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# Specific to our deploy-preview
# Our docs are published using CircleCI + GitBook
# Confgure redirects using netlify.toml
# PWA Demo
/pwa/* /pwa/index.html 200
# UI Demo
/ui/* /ui/index.html 200
# UI Demo
/docs/* /docs/index.html 200

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.netlify/www/index.html Normal file
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<html>
<head>
<title>OHIF Viewer: Deploy Preview</title>
</head>
<body>
<h1>Index of Previews</h1>
<ul>
<li>
<a href="/pwa">OHIF Viewer</a>
</li>
<li>
<a href="/docs">Documentation</a>
</li>
<li>
<a href="/ui">UI: Component Library</a>
</li>
</ul>
</body>
</html>

1
.node-version Normal file
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20.9.0

1
.prettierignore Normal file
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*.md

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.prettierrc Normal file
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{
"plugins": ["prettier-plugin-tailwindcss"],
"trailingComma": "es5",
"printWidth": 100,
"proseWrap": "always",
"tabWidth": 2,
"semi": true,
"singleQuote": true,
"arrowParens": "avoid",
"singleAttributePerLine": true,
"endOfLine": "auto"
}

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.scripts/dev.sh Executable file
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#!/bin/bash
# https://github.com/shelljs/shelljs
# https://github.com/shelljs/shelljs#exclude-options
PROJECT=$1
if [ -z "$PROJECT" ]
then
# Default
npx lerna run dev:viewer
else
eval "npx lerna run dev:$PROJECT"
fi
read -p 'Press [Enter] key to continue...'

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.scripts/dicom-json-generator.js Normal file
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/*
* This script uses nodejs to generate a JSON file from a DICOM study folder.
* You need to have dcmjs installed in your project.
* The JSON file can be used to load the study into the OHIF Viewer. You can get more detail
* in the DICOM JSON Data source on docs.ohif.org
*
* Usage: node dicom-json-generator.js <studyFolder> <urlPrefix> <outputJSONPath> <optional scheme>
*
* params:
* - studyFolder: path to the study folder which contains the DICOM files
* - urlPrefix: prefix to the url that will be used to load the study into the viewer. For instance
* we use https://ohif-assets.s3.us-east-2.amazonaws.com/dicom-json/data as the urlPrefix for the
* example since the data is hosted on S3 and each study is in a folder. So the url in the generated
* json file for the first instance of the first series of the first study will be
* dicomweb:https://ohif-assets.s3.us-east-2.amazonaws.com/dicom-json/data/Series1/Instance1
*
* as you see the dicomweb is a prefix that is used to load the data into the viewer, which is suited when
* the .dcm file is hosted statically and can be accessed via a URL (like our example above)
* However, you can specify a new scheme bellow.
*
* - outputJSONPath: path to the output JSON file
* - scheme: default dicomweb if not provided
*/
const dcmjs = require('dcmjs');
const path = require('path');
const fs = require('fs').promises;
const args = process.argv.slice(2);
const [studyDirectory, urlPrefix, outputPath, scheme = 'dicomweb'] = args;
if (args.length < 3 || args.length > 4) {
console.error(
'Usage: node dicom-json-generator.js <studyFolder> <urlPrefix> <outputJSONPath> [scheme]'
);
process.exit(1);
}
const model = {
studies: [],
};
async function convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme) {
try {
const files = await recursiveReadDir(studyDirectory);
console.debug('Processing...');
for (const file of files) {
if (!file.includes('.DS_Store') && !file.includes('.xml')) {
const arrayBuffer = await fs.readFile(file);
const dicomDict = dcmjs.data.DicomMessage.readFile(arrayBuffer.buffer);
const instance = dcmjs.data.DicomMetaDictionary.naturalizeDataset(dicomDict.dict);
instance.fileLocation = createImageId(file, urlPrefix, studyDirectory, scheme);
processInstance(instance);
}
}
console.log('Successfully loaded data');
model.studies.forEach(study => {
study.NumInstances = findInstancesNumber(study);
study.Modalities = findModalities(study).join('/');
});
await fs.writeFile(outputPath, JSON.stringify(model, null, 2));
console.log('JSON saved');
} catch (error) {
console.error(error);
}
}
async function recursiveReadDir(dir) {
let results = [];
const list = await fs.readdir(dir);
for (const file of list) {
const filePath = path.resolve(dir, file);
const stat = await fs.stat(filePath);
if (stat.isDirectory()) {
const res = await recursiveReadDir(filePath);
results = results.concat(res);
} else {
results.push(filePath);
}
}
return results;
}
function createImageId(fileLocation, urlPrefix, studyDirectory, scheme) {
const relativePath = path.relative(studyDirectory, fileLocation);
const normalizedPath = path.normalize(relativePath).replace(/\\/g, '/');
return `${scheme}:${urlPrefix}${normalizedPath}`;
}
function processInstance(instance) {
const { StudyInstanceUID, SeriesInstanceUID } = instance;
let study = getStudy(StudyInstanceUID);
if (!study) {
study = createStudyMetadata(StudyInstanceUID, instance);
model.studies.push(study);
}
let series = getSeries(StudyInstanceUID, SeriesInstanceUID);
if (!series) {
series = createSeriesMetadata(instance);
study.series.push(series);
}
const instanceMetaData =
instance.NumberOfFrames > 1
? createInstanceMetaDataMultiFrame(instance)
: createInstanceMetaData(instance);
series.instances.push(...[].concat(instanceMetaData));
}
function getStudy(StudyInstanceUID) {
return model.studies.find(study => study.StudyInstanceUID === StudyInstanceUID);
}
function getSeries(StudyInstanceUID, SeriesInstanceUID) {
const study = getStudy(StudyInstanceUID);
return study
? study.series.find(series => series.SeriesInstanceUID === SeriesInstanceUID)
: undefined;
}
const findInstancesNumber = study => {
let numInstances = 0;
study.series.forEach(aSeries => {
numInstances = numInstances + aSeries.instances.length;
});
return numInstances;
};
const findModalities = study => {
let modalities = new Set();
study.series.forEach(aSeries => {
modalities.add(aSeries.Modality);
});
return Array.from(modalities);
};
function createStudyMetadata(StudyInstanceUID, instance) {
return {
StudyInstanceUID,
StudyDescription: instance.StudyDescription,
StudyDate: instance.StudyDate,
StudyTime: instance.StudyTime,
PatientName: instance.PatientName,
PatientID: instance.PatientID || '1234', // this is critical to have
AccessionNumber: instance.AccessionNumber,
PatientAge: instance.PatientAge,
PatientSex: instance.PatientSex,
PatientWeight: instance.PatientWeight,
series: [],
};
}
function createSeriesMetadata(instance) {
return {
SeriesInstanceUID: instance.SeriesInstanceUID,
SeriesDescription: instance.SeriesDescription,
SeriesNumber: instance.SeriesNumber,
SeriesTime: instance.SeriesTime,
Modality: instance.Modality,
SliceThickness: instance.SliceThickness,
instances: [],
};
}
function commonMetaData(instance) {
return {
Columns: instance.Columns,
Rows: instance.Rows,
InstanceNumber: instance.InstanceNumber,
SOPClassUID: instance.SOPClassUID,
AcquisitionNumber: instance.AcquisitionNumber,
PhotometricInterpretation: instance.PhotometricInterpretation,
BitsAllocated: instance.BitsAllocated,
BitsStored: instance.BitsStored,
PixelRepresentation: instance.PixelRepresentation,
SamplesPerPixel: instance.SamplesPerPixel,
PixelSpacing: instance.PixelSpacing,
HighBit: instance.HighBit,
ImageOrientationPatient: instance.ImageOrientationPatient,
ImagePositionPatient: instance.ImagePositionPatient,
FrameOfReferenceUID: instance.FrameOfReferenceUID,
ImageType: instance.ImageType,
Modality: instance.Modality,
SOPInstanceUID: instance.SOPInstanceUID,
SeriesInstanceUID: instance.SeriesInstanceUID,
StudyInstanceUID: instance.StudyInstanceUID,
WindowCenter: instance.WindowCenter,
WindowWidth: instance.WindowWidth,
RescaleIntercept: instance.RescaleIntercept,
RescaleSlope: instance.RescaleSlope,
};
}
function conditionalMetaData(instance) {
return {
...(instance.ConceptNameCodeSequence && {
ConceptNameCodeSequence: instance.ConceptNameCodeSequence,
}),
...(instance.SeriesDate && { SeriesDate: instance.SeriesDate }),
...(instance.ReferencedSeriesSequence && {
ReferencedSeriesSequence: instance.ReferencedSeriesSequence,
}),
...(instance.SharedFunctionalGroupsSequence && {
SharedFunctionalGroupsSequence: instance.SharedFunctionalGroupsSequence,
}),
...(instance.PerFrameFunctionalGroupsSequence && {
PerFrameFunctionalGroupsSequence: instance.PerFrameFunctionalGroupsSequence,
}),
...(instance.ContentSequence && { ContentSequence: instance.ContentSequence }),
...(instance.ContentTemplateSequence && {
ContentTemplateSequence: instance.ContentTemplateSequence,
}),
...(instance.CurrentRequestedProcedureEvidenceSequence && {
CurrentRequestedProcedureEvidenceSequence: instance.CurrentRequestedProcedureEvidenceSequence,
}),
...(instance.CodingSchemeIdentificationSequence && {
CodingSchemeIdentificationSequence: instance.CodingSchemeIdentificationSequence,
}),
...(instance.RadiopharmaceuticalInformationSequence && {
RadiopharmaceuticalInformationSequence: instance.RadiopharmaceuticalInformationSequence,
}),
...(instance.ROIContourSequence && {
ROIContourSequence: instance.ROIContourSequence,
}),
...(instance.StructureSetROISequence && {
StructureSetROISequence: instance.StructureSetROISequence,
}),
...(instance.ReferencedFrameOfReferenceSequence && {
ReferencedFrameOfReferenceSequence: instance.ReferencedFrameOfReferenceSequence,
}),
...(instance.CorrectedImage && { CorrectedImage: instance.CorrectedImage }),
...(instance.Units && { Units: instance.Units }),
...(instance.DecayCorrection && { DecayCorrection: instance.DecayCorrection }),
...(instance.AcquisitionDate && { AcquisitionDate: instance.AcquisitionDate }),
...(instance.AcquisitionTime && { AcquisitionTime: instance.AcquisitionTime }),
...(instance.PatientWeight && { PatientWeight: instance.PatientWeight }),
...(instance.NumberOfFrames && { NumberOfFrames: instance.NumberOfFrames }),
...(instance.FrameTime && { FrameTime: instance.FrameTime }),
...(instance.EncapsulatedDocument && { EncapsulatedDocument: instance.EncapsulatedDocument }),
...(instance.SequenceOfUltrasoundRegions && {
SequenceOfUltrasoundRegions: instance.SequenceOfUltrasoundRegions,
}),
};
}
function createInstanceMetaData(instance) {
const metadata = {
...commonMetaData(instance),
...conditionalMetaData(instance),
};
return { metadata, url: instance.fileLocation };
}
function createInstanceMetaDataMultiFrame(instance) {
const instances = [];
const commonData = commonMetaData(instance);
const conditionalData = conditionalMetaData(instance);
for (let i = 1; i <= instance.NumberOfFrames; i++) {
const metadata = { ...commonData, ...conditionalData };
const result = { metadata, url: instance.fileLocation + `?frame=${i}` };
instances.push(result);
}
return instances;
}
convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme);

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.vscode/extensions.json vendored Normal file
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{
"recommendations": [
"esbenp.prettier-vscode",
"streetsidesoftware.code-spell-checker",
"dbaeumer.vscode-eslint",
"mikestead.dotenv",
"bungcip.better-toml",
"silvenon.mdx",
"gruntfuggly.todo-tree",
"wayou.vscode-todo-highlight",
"bradlc.vscode-tailwindcss"
]
}

28
.vscode/launch.json vendored Normal file
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{
// Use IntelliSense to learn about possible attributes.
// Hover to view descriptions of existing attributes.
// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
"version": "0.2.0",
"configurations": [
{
"type": "pwa-chrome",
"request": "launch",
"name": "Launch Chrome against localhost",
"url": "http://localhost:3000",
"webRoot": "${workspaceFolder}"
}
// {
// "name": "Debug Jest Tests",
// "type": "node",
// "request": "launch",
// "runtimeArgs": [
// "--inspect-brk",
// "${workspaceRoot}/node_modules/.bin/jest",
// "--runInBand"
// ],
// "console": "integratedTerminal",
// "internalConsoleOptions": "neverOpen",
// "port": 9229
// }
]
}

114
.vscode/settings.json vendored Normal file
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{
"editor.defaultFormatter": "esbenp.prettier-vscode",
"editor.rulers": [80, 120],
// ===
// Spacing
// ===
"editor.insertSpaces": true,
"editor.tabSize": 2,
"editor.trimAutoWhitespace": true,
"files.trimTrailingWhitespace": true,
"files.eol": "\n",
"files.insertFinalNewline": true,
"files.trimFinalNewlines": true,
// ===
// Event Triggers
// ===
"editor.formatOnSave": true,
"eslint.run": "onSave",
"jest.autoRun": "off",
"prettier.disableLanguages": ["html"],
"prettier.endOfLine": "lf",
"workbench.colorCustomizations": {},
"editor.codeActionsOnSave": {
"source.fixAll.eslint": "explicit"
},
"cSpell.userWords": [
"aabb",
"architectured",
"attrname",
"Barksy",
"browserslist",
"bulkdata",
"Cacheable",
"cfun",
"clonedeep",
"Colormap",
"Colormaps",
"Comlink",
"cornerstonejs",
"Crosshairs",
"datasource",
"dcmjs",
"decache",
"decached",
"decaching",
"deepmerge",
"Dicom",
"dicomweb",
"DISPLAYSETS",
"glwindow",
"grababble",
"grabbable",
"Hounsfield",
"Interactable",
"Interactor",
"istyle",
"kitware",
"labelmap",
"labelmaps",
"livewire",
"Mergeable",
"multiframe",
"nifti",
"ofun",
"OHIF",
"polylines",
"POLYSEG",
"prapogation",
"precisionmetrics",
"prefetch",
"Prescaled",
"pydicom",
"Radiopharmaceutical",
"rasterizing",
"reconstructable",
"Rehydratable",
"renderable",
"resampler",
"resemblejs",
"reslice",
"resliced",
"Reslices",
"roadmap",
"ROADMAPS",
"Segmentations",
"semibold",
"sitk",
"SUBRESOLUTION",
"suvbsa",
"suvbw",
"suvlbm",
"textbox",
"thresholded",
"thresholding",
"timepoint",
"timepoints",
"TMTV",
"TOOLGROUP",
"tqdm",
"transferables",
"typedoc",
"unsubscriptions",
"uuidv",
"viewplane",
"viewports",
"Voxel",
"Voxels",
"Vtkjs",
"wado",
"wadors",
"wadouri",
"workerpool"
]
}

22
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const path = require('path');
function excludeNodeModulesExcept(modules) {
var pathSep = path.sep;
if (pathSep == '\\')
// must be quoted for use in a regexp:
pathSep = '\\\\';
var moduleRegExps = modules.map(function (modName) {
return new RegExp('node_modules' + pathSep + modName);
});
return function (modulePath) {
if (/node_modules/.test(modulePath)) {
for (var i = 0; i < moduleRegExps.length; i++)
if (moduleRegExps[i].test(modulePath)) return false;
return true;
}
return false;
};
}
module.exports = excludeNodeModulesExcept;

29
.webpack/rules/cssToJavaScript.js Normal file
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const autoprefixer = require('autoprefixer');
const path = require('path');
const tailwindcss = require('tailwindcss');
const tailwindConfigPath = path.resolve('../../platform/app/tailwind.config.js');
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const devMode = process.env.NODE_ENV !== 'production';
const cssToJavaScript = {
test: /\.css$/,
use: [
//'style-loader',
devMode ? 'style-loader' : MiniCssExtractPlugin.loader,
{ loader: 'css-loader', options: { importLoaders: 1 } },
{
loader: 'postcss-loader',
options: {
postcssOptions: {
verbose: true,
plugins: [
[tailwindcss(tailwindConfigPath)],
[autoprefixer('last 2 version', 'ie >= 11')],
],
},
},
},
],
};
module.exports = cssToJavaScript;

10
.webpack/rules/loadShaders.js Normal file
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/**
* This is exclusively used by `vtk.js` to bundle glsl files.
*/
const loadShaders = {
test: /\.glsl$/i,
include: /vtk\.js[\/\\]Sources/,
loader: 'shader-loader',
};
module.exports = loadShaders;

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.webpack/rules/loadWebWorkers.js Normal file
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/**
* This allows us to include web workers in our bundle, and VTK.js
* web workers in our bundle. While this increases bundle size, it
* cuts down on the number of includes we need for `script tag` usage.
*/
const loadWebWorkers = {
test: /\.worker\.js$/,
include: /vtk\.js[\/\\]Sources/,
use: [
{
loader: 'worker-loader',
options: { inline: true, fallback: false },
},
],
};
module.exports = loadWebWorkers;

10
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const stylusToJavaScript = {
test: /\.styl$/,
use: [
{ loader: 'style-loader' }, // 3. Style nodes from JS Strings
{ loader: 'css-loader' }, // 2. CSS to CommonJS
{ loader: 'stylus-loader' }, // 1. Stylus to CSS
],
};
module.exports = stylusToJavaScript;

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const excludeNodeModulesExcept = require('./../helpers/excludeNodeModulesExcept.js');
function transpileJavaScript(mode) {
const exclude =
mode === 'production'
? excludeNodeModulesExcept([
// 'dicomweb-client',
// https://github.com/react-dnd/react-dnd/blob/master/babel.config.js
'react-dnd',
// https://github.com/dcmjs-org/dcmjs/blob/master/.babelrc
// https://github.com/react-dnd/react-dnd/issues/1342
// 'dcmjs', // contains: loglevelnext
// https://github.com/shellscape/loglevelnext#browser-support
// 'loglevelnext',
// https://github.com/dcmjs-org/dicom-microscopy-viewer/issues/35
// 'dicom-microscopy-viewer',
// https://github.com/openlayers/openlayers#supported-browsers
// 'ol', --> Should be fine
])
: excludeNodeModulesExcept([]);
return {
// Include mjs, ts, tsx, js, and jsx files.
test: /\.(mjs|ts|js)x?$/,
// These are packages that are not transpiled to our lowest supported
// JS version (currently ES5). Most of these leverage ES6+ features,
// that we need to transpile to a different syntax.
exclude: [/(codecs)/, /(dicomicc)/, exclude],
loader: 'babel-loader',
options: {
// Find babel.config.js in monorepo root
// https://babeljs.io/docs/en/options#rootmode
rootMode: 'upward',
envName: mode,
cacheCompression: false,
// Note: This was causing a lot of issues with yarn link of the cornerstone
// only set this to true if you don't have a yarn link to external libs
// otherwise expect the lib changes not to be reflected in the dev server
// as it will be cached
cacheDirectory: false,
},
};
}
module.exports = transpileJavaScript;

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// ~~ ENV
const dotenv = require('dotenv');
//
const path = require('path');
const fs = require('fs');
const webpack = require('webpack');
// ~~ PLUGINS
// const BundleAnalyzerPlugin = require('webpack-bundle-analyzer').BundleAnalyzerPlugin;
const TerserJSPlugin = require('terser-webpack-plugin');
// ~~ PackageJSON
// const vtkRules = require('vtk.js/Utilities/config/dependency.js').webpack.core
// .rules;
// ~~ RULES
// const loadShadersRule = require('./rules/loadShaders.js');
const loadWebWorkersRule = require('./rules/loadWebWorkers.js');
const transpileJavaScriptRule = require('./rules/transpileJavaScript.js');
const cssToJavaScript = require('./rules/cssToJavaScript.js');
// Only uncomment for old v2 stylus
// const stylusToJavaScript = require('./rules/stylusToJavaScript.js');
const ReactRefreshWebpackPlugin = require('@pmmmwh/react-refresh-webpack-plugin');
// ~~ ENV VARS
const NODE_ENV = process.env.NODE_ENV;
const QUICK_BUILD = process.env.QUICK_BUILD;
const BUILD_NUM = process.env.CIRCLE_BUILD_NUM || '0';
// read from ../version.txt
const VERSION_NUMBER = fs.readFileSync(path.join(__dirname, '../version.txt'), 'utf8') || '';
const COMMIT_HASH = fs.readFileSync(path.join(__dirname, '../commit.txt'), 'utf8') || '';
//
dotenv.config();
const defineValues = {
/* Application */
'process.env.NODE_ENV': JSON.stringify(process.env.NODE_ENV),
'process.env.NODE_DEBUG': JSON.stringify(process.env.NODE_DEBUG),
'process.env.DEBUG': JSON.stringify(process.env.DEBUG),
'process.env.PUBLIC_URL': JSON.stringify(process.env.PUBLIC_URL || '/'),
'process.env.BUILD_NUM': JSON.stringify(BUILD_NUM),
'process.env.VERSION_NUMBER': JSON.stringify(VERSION_NUMBER),
'process.env.COMMIT_HASH': JSON.stringify(COMMIT_HASH),
/* i18n */
'process.env.USE_LOCIZE': JSON.stringify(process.env.USE_LOCIZE || ''),
'process.env.LOCIZE_PROJECTID': JSON.stringify(process.env.LOCIZE_PROJECTID || ''),
'process.env.LOCIZE_API_KEY': JSON.stringify(process.env.LOCIZE_API_KEY || ''),
'process.env.REACT_APP_I18N_DEBUG': JSON.stringify(process.env.REACT_APP_I18N_DEBUG || ''),
};
// Only redefine updated values. This avoids warning messages in the logs
if (!process.env.APP_CONFIG) {
defineValues['process.env.APP_CONFIG'] = '';
}
module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
const mode = NODE_ENV === 'production' ? 'production' : 'development';
const isProdBuild = NODE_ENV === 'production';
const isQuickBuild = QUICK_BUILD === 'true';
const config = {
mode: isProdBuild ? 'production' : 'development',
devtool: isProdBuild ? 'source-map' : 'cheap-module-source-map',
entry: ENTRY,
optimization: {
// splitChunks: {
// // include all types of chunks
// chunks: 'all',
// },
//runtimeChunk: 'single',
minimize: isProdBuild,
sideEffects: false,
},
output: {
// clean: true,
publicPath: '/',
},
context: SRC_DIR,
stats: {
colors: true,
hash: true,
timings: true,
assets: true,
chunks: false,
chunkModules: false,
modules: false,
children: false,
warnings: true,
},
cache: {
type: 'filesystem',
},
module: {
noParse: [/(dicomicc)/],
rules: [
...(isProdBuild
? []
: [
{
test: /\.[jt]sx?$/,
exclude: /node_modules/,
loader: 'babel-loader',
options: {
plugins: isProdBuild ? [] : ['react-refresh/babel'],
},
},
]),
{
test: /\.svg?$/,
oneOf: [
{
use: [
{
loader: '@svgr/webpack',
options: {
svgoConfig: {
plugins: [
{
name: 'preset-default',
params: {
overrides: {
removeViewBox: false,
},
},
},
],
},
prettier: false,
svgo: true,
titleProp: true,
},
},
],
issuer: {
and: [/\.(ts|tsx|js|jsx|md|mdx)$/],
},
},
],
},
transpileJavaScriptRule(mode),
loadWebWorkersRule,
// loadShadersRule,
{
test: /\.m?js/,
resolve: {
fullySpecified: false,
},
},
cssToJavaScript,
// Note: Only uncomment the following if you are using the old style of stylus in v2
// Also you need to uncomment this platform/app/.webpack/rules/extractStyleChunks.js
// stylusToJavaScript,
{
test: /\.wasm/,
type: 'asset/resource',
},
{
test: /\.(png|jpe?g|gif|svg)$/i,
use: [
{
loader: 'file-loader',
options: {
name: 'assets/images/[name].[ext]',
},
},
],
},
], //.concat(vtkRules),
},
resolve: {
mainFields: ['module', 'browser', 'main'],
alias: {
// Viewer project
'@': path.resolve(__dirname, '../platform/app/src'),
'@components': path.resolve(__dirname, '../platform/app/src/components'),
'@hooks': path.resolve(__dirname, '../platform/app/src/hooks'),
'@routes': path.resolve(__dirname, '../platform/app/src/routes'),
'@state': path.resolve(__dirname, '../platform/app/src/state'),
'dicom-microscopy-viewer':
'dicom-microscopy-viewer/dist/dynamic-import/dicomMicroscopyViewer.min.js',
},
// Which directories to search when resolving modules
modules: [
// Modules specific to this package
path.resolve(__dirname, '../node_modules'),
// Hoisted Yarn Workspace Modules
path.resolve(__dirname, '../../../node_modules'),
path.resolve(__dirname, '../platform/app/node_modules'),
path.resolve(__dirname, '../platform/ui/node_modules'),
SRC_DIR,
],
// Attempt to resolve these extensions in order.
extensions: ['.js', '.jsx', '.json', '.ts', '.tsx', '*'],
// symlinked resources are resolved to their real path, not their symlinked location
symlinks: true,
fallback: {
fs: false,
path: false,
zlib: false,
buffer: require.resolve('buffer'),
},
},
plugins: [
new webpack.DefinePlugin(defineValues),
new webpack.ProvidePlugin({
Buffer: ['buffer', 'Buffer'],
}),
...(isProdBuild ? [] : [new ReactRefreshWebpackPlugin({ overlay: false })]),
// Uncomment to generate bundle analyzer
// new BundleAnalyzerPlugin(),
],
};
if (isProdBuild) {
config.optimization.minimizer = [
new TerserJSPlugin({
parallel: true,
terserOptions: {},
}),
];
}
if (isQuickBuild) {
config.optimization.minimize = false;
config.devtool = false;
}
return config;
};

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76
CODE_OF_CONDUCT.md Normal file
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# Contributor Covenant Code of Conduct
## Our Pledge
In the interest of fostering an open and welcoming environment, we as
contributors and maintainers pledge to making participation in our project and
our community a harassment-free experience for everyone, regardless of age, body
size, disability, ethnicity, sex characteristics, gender identity and expression,
level of experience, education, socio-economic status, nationality, personal
appearance, race, religion, or sexual identity and orientation.
## Our Standards
Examples of behavior that contributes to creating a positive environment
include:
* Using welcoming and inclusive language
* Being respectful of differing viewpoints and experiences
* Gracefully accepting constructive criticism
* Focusing on what is best for the community
* Showing empathy towards other community members
Examples of unacceptable behavior by participants include:
* The use of sexualized language or imagery and unwelcome sexual attention or
advances
* Trolling, insulting/derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or electronic
address, without explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting
## Our Responsibilities
Project maintainers are responsible for clarifying the standards of acceptable
behavior and are expected to take appropriate and fair corrective action in
response to any instances of unacceptable behavior.
Project maintainers have the right and responsibility to remove, edit, or
reject comments, commits, code, wiki edits, issues, and other contributions
that are not aligned to this Code of Conduct, or to ban temporarily or
permanently any contributor for other behaviors that they deem inappropriate,
threatening, offensive, or harmful.
## Scope
This Code of Conduct applies both within project spaces and in public spaces
when an individual is representing the project or its community. Examples of
representing a project or community include using an official project e-mail
address, posting via an official social media account, or acting as an appointed
representative at an online or offline event. Representation of a project may be
further defined and clarified by project maintainers.
## Enforcement
Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported by contacting the project team at danny.ri.brown+OHIFcoc@gmail.com. All
complaints will be reviewed and investigated and will result in a response that
is deemed necessary and appropriate to the circumstances. The project team is
obligated to maintain confidentiality with regard to the reporter of an incident.
Further details of specific enforcement policies may be posted separately.
Project maintainers who do not follow or enforce the Code of Conduct in good
faith may face temporary or permanent repercussions as determined by other
members of the project's leadership.
## Attribution
This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
[homepage]: https://www.contributor-covenant.org
For answers to common questions about this code of conduct, see
https://www.contributor-covenant.org/faq

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CONTRIBUTING.md Normal file
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See our contributing guidelines at [`https://docs.ohif.org`](https://docs.ohif.org/development/contributing.html)

297
DATACITATION.md Normal file
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# OHIF public demo data sets
The OHIF Viewer's public demo page, available at https://viewer.ohif.org/, uses publicly anonymized demo datasets.
These datasets were mostly obtained from the [NIH NCI Imaging Data Commons](https://datacommons.cancer.gov/repository/imaging-data-commons)
and [NIH NCI TCIA](https://www.cancerimagingarchive.net/). Before listing the datasets,
we would like to extend a special thank you to all groups who have made their datasets publicly available.
Without them, we would not have been able to create this demo page.
Please find below the list of datasets used on the demo page, along with their respective citations.
## Platforms
### NIH NCI IDC
- Fedorov, A., Longabaugh, W.J., Pot, D., Clunie, D.A., Pieper, S., Aerts, H.J., Homeyer, A., Lewis, R., Akbarzadeh, A., Bontempi, D. and Clifford, W., 2021. NCI imaging data commons. Cancer research, 81(16), p.4188.
### NIH NCI TCIA
- Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. Journal of Digital Imaging, 26(6), 1045–1057. https://doi.org/10.1007/s10278-013-9622-7
## Datasets
Below you can find the StudyInstanceUID of the studies that are used in the demo page along with their citations.
### 1.3.6.1.4.1.14519.5.2.1.267424821384663813780850856506829388886
Segmentation of Vestibular Schwannoma from Magnetic Resonance Imaging: An Open Annotated Dataset and Baseline Algorithm (Vestibular-Schwannoma-SEG)
- Shapey, J., Kujawa, A., Dorent, R., Wang, G., Bisdas, S., Dimitriadis, A., Grishchuck, D., Paddick, I., Kitchen, N., Bradford, R., Saeed, S., Ourselin, S., & Vercauteren, T. (2021). Segmentation of Vestibular Schwannoma from Magnetic Resonance Imaging: An Open Annotated Dataset and Baseline Algorithm [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.9YTJ-5Q73
- Shapey, J., Kujawa, A., Dorent, R., Wang, G., Dimitriadis, A., Grishchuk, D., Paddick, I., Kitchen, N., Bradford, R., Saeed, S. R., Bisdas, S., Ourselin, S., & Vercauteren, T. (2021). Segmentation of vestibular schwannoma from MRI, an open annotated dataset and baseline algorithm. In Scientific Data (Vol. 8, Issue 1). Springer Science and Business Media LLC. https://doi.org/10.1038/s41597-021-01064-w
### 1.3.6.1.4.1.14519.5.2.1.7009.2403.334240657131972136850343327463
### 1.3.6.1.4.1.14519.5.2.1.7009.2403.871108593056125491804754960339
ACRIN-NSCLC-FDG-PET (ACRIN 6668)
- Kinahan, P., Muzi, M., Bialecki, B., Herman, B., & Coombs, L. (2019). Data from the ACRIN 6668 Trial NSCLC-FDG-PET (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/tcia.2019.30ilqfcl
- Machtay, M., Duan, F., Siegel, B. A., Snyder, B. S., Gorelick, J. J., Reddin, J. S., Munden, R., Johnson, D. W., Wilf, L. H., DeNittis, A., Sherwin, N., Cho, K. H., Kim, S., Videtic, G., Neumann, D. R., Komaki, R., Macapinlac, H., Bradley, J. D., & Alavi, A. (2013). Prediction of Survival by [18F]Fluorodeoxyglucose Positron Emission Tomography in Patients With Locally Advanced Non–Small-Cell Lung Cancer Undergoing Definitive Chemoradiation Therapy: Results of the ACRIN 6668/RTOG 0235 Trial. In Journal of Clinical Oncology (Vol. 31, Issue 30, pp. 3823–3830). American Society of Clinical Oncology (ASCO). https://doi.org/10.1200/jco.2012.47.5947
### 2.25.103659964951665749659160840573802789777
The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM)
- Scarpace, L., Mikkelsen, T., Cha, S., Rao, S., Tekchandani, S., Gutman, D., Saltz, J. H., Erickson, B. J., Pedano, N., Flanders, A. E., Barnholtz-Sloan, J., Ostrom, Q., Barboriak, D., & Pierce, L. J. (2016). The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM) (Version 4) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.RNYFUYE9
### 1.3.6.1.4.1.14519.5.2.1.256467663913010332776401703474716742458
Abdominal or pelvic enhanced CT images within 10 days before surgery of 230 patients with stage II colorectal cancer (StageII-Colorectal-CT)
- Tong T., Li M. (2022) Abdominal or pelvic enhanced CT images within 10 days before surgery of 230 patients with stage II colorectal cancer (StageII-Colorectal-CT) [Dataset]. The Cancer Imaging Archive. DOI: https://doi.org/10.7937/p5k5-tg43
- Li, M., Gong, J., Bao, Y., Huang, D., Peng, J., & Tong, T. (2022). Special issue “The advance of solid tumor research in China”: Prognosis prediction for stage II colorectal cancer by fusing computed tomography radiomics and deep‐learning features of primary lesions and peripheral lymph nodes. In International Journal of Cancer. Wiley. https://doi.org/10.1002/ijc.34053
### 1.3.6.1.4.1.14519.5.2.1.3023.4024.215308722288168917637555384485
The Cancer Genome Atlas Sarcoma Collection (TCGA-SARC)
- Roche, C., Bonaccio, E., & Filippini, J. (2016). The Cancer Genome Atlas Sarcoma Collection (TCGA-SARC) (Version 3) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.CX6YLSUX
### 1.3.6.1.4.1.14519.5.2.1.4792.2001.105216574054253895819671475627
BREAST-DIAGNOSIS
- Bloch, B. Nicolas, Jain, Ashali, & Jaffe, C. Carl. (2015). BREAST-DIAGNOSIS [Data set]. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2015.SDNRQXXR
### 1.3.6.1.4.1.14519.5.2.1.1706.8374.643249677828306008300337414785
Multimodality annotated HCC cases with and without advanced imaging segmentation (HCC-TACE-Seg)
- Moawad, A. W., Fuentes, D., Morshid, A., Khalaf, A. M., Elmohr, M. M., Abusaif, A., Hazle, J. D., Kaseb, A. O., Hassan, M., Mahvash, A., Szklaruk, J., Qayyom, A., & Elsayes, K. (2021). Multimodality annotated HCC cases with and without advanced imaging segmentation [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.5FNA-0924
- Morshid, A., Elsayes, K. M., Khalaf, A. M., Elmohr, M. M., Yu, J., Kaseb, A. O., Hassan, M., Mahvash, A., Wang, Z., Hazle, J. D., & Fuentes, D. (2019). A Machine Learning Model to Predict Hepatocellular Carcinoma Response to Transcatheter Arterial Chemoembolization. Radiology: Artificial Intelligence, 1(5), e180021. https://doi.org/10.1148/ryai.2019180021
### 1.3.6.1.4.1.14519.5.2.1.1188.2803.137585363493444318569098508293
Ultrasound data of a variety of liver masses (B-mode-and-CEUS-Liver)
- Eisenbrey, J., Lyshchik, A., & Wessner, C. (2021). Ultrasound data of a variety of liver masses [Data set]. The Cancer Imaging Archive. DOI: https://doi.org/10.7937/TCIA.2021.v4z7-tc39
### 1.3.6.1.4.1.32722.99.99.62087908186665265759322018723889952421
NSCLC-Radiomics
- Aerts, H. J. W. L., Wee, L., Rios Velazquez, E., Leijenaar, R. T. H., Parmar, C., Grossmann, P., Carvalho, S., Bussink, J., Monshouwer, R., Haibe-Kains, B., Rietveld, D., Hoebers, F., Rietbergen, M. M., Leemans, C. R., Dekker, A., Quackenbush, J., Gillies, R. J., Lambin, P. (2019). Data From NSCLC-Radiomics (version 4) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2015.PF0M9REI
- Aerts, H. J. W. L., Velazquez, E. R., Leijenaar, R. T. H., Parmar, C., Grossmann, P., Carvalho, S., Bussink, J., Monshouwer, R., Haibe-Kains, B., Rietveld, D., Hoebers, F., Rietbergen, M. M., Leemans, C. R., Dekker, A., Quackenbush, J., Gillies, R. J., Lambin, P. (2014, June 3). Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms5006 (link)
### 1.3.6.1.4.1.14519.5.2.1.3671.4754.298665348758363466150039312520
QIN-PROSTATE-Repeatability
- Fedorov, A; Schwier, M; Clunie, D; Herz, C; Pieper, S; Kikinis, R; Tempany, C; Fennessy, F. (2018). Data From QIN-PROSTATE-Repeatability. The Cancer Imaging Archive. DOI: 10.7937/K9/TCIA.2018.MR1CKGND
- Fedorov A, Vangel MG, Tempany CM, Fennessy FM. Multiparametric Magnetic Resonance Imaging of the Prostate: Repeatability of Volume and Apparent Diffusion Coefficient Quantification. Investigative Radiology. 52, 538–546 (2017). DOI: 10.1097/RLI.0000000000000382
- Fedorov, A., Schwier, M., Clunie, D., Herz, C., Pieper, S., Kikinis,R., Tempany, C. & Fennessy, F. An annotated test-retest collection of prostate multiparametric MRI. Scientific Data 5, 180281 (2018). DOI:
### 2.25.141277760791347900862109212450152067508
The Clinical Proteomic Tumor Analysis Consortium Clear Cell Renal Cell Carcinoma Collection (CPTAC-CCRCC)
- National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Clear Cell Renal Cell Carcinoma Collection (CPTAC-CCRCC) (Version 10) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.OBLAMN27
- The CPTAC program requests that publications using data from this program include the following statement: “Data used in this publication were generated by the National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC).”
### 2.25.275741864483510678566144889372061815320
National Lung Screening Trial
- National Lung Screening Trial Research Team. (2013). Data from the National Lung Screening Trial (NLST) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.HMQ8-J677
- National Lung Screening Trial Research Team*; Aberle DR, Adams AM, Berg CD, Black WC, Clapp JD, Fagerstrom RM, Gareen IF, Gatsonis C, Marcus PM, Sicks JD (2011). Reduced Lung-Cancer Mortality with Low-Dose Computed Tomographic Screening. New England Journal of Medicine, 365(5), 395–409. https://doi.org/10.1056/nejmoa1102873
### 1.3.6.1.4.1.14519.5.2.1.99.1071.26968527900428638961173806140069
Stony Brook University COVID-19 Positive Cases (COVID-19-NY-SBU)
- Saltz, J., Saltz, M., Prasanna, P., Moffitt, R., Hajagos, J., Bremer, E., Balsamo, J., & Kurc, T. (2021). Stony Brook University COVID-19 Positive Cases [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.BBAG-2923
### 2.16.840.1.114362.1.11972228.22789312658.616067305.306.2
https://data.kitware.com/
### 1.2.276.0.7230010.3.1.2.296485376.1.1665793212.499772
### 2.25.269859997690759739055099378767846712697
### 1.3.6.1.4.1.14519.5.2.1.5099.8010.217836670708542506360829799868
### 1.3.6.1.4.1.14519.5.2.1.4792.2001.232252967813565730694525674696
### 1.3.6.1.4.1.14519.5.2.1.4792.2001.105216574054253895819671475627
### 1.3.6.1.4.1.5962.99.1.1117.5035.1620319789811.1.2.1
### 1.3.6.1.4.1.5962.99.1.1123.9231.1620326176300.1.2.1
### 1.3.6.1.4.1.5962.99.1.1126.3483.1620329455972.1.2.1
https://github.com/ImagingInformatics/hackathon-images
### 2.16.124.113543.6004.101.103.20021117.162333.1
### 2.16.124.113543.6004.101.103.20021117.190619.1
### 2.16.124.113543.6004.101.103.20021117.123455.1
### 2.16.124.113543.6004.101.103.20021117.061159.1
https://www.aapm.org/
### 1.2.840.113619.2.30.1.1762295590.1623.978668949.886
### 1.2.276.0.7230010.3.1.2.447481088.1.1669202398.851612
Custom data SPECT, specifically I123-FP-CIT (DaTSCAN) SPECT, evaluates the dopaminergic system to diagnose Parkinson's disease, especially when tremor symptoms are unclear. It helps distinguish Parkinson's disease from treatment-related tremor.
### 1.3.6.1.4.1.9328.50.1.54652
https://www.cancerimagingarchive.net/collection/rider-pilot/
Lung Image Database Consortium (LIDC). (2023) RIDER Pilot [Data set]. The Cancer Imaging Archive (TCIA). https://doi.org/10.7937/m87f-mz83
### 1.3.6.1.4.1.14519.5.2.1.331759366792756327296606233801322964986
Mayr, N., Yuh, W. T. C., Bowen, S., Harkenrider, M., Knopp, M. V., Lee, E. Y.-P., Leung, E., Lo, S. S., Small Jr., W., & Wolfson, A. H. (2023). Cervical Cancer – Tumor Heterogeneity: Serial Functional and Molecular Imaging Across the Radiation Therapy Course in Advanced Cervical Cancer (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/ERZ5-QZ59
https://www.cancerimagingarchive.net/collection/cc-tumor-heterogeneity/
### 1.3.6.1.4.1.14519.5.2.1.297577087050970310787702792940607009472
Eslick, E. M., Kipritidis, J., Gradinscak, D., Stevens, M. J., Bailey, D. L., Harris, B., Booth, J. T., & Keall, P. J. (2022). CT Ventilation as a functional imaging modality for lung cancer radiotherapy (CT-vs-PET-Ventilation-Imaging) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/3ppx-7s22
https://www.cancerimagingarchive.net/collection/ct-vs-pet-ventilation-imaging/
### 1.3.6.1.4.1.14519.5.2.1.2103.7010.634114621738943599785009586807
### 1.3.6.1.4.1.14519.5.2.1.2103.7010.135953723682765205394176991681
Huang, W., Tudorica, A., Chui, S., Kemmer, K., Naik, A., Troxell, M., Oh, K., Roy, N., Afzal, A., & Holtorf, M. (2014). Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge (QIN Breast DCE-MRI) (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/k9/tcia.2014.a2n1ixox
https://www.cancerimagingarchive.net/collection/qin-breast-dce-mri/
### 1.3.6.1.4.1.14519.5.2.1.1.24766180081901755714059656629507905556
Cancer Moonshot Biobank. (2023). Cancer Moonshoot Biobank – Acute Myeloid Leukemia (CMB-AML) (Version 4) [Dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/PCTE-6M66
https://www.cancerimagingarchive.net/collection/cmb-aml/
### 1.3.6.1.4.1.14519.5.2.1.3098.5025.285242291560760827564488897577
https://www.cancerimagingarchive.net/collection/anti-pd-1_lung/
Madhavi, P., Patel, S., & Tsao, A. S. (2019). Data from Anti-PD-1 Immunotherapy Lung [Data set]. The Cancer Imaging Archive. DOI: 10.7937/tcia.2019.zjjwb9ip
### 1.3.6.1.4.1.14519.5.2.1.1.84416332615988066829602832830236187384
https://www.cancerimagingarchive.net/collection/cmb-pca/
Cancer Moonshot Biobank. (2022). Cancer Moonshot Biobank – Prostate Cancer Collection (CMB-PCA) (Version 7) [Dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/25T7-6Y12
### 1.3.6.1.4.1.32722.99.99.239341353911714368772597187099978969331
Aerts, H. J. W. L., Wee, L., Rios Velazquez, E., Leijenaar, R. T. H., Parmar, C., Grossmann, P., Carvalho, S., Bussink, J., Monshouwer, R., Haibe-Kains, B., Rietveld, D., Hoebers, F., Rietbergen, M. M., Leemans, C. R., Dekker, A., Quackenbush, J., Gillies, R. J., Lambin, P. (2014). Data From NSCLC-Radiomics (version 4) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2015.PF0M9REI
https://www.cancerimagingarchive.net/collection/nsclc-radiomics/
### 1.3.6.1.4.1.14519.5.2.1.7085.2626.494695569589117268722281491772
https://www.cancerimagingarchive.net/collection/cptac-ucec/
National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2019). The Clinical Proteomic Tumor Analysis Consortium Uterine Corpus Endometrial Carcinoma Collection (CPTAC-UCEC) (Version 12) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.3R3JUISW
### 1.3.6.1.4.1.14519.5.2.1.207544490797667703011829289839681390478
https://www.cancerimagingarchive.net/collection/remind/
Juvekar, P., Dorent, R., Kögl, F., Torio, E., Barr, C., Rigolo, L., Galvin, C., Jowkar, N., Kazi, A., Haouchine, N., Cheema, H., Navab, N., Pieper, S., Wells, W. M., Bi, W. L., Golby, A., Frisken, S., & Kapur, T. (2023). The Brain Resection Multimodal Imaging Database (ReMIND) (Version 1) [dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/3RAG-D070
### 1.3.12.2.1107.5.1.4.60175.30000008042114404745300000010
Gavrielides, M. A., Kinnard, L. M., Myers, K. J., Peregoy, J., Pritchard, W. F., Zeng, R., Esparza, J., Karanian, J., & Petrick, N. (2015). Data From Phantom FDA [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/k9/TCIA.2015.orbjkmux
https://www.cancerimagingarchive.net/collection/phantom-fda/
### 1.3.6.1.4.1.14519.5.2.1.6834.5010.992793141464713669479982159310
https://www.cancerimagingarchive.net/collection/4d-lung/
Hugo, G. D., Weiss, E., Sleeman, W. C., Balik, S., Keall, P. J., Lu, J., & Williamson, J. F. (2016). Data from 4D Lung Imaging of NSCLC Patients (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.ELN8YGLE
### 1.3.6.1.4.1.9328.50.17.15423521354819720574322014551955370036
https://www.cancerimagingarchive.net/collection/rider-lung-pet-ct/
Muzi P, Wanner M, & Kinahan P. (2015). Data From RIDER Lung PET-CT. The Cancer Imaging Archive. https://doi.org/10.7937/k9/tcia.2015.ofip7tvm
### 1.3.6.1.4.1.14519.5.2.1.9823.1001.134394060407147891170882809392
https://www.cancerimagingarchive.net/collection/prostate-mri/
Choyke P, Turkbey B, Pinto P, Merino M, Wood B. (2016). Data From PROSTATE-MRI. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2016.6046GUDv
### 1.3.6.1.4.1.14519.5.2.1.191696062987463500085282581898315738844
https://www.cancerimagingarchive.net/collection/upenn-gbm/
Bakas, S., Sako, C., Akbari, H., Bilello, M., Sotiras, A., Shukla, G., Rudie, J. D., Flores Santamaria, N., Fathi Kazerooni, A., Pati, S., Rathore, S., Mamourian, E., Ha, S. M., Parker, W., Doshi, J., Baid, U., Bergman, M., Binder, Z. A., Verma, R., … Davatzikos, C. (2021). Multi-parametric magnetic resonance imaging (mpMRI) scans for de novo Glioblastoma (GBM) patients from the University of Pennsylvania Health System (UPENN-GBM) (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.709X-DN49
### 1.3.6.1.4.1.14519.5.2.1.4792.2001.921758700577562664959693695481
https://www.cancerimagingarchive.net/collection/breast-diagnosis/
Bloch, B. Nicolas, Jain, Ashali, & Jaffe, C. Carl. (2015). BREAST-DIAGNOSIS [Data set]. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2015.SDNRQXXR
### 1.3.6.1.4.1.14519.5.2.1.1620.1225.189514895974227080410265976065
Comstock, C. E., Gatsonis, C., Newstead, G. M., Snyder, B. S., Gareen, I. F., Bergin, J. T., Rahbar, H., Sung, J. S., Jacobs, C., Harvey, J. A., Nicholson, M. H., Ward, R. C., Holt, J., Prather, A., Miller, K. D., Schnall, M. D., & Kuhl, C. K. (2023). Abbreviated Breast MRI and Digital Tomosynthesis Mammography in Screening Women With Dense Breasts (EA1141) (Version 1) [dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/2BAS-HR33
https://www.cancerimagingarchive.net/collection/ea1141/
### 1.2.276.0.7230010.3.1.2.2155604110.4180.1021041295.21
From OFFIS DICOM-Team
https://www.offis.de/
OFFIS DICOM-Team

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# syntax=docker/dockerfile:1.7-labs
# This dockerfile is used to publish the `ohif/app` image on dockerhub.
#
# It's a good example of how to build our static application and package it
# with a web server capable of hosting it as static content.
#
# docker build
# --------------
# If you would like to use this dockerfile to build and tag an image, make sure
# you set the context to the project's root directory:
# https://docs.docker.com/engine/reference/commandline/build/
#
#
# SUMMARY
# --------------
# This dockerfile has two stages:
#
# 1. Building the React application for production
# 2. Setting up our Nginx (Alpine Linux) image w/ step one's output
#
# syntax=docker/dockerfile:1.7-labs
# This dockerfile is used to publish the `ohif/app` image on dockerhub.
#
# It's a good example of how to build our static application and package it
# with a web server capable of hosting it as static content.
#
# docker build
# --------------
# If you would like to use this dockerfile to build and tag an image, make sure
# you set the context to the project's root directory:
# https://docs.docker.com/engine/reference/commandline/build/
#
#
# SUMMARY
# --------------
# This dockerfile is used as an input for a second stage to make things run faster.
#
# Stage 1: Build the application
# docker build -t ohif/viewer:latest .
# Copy Files
FROM node:20.18.1-slim as builder
RUN apt-get update && apt-get install -y build-essential python3
RUN mkdir /usr/src/app
WORKDIR /usr/src/app
RUN npm install -g bun
# RUN npm install -g lerna@7.4.2
ENV PATH=/usr/src/app/node_modules/.bin:$PATH
# Do an initial install and then a final install
COPY package.json yarn.lock preinstall.js lerna.json ./
COPY --parents ./addOns/package.json ./addOns/*/*/package.json ./extensions/*/package.json ./modes/*/package.json ./platform/*/package.json ./
# Run the install before copying the rest of the files
RUN bun pm cache rm
RUN bun install
# Copy the local directory
COPY --link --exclude=yarn.lock --exclude=package.json --exclude=Dockerfile . .
# Do a second install to finalize things after the copy
RUN bun run show:config
RUN bun install
# Build here
# After install it should hopefully be stable until the local directory changes
ENV QUICK_BUILD true
# ENV GENERATE_SOURCEMAP=false
ARG APP_CONFIG=config/default.js
ARG PUBLIC_URL=/
RUN bun run show:config
RUN bun run build
# Precompress files
RUN chmod u+x .docker/compressDist.sh
RUN ./.docker/compressDist.sh
# Stage 3: Bundle the built application into a Docker container
# which runs Nginx using Alpine Linux
FROM nginxinc/nginx-unprivileged:1.27-alpine as final
#RUN apk add --no-cache bash
ARG PORT=80
ENV PORT=${PORT}
ARG PUBLIC_URL=/
ENV PUBLIC_URL=${PUBLIC_URL}
RUN rm /etc/nginx/conf.d/default.conf
USER nginx
COPY --chown=nginx:nginx .docker/Viewer-v3.x /usr/src
RUN chmod 777 /usr/src/entrypoint.sh
COPY --from=builder /usr/src/app/platform/app/dist /usr/share/nginx/html${PUBLIC_URL}
COPY --from=builder /usr/src/app/platform/app/dist/index.html /usr/share/nginx/html
# In entrypoint.sh, app-config.js might be overwritten, so chmod it to be writeable.
# The nginx user cannot chmod it, so change to root.
USER root
RUN chown -R nginx:nginx /usr/share/nginx/html
USER nginx
ENTRYPOINT ["/usr/src/entrypoint.sh"]
CMD ["nginx", "-g", "daemon off;"]

21
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@@ -0,0 +1,21 @@
MIT License
Copyright (c) 2018 Open Health Imaging Foundation
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

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<!-- prettier-ignore-start -->
<!-- markdownlint-disable -->
<div align="center">
<h1>OHIF Medical Imaging Viewer</h1>
<p><strong>The OHIF Viewer</strong> is a zero-footprint medical image viewer
provided by the <a href="https://ohif.org/">Open Health Imaging Foundation (OHIF)</a>. It is a configurable and extensible progressive web application with out-of-the-box support for image archives which support <a href="https://www.dicomstandard.org/using/dicomweb/">DICOMweb</a>.</p>
</div>
<div align="center">
<a href="https://docs.ohif.org/"><strong>Read The Docs</strong></a>
</div>
<div align="center">
<a href="https://viewer.ohif.org/">Live Demo</a> |
<a href="https://ui.ohif.org/">Component Library</a>
</div>
<div align="center">
📰 <a href="https://ohif.org/news/"><strong>Join OHIF Newsletter</strong></a> 📰
</div>
<div align="center">
📰 <a href="https://ohif.org/news/"><strong>Join OHIF Newsletter</strong></a> 📰
</div>
<hr />
[![NPM version][npm-version-image]][npm-url]
[![MIT License][license-image]][license-url]
[![This project is using Percy.io for visual regression testing.][percy-image]](percy-url)
<!-- [![NPM downloads][npm-downloads-image]][npm-url] -->
<!-- [![Pulls][docker-pulls-img]][docker-image-url] -->
<!-- [![FOSSA Status](https://app.fossa.io/api/projects/git%2Bgithub.com%2FOHIF%2FViewers.svg?type=shield)](https://app.fossa.io/projects/git%2Bgithub.com%2FOHIF%2FViewers?ref=badge_shield) -->
<!-- [![Netlify Status][netlify-image]][netlify-url] -->
<!-- [![CircleCI][circleci-image]][circleci-url] -->
<!-- [![codecov][codecov-image]][codecov-url] -->
<!-- [![All Contributors](https://img.shields.io/badge/all_contributors-10-orange.svg?style=flat-square)](#contributors) -->
<!-- prettier-ignore-end -->
| | | |
| :-: | :--- | :--- |
| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-measurements.webp?raw=true" alt="Measurement tracking" width="350"/> | Measurement Tracking | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125095438.5) |
| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-segmentation.webp?raw=true" alt="Segmentations" width="350"/> | Labelmap Segmentations | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.12.2.1107.5.2.32.35162.30000015050317233592200000046) |
| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-ptct.webp?raw=true" alt="Hanging Protocols" width="350"/> | Fusion and Custom Hanging protocols | [Demo](https://viewer.ohif.org/tmtv?StudyInstanceUIDs=1.3.6.1.4.1.14519.5.2.1.7009.2403.334240657131972136850343327463) |
| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-volume-rendering.webp?raw=true" alt="Volume Rendering" width="350"/> | Volume Rendering | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125095438.5&hangingprotocolId=mprAnd3DVolumeViewport) |
| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-pdf.webp?raw=true" alt="PDF" width="350"/> | PDF | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=2.25.317377619501274872606137091638706705333) |
| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-rtstruct.webp?raw=true" alt="RTSTRUCT" width="350"/> | RT STRUCT | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.6.1.4.1.5962.99.1.2968617883.1314880426.1493322302363.3.0) |
| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-4d.webp?raw=true" alt="4D" width="350"/> | 4D | [Demo](https://viewer.ohif.org/dynamic-volume?StudyInstanceUIDs=2.25.232704420736447710317909004159492840763) |
| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-video.webp?raw=true" alt="VIDEO" width="350"/> | Video | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=2.25.96975534054447904995905761963464388233) |
| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/microscopy.webp?raw=true" alt="microscopy" width="350"/> | Slide Microscopy | [Demo](https://viewer.ohif.org/microscopy?StudyInstanceUIDs=2.25.141277760791347900862109212450152067508) |
## About
The OHIF Viewer can retrieve
and load images from most sources and formats; render sets in 2D, 3D, and
reconstructed representations; allows for the manipulation, annotation, and
serialization of observations; supports internationalization, OpenID Connect,
offline use, hotkeys, and many more features.
Almost everything offers some degree of customization and configuration. If it
doesn't support something you need, we accept pull requests and have an ever
improving Extension System.
## Why Choose Us
### Community & Experience
The OHIF Viewer is a collaborative effort that has served as the basis for many
active, production, and FDA Cleared medical imaging viewers. It benefits from
our extensive community's collective experience, and from the sponsored
contributions of individuals, research groups, and commercial organizations.
### Built to Adapt
After more than 8-years of integrating with many companies and organizations,
The OHIF Viewer has been rebuilt from the ground up to better address the
varying workflow and configuration needs of its many users. All of the Viewer's
core features are built using it's own extension system. The same extensibility
that allows us to offer:
- 2D and 3D medical image viewing
- Multiplanar Reconstruction (MPR)
- Maximum Intensity Project (MIP)
- Whole slide microscopy viewing
- PDF and Dicom Structured Report rendering
- Segmentation rendering as labelmaps and contours
- User Access Control (UAC)
- Context specific toolbar and side panel content
- and many others
Can be leveraged by you to customize the viewer for your workflow, and to add
any new functionality you may need (and wish to maintain privately without
forking).
### Support
- [Report a Bug 🐛](https://github.com/OHIF/Viewers/issues/new?assignees=&labels=Community%3A+Report+%3Abug%3A%2CAwaiting+Reproduction&projects=&template=bug-report.yml&title=%5BBug%5D+)
- [Request a Feature 🚀](https://github.com/OHIF/Viewers/issues/new?assignees=&labels=Community%3A+Request+%3Ahand%3A&projects=&template=feature-request.yml&title=%5BFeature+Request%5D+)
- [Ask a Question 🤗](community.ohif.org)
- [Slack Channel](https://join.slack.com/t/cornerstonejs/shared_invite/zt-1r8xb2zau-dOxlD6jit3TN0Uwf928w9Q)
For commercial support, academic collaborations, and answers to common
questions; please use [Get Support](https://ohif.org/get-support/) to contact
us.
## Developing
### Branches
#### `master` branch - The latest dev (beta) release
- `master` - The latest dev release
This is typically where the latest development happens. Code that is in the master branch has passed code reviews and automated tests, but it may not be deemed ready for production. This branch usually contains the most recent changes and features being worked on by the development team. It's often the starting point for creating feature branches (where new features are developed) and hotfix branches (for urgent fixes).
Each package is tagged with beta version numbers, and published to npm such as `@ohif/ui@3.6.0-beta.1`
### `release/*` branches - The latest stable releases
Once the `master` branch code reaches a stable, release-ready state, we conduct a comprehensive code review and QA testing. Upon approval, we create a new release branch from `master`. These branches represent the latest stable version considered ready for production.
For example, `release/3.5` is the branch for version 3.5.0, and `release/3.6` is for version 3.6.0. After each release, we wait a few days to ensure no critical bugs. If any are found, we fix them in the release branch and create a new release with a minor version bump, e.g., 3.5.1 in the `release/3.5` branch.
Each package is tagged with version numbers and published to npm, such as `@ohif/ui@3.5.0`. Note that `master` is always ahead of the `release` branch. We publish docker builds for both beta and stable releases.
Here is a schematic representation of our development workflow:
![alt text](platform/docs/docs/assets/img/github-readme-branches-Jun2024.png)
### Requirements
- [Yarn 1.20.0+](https://yarnpkg.com/en/docs/install)
- [Node 18+](https://nodejs.org/en/)
- Yarn Workspaces should be enabled on your machine:
- `yarn config set workspaces-experimental true`
### Getting Started
1. [Fork this repository][how-to-fork]
2. [Clone your forked repository][how-to-clone]
- `git clone https://github.com/YOUR-USERNAME/Viewers.git`
3. Navigate to the cloned project's directory
4. Add this repo as a `remote` named `upstream`
- `git remote add upstream https://github.com/OHIF/Viewers.git`
5. `yarn install` to restore dependencies and link projects
#### To Develop
_From this repository's root directory:_
```bash
# Enable Yarn Workspaces
yarn config set workspaces-experimental true
# Restore dependencies
yarn install
```
## Commands
These commands are available from the root directory. Each project directory
also supports a number of commands that can be found in their respective
`README.md` and `package.json` files.
| Yarn Commands | Description |
| ---------------------------- | ------------------------------------------------------------- |
| **Develop** | |
| `dev` | Default development experience for Viewer |
| `dev:fast` | Our experimental fast dev mode that uses rsbuild instead of webpack |
| `test:unit` | Jest multi-project test runner; overall coverage |
| **Deploy** | |
| `build`\* | Builds production output for our PWA Viewer | |
\* - For more information on different builds, check out our [Deploy
Docs][deployment-docs]
## Project
The OHIF Medical Image Viewing Platform is maintained as a
[`monorepo`][monorepo]. This means that this repository, instead of containing a
single project, contains many projects. If you explore our project structure,
you'll see the following:
```bash
.
├── extensions #
│ ├── _example # Skeleton of example extension
│ ├── default # basic set of useful functionalities (datasources, panels, etc)
│ ├── cornerstone # image rendering and tools w/ Cornerstone3D
│ ├── cornerstone-dicom-sr # DICOM Structured Report rendering and export
│ ├── cornerstone-dicom-sr # DICOM Structured Report rendering and export
│ ├── cornerstone-dicom-seg # DICOM Segmentation rendering and export
│ ├── cornerstone-dicom-rt # DICOM RTSTRUCT rendering
│ ├── cornerstone-microscopy # Whole Slide Microscopy rendering
│ ├── dicom-pdf # PDF rendering
│ ├── dicom-video # DICOM RESTful Services
│ ├── measurement-tracking # Longitudinal measurement tracking
│ ├── tmtv # Total Metabolic Tumor Volume (TMTV) calculation
|
│
├── modes #
│ ├── _example # Skeleton of example mode
│ ├── basic-dev-mode # Basic development mode
│ ├── longitudinal # Longitudinal mode (measurement tracking)
│ ├── tmtv # Total Metabolic Tumor Volume (TMTV) calculation mode
│ └── microscopy # Whole Slide Microscopy mode
│
├── platform #
│ ├── core # Business Logic
│ ├── i18n # Internationalization Support
│ ├── ui # React component library
│ ├── docs # Documentation
│ └── viewer # Connects platform and extension projects
│
├── ... # misc. shared configuration
├── lerna.json # MonoRepo (Lerna) settings
├── package.json # Shared devDependencies and commands
└── README.md # This file
```
## Acknowledgments
To acknowledge the OHIF Viewer in an academic publication, please cite
> _Open Health Imaging Foundation Viewer: An Extensible Open-Source Framework
> for Building Web-Based Imaging Applications to Support Cancer Research_
>
> Erik Ziegler, Trinity Urban, Danny Brown, James Petts, Steve D. Pieper, Rob
> Lewis, Chris Hafey, and Gordon J. Harris
>
> _JCO Clinical Cancer Informatics_, no. 4 (2020), 336-345, DOI:
> [10.1200/CCI.19.00131](https://www.doi.org/10.1200/CCI.19.00131)
>
> Open-Access on Pubmed Central:
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7259879/
or, for v1, please cite:
> _LesionTracker: Extensible Open-Source Zero-Footprint Web Viewer for Cancer
> Imaging Research and Clinical Trials_
>
> Trinity Urban, Erik Ziegler, Rob Lewis, Chris Hafey, Cheryl Sadow, Annick D.
> Van den Abbeele and Gordon J. Harris
>
> _Cancer Research_, November 1 2017 (77) (21) e119-e122 DOI:
> [10.1158/0008-5472.CAN-17-0334](https://www.doi.org/10.1158/0008-5472.CAN-17-0334)
**Note:** If you use or find this repository helpful, please take the time to
star this repository on GitHub. This is an easy way for us to assess adoption
and it can help us obtain future funding for the project.
This work is supported primarily by the National Institutes of Health, National
Cancer Institute, Informatics Technology for Cancer Research (ITCR) program,
under a
[grant to Dr. Gordon Harris at Massachusetts General Hospital (U24 CA199460)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8971104).
[NCI Imaging Data Commons (IDC) project](https://imaging.datacommons.cancer.gov/) supported the development of new features and bug fixes marked with ["IDC:priority"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Apriority),
["IDC:candidate"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Acandidate) or ["IDC:collaboration"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Acollaboration). NCI Imaging Data Commons is supported by contract number 19X037Q from
Leidos Biomedical Research under Task Order HHSN26100071 from NCI. [IDC Viewer](https://learn.canceridc.dev/portal/visualization) is a customized version of the OHIF Viewer.
This project is tested with BrowserStack. Thank you for supporting open-source!
## License
MIT © [OHIF](https://github.com/OHIF)
<!--
Links
-->
<!-- prettier-ignore-start -->
<!-- Badges -->
[lerna-image]: https://img.shields.io/badge/maintained%20with-lerna-cc00ff.svg
[lerna-url]: https://lerna.js.org/
[netlify-image]: https://api.netlify.com/api/v1/badges/32708787-c9b0-4634-b50f-7ca41952da77/deploy-status
[netlify-url]: https://app.netlify.com/sites/ohif-dev/deploys
[all-contributors-image]: https://img.shields.io/badge/all_contributors-0-orange.svg?style=flat-square
[circleci-image]: https://circleci.com/gh/OHIF/Viewers.svg?style=svg
[circleci-url]: https://circleci.com/gh/OHIF/Viewers
[codecov-image]: https://codecov.io/gh/OHIF/Viewers/branch/master/graph/badge.svg
[codecov-url]: https://codecov.io/gh/OHIF/Viewers/branch/master
[prettier-image]: https://img.shields.io/badge/code_style-prettier-ff69b4.svg?style=flat-square
[prettier-url]: https://github.com/prettier/prettier
[semantic-image]: https://img.shields.io/badge/%20%20%F0%9F%93%A6%F0%9F%9A%80-semantic--release-e10079.svg
[semantic-url]: https://github.com/semantic-release/semantic-release
<!-- ROW -->
[npm-url]: https://npmjs.org/package/@ohif/app
[npm-downloads-image]: https://img.shields.io/npm/dm/@ohif/app.svg?style=flat-square
[npm-version-image]: https://img.shields.io/npm/v/@ohif/app.svg?style=flat-square
[docker-pulls-img]: https://img.shields.io/docker/pulls/ohif/viewer.svg?style=flat-square
[docker-image-url]: https://hub.docker.com/r/ohif/app
[license-image]: https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square
[license-url]: LICENSE
[percy-image]: https://percy.io/static/images/percy-badge.svg
[percy-url]: https://percy.io/Open-Health-Imaging-Foundation/OHIF-Viewer
<!-- Links -->
[monorepo]: https://en.wikipedia.org/wiki/Monorepo
[how-to-fork]: https://help.github.com/en/articles/fork-a-repo
[how-to-clone]: https://help.github.com/en/articles/fork-a-repo#step-2-create-a-local-clone-of-your-fork
[ohif-architecture]: https://docs.ohif.org/architecture/index.html
[ohif-extensions]: https://docs.ohif.org/architecture/index.html
[deployment-docs]: https://docs.ohif.org/deployment/
[react-url]: https://reactjs.org/
[pwa-url]: https://developers.google.com/web/progressive-web-apps/
[ohif-viewer-url]: https://www.npmjs.com/package/@ohif/app
[configuration-url]: https://docs.ohif.org/configuring/
[extensions-url]: https://docs.ohif.org/extensions/
<!-- Platform -->
[platform-core]: platform/core/README.md
[core-npm]: https://www.npmjs.com/package/@ohif/core
[platform-i18n]: platform/i18n/README.md
[i18n-npm]: https://www.npmjs.com/package/@ohif/i18n
[platform-ui]: platform/ui/README.md
[ui-npm]: https://www.npmjs.com/package/@ohif/ui
[platform-viewer]: platform/app/README.md
[viewer-npm]: https://www.npmjs.com/package/@ohif/app
<!-- Extensions -->
[extension-cornerstone]: extensions/cornerstone/README.md
[cornerstone-npm]: https://www.npmjs.com/package/@ohif/extension-cornerstone
[extension-dicom-html]: extensions/dicom-html/README.md
[html-npm]: https://www.npmjs.com/package/@ohif/extension-dicom-html
[extension-dicom-microscopy]: extensions/dicom-microscopy/README.md
[microscopy-npm]: https://www.npmjs.com/package/@ohif/extension-dicom-microscopy
[extension-dicom-pdf]: extensions/dicom-pdf/README.md
[pdf-npm]: https://www.npmjs.com/package/@ohif/extension-dicom-pdf
[extension-vtk]: extensions/vtk/README.md
[vtk-npm]: https://www.npmjs.com/package/@ohif/extension-vtk
<!-- prettier-ignore-end -->
[![FOSSA Status](https://app.fossa.com/api/projects/git%2Bgithub.com%2FOHIF%2FViewers.svg?type=large&issueType=license)](https://app.fossa.com/projects/git%2Bgithub.com%2FOHIF%2FViewers?ref=badge_large&issueType=license)

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# External Dependencies
This module contains optional dependencies and external dependencies for including in OHIF, such as the DICOM Microscopy Viewer component.

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{
"name": "@externals/devDependencies",
"description": "External dev dependencies - put dev build dependencies here",
"version": "3.10.0-beta.111",
"license": "MIT",
"private": true,
"engines": {
"node": ">=12",
"yarn": ">=1.19.1"
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@kitware/vtk.js": "32.1.1",
"clsx": "^2.1.1",
"core-js": "^3.2.1",
"moment": "^2.9.4"
},
"peerDependencies": {
"react": "^18.3.1",
"react-dom": "^18.3.1"
},
"devDependencies": {
"@pmmmwh/react-refresh-webpack-plugin": "^0.5.15",
"@rsbuild/core": "^1.1.13",
"@rsbuild/plugin-node-polyfill": "1.2.0",
"@rsbuild/plugin-react": "^1.1.0",
"@svgr/webpack": "^8.1.0",
"@swc/helpers": "^0.5.15",
"@types/jest": "^27.5.0",
"@typescript-eslint/eslint-plugin": "^6.3.0",
"@typescript-eslint/parser": "^6.3.0",
"autoprefixer": "^10.4.4",
"babel-eslint": "9.x",
"babel-loader": "^8.2.4",
"babel-plugin-module-resolver": "^5.0.0",
"clean-webpack-plugin": "^3.0.0",
"copy-webpack-plugin": "^9.0.1",
"cross-env": "^5.2.0",
"css-loader": "^6.8.1",
"dotenv": "^8.1.0",
"eslint": "^8.39.0",
"eslint-config-prettier": "^7.2.0",
"eslint-config-react-app": "^6.0.0",
"eslint-plugin-cypress": "^2.12.1",
"eslint-plugin-flowtype": "^7.0.0",
"eslint-plugin-import": "^2.26.0",
"eslint-plugin-jsx-a11y": "^6.5.1",
"eslint-plugin-node": "^11.1.0",
"eslint-plugin-prettier": "^5.0.0",
"eslint-plugin-promise": "^5.2.0",
"eslint-plugin-react": "^7.29.4",
"eslint-plugin-react-hooks": "^4.4.0",
"eslint-plugin-tsdoc": "^0.2.11",
"eslint-webpack-plugin": "^2.5.3",
"execa": "^8.0.1",
"extract-css-chunks-webpack-plugin": "^4.5.4",
"html-webpack-plugin": "^5.3.2",
"husky": "^3.0.0",
"jest": "^29.5.0",
"jest-canvas-mock": "^2.1.0",
"jest-environment-jsdom": "^29.5.0",
"jest-junit": "^6.4.0",
"lerna": "^7.2.0",
"lint-staged": "^9.0.2",
"mini-css-extract-plugin": "^2.1.0",
"optimize-css-assets-webpack-plugin": "^6.0.1",
"postcss": "^8.3.5",
"postcss-import": "^14.0.2",
"postcss-loader": "^6.1.1",
"postcss-preset-env": "^7.4.3",
"prettier": "^3.0.3",
"prettier-plugin-tailwindcss": "^0.5.4",
"react-refresh": "^0.14.2",
"semver": "^7.5.1",
"serve": "^14.2.4",
"shader-loader": "^1.3.1",
"shx": "^0.3.3",
"source-map-loader": "^4.0.1",
"start-server-and-test": "^1.10.0",
"style-loader": "^1.0.0",
"stylus": "^0.59.0",
"stylus-loader": "^7.1.3",
"terser-webpack-plugin": "^5.1.4",
"typescript": "5.5.4",
"unused-webpack-plugin": "2.4.0",
"webpack": "5.94.0",
"webpack-bundle-analyzer": "^4.8.0",
"webpack-cli": "^4.7.2",
"webpack-dev-server": "4.7.3",
"webpack-hot-middleware": "^2.25.0",
"webpack-merge": "^5.7.3",
"workbox-webpack-plugin": "^6.1.5",
"worker-loader": "^3.0.8"
},
"scripts": {
"build": "Included as direct dependency"
}
}

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{
"name": "@externals/dicom-microscopy-viewer",
"description": "External reference to dicom-microscopy-viewer",
"version": "3.10.0-beta.111",
"license": "MIT",
"dependencies": {
"dicom-microscopy-viewer": "^0.46.1"
}
}

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{
"name": "ohif-monorepo-root",
"private": true,
"packageManager": "yarn@1.22.22",
"workspaces": {
"packages": [
"../platform/i18n",
"../platform/core",
"../platform/ui",
"../platform/ui-next",
"../platform/app",
"../extensions/*",
"../modes/*",
"../addOns/externals/*"
],
"nohoist": [
"**/html-minifier-terser"
]
},
"scripts": {
"preinstall": "cd .. && node preinstall.js"
},
"devDependencies": {
"@babel/core": "7.24.7",
"@babel/plugin-proposal-class-properties": "^7.16.7",
"@babel/plugin-proposal-object-rest-spread": "^7.17.3",
"@babel/plugin-proposal-private-methods": "^7.18.6",
"@babel/plugin-proposal-private-property-in-object": "^7.21.11",
"@babel/plugin-syntax-dynamic-import": "^7.8.3",
"@babel/plugin-transform-arrow-functions": "^7.16.7",
"@babel/plugin-transform-regenerator": "^7.16.7",
"@babel/plugin-transform-runtime": "7.24.7",
"@babel/plugin-transform-typescript": "^7.13.0",
"@babel/preset-env": "7.24.7",
"@babel/preset-react": "^7.16.7",
"@babel/preset-typescript": "^7.13.0"
},
"resolutions": {
"**/@babel/runtime": "^7.20.13",
"commander": "8.3.0",
"dcmjs": "0.38.0",
"dicomweb-client": ">=0.10.4",
"nth-check": "^2.1.1",
"trim-newlines": "^5.0.0",
"glob-parent": "^6.0.2",
"trim": "^1.0.0",
"package-json": "^8.1.0",
"typescript": "5.5.4",
"sharp": "^0.32.6"
}
}

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/* Used by webpack, babel and eslint */
const path = require('path');
module.exports = {
'@codinsky/parse-js': path.resolve(__dirname, 'packages/parse/src'),
'@codinsky/curate': path.resolve(__dirname, 'packages/curate/src'),
};

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// https://babeljs.io/docs/en/options#babelrcroots
const { extendDefaultPlugins } = require('svgo');
module.exports = {
babelrcRoots: ['./platform/*', './extensions/*', './modes/*'],
presets: ['@babel/preset-env', '@babel/preset-react', '@babel/preset-typescript'],
plugins: [
['@babel/plugin-proposal-class-properties', { loose: true }],
'@babel/plugin-transform-typescript',
['@babel/plugin-proposal-private-property-in-object', { loose: true }],
['@babel/plugin-proposal-private-methods', { loose: true }],
'@babel/plugin-transform-class-static-block',
],
env: {
test: {
presets: [
[
// TODO: https://babeljs.io/blog/2019/03/19/7.4.0#migration-from-core-js-2
'@babel/preset-env',
{
modules: 'commonjs',
debug: false,
},
],
'@babel/preset-react',
'@babel/preset-typescript',
],
plugins: [
'@babel/plugin-proposal-object-rest-spread',
'@babel/plugin-syntax-dynamic-import',
'@babel/plugin-transform-regenerator',
'@babel/transform-destructuring',
'@babel/plugin-transform-runtime',
'@babel/plugin-transform-typescript',
'@babel/plugin-transform-class-static-block',
],
},
production: {
presets: [
// WebPack handles ES6 --> Target Syntax
['@babel/preset-env', { modules: false }],
'@babel/preset-react',
'@babel/preset-typescript',
],
ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
},
development: {
presets: [
// WebPack handles ES6 --> Target Syntax
['@babel/preset-env', { modules: false }],
'@babel/preset-react',
'@babel/preset-typescript',
],
ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
},
},
};

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fdb073c216013477c8545db34d254a9ad328fe48

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module.exports.interfaceVersion = 2;
module.exports.resolve = (source, file, aliases) => {
if (aliases[source]) {
return { found: true, path: aliases[source] };
}
return { found: false };
};

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const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
const ENTRY = {
app: `${SRC_DIR}/index.tsx`,
};
module.exports = (env, argv) => {
return webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
};

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const webpack = require('webpack');
const { merge } = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const pkg = require('./../package.json');
const ROOT_DIR = path.join(__dirname, '../');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
const ENTRY = {
app: `${SRC_DIR}/index.tsx`,
};
const outputName = `ohif-${pkg.name.split('/').pop()}`;
module.exports = (env, argv) => {
const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
return merge(commonConfig, {
stats: {
colors: true,
hash: true,
timings: true,
assets: true,
chunks: false,
chunkModules: false,
modules: false,
children: false,
warnings: true,
},
optimization: {
minimize: true,
sideEffects: true,
},
output: {
path: ROOT_DIR,
library: 'ohif-extension-cornerstone-dicom-pmap',
libraryTarget: 'umd',
filename: pkg.main,
},
externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
plugins: [
new webpack.optimize.LimitChunkCountPlugin({
maxChunks: 1,
}),
new MiniCssExtractPlugin({
filename: `./dist/${outputName}.css`,
chunkFilename: `./dist/${outputName}.css`,
}),
],
});
};

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MIT License
Copyright (c) 2023 Open Health Imaging Foundation
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
the Software, and to permit persons to whom the Software is furnished to do so,
subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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# dicom-pmap
## Description
DICOM PMAP read workflow. This extension will allow you to load a DICOM Parametric
Map image and display it on OHIF.
## Author
OHIF
## License
MIT

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module.exports = {
plugins: ['@babel/plugin-proposal-class-properties'],
env: {
test: {
presets: [
[
// TODO: https://babeljs.io/blog/2019/03/19/7.4.0#migration-from-core-js-2
'@babel/preset-env',
{
modules: 'commonjs',
debug: false,
},
'@babel/preset-typescript',
],
'@babel/preset-react',
],
plugins: [
'@babel/plugin-proposal-object-rest-spread',
'@babel/plugin-syntax-dynamic-import',
'@babel/plugin-transform-regenerator',
'@babel/plugin-transform-runtime',
],
},
production: {
presets: [
// WebPack handles ES6 --> Target Syntax
['@babel/preset-env', { modules: false }],
'@babel/preset-react',
'@babel/preset-typescript',
],
ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
},
development: {
presets: [
// WebPack handles ES6 --> Target Syntax
['@babel/preset-env', { modules: false }],
'@babel/preset-react',
'@babel/preset-typescript',
],
plugins: ['react-hot-loader/babel'],
ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
},
},
};

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{
"name": "@ohif/extension-cornerstone-dicom-pmap",
"version": "3.10.0-beta.111",
"description": "DICOM Parametric Map read workflow",
"author": "OHIF",
"license": "MIT",
"main": "dist/ohif-extension-cornerstone-dicom-pmap.umd.js",
"module": "src/index.tsx",
"files": [
"dist/**",
"public/**",
"README.md"
],
"repository": "OHIF/Viewers",
"keywords": [
"ohif-extension"
],
"publishConfig": {
"access": "public"
},
"engines": {
"node": ">=14",
"npm": ">=6",
"yarn": ">=1.18.0"
},
"scripts": {
"clean": "shx rm -rf dist",
"clean:deep": "yarn run clean && shx rm -rf node_modules",
"dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --output-pathinfo",
"dev:dicom-pmap": "yarn run dev",
"build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
"build:package-1": "yarn run build",
"start": "yarn run dev"
},
"peerDependencies": {
"@ohif/core": "3.10.0-beta.111",
"@ohif/extension-cornerstone": "3.10.0-beta.111",
"@ohif/extension-default": "3.10.0-beta.111",
"@ohif/i18n": "3.10.0-beta.111",
"prop-types": "^15.6.2",
"react": "^18.3.1",
"react-dom": "^18.3.1",
"react-i18next": "^12.2.2",
"react-router": "^6.8.1",
"react-router-dom": "^6.8.1"
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^2.19.14",
"@cornerstonejs/core": "^2.19.14",
"@kitware/vtk.js": "32.1.1",
"react-color": "^2.19.3"
}
}

244
extensions/cornerstone-dicom-pmap/src/getSopClassHandlerModule.ts Normal file
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import { utils } from '@ohif/core';
import { metaData, cache, utilities as csUtils, volumeLoader } from '@cornerstonejs/core';
import { adaptersPMAP } from '@cornerstonejs/adapters';
import { SOPClassHandlerId } from './id';
import { dicomLoaderService } from '@ohif/extension-cornerstone';
const VOLUME_LOADER_SCHEME = 'cornerstoneStreamingImageVolume';
const sopClassUids = ['1.2.840.10008.5.1.4.1.1.30'];
function _getDisplaySetsFromSeries(
instances,
servicesManager: AppTypes.ServicesManager,
extensionManager
) {
const instance = instances[0];
const {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPClassUID,
wadoRoot,
wadoUri,
wadoUriRoot,
} = instance;
const displaySet = {
// Parametric map use to have the same modality as its referenced volume but
// "PMAP" is used in the viewer even though this is not a valid DICOM modality
Modality: 'PMAP',
isReconstructable: true, // by default for now
displaySetInstanceUID: `pmap.${utils.guid()}`,
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
SOPClassHandlerId,
SOPClassUID,
referencedImages: null,
referencedSeriesInstanceUID: null,
referencedDisplaySetInstanceUID: null,
referencedVolumeURI: null,
referencedVolumeId: null,
isDerivedDisplaySet: true,
loadStatus: {
loading: false,
loaded: false,
},
sopClassUids,
instance,
instances: [instance],
wadoRoot,
wadoUriRoot,
wadoUri,
isOverlayDisplaySet: true,
};
const referencedSeriesSequence = instance.ReferencedSeriesSequence;
if (!referencedSeriesSequence) {
console.error('ReferencedSeriesSequence is missing for the parametric map');
return;
}
const referencedSeries = referencedSeriesSequence[0] || referencedSeriesSequence;
displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
// Does not get the referenced displaySet during parametric displaySet creation
// because it is still not available (getDisplaySetByUID returns `undefined`).
displaySet.getReferenceDisplaySet = () => {
const { displaySetService } = servicesManager.services;
if (displaySet.referencedDisplaySetInstanceUID) {
return displaySetService.getDisplaySetByUID(displaySet.referencedDisplaySetInstanceUID);
}
const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
displaySet.referencedSeriesInstanceUID
);
if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
throw new Error('Referenced displaySet is missing for the parametric map');
}
const referencedDisplaySet = referencedDisplaySets[0];
displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
return referencedDisplaySet;
};
// Does not get the referenced volumeId during parametric displaySet creation because the
// referenced displaySet is still not available (getDisplaySetByUID returns `undefined`).
displaySet.getReferencedVolumeId = () => {
if (displaySet.referencedVolumeId) {
return displaySet.referencedVolumeId;
}
const referencedDisplaySet = displaySet.getReferenceDisplaySet();
const referencedVolumeURI = referencedDisplaySet.displaySetInstanceUID;
const referencedVolumeId = `${VOLUME_LOADER_SCHEME}:${referencedVolumeURI}`;
displaySet.referencedVolumeURI = referencedVolumeURI;
displaySet.referencedVolumeId = referencedVolumeId;
return referencedVolumeId;
};
displaySet.load = async ({ headers }) =>
await _load(displaySet, servicesManager, extensionManager, headers);
return [displaySet];
}
const getRangeFromPixelData = (pixelData: Float32Array) => {
let lowest = pixelData[0];
let highest = pixelData[0];
for (let i = 1; i < pixelData.length; i++) {
if (pixelData[i] < lowest) {
lowest = pixelData[i];
}
if (pixelData[i] > highest) {
highest = pixelData[i];
}
}
return [lowest, highest];
};
async function _load(
displaySet,
servicesManager: AppTypes.ServicesManager,
extensionManager,
headers
) {
const volumeId = `${VOLUME_LOADER_SCHEME}:${displaySet.displaySetInstanceUID}`;
const volumeLoadObject = cache.getVolumeLoadObject(volumeId);
if (volumeLoadObject) {
return volumeLoadObject.promise;
}
displaySet.loading = true;
displaySet.isLoaded = false;
// We don't want to fire multiple loads, so we'll wait for the first to finish
// and also return the same promise to any other callers.
const promise = _loadParametricMap({
extensionManager,
displaySet,
headers,
});
cache.putVolumeLoadObject(volumeId, { promise }).catch(err => {
throw err;
});
promise
.then(() => {
displaySet.loading = false;
displaySet.isLoaded = true;
// Broadcast that loading is complete
servicesManager.services.segmentationService._broadcastEvent(
servicesManager.services.segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
{
pmapDisplaySet: displaySet,
}
);
})
.catch(err => {
displaySet.loading = false;
displaySet.isLoaded = false;
throw err;
});
return promise;
}
async function _loadParametricMap({ displaySet, headers }: withAppTypes) {
const arrayBuffer = await dicomLoaderService.findDicomDataPromise(displaySet, null, headers);
const referencedVolumeId = displaySet.getReferencedVolumeId();
const cachedReferencedVolume = cache.getVolume(referencedVolumeId);
// Parametric map can be loaded only if its referenced volume exists otherwise it will fail
if (!cachedReferencedVolume) {
throw new Error(
'Referenced Volume is missing for the PMAP, and stack viewport PMAP is not supported yet'
);
}
const { imageIds } = cachedReferencedVolume;
const results = await adaptersPMAP.Cornerstone3D.ParametricMap.generateToolState(
imageIds,
arrayBuffer,
metaData
);
const { pixelData } = results;
const TypedArrayConstructor = pixelData.constructor;
const paramMapId = displaySet.displaySetInstanceUID;
const derivedVolume = await volumeLoader.createAndCacheDerivedVolume(referencedVolumeId, {
volumeId: paramMapId,
targetBuffer: {
type: TypedArrayConstructor.name,
},
});
const newPixelData = new TypedArrayConstructor(pixelData.length);
for (let i = 0; i < pixelData.length; i++) {
newPixelData[i] = pixelData[i] * 100;
}
derivedVolume.voxelManager.setCompleteScalarDataArray(newPixelData);
const range = getRangeFromPixelData(newPixelData);
const windowLevel = csUtils.windowLevel.toWindowLevel(range[0], range[1]);
derivedVolume.metadata.voiLut = [windowLevel];
derivedVolume.loadStatus = { loaded: true };
return derivedVolume;
}
function getSopClassHandlerModule({ servicesManager, extensionManager }) {
const getDisplaySetsFromSeries = instances => {
return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
};
return [
{
name: 'dicom-pmap',
sopClassUids,
getDisplaySetsFromSeries,
},
];
}
export default getSopClassHandlerModule;

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extensions/cornerstone-dicom-pmap/src/id.js Normal file
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import packageJson from '../package.json';
const id = packageJson.name;
const SOPClassHandlerName = 'dicom-pmap';
const SOPClassHandlerId = `${id}.sopClassHandlerModule.${SOPClassHandlerName}`;
export { id, SOPClassHandlerId, SOPClassHandlerName };

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extensions/cornerstone-dicom-pmap/src/index.tsx Normal file
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import { id } from './id';
import React from 'react';
import getSopClassHandlerModule from './getSopClassHandlerModule';
const Component = React.lazy(() => {
return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstonePMAPViewport');
});
const OHIFCornerstonePMAPViewport = props => {
return (
<React.Suspense fallback={<div>Loading...</div>}>
<Component {...props} />
</React.Suspense>
);
};
/**
* You can remove any of the following modules if you don't need them.
*/
const extension = {
id,
getViewportModule({ servicesManager, extensionManager, commandsManager }) {
const ExtendedOHIFCornerstonePMAPViewport = props => {
return (
<OHIFCornerstonePMAPViewport
servicesManager={servicesManager}
extensionManager={extensionManager}
commandsManager={commandsManager}
{...props}
/>
);
};
return [{ name: 'dicom-pmap', component: ExtendedOHIFCornerstonePMAPViewport }];
},
getSopClassHandlerModule,
};
export default extension;

210
extensions/cornerstone-dicom-pmap/src/viewports/OHIFCornerstonePMAPViewport.tsx Normal file
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import PropTypes from 'prop-types';
import React, { useCallback, useEffect, useRef, useState } from 'react';
import { useViewportGrid } from '@ohif/ui-next';
function OHIFCornerstonePMAPViewport(props: withAppTypes) {
const {
displaySets,
children,
viewportOptions,
displaySetOptions,
servicesManager,
extensionManager,
} = props;
const viewportId = viewportOptions.viewportId;
const { displaySetService, segmentationService, uiNotificationService, customizationService } =
servicesManager.services;
// PMAP viewport will always have a single display set
if (displaySets.length !== 1) {
throw new Error('PMAP viewport must have a single display set');
}
const LoadingIndicatorTotalPercent = customizationService.getCustomization(
'ui.loadingIndicatorTotalPercent'
);
const pmapDisplaySet = displaySets[0];
const [viewportGrid, viewportGridService] = useViewportGrid();
const referencedDisplaySetRef = useRef(null);
const { viewports, activeViewportId } = viewportGrid;
const referencedDisplaySet = pmapDisplaySet.getReferenceDisplaySet();
const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(
referencedDisplaySet,
pmapDisplaySet
);
referencedDisplaySetRef.current = {
displaySet: referencedDisplaySet,
metadata: referencedDisplaySetMetadata,
};
const [pmapIsLoading, setPmapIsLoading] = useState(!pmapDisplaySet.isLoaded);
// Add effect to listen for loading complete
useEffect(() => {
const { unsubscribe } = segmentationService.subscribe(
segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
evt => {
if (evt.pmapDisplaySet?.displaySetInstanceUID === pmapDisplaySet.displaySetInstanceUID) {
setPmapIsLoading(false);
}
}
);
return () => {
unsubscribe();
};
}, [pmapDisplaySet]);
const getCornerstoneViewport = useCallback(() => {
const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
const { component: Component } = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.viewportModule.cornerstone'
);
displaySetOptions.unshift({});
const [pmapDisplaySetOptions] = displaySetOptions;
// Make sure `options` exists
pmapDisplaySetOptions.options = pmapDisplaySetOptions.options ?? {};
Object.assign(pmapDisplaySetOptions.options, {
colormap: {
name: 'rainbow_2',
opacity: [
{ value: 0, opacity: 0 },
{ value: 0.25, opacity: 0.25 },
{ value: 0.5, opacity: 0.5 },
{ value: 0.75, opacity: 0.75 },
{ value: 0.9, opacity: 0.99 },
],
},
voi: {
windowCenter: 50,
windowWidth: 100,
},
});
uiNotificationService.show({
title: 'Parametric Map',
type: 'warning',
message: 'The values are multiplied by 100 in the viewport for better visibility',
});
return (
<Component
{...props}
// Referenced + PMAP displaySets must be passed as parameter in this order
displaySets={[referencedDisplaySet, pmapDisplaySet]}
viewportOptions={{
viewportType: 'volume',
orientation: viewportOptions.orientation,
viewportId: viewportOptions.viewportId,
presentationIds: viewportOptions.presentationIds,
}}
displaySetOptions={[{}, pmapDisplaySetOptions]}
></Component>
);
}, [
extensionManager,
displaySetOptions,
props,
pmapDisplaySet,
viewportOptions.orientation,
viewportOptions.viewportId,
]);
// Cleanup the PMAP viewport when the viewport is destroyed
useEffect(() => {
const onDisplaySetsRemovedSubscription = displaySetService.subscribe(
displaySetService.EVENTS.DISPLAY_SETS_REMOVED,
({ displaySetInstanceUIDs }) => {
const activeViewport = viewports.get(activeViewportId);
if (displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)) {
viewportGridService.setDisplaySetsForViewport({
viewportId: activeViewportId,
displaySetInstanceUIDs: [],
});
}
}
);
return () => {
onDisplaySetsRemovedSubscription.unsubscribe();
};
}, [activeViewportId, displaySetService, viewportGridService, viewports]);
let childrenWithProps = null;
if (children && children.length) {
childrenWithProps = children.map((child, index) => {
return (
child &&
React.cloneElement(child, {
viewportId,
key: index,
})
);
});
}
return (
<>
<div className="relative flex h-full w-full flex-row overflow-hidden">
{pmapIsLoading && (
<LoadingIndicatorTotalPercent
className="h-full w-full"
totalNumbers={null}
percentComplete={null}
loadingText="Loading Parametric Map..."
/>
)}
{getCornerstoneViewport()}
{childrenWithProps}
</div>
</>
);
}
OHIFCornerstonePMAPViewport.propTypes = {
displaySets: PropTypes.arrayOf(PropTypes.object),
viewportId: PropTypes.string.isRequired,
dataSource: PropTypes.object,
children: PropTypes.node,
};
function _getReferencedDisplaySetMetadata(referencedDisplaySet, pmapDisplaySet) {
const { SharedFunctionalGroupsSequence } = pmapDisplaySet.instance;
const SharedFunctionalGroup = Array.isArray(SharedFunctionalGroupsSequence)
? SharedFunctionalGroupsSequence[0]
: SharedFunctionalGroupsSequence;
const { PixelMeasuresSequence } = SharedFunctionalGroup;
const PixelMeasures = Array.isArray(PixelMeasuresSequence)
? PixelMeasuresSequence[0]
: PixelMeasuresSequence;
const { SpacingBetweenSlices, SliceThickness } = PixelMeasures;
const image0 = referencedDisplaySet.images[0];
const referencedDisplaySetMetadata = {
PatientID: image0.PatientID,
PatientName: image0.PatientName,
PatientSex: image0.PatientSex,
PatientAge: image0.PatientAge,
SliceThickness: image0.SliceThickness || SliceThickness,
StudyDate: image0.StudyDate,
SeriesDescription: image0.SeriesDescription,
SeriesInstanceUID: image0.SeriesInstanceUID,
SeriesNumber: image0.SeriesNumber,
ManufacturerModelName: image0.ManufacturerModelName,
SpacingBetweenSlices: image0.SpacingBetweenSlices || SpacingBetweenSlices,
};
return referencedDisplaySetMetadata;
}
export default OHIFCornerstonePMAPViewport;

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extensions/cornerstone-dicom-rt/.webpack/webpack.dev.js Normal file
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const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
const ENTRY = {
app: `${SRC_DIR}/index.tsx`,
};
module.exports = (env, argv) => {
return webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
};

48
extensions/cornerstone-dicom-rt/.webpack/webpack.prod.js Normal file
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const webpack = require('webpack');
const { merge } = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const pkg = require('./../package.json');
const BundleAnalyzerPlugin = require('webpack-bundle-analyzer').BundleAnalyzerPlugin;
const ROOT_DIR = path.join(__dirname, './..');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
const ENTRY = {
app: `${SRC_DIR}/index.tsx`,
};
module.exports = (env, argv) => {
const commonConfig = webpackCommon(env, argv, { SRC_DIR, ENTRY, DIST_DIR });
return merge(commonConfig, {
stats: {
colors: true,
hash: true,
timings: true,
assets: true,
chunks: false,
chunkModules: false,
modules: false,
children: false,
warnings: true,
},
optimization: {
minimize: true,
sideEffects: false,
},
output: {
path: ROOT_DIR,
library: 'ohif-extension-cornerstone-dicom-rt',
libraryTarget: 'umd',
filename: pkg.main,
},
externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
plugins: [
new webpack.optimize.LimitChunkCountPlugin({
maxChunks: 1,
}),
// new BundleAnalyzerPlugin(),
],
});
};

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extensions/cornerstone-dicom-rt/CHANGELOG.md Normal file
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20
extensions/cornerstone-dicom-rt/LICENSE Normal file
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MIT License
Copyright (c) 2023 Open Health Imaging Foundation
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
the Software, and to permit persons to whom the Software is furnished to do so,
subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

13
extensions/cornerstone-dicom-rt/README.md Normal file
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# dicom-rt
## Description
DICOM RT read workflow. This extension will allow you to load a DICOM RTSS image
and display it in OHIF.
## Author
OHIF
## License
MIT

43
extensions/cornerstone-dicom-rt/babel.config.js Normal file
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module.exports = {
plugins: ['@babel/plugin-proposal-class-properties'],
env: {
test: {
presets: [
[
// TODO: https://babeljs.io/blog/2019/03/19/7.4.0#migration-from-core-js-2
'@babel/preset-env',
{
modules: 'commonjs',
debug: false,
},
'@babel/preset-typescript',
],
'@babel/preset-react',
],
plugins: [
'@babel/plugin-proposal-object-rest-spread',
'@babel/plugin-syntax-dynamic-import',
'@babel/plugin-transform-regenerator',
'@babel/plugin-transform-runtime',
],
},
production: {
presets: [
// WebPack handles ES6 --> Target Syntax
['@babel/preset-env', { modules: false }],
'@babel/preset-react',
'@babel/preset-typescript',
],
ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
},
development: {
presets: [
// WebPack handles ES6 --> Target Syntax
['@babel/preset-env', { modules: false }],
'@babel/preset-react',
'@babel/preset-typescript',
],
ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
},
},
};

51
extensions/cornerstone-dicom-rt/package.json Normal file
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{
"name": "@ohif/extension-cornerstone-dicom-rt",
"version": "3.10.0-beta.111",
"description": "DICOM RT read workflow",
"author": "OHIF",
"license": "MIT",
"main": "dist/ohif-extension-cornerstone-dicom-rt.umd.js",
"module": "src/index.tsx",
"files": [
"dist/**",
"public/**",
"README.md"
],
"publishConfig": {
"access": "public"
},
"repository": "OHIF/Viewers",
"keywords": [
"ohif-extension"
],
"engines": {
"node": ">=14",
"npm": ">=6",
"yarn": ">=1.18.0"
},
"scripts": {
"clean": "shx rm -rf dist",
"clean:deep": "yarn run clean && shx rm -rf node_modules",
"dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --output-pathinfo",
"dev:dicom-seg": "yarn run dev",
"build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
"build:package-1": "yarn run build",
"start": "yarn run dev"
},
"peerDependencies": {
"@ohif/core": "3.10.0-beta.111",
"@ohif/extension-cornerstone": "3.10.0-beta.111",
"@ohif/extension-default": "3.10.0-beta.111",
"@ohif/i18n": "3.10.0-beta.111",
"prop-types": "^15.6.2",
"react": "^18.3.1",
"react-dom": "^18.3.1",
"react-i18next": "^10.11.0",
"react-router": "^6.23.1",
"react-router-dom": "^6.23.1"
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"react-color": "^2.19.3"
}
}

55
extensions/cornerstone-dicom-rt/src/getCommandsModule.ts Normal file
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import { SegmentationRepresentations } from '@cornerstonejs/tools/enums';
const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
const services = servicesManager.services;
const { displaySetService, viewportGridService } = services;
const actions = {
hydrateRTSDisplaySet: ({ displaySet, viewportId }) => {
if (displaySet.Modality !== 'RTSTRUCT') {
throw new Error('Display set is not an RTSTRUCT');
}
const referencedDisplaySet = displaySetService.getDisplaySetByUID(
displaySet.referencedDisplaySetInstanceUID
);
// update the previously stored segmentationPresentation with the new viewportId
// presentation so that when we put the referencedDisplaySet back in the viewport
// it will have the correct segmentation representation hydrated
commandsManager.runCommand('updateStoredSegmentationPresentation', {
displaySet: displaySet,
type: SegmentationRepresentations.Contour,
});
// update the previously stored positionPresentation with the new viewportId
// presentation so that when we put the referencedDisplaySet back in the viewport
// it will be in the correct position zoom and pan
commandsManager.runCommand('updateStoredPositionPresentation', {
viewportId,
displaySetInstanceUID: referencedDisplaySet.displaySetInstanceUID,
});
viewportGridService.setDisplaySetsForViewport({
viewportId,
displaySetInstanceUIDs: [referencedDisplaySet.displaySetInstanceUID],
});
},
};
const definitions = {
hydrateRTSDisplaySet: {
commandFn: actions.hydrateRTSDisplaySet,
storeContexts: [],
options: {},
},
};
return {
actions,
definitions,
defaultContext: 'cornerstone-dicom-rt',
};
};
export default commandsModule;

199
extensions/cornerstone-dicom-rt/src/getSopClassHandlerModule.ts Normal file
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import { utils } from '@ohif/core';
import { SOPClassHandlerId } from './id';
import loadRTStruct from './loadRTStruct';
const sopClassUids = ['1.2.840.10008.5.1.4.1.1.481.3'];
const loadPromises = {};
function _getDisplaySetsFromSeries(
instances,
servicesManager: AppTypes.ServicesManager,
extensionManager
) {
const instance = instances[0];
const {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPClassUID,
wadoRoot,
wadoUri,
wadoUriRoot,
} = instance;
const displaySet = {
Modality: 'RTSTRUCT',
loading: false,
isReconstructable: false, // by default for now since it is a volumetric SEG currently
displaySetInstanceUID: utils.guid(),
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
SOPClassHandlerId,
SOPClassUID,
referencedImages: null,
referencedSeriesInstanceUID: null,
referencedDisplaySetInstanceUID: null,
isDerivedDisplaySet: true,
isLoaded: false,
isHydrated: false,
structureSet: null,
sopClassUids,
instance,
wadoRoot,
wadoUriRoot,
wadoUri,
isOverlayDisplaySet: true,
};
let referencedSeriesSequence = instance.ReferencedSeriesSequence;
if (instance.ReferencedFrameOfReferenceSequence && !instance.ReferencedSeriesSequence) {
instance.ReferencedSeriesSequence = _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
instance.ReferencedFrameOfReferenceSequence
);
referencedSeriesSequence = instance.ReferencedSeriesSequence;
}
if (!referencedSeriesSequence) {
throw new Error('ReferencedSeriesSequence is missing for the RTSTRUCT');
}
const referencedSeries = referencedSeriesSequence[0];
displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
const { displaySetService } = servicesManager.services;
const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
displaySet.referencedSeriesInstanceUID
);
if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
// Instead of throwing error, subscribe to display sets added
const { unsubscribe } = displaySetService.subscribe(
displaySetService.EVENTS.DISPLAY_SETS_ADDED,
({ displaySetsAdded }) => {
const addedDisplaySet = displaySetsAdded[0];
if (addedDisplaySet.SeriesInstanceUID === displaySet.referencedSeriesInstanceUID) {
displaySet.referencedDisplaySetInstanceUID = addedDisplaySet.displaySetInstanceUID;
unsubscribe();
}
}
);
} else {
const referencedDisplaySet = referencedDisplaySets[0];
displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
}
displaySet.load = ({ headers }) => _load(displaySet, servicesManager, extensionManager, headers);
return [displaySet];
}
function _load(rtDisplaySet, servicesManager: AppTypes.ServicesManager, extensionManager, headers) {
const { SOPInstanceUID } = rtDisplaySet;
const { segmentationService } = servicesManager.services;
if (
(rtDisplaySet.loading || rtDisplaySet.isLoaded) &&
loadPromises[SOPInstanceUID] &&
_segmentationExistsInCache(rtDisplaySet, segmentationService)
) {
return loadPromises[SOPInstanceUID];
}
rtDisplaySet.loading = true;
// We don't want to fire multiple loads, so we'll wait for the first to finish
// and also return the same promise to any other callers.
loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => {
if (!rtDisplaySet.structureSet) {
const structureSet = await loadRTStruct(extensionManager, rtDisplaySet, headers);
rtDisplaySet.structureSet = structureSet;
}
segmentationService
.createSegmentationForRTDisplaySet(rtDisplaySet)
.then(() => {
rtDisplaySet.loading = false;
resolve();
})
.catch(error => {
rtDisplaySet.loading = false;
reject(error);
});
});
return loadPromises[SOPInstanceUID];
}
function _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
ReferencedFrameOfReferenceSequence
) {
const ReferencedSeriesSequence = [];
ReferencedFrameOfReferenceSequence.forEach(referencedFrameOfReference => {
const { RTReferencedStudySequence } = referencedFrameOfReference;
RTReferencedStudySequence.forEach(rtReferencedStudy => {
const { RTReferencedSeriesSequence } = rtReferencedStudy;
RTReferencedSeriesSequence.forEach(rtReferencedSeries => {
const ReferencedInstanceSequence = [];
const { ContourImageSequence, SeriesInstanceUID } = rtReferencedSeries;
ContourImageSequence.forEach(contourImage => {
ReferencedInstanceSequence.push({
ReferencedSOPInstanceUID: contourImage.ReferencedSOPInstanceUID,
ReferencedSOPClassUID: contourImage.ReferencedSOPClassUID,
});
});
const referencedSeries = {
SeriesInstanceUID,
ReferencedInstanceSequence,
};
ReferencedSeriesSequence.push(referencedSeries);
});
});
});
return ReferencedSeriesSequence;
}
function _segmentationExistsInCache(
rtDisplaySet,
segmentationService: AppTypes.SegmentationService
) {
// Todo: fix this
return false;
// This should be abstracted with the CornerstoneCacheService
const rtContourId = rtDisplaySet.displaySetInstanceUID;
const contour = segmentationService.getContour(rtContourId);
return contour !== undefined;
}
function getSopClassHandlerModule({ servicesManager, extensionManager }) {
return [
{
name: 'dicom-rt',
sopClassUids,
getDisplaySetsFromSeries: instances => {
return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
},
},
];
}
export default getSopClassHandlerModule;

7
extensions/cornerstone-dicom-rt/src/id.js Normal file
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import packageJson from '../package.json';
const id = packageJson.name;
const SOPClassHandlerName = 'dicom-rt';
const SOPClassHandlerId = `${id}.sopClassHandlerModule.${SOPClassHandlerName}`;
export { id, SOPClassHandlerId, SOPClassHandlerName };

63
extensions/cornerstone-dicom-rt/src/index.tsx Normal file
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import { id } from './id';
import React from 'react';
import { Types } from '@ohif/core';
import getSopClassHandlerModule from './getSopClassHandlerModule';
import getCommandsModule from './getCommandsModule';
const Component = React.lazy(() => {
return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneRTViewport');
});
const OHIFCornerstoneRTViewport = props => {
return (
<React.Suspense fallback={<div>Loading...</div>}>
<Component {...props} />
</React.Suspense>
);
};
/**
* You can remove any of the following modules if you don't need them.
*/
const extension: Types.Extensions.Extension = {
/**
* Only required property. Should be a unique value across all extensions.
* You ID can be anything you want, but it should be unique.
*/
id,
getCommandsModule,
/**
* PanelModule should provide a list of panels that will be available in OHIF
* for Modes to consume and render. Each panel is defined by a {name,
* iconName, iconLabel, label, component} object. Example of a panel module
* is the StudyBrowserPanel that is provided by the default extension in OHIF.
*/
getViewportModule({
servicesManager,
extensionManager,
commandsManager,
}: Types.Extensions.ExtensionParams) {
const ExtendedOHIFCornerstoneRTViewport = props => {
return (
<OHIFCornerstoneRTViewport
servicesManager={servicesManager}
extensionManager={extensionManager}
commandsManager={commandsManager}
{...props}
/>
);
};
return [{ name: 'dicom-rt', component: ExtendedOHIFCornerstoneRTViewport }];
},
/**
* SopClassHandlerModule should provide a list of sop class handlers that will be
* available in OHIF for Modes to consume and use to create displaySets from Series.
* Each sop class handler is defined by a { name, sopClassUids, getDisplaySetsFromSeries}.
* Examples include the default sop class handler provided by the default extension
*/
getSopClassHandlerModule,
};
export default extension;

267
extensions/cornerstone-dicom-rt/src/loadRTStruct.js Normal file
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import dcmjs from 'dcmjs';
const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
const dicomlab2RGB = dcmjs.data.Colors.dicomlab2RGB;
async function checkAndLoadContourData(instance, datasource) {
if (!instance || !instance.ROIContourSequence) {
return Promise.reject('Invalid instance object or ROIContourSequence');
}
const promisesMap = new Map();
for (const ROIContour of instance.ROIContourSequence) {
const referencedROINumber = ROIContour.ReferencedROINumber;
if (!ROIContour || !ROIContour.ContourSequence) {
promisesMap.set(referencedROINumber, [Promise.resolve([])]);
continue;
}
for (const Contour of ROIContour.ContourSequence) {
if (!Contour || !Contour.ContourData) {
return Promise.reject('Invalid Contour or ContourData');
}
const contourData = Contour.ContourData;
if (Array.isArray(contourData)) {
promisesMap.has(referencedROINumber)
? promisesMap.get(referencedROINumber).push(Promise.resolve(contourData))
: promisesMap.set(referencedROINumber, [Promise.resolve(contourData)]);
} else if (contourData && contourData.BulkDataURI) {
const bulkDataURI = contourData.BulkDataURI;
if (!datasource || !datasource.retrieve || !datasource.retrieve.bulkDataURI) {
return Promise.reject('Invalid datasource object or retrieve function');
}
const bulkDataPromise = datasource.retrieve.bulkDataURI({
BulkDataURI: bulkDataURI,
StudyInstanceUID: instance.StudyInstanceUID,
SeriesInstanceUID: instance.SeriesInstanceUID,
SOPInstanceUID: instance.SOPInstanceUID,
});
promisesMap.has(referencedROINumber)
? promisesMap.get(referencedROINumber).push(bulkDataPromise)
: promisesMap.set(referencedROINumber, [bulkDataPromise]);
} else {
return Promise.reject(`Invalid ContourData: ${contourData}`);
}
}
}
const resolvedPromisesMap = new Map();
for (const [key, promiseArray] of promisesMap.entries()) {
resolvedPromisesMap.set(key, await Promise.allSettled(promiseArray));
}
instance.ROIContourSequence.forEach(ROIContour => {
try {
const referencedROINumber = ROIContour.ReferencedROINumber;
const resolvedPromises = resolvedPromisesMap.get(referencedROINumber);
if (ROIContour.ContourSequence) {
ROIContour.ContourSequence.forEach((Contour, index) => {
const promise = resolvedPromises[index];
if (promise.status === 'fulfilled') {
if (Array.isArray(promise.value) && promise.value.every(Number.isFinite)) {
// If promise.value is already an array of numbers, use it directly
Contour.ContourData = promise.value;
} else {
// If the resolved promise value is a byte array (Blob), it needs to be decoded
const uint8Array = new Uint8Array(promise.value);
const textDecoder = new TextDecoder();
const dataUint8Array = textDecoder.decode(uint8Array);
if (typeof dataUint8Array === 'string' && dataUint8Array.includes('\\')) {
Contour.ContourData = dataUint8Array.split('\\').map(parseFloat);
} else {
Contour.ContourData = [];
}
}
} else {
console.error(promise.reason);
}
});
}
} catch (error) {
console.error(error);
}
});
}
export default async function loadRTStruct(extensionManager, rtStructDisplaySet, headers) {
const utilityModule = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.utilityModule.common'
);
const dataSource = extensionManager.getActiveDataSource()[0];
const { bulkDataURI } = dataSource.getConfig?.() || {};
const { dicomLoaderService } = utilityModule.exports;
// Set here is loading is asynchronous.
// If this function throws its set back to false.
rtStructDisplaySet.isLoaded = true;
let instance = rtStructDisplaySet.instance;
if (!bulkDataURI || !bulkDataURI.enabled) {
const segArrayBuffer = await dicomLoaderService.findDicomDataPromise(
rtStructDisplaySet,
null,
headers
);
const dicomData = DicomMessage.readFile(segArrayBuffer);
const rtStructDataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
rtStructDataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
instance = rtStructDataset;
} else {
await checkAndLoadContourData(instance, dataSource);
}
const { StructureSetROISequence, ROIContourSequence, RTROIObservationsSequence } = instance;
// Define our structure set entry and add it to the rtstruct module state.
const structureSet = {
StructureSetLabel: instance.StructureSetLabel,
SeriesInstanceUID: instance.SeriesInstanceUID,
ROIContours: [],
visible: true,
ReferencedSOPInstanceUIDsSet: new Set(),
};
for (let i = 0; i < ROIContourSequence.length; i++) {
const ROIContour = ROIContourSequence[i];
const { ContourSequence } = ROIContour;
if (!ContourSequence) {
continue;
}
const isSupported = false;
const ContourSequenceArray = _toArray(ContourSequence);
const contourPoints = [];
for (let c = 0; c < ContourSequenceArray.length; c++) {
const { ContourData, NumberOfContourPoints, ContourGeometricType, ContourImageSequence } =
ContourSequenceArray[c];
let isSupported = false;
const points = [];
for (let p = 0; p < NumberOfContourPoints * 3; p += 3) {
points.push({
x: ContourData[p],
y: ContourData[p + 1],
z: ContourData[p + 2],
});
}
switch (ContourGeometricType) {
case 'CLOSED_PLANAR':
case 'OPEN_PLANAR':
case 'POINT':
isSupported = true;
break;
default:
continue;
}
contourPoints.push({
numberOfPoints: NumberOfContourPoints,
points,
type: ContourGeometricType,
isSupported,
});
if (ContourImageSequence?.ReferencedSOPInstanceUID) {
structureSet.ReferencedSOPInstanceUIDsSet.add(
ContourImageSequence?.ReferencedSOPInstanceUID
);
}
}
_setROIContourMetadata(
structureSet,
StructureSetROISequence,
RTROIObservationsSequence,
ROIContour,
contourPoints,
isSupported
);
}
return structureSet;
}
function _setROIContourMetadata(
structureSet,
StructureSetROISequence,
RTROIObservationsSequence,
ROIContour,
contourPoints,
isSupported
) {
const StructureSetROI = StructureSetROISequence.find(
structureSetROI => structureSetROI.ROINumber === ROIContour.ReferencedROINumber
);
const ROIContourData = {
ROINumber: StructureSetROI.ROINumber,
ROIName: StructureSetROI.ROIName,
ROIGenerationAlgorithm: StructureSetROI.ROIGenerationAlgorithm,
ROIDescription: StructureSetROI.ROIDescription,
isSupported,
contourPoints,
visible: true,
};
_setROIContourDataColor(ROIContour, ROIContourData);
if (RTROIObservationsSequence) {
// If present, add additional RTROIObservations metadata.
_setROIContourRTROIObservations(
ROIContourData,
RTROIObservationsSequence,
ROIContour.ReferencedROINumber
);
}
structureSet.ROIContours.push(ROIContourData);
}
function _setROIContourDataColor(ROIContour, ROIContourData) {
let { ROIDisplayColor, RecommendedDisplayCIELabValue } = ROIContour;
if (!ROIDisplayColor && RecommendedDisplayCIELabValue) {
// If ROIDisplayColor is absent, try using the RecommendedDisplayCIELabValue color.
ROIDisplayColor = dicomlab2RGB(RecommendedDisplayCIELabValue);
}
if (ROIDisplayColor) {
ROIContourData.colorArray = [...ROIDisplayColor];
}
}
function _setROIContourRTROIObservations(ROIContourData, RTROIObservationsSequence, ROINumber) {
const RTROIObservations = RTROIObservationsSequence.find(
RTROIObservations => RTROIObservations.ReferencedROINumber === ROINumber
);
if (RTROIObservations) {
// Deep copy so we don't keep the reference to the dcmjs dataset entry.
const { ObservationNumber, ROIObservationDescription, RTROIInterpretedType, ROIInterpreter } =
RTROIObservations;
ROIContourData.RTROIObservations = {
ObservationNumber,
ROIObservationDescription,
RTROIInterpretedType,
ROIInterpreter,
};
}
}
function _toArray(objOrArray) {
return Array.isArray(objOrArray) ? objOrArray : [objOrArray];
}

7
extensions/cornerstone-dicom-rt/src/utils/initRTToolGroup.ts Normal file
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function createRTToolGroupAndAddTools(ToolGroupService, customizationService, toolGroupId) {
const tools = customizationService.getCustomization('cornerstone.overlayViewportTools');
return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools);
}
export default createRTToolGroupAndAddTools;

82
extensions/cornerstone-dicom-rt/src/utils/promptHydrateRT.ts Normal file
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import { ButtonEnums } from '@ohif/ui';
const RESPONSE = {
NO_NEVER: -1,
CANCEL: 0,
HYDRATE_SEG: 5,
};
function promptHydrateRT({
servicesManager,
rtDisplaySet,
viewportId,
preHydrateCallbacks,
hydrateRTDisplaySet,
}: withAppTypes) {
const { uiViewportDialogService } = servicesManager.services;
const extensionManager = servicesManager._extensionManager;
const appConfig = extensionManager._appConfig;
return new Promise(async function (resolve, reject) {
const promptResult = appConfig?.disableConfirmationPrompts
? RESPONSE.HYDRATE_SEG
: await _askHydrate(uiViewportDialogService, viewportId);
if (promptResult === RESPONSE.HYDRATE_SEG) {
preHydrateCallbacks?.forEach(callback => {
callback();
});
const isHydrated = await hydrateRTDisplaySet({
rtDisplaySet,
viewportId,
servicesManager,
});
resolve(isHydrated);
}
});
}
function _askHydrate(uiViewportDialogService: AppTypes.UIViewportDialogService, viewportId) {
return new Promise(function (resolve, reject) {
const message = 'Do you want to open this Segmentation?';
const actions = [
{
id: 'no-hydrate',
type: ButtonEnums.type.secondary,
text: 'No',
value: RESPONSE.CANCEL,
},
{
id: 'yes-hydrate',
type: ButtonEnums.type.primary,
text: 'Yes',
value: RESPONSE.HYDRATE_SEG,
},
];
const onSubmit = result => {
uiViewportDialogService.hide();
resolve(result);
};
uiViewportDialogService.show({
id: 'promptHydrateRT',
viewportId,
type: 'info',
message,
actions,
onSubmit,
onOutsideClick: () => {
uiViewportDialogService.hide();
resolve(RESPONSE.CANCEL);
},
onKeyPress: event => {
if (event.key === 'Enter') {
onSubmit(RESPONSE.HYDRATE_SEG);
}
},
});
});
}
export default promptHydrateRT;

397
extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx Normal file
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import React, { useCallback, useEffect, useRef, useState } from 'react';
import PropTypes from 'prop-types';
import { ViewportActionArrows } from '@ohif/ui';
import { useViewportGrid } from '@ohif/ui-next';
import { utils } from '@ohif/extension-cornerstone';
import promptHydrateRT from '../utils/promptHydrateRT';
import _getStatusComponent from './_getStatusComponent';
import createRTToolGroupAndAddTools from '../utils/initRTToolGroup';
import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
const RT_TOOLGROUP_BASE_NAME = 'RTToolGroup';
function OHIFCornerstoneRTViewport(props: withAppTypes) {
const {
children,
displaySets,
viewportOptions,
servicesManager,
extensionManager,
commandsManager,
} = props;
const {
displaySetService,
toolGroupService,
segmentationService,
uiNotificationService,
customizationService,
viewportActionCornersService,
} = servicesManager.services;
const viewportId = viewportOptions.viewportId;
const toolGroupId = `${RT_TOOLGROUP_BASE_NAME}-${viewportId}`;
// RT viewport will always have a single display set
if (displaySets.length > 1) {
throw new Error('RT viewport should only have a single display set');
}
const LoadingIndicatorTotalPercent = customizationService.getCustomization(
'ui.loadingIndicatorTotalPercent'
);
const rtDisplaySet = displaySets[0];
const [viewportGrid, viewportGridService] = useViewportGrid();
// States
const selectedSegmentObjectIndex: number = 0;
const { setPositionPresentation } = usePositionPresentationStore();
// Hydration means that the RT is opened and segments are loaded into the
// segmentation panel, and RT is also rendered on any viewport that is in the
// same frameOfReferenceUID as the referencedSeriesUID of the RT. However,
// loading basically means RT loading over network and bit unpacking of the
// RT data.
const [isHydrated, setIsHydrated] = useState(rtDisplaySet.isHydrated);
const [rtIsLoading, setRtIsLoading] = useState(!rtDisplaySet.isLoaded);
const [element, setElement] = useState(null);
const [processingProgress, setProcessingProgress] = useState({
percentComplete: null,
totalSegments: null,
});
// refs
const referencedDisplaySetRef = useRef(null);
const { viewports, activeViewportId } = viewportGrid;
const referencedDisplaySetInstanceUID = rtDisplaySet.referencedDisplaySetInstanceUID;
const referencedDisplaySet = displaySetService.getDisplaySetByUID(
referencedDisplaySetInstanceUID
);
const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(referencedDisplaySet);
referencedDisplaySetRef.current = {
displaySet: referencedDisplaySet,
metadata: referencedDisplaySetMetadata,
};
/**
* OnElementEnabled callback which is called after the cornerstoneExtension
* has enabled the element. Note: we delegate all the image rendering to
* cornerstoneExtension, so we don't need to do anything here regarding
* the image rendering, element enabling etc.
*/
const onElementEnabled = evt => {
setElement(evt.detail.element);
};
const onElementDisabled = () => {
setElement(null);
};
const storePresentationState = useCallback(() => {
viewportGrid?.viewports.forEach(({ viewportId }) => {
commandsManager.runCommand('storePresentation', {
viewportId,
});
});
}, [viewportGrid]);
const hydrateRTDisplaySet = useCallback(
({ rtDisplaySet, viewportId }) => {
commandsManager.runCommand('hydrateRTSDisplaySet', {
displaySet: rtDisplaySet,
viewportId,
});
},
[commandsManager]
);
const getCornerstoneViewport = useCallback(() => {
const { component: Component } = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.viewportModule.cornerstone'
);
const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
// Todo: jump to the center of the first segment
return (
<Component
{...props}
displaySets={[referencedDisplaySet, rtDisplaySet]}
viewportOptions={{
viewportType: 'stack',
toolGroupId: toolGroupId,
orientation: viewportOptions.orientation,
viewportId: viewportOptions.viewportId,
presentationIds: viewportOptions.presentationIds,
}}
onElementEnabled={evt => {
props.onElementEnabled?.(evt);
onElementEnabled(evt);
}}
onElementDisabled={onElementDisabled}
></Component>
);
}, [viewportId, rtDisplaySet, toolGroupId]);
const onSegmentChange = useCallback(
direction => {
utils.handleSegmentChange({
direction,
segDisplaySet: rtDisplaySet,
viewportId,
selectedSegmentObjectIndex,
segmentationService,
});
},
[selectedSegmentObjectIndex]
);
useEffect(() => {
if (rtIsLoading) {
return;
}
promptHydrateRT({
servicesManager,
viewportId,
rtDisplaySet,
preHydrateCallbacks: [storePresentationState],
hydrateRTDisplaySet,
}).then(isHydrated => {
if (isHydrated) {
setIsHydrated(true);
}
});
}, [servicesManager, viewportId, rtDisplaySet, rtIsLoading]);
useEffect(() => {
// I'm not sure what is this, since in RT we support Overlapping segments
// via contours
const { unsubscribe } = segmentationService.subscribe(
segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
evt => {
if (evt.rtDisplaySet.displaySetInstanceUID === rtDisplaySet.displaySetInstanceUID) {
setRtIsLoading(false);
}
if (rtDisplaySet?.firstSegmentedSliceImageId && viewportOptions?.presentationIds) {
const { firstSegmentedSliceImageId } = rtDisplaySet;
const { presentationIds } = viewportOptions;
setPositionPresentation(presentationIds.positionPresentationId, {
viewportType: 'stack',
viewReference: {
referencedImageId: firstSegmentedSliceImageId,
},
viewPresentation: {},
});
}
if (evt.overlappingSegments) {
uiNotificationService.show({
title: 'Overlapping Segments',
message: 'Overlapping segments detected which is not currently supported',
type: 'warning',
});
}
}
);
return () => {
unsubscribe();
};
}, [rtDisplaySet]);
useEffect(() => {
const { unsubscribe } = segmentationService.subscribe(
segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE,
({ percentComplete, numSegments }) => {
setProcessingProgress({
percentComplete,
totalSegments: numSegments,
});
}
);
return () => {
unsubscribe();
};
}, [rtDisplaySet]);
/**
Cleanup the SEG viewport when the viewport is destroyed
*/
useEffect(() => {
const onDisplaySetsRemovedSubscription = displaySetService.subscribe(
displaySetService.EVENTS.DISPLAY_SETS_REMOVED,
({ displaySetInstanceUIDs }) => {
const activeViewport = viewports.get(activeViewportId);
if (displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)) {
viewportGridService.setDisplaySetsForViewport({
viewportId: activeViewportId,
displaySetInstanceUIDs: [],
});
}
}
);
return () => {
onDisplaySetsRemovedSubscription.unsubscribe();
};
}, []);
useEffect(() => {
let toolGroup = toolGroupService.getToolGroup(toolGroupId);
if (toolGroup) {
return;
}
toolGroup = createRTToolGroupAndAddTools(toolGroupService, customizationService, toolGroupId);
return () => {
// remove the segmentation representations if seg displayset changed
segmentationService.removeSegmentationRepresentations(viewportId);
toolGroupService.destroyToolGroup(toolGroupId);
};
}, []);
useEffect(() => {
setIsHydrated(rtDisplaySet.isHydrated);
return () => {
// remove the segmentation representations if seg displayset changed
segmentationService.removeSegmentationRepresentations(viewportId);
referencedDisplaySetRef.current = null;
};
}, [rtDisplaySet]);
const onStatusClick = useCallback(async () => {
// Before hydrating a RT and make it added to all viewports in the grid
// that share the same frameOfReferenceUID, we need to store the viewport grid
// presentation state, so that we can restore it after hydrating the RT. This is
// required if the user has changed the viewport (other viewport than RT viewport)
// presentation state (w/l and invert) and then opens the RT. If we don't store
// the presentation state, the viewport will be reset to the default presentation
storePresentationState();
const isHydrated = await hydrateRTDisplaySet({
rtDisplaySet,
viewportId,
});
setIsHydrated(isHydrated);
}, [hydrateRTDisplaySet, rtDisplaySet, storePresentationState, viewportId]);
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
let childrenWithProps = null;
if (
!referencedDisplaySetRef.current ||
referencedDisplaySet.displaySetInstanceUID !==
referencedDisplaySetRef.current.displaySet.displaySetInstanceUID
) {
return null;
}
if (children && children.length) {
childrenWithProps = children.map((child, index) => {
return (
child &&
React.cloneElement(child, {
viewportId,
key: index,
})
);
});
}
useEffect(() => {
viewportActionCornersService.addComponents([
{
viewportId,
id: 'viewportStatusComponent',
component: _getStatusComponent({
isHydrated,
onStatusClick,
}),
indexPriority: -100,
location: viewportActionCornersService.LOCATIONS.topLeft,
},
{
viewportId,
id: 'viewportActionArrowsComponent',
component: (
<ViewportActionArrows
key="actionArrows"
onArrowsClick={onSegmentChange}
className={
viewportId === activeViewportId ? 'visible' : 'invisible group-hover/pane:visible'
}
></ViewportActionArrows>
),
indexPriority: 0,
location: viewportActionCornersService.LOCATIONS.topRight,
},
]);
}, [
activeViewportId,
isHydrated,
onSegmentChange,
onStatusClick,
viewportActionCornersService,
viewportId,
]);
return (
<>
<div className="relative flex h-full w-full flex-row overflow-hidden">
{rtIsLoading && (
<LoadingIndicatorTotalPercent
className="h-full w-full"
totalNumbers={processingProgress.totalSegments}
percentComplete={processingProgress.percentComplete}
loadingText="Loading RTSTRUCT..."
/>
)}
{getCornerstoneViewport()}
{childrenWithProps}
</div>
</>
);
}
OHIFCornerstoneRTViewport.propTypes = {
displaySets: PropTypes.arrayOf(PropTypes.object),
viewportId: PropTypes.string.isRequired,
dataSource: PropTypes.object,
children: PropTypes.node,
};
function _getReferencedDisplaySetMetadata(referencedDisplaySet) {
const image0 = referencedDisplaySet.images[0];
const referencedDisplaySetMetadata = {
PatientID: image0.PatientID,
PatientName: image0.PatientName,
PatientSex: image0.PatientSex,
PatientAge: image0.PatientAge,
SliceThickness: image0.SliceThickness,
StudyDate: image0.StudyDate,
SeriesDescription: image0.SeriesDescription,
SeriesInstanceUID: image0.SeriesInstanceUID,
SeriesNumber: image0.SeriesNumber,
ManufacturerModelName: image0.ManufacturerModelName,
SpacingBetweenSlices: image0.SpacingBetweenSlices,
};
return referencedDisplaySetMetadata;
}
export default OHIFCornerstoneRTViewport;

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import React from 'react';
import { useTranslation } from 'react-i18next';
import { ViewportActionButton } from '@ohif/ui';
import { Icons, Tooltip, TooltipTrigger, TooltipContent } from '@ohif/ui-next';
export default function _getStatusComponent({ isHydrated, onStatusClick }) {
let ToolTipMessage = null;
let StatusIcon = null;
switch (isHydrated) {
case true:
StatusIcon = () => <Icons.ByName name="status-alert" />;
ToolTipMessage = () => <div>This Segmentation is loaded in the segmentation panel</div>;
break;
case false:
StatusIcon = () => (
<Icons.ByName
className="text-aqua-pale"
name="status-untracked"
/>
);
ToolTipMessage = () => <div>Click LOAD to load RTSTRUCT.</div>;
}
const StatusArea = () => {
const { t } = useTranslation('Common');
const loadStr = t('LOAD');
return (
<div className="flex h-6 cursor-default text-sm leading-6 text-white">
<div className="bg-customgray-100 flex min-w-[45px] items-center rounded-l-xl rounded-r p-1">
<StatusIcon />
<span className="ml-1">RTSTRUCT</span>
</div>
{!isHydrated && (
<ViewportActionButton onInteraction={onStatusClick}>{loadStr}</ViewportActionButton>
)}
</div>
);
};
return (
<>
{ToolTipMessage && (
<Tooltip>
<TooltipTrigger asChild>
<span>
<StatusArea />
</span>
</TooltipTrigger>
<TooltipContent side="bottom">
<ToolTipMessage />
</TooltipContent>
</Tooltip>
)}
{!ToolTipMessage && <StatusArea />}
</>
);
}

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const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
const ENTRY = {
app: `${SRC_DIR}/index.tsx`,
};
module.exports = (env, argv) => {
return webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
};

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const webpack = require('webpack');
const { merge } = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const pkg = require('./../package.json');
const ROOT_DIR = path.join(__dirname, '../');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
const ENTRY = {
app: `${SRC_DIR}/index.tsx`,
};
const outputName = `ohif-${pkg.name.split('/').pop()}`;
module.exports = (env, argv) => {
const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
return merge(commonConfig, {
stats: {
colors: true,
hash: true,
timings: true,
assets: true,
chunks: false,
chunkModules: false,
modules: false,
children: false,
warnings: true,
},
optimization: {
minimize: true,
sideEffects: true,
},
output: {
path: ROOT_DIR,
library: 'ohif-extension-cornerstone-dicom-seg',
libraryTarget: 'umd',
filename: pkg.main,
},
externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
plugins: [
new webpack.optimize.LimitChunkCountPlugin({
maxChunks: 1,
}),
new MiniCssExtractPlugin({
filename: `./dist/${outputName}.css`,
chunkFilename: `./dist/${outputName}.css`,
}),
],
});
};

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MIT License
Copyright (c) 2023 Open Health Imaging Foundation
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
the Software, and to permit persons to whom the Software is furnished to do so,
subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

18
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# dicom-seg
## Description
DICOM SEG read workflow. This extension will allow you to load a DICOM SEG image
and display it on OHIF. Currently Segmentations are loaded as a volumetric labelmap
and displayed as a 3D volume.
This extension provides a SEG viewport, which enables rendering and reviewing
of the DICOM SEG images. However, in order to fully load all the segments
you will need to click on the SEG Pill button on the viewport action bar
to fully load the segments.
## Author
OHIF
## License
MIT

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extensions/cornerstone-dicom-seg/babel.config.js Normal file
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module.exports = {
plugins: ['@babel/plugin-proposal-class-properties'],
env: {
test: {
presets: [
[
// TODO: https://babeljs.io/blog/2019/03/19/7.4.0#migration-from-core-js-2
'@babel/preset-env',
{
modules: 'commonjs',
debug: false,
},
'@babel/preset-typescript',
],
'@babel/preset-react',
],
plugins: [
'@babel/plugin-proposal-object-rest-spread',
'@babel/plugin-syntax-dynamic-import',
'@babel/plugin-transform-regenerator',
'@babel/plugin-transform-runtime',
],
},
production: {
presets: [
// WebPack handles ES6 --> Target Syntax
['@babel/preset-env', { modules: false }],
'@babel/preset-react',
'@babel/preset-typescript',
],
ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
},
development: {
presets: [
// WebPack handles ES6 --> Target Syntax
['@babel/preset-env', { modules: false }],
'@babel/preset-react',
'@babel/preset-typescript',
],
ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
},
},
};

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{
"name": "@ohif/extension-cornerstone-dicom-seg",
"version": "3.10.0-beta.111",
"description": "DICOM SEG read workflow",
"author": "OHIF",
"license": "MIT",
"main": "dist/ohif-extension-cornerstone-dicom-seg.umd.js",
"module": "src/index.tsx",
"files": [
"dist/**",
"public/**",
"README.md"
],
"repository": "OHIF/Viewers",
"keywords": [
"ohif-extension"
],
"publishConfig": {
"access": "public"
},
"engines": {
"node": ">=14",
"npm": ">=6",
"yarn": ">=1.18.0"
},
"scripts": {
"clean": "shx rm -rf dist",
"clean:deep": "yarn run clean && shx rm -rf node_modules",
"dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --output-pathinfo",
"dev:dicom-seg": "yarn run dev",
"build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
"build:package-1": "yarn run build",
"start": "yarn run dev"
},
"peerDependencies": {
"@ohif/core": "3.10.0-beta.111",
"@ohif/extension-cornerstone": "3.10.0-beta.111",
"@ohif/extension-default": "3.10.0-beta.111",
"@ohif/i18n": "3.10.0-beta.111",
"prop-types": "^15.6.2",
"react": "^18.3.1",
"react-dom": "^18.3.1",
"react-i18next": "^12.2.2",
"react-router": "^6.23.1",
"react-router-dom": "^6.23.1"
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^2.19.14",
"@cornerstonejs/core": "^2.19.14",
"@kitware/vtk.js": "32.1.1",
"react-color": "^2.19.3"
}
}

379
extensions/cornerstone-dicom-seg/src/commandsModule.ts Normal file
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import dcmjs from 'dcmjs';
import { createReportDialogPrompt } from '@ohif/extension-default';
import { Types } from '@ohif/core';
import { cache, metaData } from '@cornerstonejs/core';
import {
segmentation as cornerstoneToolsSegmentation,
Enums as cornerstoneToolsEnums,
utilities,
} from '@cornerstonejs/tools';
import { adaptersRT, helpers, adaptersSEG } from '@cornerstonejs/adapters';
import { classes, DicomMetadataStore } from '@ohif/core';
import vtkImageMarchingSquares from '@kitware/vtk.js/Filters/General/ImageMarchingSquares';
import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
const { segmentation: segmentationUtils } = utilities;
const { datasetToBlob } = dcmjs.data;
const getTargetViewport = ({ viewportId, viewportGridService }) => {
const { viewports, activeViewportId } = viewportGridService.getState();
const targetViewportId = viewportId || activeViewportId;
const viewport = viewports.get(targetViewportId);
return viewport;
};
const {
Cornerstone3D: {
Segmentation: { generateSegmentation },
},
} = adaptersSEG;
const {
Cornerstone3D: {
RTSS: { generateRTSSFromSegmentations },
},
} = adaptersRT;
const { downloadDICOMData } = helpers;
const commandsModule = ({
servicesManager,
extensionManager,
}: Types.Extensions.ExtensionParams): Types.Extensions.CommandsModule => {
const {
segmentationService,
uiDialogService,
displaySetService,
viewportGridService,
toolGroupService,
} = servicesManager.services as AppTypes.Services;
const actions = {
/**
* Loads segmentations for a specified viewport.
* The function prepares the viewport for rendering, then loads the segmentation details.
* Additionally, if the segmentation has scalar data, it is set for the corresponding label map volume.
*
* @param {Object} params - Parameters for the function.
* @param params.segmentations - Array of segmentations to be loaded.
* @param params.viewportId - the target viewport ID.
*
*/
loadSegmentationsForViewport: async ({ segmentations, viewportId }) => {
// Todo: handle adding more than one segmentation
const viewport = getTargetViewport({ viewportId, viewportGridService });
const displaySetInstanceUID = viewport.displaySetInstanceUIDs[0];
const segmentation = segmentations[0];
const segmentationId = segmentation.segmentationId;
const label = segmentation.config.label;
const segments = segmentation.config.segments;
const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
await segmentationService.createLabelmapForDisplaySet(displaySet, {
segmentationId,
segments,
label,
});
segmentationService.addOrUpdateSegmentation(segmentation);
await segmentationService.addSegmentationRepresentation(viewport.viewportId, {
segmentationId,
});
return segmentationId;
},
/**
* Generates a segmentation from a given segmentation ID.
* This function retrieves the associated segmentation and
* its referenced volume, extracts label maps from the
* segmentation volume, and produces segmentation data
* alongside associated metadata.
*
* @param {Object} params - Parameters for the function.
* @param params.segmentationId - ID of the segmentation to be generated.
* @param params.options - Optional configuration for the generation process.
*
* @returns Returns the generated segmentation data.
*/
generateSegmentation: ({ segmentationId, options = {} }) => {
const segmentation = cornerstoneToolsSegmentation.state.getSegmentation(segmentationId);
const { imageIds } = segmentation.representationData.Labelmap;
const segImages = imageIds.map(imageId => cache.getImage(imageId));
const referencedImages = segImages.map(image => cache.getImage(image.referencedImageId));
const labelmaps2D = [];
let z = 0;
for (const segImage of segImages) {
const segmentsOnLabelmap = new Set();
const pixelData = segImage.getPixelData();
const { rows, columns } = segImage;
// Use a single pass through the pixel data
for (let i = 0; i < pixelData.length; i++) {
const segment = pixelData[i];
if (segment !== 0) {
segmentsOnLabelmap.add(segment);
}
}
labelmaps2D[z++] = {
segmentsOnLabelmap: Array.from(segmentsOnLabelmap),
pixelData,
rows,
columns,
};
}
const allSegmentsOnLabelmap = labelmaps2D.map(labelmap => labelmap.segmentsOnLabelmap);
const labelmap3D = {
segmentsOnLabelmap: Array.from(new Set(allSegmentsOnLabelmap.flat())),
metadata: [],
labelmaps2D,
};
const segmentationInOHIF = segmentationService.getSegmentation(segmentationId);
const representations = segmentationService.getRepresentationsForSegmentation(segmentationId);
Object.entries(segmentationInOHIF.segments).forEach(([segmentIndex, segment]) => {
// segmentation service already has a color for each segment
if (!segment) {
return;
}
const { label } = segment;
const firstRepresentation = representations[0];
const color = segmentationService.getSegmentColor(
firstRepresentation.viewportId,
segmentationId,
segment.segmentIndex
);
const RecommendedDisplayCIELabValue = dcmjs.data.Colors.rgb2DICOMLAB(
color.slice(0, 3).map(value => value / 255)
).map(value => Math.round(value));
const segmentMetadata = {
SegmentNumber: segmentIndex.toString(),
SegmentLabel: label,
SegmentAlgorithmType: segment?.algorithmType || 'MANUAL',
SegmentAlgorithmName: segment?.algorithmName || 'OHIF Brush',
RecommendedDisplayCIELabValue,
SegmentedPropertyCategoryCodeSequence: {
CodeValue: 'T-D0050',
CodingSchemeDesignator: 'SRT',
CodeMeaning: 'Tissue',
},
SegmentedPropertyTypeCodeSequence: {
CodeValue: 'T-D0050',
CodingSchemeDesignator: 'SRT',
CodeMeaning: 'Tissue',
},
};
labelmap3D.metadata[segmentIndex] = segmentMetadata;
});
const generatedSegmentation = generateSegmentation(
referencedImages,
labelmap3D,
metaData,
options
);
return generatedSegmentation;
},
/**
* Downloads a segmentation based on the provided segmentation ID.
* This function retrieves the associated segmentation and
* uses it to generate the corresponding DICOM dataset, which
* is then downloaded with an appropriate filename.
*
* @param {Object} params - Parameters for the function.
* @param params.segmentationId - ID of the segmentation to be downloaded.
*
*/
downloadSegmentation: ({ segmentationId }) => {
const segmentationInOHIF = segmentationService.getSegmentation(segmentationId);
const generatedSegmentation = actions.generateSegmentation({
segmentationId,
});
downloadDICOMData(generatedSegmentation.dataset, `${segmentationInOHIF.label}`);
},
/**
* Stores a segmentation based on the provided segmentationId into a specified data source.
* The SeriesDescription is derived from user input or defaults to the segmentation label,
* and in its absence, defaults to 'Research Derived Series'.
*
* @param {Object} params - Parameters for the function.
* @param params.segmentationId - ID of the segmentation to be stored.
* @param params.dataSource - Data source where the generated segmentation will be stored.
*
* @returns {Object|void} Returns the naturalized report if successfully stored,
* otherwise throws an error.
*/
storeSegmentation: async ({ segmentationId, dataSource }) => {
const promptResult = await createReportDialogPrompt(uiDialogService, {
extensionManager,
});
if (promptResult.action !== 1 && !promptResult.value) {
return;
}
const segmentation = segmentationService.getSegmentation(segmentationId);
if (!segmentation) {
throw new Error('No segmentation found');
}
const { label } = segmentation;
const SeriesDescription = promptResult.value || label || 'Research Derived Series';
const generatedData = actions.generateSegmentation({
segmentationId,
options: {
SeriesDescription,
},
});
if (!generatedData || !generatedData.dataset) {
throw new Error('Error during segmentation generation');
}
const { dataset: naturalizedReport } = generatedData;
await dataSource.store.dicom(naturalizedReport);
// The "Mode" route listens for DicomMetadataStore changes
// When a new instance is added, it listens and
// automatically calls makeDisplaySets
// add the information for where we stored it to the instance as well
naturalizedReport.wadoRoot = dataSource.getConfig().wadoRoot;
DicomMetadataStore.addInstances([naturalizedReport], true);
return naturalizedReport;
},
/**
* Converts segmentations into RTSS for download.
* This sample function retrieves all segentations and passes to
* cornerstone tool adapter to convert to DICOM RTSS format. It then
* converts dataset to downloadable blob.
*
*/
downloadRTSS: ({ segmentationId }) => {
const segmentations = segmentationService.getSegmentation(segmentationId);
const vtkUtils = {
vtkImageMarchingSquares,
vtkDataArray,
vtkImageData,
};
const RTSS = generateRTSSFromSegmentations(
segmentations,
classes.MetadataProvider,
DicomMetadataStore,
cache,
cornerstoneToolsEnums,
vtkUtils
);
try {
const reportBlob = datasetToBlob(RTSS);
//Create a URL for the binary.
const objectUrl = URL.createObjectURL(reportBlob);
window.location.assign(objectUrl);
} catch (e) {
console.warn(e);
}
},
setBrushSize: ({ value, toolNames }) => {
const brushSize = Number(value);
toolGroupService.getToolGroupIds()?.forEach(toolGroupId => {
if (toolNames?.length === 0) {
segmentationUtils.setBrushSizeForToolGroup(toolGroupId, brushSize);
} else {
toolNames?.forEach(toolName => {
segmentationUtils.setBrushSizeForToolGroup(toolGroupId, brushSize, toolName);
});
}
});
},
setThresholdRange: ({
value,
toolNames = ['ThresholdCircularBrush', 'ThresholdSphereBrush'],
}) => {
toolGroupService.getToolGroupIds()?.forEach(toolGroupId => {
const toolGroup = toolGroupService.getToolGroup(toolGroupId);
toolNames?.forEach(toolName => {
toolGroup.setToolConfiguration(toolName, {
strategySpecificConfiguration: {
THRESHOLD: {
threshold: value,
},
},
});
});
});
},
};
const definitions = {
/**
* Obsolete?
*/
loadSegmentationDisplaySetsForViewport: {
commandFn: actions.loadSegmentationDisplaySetsForViewport,
},
/**
* Obsolete?
*/
loadSegmentationsForViewport: {
commandFn: actions.loadSegmentationsForViewport,
},
generateSegmentation: {
commandFn: actions.generateSegmentation,
},
downloadSegmentation: {
commandFn: actions.downloadSegmentation,
},
storeSegmentation: {
commandFn: actions.storeSegmentation,
},
downloadRTSS: {
commandFn: actions.downloadRTSS,
},
setBrushSize: {
commandFn: actions.setBrushSize,
},
setThresholdRange: {
commandFn: actions.setThresholdRange,
},
};
return {
actions,
definitions,
defaultContext: 'SEGMENTATION',
};
};
export default commandsModule;

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import { Types } from '@ohif/core';
const segProtocol: Types.HangingProtocol.Protocol = {
id: '@ohif/seg',
// Don't store this hanging protocol as it applies to the currently active
// display set by default
// cacheId: null,
name: 'Segmentations',
// Just apply this one when specifically listed
protocolMatchingRules: [],
toolGroupIds: ['default'],
// -1 would be used to indicate active only, whereas other values are
// the number of required priors referenced - so 0 means active with
// 0 or more priors.
numberOfPriorsReferenced: 0,
// Default viewport is used to define the viewport when
// additional viewports are added using the layout tool
defaultViewport: {
viewportOptions: {
viewportType: 'stack',
toolGroupId: 'default',
allowUnmatchedView: true,
syncGroups: [
{
type: 'hydrateseg',
id: 'sameFORId',
source: true,
target: true,
// options: {
// matchingRules: ['sameFOR'],
// },
},
],
},
displaySets: [
{
id: 'segDisplaySetId',
matchedDisplaySetsIndex: -1,
},
],
},
displaySetSelectors: {
segDisplaySetId: {
seriesMatchingRules: [
{
attribute: 'Modality',
constraint: {
equals: 'SEG',
},
},
],
},
},
stages: [
{
name: 'Segmentations',
viewportStructure: {
layoutType: 'grid',
properties: {
rows: 1,
columns: 1,
},
},
viewports: [
{
viewportOptions: {
allowUnmatchedView: true,
syncGroups: [
{
type: 'hydrateseg',
id: 'sameFORId',
source: true,
target: true,
// options: {
// matchingRules: ['sameFOR'],
// },
},
],
},
displaySets: [
{
id: 'segDisplaySetId',
},
],
},
],
},
],
};
function getHangingProtocolModule() {
return [
{
name: segProtocol.id,
protocol: segProtocol,
},
];
}
export default getHangingProtocolModule;
export { segProtocol };

255
extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.ts Normal file
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import { utils } from '@ohif/core';
import { metaData, triggerEvent, eventTarget } from '@cornerstonejs/core';
import { CONSTANTS, segmentation as cstSegmentation } from '@cornerstonejs/tools';
import { adaptersSEG, Enums } from '@cornerstonejs/adapters';
import { SOPClassHandlerId } from './id';
import { dicomlabToRGB } from './utils/dicomlabToRGB';
const sopClassUids = ['1.2.840.10008.5.1.4.1.1.66.4'];
const loadPromises = {};
function _getDisplaySetsFromSeries(
instances,
servicesManager: AppTypes.ServicesManager,
extensionManager
) {
const instance = instances[0];
const {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPClassUID,
wadoRoot,
wadoUri,
wadoUriRoot,
} = instance;
const displaySet = {
Modality: 'SEG',
loading: false,
isReconstructable: true, // by default for now since it is a volumetric SEG currently
displaySetInstanceUID: utils.guid(),
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
SOPClassHandlerId,
SOPClassUID,
referencedImages: null,
referencedSeriesInstanceUID: null,
referencedDisplaySetInstanceUID: null,
isDerivedDisplaySet: true,
isLoaded: false,
isHydrated: false,
segments: {},
sopClassUids,
instance,
instances: [instance],
wadoRoot,
wadoUriRoot,
wadoUri,
isOverlayDisplaySet: true,
};
const referencedSeriesSequence = instance.ReferencedSeriesSequence;
if (!referencedSeriesSequence) {
console.error('ReferencedSeriesSequence is missing for the SEG');
return;
}
const referencedSeries = referencedSeriesSequence[0] || referencedSeriesSequence;
displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
const { displaySetService } = servicesManager.services;
const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
displaySet.referencedSeriesInstanceUID
);
const referencedDisplaySet = referencedDisplaySets[0];
if (!referencedDisplaySet) {
// subscribe to display sets added which means at some point it will be available
const { unsubscribe } = displaySetService.subscribe(
displaySetService.EVENTS.DISPLAY_SETS_ADDED,
({ displaySetsAdded }) => {
// here we can also do a little bit of search, since sometimes DICOM SEG
// does not contain the referenced display set uid , and we can just
// see which of the display sets added is more similar and assign it
// to the referencedDisplaySet
const addedDisplaySet = displaySetsAdded[0];
if (addedDisplaySet.SeriesInstanceUID === displaySet.referencedSeriesInstanceUID) {
displaySet.referencedDisplaySetInstanceUID = addedDisplaySet.displaySetInstanceUID;
unsubscribe();
}
}
);
} else {
displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
}
displaySet.load = async ({ headers }) =>
await _load(displaySet, servicesManager, extensionManager, headers);
return [displaySet];
}
function _load(
segDisplaySet,
servicesManager: AppTypes.ServicesManager,
extensionManager,
headers
) {
const { SOPInstanceUID } = segDisplaySet;
const { segmentationService } = servicesManager.services;
if (
(segDisplaySet.loading || segDisplaySet.isLoaded) &&
loadPromises[SOPInstanceUID] &&
_segmentationExists(segDisplaySet)
) {
return loadPromises[SOPInstanceUID];
}
segDisplaySet.loading = true;
// We don't want to fire multiple loads, so we'll wait for the first to finish
// and also return the same promise to any other callers.
loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => {
if (!segDisplaySet.segments || Object.keys(segDisplaySet.segments).length === 0) {
try {
await _loadSegments({
extensionManager,
servicesManager,
segDisplaySet,
headers,
});
} catch (e) {
segDisplaySet.loading = false;
return reject(e);
}
}
segmentationService
.createSegmentationForSEGDisplaySet(segDisplaySet)
.then(() => {
segDisplaySet.loading = false;
resolve();
})
.catch(error => {
segDisplaySet.loading = false;
reject(error);
});
});
return loadPromises[SOPInstanceUID];
}
async function _loadSegments({
extensionManager,
servicesManager,
segDisplaySet,
headers,
}: withAppTypes) {
const utilityModule = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.utilityModule.common'
);
const { segmentationService, uiNotificationService } = servicesManager.services;
const { dicomLoaderService } = utilityModule.exports;
const arrayBuffer = await dicomLoaderService.findDicomDataPromise(segDisplaySet, null, headers);
const referencedDisplaySet = servicesManager.services.displaySetService.getDisplaySetByUID(
segDisplaySet.referencedDisplaySetInstanceUID
);
if (!referencedDisplaySet) {
throw new Error('referencedDisplaySet is missing for SEG');
}
const { instances: images } = referencedDisplaySet;
const imageIds = images.map(({ imageId }) => imageId);
// Todo: what should be defaults here
const tolerance = 0.001;
const skipOverlapping = true;
eventTarget.addEventListener(Enums.Events.SEGMENTATION_LOAD_PROGRESS, evt => {
const { percentComplete } = evt.detail;
segmentationService._broadcastEvent(segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE, {
percentComplete,
});
});
const results = await adaptersSEG.Cornerstone3D.Segmentation.generateToolState(
imageIds,
arrayBuffer,
metaData,
{ skipOverlapping, tolerance, eventTarget, triggerEvent }
);
let usedRecommendedDisplayCIELabValue = true;
results.segMetadata.data.forEach((data, i) => {
if (i > 0) {
data.rgba = data.RecommendedDisplayCIELabValue;
if (data.rgba) {
data.rgba = dicomlabToRGB(data.rgba);
} else {
usedRecommendedDisplayCIELabValue = false;
data.rgba = CONSTANTS.COLOR_LUT[i % CONSTANTS.COLOR_LUT.length];
}
}
});
if (results.overlappingSegments) {
uiNotificationService.show({
title: 'Overlapping Segments',
message:
'Unsupported overlapping segments detected, segmentation rendering results may be incorrect.',
type: 'warning',
});
}
if (!usedRecommendedDisplayCIELabValue) {
// Display a notification about the non-utilization of RecommendedDisplayCIELabValue
uiNotificationService.show({
title: 'DICOM SEG import',
message:
'RecommendedDisplayCIELabValue not found for one or more segments. The default color was used instead.',
type: 'warning',
duration: 5000,
});
}
Object.assign(segDisplaySet, results);
}
function _segmentationExists(segDisplaySet) {
return cstSegmentation.state.getSegmentation(segDisplaySet.displaySetInstanceUID);
}
function getSopClassHandlerModule({ servicesManager, extensionManager }) {
const getDisplaySetsFromSeries = instances => {
return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
};
return [
{
name: 'dicom-seg',
sopClassUids,
getDisplaySetsFromSeries,
},
];
}
export default getSopClassHandlerModule;

65
extensions/cornerstone-dicom-seg/src/getToolbarModule.ts Normal file
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export function getToolbarModule({ servicesManager }: withAppTypes) {
const { segmentationService, toolbarService, toolGroupService } = servicesManager.services;
return [
{
name: 'evaluate.cornerstone.hasSegmentation',
evaluate: ({ viewportId }) => {
const segmentations = segmentationService.getSegmentationRepresentations(viewportId);
return {
disabled: !segmentations?.length,
};
},
},
{
name: 'evaluate.cornerstone.segmentation',
evaluate: ({ viewportId, button, toolNames, disabledText }) => {
// Todo: we need to pass in the button section Id since we are kind of
// forcing the button to have black background since initially
// it is designed for the toolbox not the toolbar on top
// we should then branch the buttonSectionId to have different styles
const segmentations = segmentationService.getSegmentationRepresentations(viewportId);
if (!segmentations?.length) {
return {
disabled: true,
disabledText: disabledText ?? 'No segmentations available',
};
}
const activeSegmentation = segmentationService.getActiveSegmentation(viewportId);
if (!Object.keys(activeSegmentation.segments).length) {
return {
disabled: true,
disabledText: 'Add segment to enable this tool',
};
}
const toolGroup = toolGroupService.getToolGroupForViewport(viewportId);
if (!toolGroup) {
return {
disabled: true,
disabledText: disabledText ?? 'Not available on the current viewport',
};
}
const toolName = toolbarService.getToolNameForButton(button);
if (!toolGroup.hasTool(toolName) && !toolNames) {
return {
disabled: true,
disabledText: disabledText ?? 'Not available on the current viewport',
};
}
const isPrimaryActive = toolNames
? toolNames.includes(toolGroup.getActivePrimaryMouseButtonTool())
: toolGroup.getActivePrimaryMouseButtonTool() === toolName;
return {
disabled: false,
isActive: isPrimaryActive,
};
},
},
];
}

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extensions/cornerstone-dicom-seg/src/id.js Normal file
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import packageJson from '../package.json';
const id = packageJson.name;
const SOPClassHandlerName = 'dicom-seg';
const SOPClassHandlerId = `${id}.sopClassHandlerModule.${SOPClassHandlerName}`;
export { id, SOPClassHandlerId, SOPClassHandlerName };

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extensions/cornerstone-dicom-seg/src/index.tsx Normal file
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import { id } from './id';
import React from 'react';
import getSopClassHandlerModule from './getSopClassHandlerModule';
import getHangingProtocolModule from './getHangingProtocolModule';
import getCommandsModule from './commandsModule';
import { getToolbarModule } from './getToolbarModule';
const Component = React.lazy(() => {
return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneSEGViewport');
});
const OHIFCornerstoneSEGViewport = props => {
return (
<React.Suspense fallback={<div>Loading...</div>}>
<Component {...props} />
</React.Suspense>
);
};
/**
* You can remove any of the following modules if you don't need them.
*/
const extension = {
/**
* Only required property. Should be a unique value across all extensions.
* You ID can be anything you want, but it should be unique.
*/
id,
getCommandsModule,
getToolbarModule,
getViewportModule({ servicesManager, extensionManager, commandsManager }) {
const ExtendedOHIFCornerstoneSEGViewport = props => {
return (
<OHIFCornerstoneSEGViewport
servicesManager={servicesManager}
extensionManager={extensionManager}
commandsManager={commandsManager}
{...props}
/>
);
};
return [{ name: 'dicom-seg', component: ExtendedOHIFCornerstoneSEGViewport }];
},
/**
* SopClassHandlerModule should provide a list of sop class handlers that will be
* available in OHIF for Modes to consume and use to create displaySets from Series.
* Each sop class handler is defined by a { name, sopClassUids, getDisplaySetsFromSeries}.
* Examples include the default sop class handler provided by the default extension
*/
getSopClassHandlerModule,
getHangingProtocolModule,
};
export default extension;

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extensions/cornerstone-dicom-seg/src/types/segmentation.tsx Normal file
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export enum SegmentationPanelMode {
Expanded = 'expanded',
Dropdown = 'dropdown',
}

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