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Author SHA1 Message Date
ohif-bot 29eca3bd20 chore(version): Update package versions [skip ci] 2025-07-23 15:55:11 +00:00
ohif-bot 38bc497545 chore(version): version.json [skip ci] 2025-07-23 15:55:05 +00:00
Joe Boccanfuso d383be7c72 fix(security): Removed stylus package due to potential security vulnerability and we don't use it. (#5251) 2025-07-23 11:49:30 -04:00
Joe Boccanfuso d206cf9ba5 fix(security): Pin eslint-config-prettier and eslint-plugin-prettier versions. (#5246) 2025-07-22 12:02:57 -04:00
ohif-bot 1ad5acae9d chore(version): Update package versions [skip ci] 2025-06-09 15:06:36 +00:00
ohif-bot c19e32e0d1 chore(version): version.json [skip ci] 2025-06-09 15:06:30 +00:00
36813e0c2f chore: recovery 2 (#5014)
Co-authored-by: Dan Rukas <dan.rukas@gmail.com>
Co-authored-by: Tang Cheng <45505657+tctco@users.noreply.github.com>
2025-06-09 10:58:06 -04:00
ohif-bot 9a4a40468f chore(version): Update package versions [skip ci] 2025-04-11 20:02:21 +00:00
ohif-bot 466a867e6a chore(version): version.json [skip ci] 2025-04-11 20:02:14 +00:00
aaba8bf1b0 fix: make datasource selection work and UI fixes (#4952)
Co-authored-by: Pedro Köhler <pedrokohlerbh@gmail.com>
Co-authored-by: Dan Rukas <dan.rukas@gmail.com>
2025-04-11 15:57:29 -04:00
ohif-bot 0b6e9cba76 chore(version): Update package versions [skip ci] 2025-04-10 02:48:32 +00:00
ohif-bot 963664cb63 chore(version): version.json [skip ci] 2025-04-10 02:48:27 +00:00
sedghi 12fe1e107d chore: release 3p10 2025-04-09 22:41:26 -04:00
2221 changed files with 81606 additions and 195762 deletions

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+48 -133
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@@ -1,47 +1,52 @@
version: 2.1
# ci: re-trigger pipeline
orbs:
codecov: codecov/codecov@1.0.5
cypress: cypress-io/cypress@3.4.2
defaults: &defaults
docker:
- image: cimg/node:24.0.0
- image: cimg/node:20.18.1
environment:
TERM: xterm
QUICK_BUILD: true
working_directory: ~/repo
commands:
install_pnpm:
install_bun:
steps:
- restore_cache:
keys:
- bun-cache-v2-{{ arch }}-latest
- run:
name: Install pnpm
name: Install Bun
command: |
# The cimg/node global modules dir (/usr/local/lib/node_modules) is
# root-owned, so a plain `npm install -g` fails with EACCES. Install
# with sudo so the global pnpm binary lands in the shared prefix.
sudo npm install -g pnpm@11.5.2
echo 'export PATH="$(pnpm store path)/../.bin:$PATH"' >> $BASH_ENV
if [ ! -d "$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 $BASH_ENV
- save_cache:
key: bun-cache-v2-{{ arch }}-latest
paths:
- ~/.bun
jobs:
UNIT_TESTS:
<<: *defaults
resource_class: large
steps:
- install_pnpm
- install_bun
- run: node --version
- checkout
- run:
name: Install Dependencies
command: pnpm install --frozen-lockfile
command: bun install --no-save
# RUN TESTS
- run:
name: 'JavaScript Test Suite'
command: pnpm run test:unit:ci
command: bun run test:unit:ci
# platform/app
- run:
name: 'VIEWER: Combine report output'
@@ -75,17 +80,17 @@ jobs:
steps:
# Checkout code and ALL Git Tags
- checkout
- install_pnpm
- install_bun
- run:
name: Install Dependencies
command: pnpm install --frozen-lockfile
command: bun install --no-save
# Build & Test
- run:
name: 'Perform the versioning before build'
command: node ./version.mjs
command: bun ./version.mjs
- run:
name: 'Build the OHIF Viewer'
command: pnpm run build
command: bun run build
no_output_timeout: 45m
- run:
name: 'Upload SourceMaps, Send Deploy Notification'
@@ -111,55 +116,14 @@ jobs:
<<: *defaults
resource_class: large
steps:
- install_pnpm
- install_bun
# Checkout code and ALL Git Tags
- checkout
- attach_workspace:
at: ~/repo
# SECURITY AUDIT - only when pnpm-lock.yaml has changed
- run:
name: 'Security Audit - High Risk Vulnerabilities'
command: |
git fetch origin master 2>/dev/null || true
BASE_REF=$(git merge-base HEAD origin/master 2>/dev/null)
if [[ -z "$BASE_REF" ]]; then
echo "Could not determine base ref (e.g. shallow clone or no origin/master), skipping security audit."
exit 0
fi
CHANGED_FILES=$(git diff --name-only origin/master...HEAD 2>/dev/null || echo "")
if ! echo "$CHANGED_FILES" | grep -qx 'pnpm-lock.yaml'; then
echo "pnpm-lock.yaml unchanged - skipping security audit."
exit 0
fi
echo "pnpm-lock.yaml changed - running pnpm audit for security vulnerabilities..."
echo "Checking for HIGH-RISK vulnerabilities..."
if pnpm audit --audit-level high; then
echo "No high-risk vulnerabilities found"
echo "Security audit passed!"
else
echo ""
echo "HIGH-RISK VULNERABILITIES DETECTED!"
echo "======================================"
echo ""
echo "To fix these issues:"
echo " 1. Run: pnpm audit"
echo " 2. Review the vulnerability details"
echo " 3. Update affected packages to secure versions"
echo " 4. Test your changes"
echo " 5. Re-run: pnpm audit --audit-level high"
echo ""
echo "Full audit report:"
pnpm audit || true
echo ""
echo "This build cannot proceed until high-risk vulnerabilities are resolved."
exit 1
fi
- run:
name: Install Dependencies
command: pnpm install
command: bun install --frozen-lockfile
- run:
name: Avoid hosts unknown for github
command: |
@@ -170,34 +134,28 @@ jobs:
git config --global user.name "ohif-bot"
- run:
name: Authenticate with NPM registry
# Write the auth token to npm's per-user config (~/.npmrc), not the
# repo root. publish-package.mjs chdir's into each package dir to run
# `npm publish`, and npm only reads the project .npmrc from that dir
# plus the user .npmrc from $HOME -- it never sees ~/repo/.npmrc, so a
# root-level token yields ENEEDAUTH. Using ~/.npmrc also avoids
# clobbering the committed workspace-config .npmrc (node-linker=hoisted).
command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/.npmrc
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: |
pnpm run build:package-all
bun run build:package-all
- run:
name: build the other half of the packages
command: |
pnpm run build:package-all-1
bun run build:package-all-1
NPM_PUBLISH:
<<: *defaults
resource_class: large
steps:
- install_pnpm
- install_bun
# Checkout code and ALL Git Tags
- checkout
- attach_workspace:
at: ~/repo
- run:
name: Install Dependencies
command: pnpm install --frozen-lockfile
command: bun install --no-save
- run:
name: Avoid hosts unknown for github
command: |
@@ -208,21 +166,15 @@ jobs:
git config --global user.name "ohif-bot"
- run:
name: Authenticate with NPM registry
# Write the auth token to npm's per-user config (~/.npmrc), not the
# repo root. publish-package.mjs chdir's into each package dir to run
# `npm publish`, and npm only reads the project .npmrc from that dir
# plus the user .npmrc from $HOME -- it never sees ~/repo/.npmrc, so a
# root-level token yields ENEEDAUTH. Using ~/.npmrc also avoids
# clobbering the committed workspace-config .npmrc (node-linker=hoisted).
command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/.npmrc
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: |
pnpm run build:package-all
bun run build:package-all
- run:
name: build the other half of the packages
command: |
pnpm run build:package-all-1
bun run build:package-all-1
- run:
name: increase min time out
command: |
@@ -234,20 +186,14 @@ jobs:
- run:
name: publish package versions
command: |
node ./publish-version.mjs
bun ./publish-version.mjs
- run:
name: Re-assert the NPM auth token before publishing
# Write the auth token to npm's per-user config (~/.npmrc), not the
# repo root. publish-package.mjs chdir's into each package dir to run
# `npm publish`, and npm only reads the project .npmrc from that dir
# plus the user .npmrc from $HOME -- it never sees ~/repo/.npmrc, so a
# root-level token yields ENEEDAUTH. Using ~/.npmrc also avoids
# clobbering the committed workspace-config .npmrc (node-linker=hoisted).
command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/.npmrc
name: Again set the NPM registry (was deleted in the version script)
command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
- run:
name: publish package dist
command: |
node ./publish-package.mjs
bun ./publish-package.mjs
- persist_to_workspace:
root: ~/repo
paths:
@@ -269,11 +215,8 @@ jobs:
if [[ ! -e version.txt ]]; then
exit 0
else
# Restore the committed .npmrc (pnpm workspace config such as
# node-linker=hoisted). NPM_PUBLISH overwrote it with a publish
# auth token, but the Dockerfile COPYs .npmrc for the in-image
# pnpm install, so it needs the config file present and token-free.
git checkout -- .npmrc
# Remove npm config
rm -f ./.npmrc
# Set our version number using vars
export IMAGE_VERSION=$(cat version.txt)
export IMAGE_VERSION_FULL=v$IMAGE_VERSION
@@ -306,11 +249,8 @@ jobs:
if [[ ! -e version.txt ]]; then
exit 0
else
# Restore the committed .npmrc (pnpm workspace config such as
# node-linker=hoisted). NPM_PUBLISH overwrote it with a publish
# auth token, but the Dockerfile COPYs .npmrc for the in-image
# pnpm install, so it needs the config file present and token-free.
git checkout -- .npmrc
# Remove npm config
rm -f ./.npmrc
# Set our version number using vars
export IMAGE_VERSION=$(cat version.txt)
export IMAGE_VERSION_FULL=v$IMAGE_VERSION
@@ -347,11 +287,7 @@ jobs:
exit 0
else
echo "Building and pushing Docker image from the master branch (beta releases)"
# Restore the committed .npmrc (pnpm workspace config such as
# node-linker=hoisted). NPM_PUBLISH overwrote it with a publish
# auth token, but the Dockerfile COPYs .npmrc for the in-image
# pnpm install, so it needs the config file present and token-free.
git checkout -- .npmrc
rm -f ./.npmrc
# Set our version number using vars
export IMAGE_VERSION=$(cat version.txt)
@@ -385,11 +321,7 @@ jobs:
exit 0
else
echo "Building and pushing ARM64 Docker image from the master branch (beta releases)"
# Restore the committed .npmrc (pnpm workspace config such as
# node-linker=hoisted). NPM_PUBLISH overwrote it with a publish
# auth token, but the Dockerfile COPYs .npmrc for the in-image
# pnpm install, so it needs the config file present and token-free.
git checkout -- .npmrc
rm -f ./.npmrc
# Set our version number using vars
export IMAGE_VERSION=$(cat version.txt)
export IMAGE_VERSION_FULL=v$IMAGE_VERSION
@@ -407,20 +339,11 @@ jobs:
resource_class: large
parallelism: 8
steps:
- install_pnpm
- install_bun
- run:
name: Install System Dependencies
command: |
# CircleCI's base image registers third-party apt sources (git-lfs via
# packagecloud, git-core PPA via launchpad) that periodically hang
# `apt-get update`. The Cypress libs below all come from the Ubuntu
# archive, so drop those sources and bound the update with timeouts +
# retries so a slow mirror can't stall the job indefinitely.
sudo rm -f /etc/apt/sources.list.d/*git* || true
sudo apt-get update \
-o Acquire::Retries=3 \
-o Acquire::http::Timeout=20 \
-o Acquire::https::Timeout=20
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
@@ -430,15 +353,12 @@ jobs:
name: Export Display Variable
command: export DISPLAY=:99
- cypress/install:
install-command: pnpm install
install-command: bun install --no-save
package-manager: yarn
- cypress/run-tests:
# CI runs headless under Xvfb with no GPU, so Electron uses software
# WebGL. Newer Chromium deprecated that implicit fallback (canvas
# rendering degrades and races with element clicks). ELECTRON_EXTRA_LAUNCH_ARGS
# is the reliable way to pass the opt-in flag to Cypress's Electron browser.
cypress-command: |
npx wait-on@latest http://localhost:3000 && cd platform/app && ELECTRON_EXTRA_LAUNCH_ARGS="--enable-unsafe-swiftshader" npx cypress run --record --parallel
start-command: pnpm run test:data && pnpm run test:e2e:serve
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
@@ -537,13 +457,8 @@ workflows:
filters:
branches:
only: master
# - HOLD_FOR_APPROVAL:
# type: approval
# requires:
# - BUILD
- NPM_PUBLISH:
requires:
# - HOLD_FOR_APPROVAL
- BUILD
- DOCKER_BETA_PUBLISH:
requires:
+9 -3
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@@ -1,9 +1,15 @@
version: 2
enable-beta-ecosystems: true
updates:
- package-ecosystem: 'npm'
# Disable all pull requests for npm/pnpm version updates.
open-pull-requests-limit: 0
- package-ecosystem: 'bun'
directory: '/'
schedule:
interval: 'daily'
labels: ['dependencies']
commit-message:
prefix: 'chore'
include: 'scope'
- package-ecosystem: 'npm'
directory: '/'
schedule:
interval: 'daily'
+21 -22
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@@ -51,29 +51,28 @@ body:
validations:
required: true
- type: textarea
id: system_info
- type: input
id: os
attributes:
label: 'System Information'
description: 'Please run the following command in your terminal and paste the output:'
placeholder: |
Run: npx envinfo --system --binaries --browsers
Then paste the output here. It should look something like:
System:
OS: Windows 10 10.0.19042
CPU: (8) x64 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
Memory: 15.89 GB / 31.74 GB
Shell: 1.0.0 - C:\WINDOWS\System32\WindowsPowerShell\v1.0\powershell.exe
Binaries:
Node: 20.18.1 - C:\Program Files\nodejs\node.EXE
Yarn: 1.22.22 - C:\Users\user\AppData\Roaming\npm\yarn.CMD
npm: 10.8.2 - C:\Program Files\nodejs\npm.CMD
Browsers:
Chrome: 83.0.4103.116
Edge: Spartan (44.19041.1266.0), Chromium (83.0.478.58)
Firefox: 77.0.1
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
-124
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@@ -1,124 +0,0 @@
name: Build and Deploy Docs
on:
push:
branches: [master]
env:
ACTIONS_STEP_DEBUG: true
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
build-and-deploy-docs:
timeout-minutes: 60
runs-on: ubuntu-latest
# Need permissions to read actions and pull requests
permissions:
actions: read
contents: read
pull-requests: read
steps:
- uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
with:
persist-credentials: false
- uses: pnpm/action-setup@0e279bb959325dab635dd2c09392533439d90093 # v6.0.8
- uses: actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
with:
node-version: 24
cache: pnpm
- name: Configure git for private repos
run: git config --global url."https://${GITHUB_TOKEN}:x-oauth-basic@github.com/".insteadOf ssh://git@github.com/
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Install dependencies
# Internal @ohif/* deps are workspace:* in the committed manifests and the
# lockfile records them as links, so pnpm-lock.yaml stays in sync across
# version bumps and a frozen install passes. Frozen is the right choice
# for a deploy job: it fails fast if a PR ever changed a real dependency
# without committing the lockfile update, instead of silently reconciling.
# (Exact versions appear only in published tarballs, where pnpm publish
# rewrites workspace:* at pack time -- not publish-version.mjs.)
run: pnpm install --frozen-lockfile
# Removed Playwright tests and coverage generation steps
- name: Find PR and associated workflow run
id: find_pr_run
env:
GH_TOKEN: ${{ github.token }}
MERGE_COMMIT_SHA: ${{ github.sha }}
run: |
# Find the PR associated with the merge commit SHA
# Note: This relies on the merge commit being directly pushed to main
PR_DATA=$(gh pr list --state merged --search "$MERGE_COMMIT_SHA" --json number,headRefOid --jq '.[0]')
if [ -z "$PR_DATA" ]; then
echo "::warning::Could not find merged PR for commit $MERGE_COMMIT_SHA. Skipping coverage embedding."
echo "coverage_found=false" >> $GITHUB_OUTPUT
exit 0
fi
PR_HEAD_SHA=$(echo "$PR_DATA" | jq -r '.headRefOid')
PR_NUMBER=$(echo "$PR_DATA" | jq -r '.number')
echo "Found PR Number: $PR_NUMBER"
echo "Found PR Head SHA: $PR_HEAD_SHA"
# Find the latest *successful* playwright.yml run for the PR head commit so we
# never embed coverage from a failed/incomplete run.
RUN_ID=$(gh run list --workflow playwright.yml --commit "$PR_HEAD_SHA" --event pull_request --status success --json databaseId --jq '.[0].databaseId')
if [ -z "$RUN_ID" ]; then
echo "::warning::Could not find a successful 'playwright.yml' run for PR $PR_NUMBER (Head SHA: $PR_HEAD_SHA). Skipping coverage embedding."
echo "coverage_found=false" >> $GITHUB_OUTPUT
exit 0
fi
echo "Found Run ID: $RUN_ID"
echo "run_id=$RUN_ID" >> $GITHUB_OUTPUT
echo "coverage_found=true" >> $GITHUB_OUTPUT
- name: Download coverage artifact from PR run
if: steps.find_pr_run.outputs.coverage_found == 'true'
env:
GH_TOKEN: ${{ github.token }}
run: |
mkdir -p ./coverage-artifact
gh run download ${{ steps.find_pr_run.outputs.run_id }} -n coverage-report-pr --dir ./coverage-artifact
# Verify the artifact contains an HTML coverage report rather than checking a single asset
if [ -z "$(ls -A ./coverage-artifact)" ] || ! ls ./coverage-artifact/*.html >/dev/null 2>&1; then
echo "Failed to download or find an HTML coverage report in artifact 'coverage-report-pr' from run ${{ steps.find_pr_run.outputs.run_id }}."
exit 1
fi
echo "Artifact downloaded successfully."
- name: Copy coverage to docs static directory
if: steps.find_pr_run.outputs.coverage_found == 'true'
run: |
# Copy files from the downloaded artifact directory
mkdir -p platform/docs/static/coverage
cp -r ./coverage-artifact/* platform/docs/static/coverage/
# Copy specific asset files from the downloaded artifact root to static root
cp ./coverage-artifact/base.css platform/docs/static/
cp ./coverage-artifact/block-navigation.js platform/docs/static/
cp ./coverage-artifact/prettify.css platform/docs/static/
cp ./coverage-artifact/prettify.js platform/docs/static/
cp ./coverage-artifact/favicon.png platform/docs/static/
cp ./coverage-artifact/sort-arrow-sprite.png platform/docs/static/
cp ./coverage-artifact/sorter.js platform/docs/static/
- name: Build docs
run: pnpm --filter ohif-docs run build
- name: Deploy to Netlify
# The docs are already built by the "Build docs" step above, so pass
# --no-build: `netlify deploy` runs the build command by default, which
# would otherwise pick up the repo-root netlify.toml (configured for the
# main viewer app) and build the wrong project. --dir is resolved
# relative to the repo root (the netlify.toml base), not the cwd, so it
# must be the full path to the prebuilt docs output.
run: npx netlify-cli deploy --dir=platform/docs/build --prod --no-build
env:
NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
-100
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@@ -1,100 +0,0 @@
# For most projects, this workflow file will not need changing; you simply need
# to commit it to your repository.
#
# You may wish to alter this file to override the set of languages analyzed,
# or to provide custom queries or build logic.
#
# ******** NOTE ********
# We have attempted to detect the languages in your repository. Please check
# the `language` matrix defined below to confirm you have the correct set of
# supported CodeQL languages.
#
name: "CodeQL Advanced"
on:
pull_request:
branches: [ "main" ]
schedule:
- cron: '15 1 * * 5'
jobs:
analyze:
name: Analyze (${{ matrix.language }})
# Runner size impacts CodeQL analysis time. To learn more, please see:
# - https://gh.io/recommended-hardware-resources-for-running-codeql
# - https://gh.io/supported-runners-and-hardware-resources
# - https://gh.io/using-larger-runners (GitHub.com only)
# Consider using larger runners or machines with greater resources for possible analysis time improvements.
runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
permissions:
# required for all workflows
security-events: write
# required to fetch internal or private CodeQL packs
packages: read
# only required for workflows in private repositories
actions: read
contents: read
strategy:
fail-fast: false
matrix:
include:
- language: actions
build-mode: none
- language: javascript-typescript
build-mode: none
# CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
# Use `c-cpp` to analyze code written in C, C++ or both
# Use 'java-kotlin' to analyze code written in Java, Kotlin or both
# Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
# To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
# see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
# If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
# your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
steps:
- name: Checkout repository
uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
with:
persist-credentials: false
# Add any setup steps before running the `github/codeql-action/init` action.
# This includes steps like installing compilers or runtimes (`actions/setup-node`
# or others). This is typically only required for manual builds.
# - name: Setup runtime (example)
# uses: actions/setup-example@v1
# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@dd903d2e4f5405488e5ef1422510ee31c8b32357 # v3.36.2
with:
languages: ${{ matrix.language }}
build-mode: ${{ matrix.build-mode }}
# If you wish to specify custom queries, you can do so here or in a config file.
# By default, queries listed here will override any specified in a config file.
# Prefix the list here with "+" to use these queries and those in the config file.
# For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
# queries: security-extended,security-and-quality
# If the analyze step fails for one of the languages you are analyzing with
# "We were unable to automatically build your code", modify the matrix above
# to set the build mode to "manual" for that language. Then modify this step
# to build your code.
# ℹ️ Command-line programs to run using the OS shell.
# 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
- if: matrix.build-mode == 'manual'
shell: bash
run: |
echo 'If you are using a "manual" build mode for one or more of the' \
'languages you are analyzing, replace this with the commands to build' \
'your code, for example:'
echo ' make bootstrap'
echo ' make release'
exit 1
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@dd903d2e4f5405488e5ef1422510ee31c8b32357 # v3.36.2
with:
category: "/language:${{matrix.language}}"
+55 -211
View File
@@ -1,231 +1,75 @@
name: Playwright Tests
on:
push:
branches: [main, master]
pull_request:
branches: [master, release/*]
workflow_dispatch:
inputs:
cs3d_ref:
description: >-
CS3D branch (e.g. main, origin:feat/foo) or version (e.g. 4.18.2, 4.19+, 4.x). Only used
when ohif-integration label is present or via workflow_dispatch.
required: false
default: '4.19+'
permissions:
contents: read
pull-requests: read
issues: read
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
branches: [main, master]
jobs:
playwright-tests:
timeout-minutes: 120
runs-on: [self-hosted, nashua]
timeout-minutes: 60
runs-on: ubuntu-latest
container:
image: mcr.microsoft.com/playwright:v1.51.1-noble
strategy:
fail-fast: false
matrix:
node-version: [24]
shardIndex: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
shardTotal: [10]
steps:
- uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
- 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:
persist-credentials: false
- uses: actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
with:
node-version: ${{ matrix.node-version }}
# No `cache: pnpm`: this is a self-hosted runner with a persistent
# pnpm store on local disk. The Actions cache doesn't preserve the
# pnpm self-install's links faithfully, dropping pnpm/dist/worker.js
# and breaking `pnpm install` with MODULE_NOT_FOUND.
# Install pnpm via Corepack instead of pnpm/action-setup. The action's
# self-installer is a JS action run under the runner's bundled
# externals/node{version} and derives the `npm` path from that runtime — which
# on this self-hosted runner is corrupted (Cannot find module
# '../lib/cli.js'), so it dies regardless of `standalone:true`. Corepack
# ships inside the Node that setup-node just installed, reads the pinned
# `packageManager` (pnpm@11.5.2) from package.json, and fetches pnpm via
# Node's own https — it never invokes the npm CLI.
- name: Enable Corepack (pnpm)
shell: bash
run: |
corepack enable
corepack prepare --activate
# ── CS3D integration: detect label and ref type ──────────────────────
- name: Check for CS3D integration label
id: cs3d-check
run: bash .scripts/ci/cs3d-check-integration.sh
env:
GH_TOKEN: ${{ github.token }}
EVENT_NAME: ${{ github.event_name }}
CS3D_REF_INPUT: ${{ github.event.inputs.cs3d_ref || '4.19+' }}
REPO: ${{ github.repository }}
PR_NUMBER: ${{ github.event.pull_request.number }}
- name: Detect CS3D ref type
id: cs3d-ref
if: steps.cs3d-check.outputs.enabled == 'true'
run: |
REF="${CS3D_REF}"
if [[ "$REF" =~ ^[0-9]+\.[0-9x]+\+?(\.[0-9x]+)?(-[a-zA-Z0-9._]+)?$ ]]; then
echo "type=version" >> "$GITHUB_OUTPUT"
RESOLVED=$(node .scripts/cs3d-resolve-version.mjs "$REF")
echo "version=$RESOLVED" >> "$GITHUB_OUTPUT"
echo "::notice::CS3D version: $REF -> $RESOLVED"
else
echo "type=branch" >> "$GITHUB_OUTPUT"
echo "::notice::CS3D branch: $REF"
fi
env:
CS3D_REF: ${{ steps.cs3d-check.outputs.cs3d_ref }}
# ── CS3D branch path: clone and build before OHIF install ───────────
- name: Clone CS3D
if: steps.cs3d-check.outputs.enabled == 'true' && steps.cs3d-ref.outputs.type == 'branch'
run: |
REF="${CS3D_REF}"
if [[ "$REF" == *:* ]]; then
REPO="https://github.com/${REF%%:*}/cornerstone3D.git"
BRANCH="${REF#*:}"
else
REPO="https://github.com/cornerstonejs/cornerstone3D.git"
BRANCH="$REF"
fi
echo "::notice::Cloning CS3D from $REPO branch $BRANCH"
git clone --depth 1 --branch "$BRANCH" "$REPO" libs/@cornerstonejs
env:
CS3D_REF: ${{ steps.cs3d-check.outputs.cs3d_ref }}
- name: Install & Build CS3D
if: steps.cs3d-check.outputs.enabled == 'true' && steps.cs3d-ref.outputs.type == 'branch'
working-directory: libs/@cornerstonejs
run: pnpm install --frozen-lockfile && pnpm run build:esm
# ── Common: install OHIF dependencies ───────────────────────────────
node-version: 20
- name: Install dependencies
run: pnpm install --frozen-lockfile
# ── CS3D branch path: link packages after OHIF install ──────────────
- name: Link CS3D packages
if: steps.cs3d-check.outputs.enabled == 'true' && steps.cs3d-ref.outputs.type == 'branch'
working-directory: libs/@cornerstonejs
run: node scripts/link-ohif-cornerstone-node-modules.mjs "$GITHUB_WORKSPACE"
# ── CS3D version path: update versions after OHIF install ───────────
- name: Set CS3D version
if: steps.cs3d-check.outputs.enabled == 'true' && steps.cs3d-ref.outputs.type == 'version'
run: |
node .scripts/cs3d-set-version.mjs "${CS3D_VERSION}"
pnpm install --no-frozen-lockfile
env:
CS3D_VERSION: ${{ steps.cs3d-ref.outputs.version }}
# ── Common: run tests ───────────────────────────────────────────────
- name: Install Playwright browsers
# Only chromium is used (see playwright.config.ts and tests/globalSetup.ts);
# firefox/webkit projects are commented out. Scoping the install to chromium
# avoids downloading + dep-validating browsers we never launch (the WebKit
# validation is what surfaces the "missing libwoff1/libflite1/..." error on
# hosts without those libs).
run: npx playwright install chromium
run: bun install --frozen-lockfile
- name: Set up Git safe directory
run: git config --global --add safe.directory /__w/Viewers/Viewers
- name: Run Playwright tests
run: |
export NODE_OPTIONS="--max_old_space_size=10192"
pnpm run test:e2e:coverage
NODE_OPTIONS="--max_old_space_size=8192" TEST_ENV=true bun x playwright test --shard=${{ matrix.shardIndex }}/${{ matrix.shardTotal }}
# ── Common: collect test results and coverage ───────────────────────
- name: Create directory of test results
- name: Upload blob report to GitHub Actions Artifacts
if: ${{ !cancelled() }}
run: |
mkdir -p packaged-test-results
cp -r ./tests/test-results packaged-test-results/ || true
cp -r ./tests/playwright-report packaged-test-results/ || true
- name: Upload directory of test results artifact
if: ${{ !cancelled() }}
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
uses: actions/upload-artifact@v4
with:
name: playwright-results
path: packaged-test-results/
retention-days: 5
- name: create the coverage report
run: |
pnpm exec nyc report --reporter=lcov --reporter=text
- name: Upload the coverage report to GitHub Actions Artifacts
if: ${{ !cancelled() }}
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: coverage-report-pr
path: coverage
retention-days: 3
name: blob-report-${{ matrix.shardIndex }}
path: blob-report
retention-days: 1
# ── CS3D: build and deploy preview to Netlify ───────────────────────
- name: Log build context (OHIF/CS3D branch and version for build diagnosis)
if: steps.cs3d-check.outputs.enabled == 'true'
run: |
if [[ "$CS3D_REF_TYPE" == "branch" ]]; then
echo "::notice::Build type: ohif-downstream | OHIF: ${{ github.repository }}@${{ github.ref }} (${{ github.sha }}) | CS3D: branch ${{ steps.cs3d-check.outputs.cs3d_ref }}"
else
echo "::notice::Build type: ohif-upstream | OHIF: ${{ github.repository }}@${{ github.ref }} (${{ github.sha }}) | CS3D: version ${{ steps.cs3d-ref.outputs.version }}"
fi
node .scripts/log-build-context.mjs
env:
BUILD_TYPE:
${{ steps.cs3d-ref.outputs.type == 'branch' && 'ohif-downstream' || 'ohif-upstream' }}
CS3D_REF_TYPE: ${{ steps.cs3d-ref.outputs.type }}
- name: Build OHIF viewer (CS3D preview)
if: steps.cs3d-check.outputs.enabled == 'true'
run: pnpm run build:ci
- name: Deploy CS3D preview to Netlify
if: steps.cs3d-check.outputs.enabled == 'true'
run: |
RESULT=$(npx netlify-cli deploy --dir=platform/app/dist --alias="cs3d-pr-${PR_NUM}" --json --filter=@ohif/app) || {
echo "::error::Netlify deploy command failed"
exit 1
}
URL=$(echo "$RESULT" | jq -r '.deploy_url')
if [[ -z "$URL" || "$URL" == "null" ]]; then
echo "::error::Netlify deploy did not return a valid URL"
echo "$RESULT"
exit 1
fi
echo "::notice::CS3D preview deployed: $URL"
env:
NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
PR_NUM: ${{ github.event.pull_request.number || 'manual' }}
# ── CS3D: log results ───────────────────────────────────────────────
- name: Log CS3D build used
if: steps.cs3d-check.outputs.enabled == 'true'
run: |
if [[ "$CS3D_REF_TYPE" == "branch" ]]; then
echo "::notice::CS3D integration PASSED with branch ${CS3D_REF} (linked from libs/@cornerstonejs)"
else
echo "::notice::CS3D integration PASSED with @cornerstonejs/*@${CS3D_VERSION}"
fi
env:
CS3D_REF_TYPE: ${{ steps.cs3d-ref.outputs.type }}
CS3D_REF: ${{ steps.cs3d-check.outputs.cs3d_ref }}
CS3D_VERSION: ${{ steps.cs3d-ref.outputs.version }}
# ── Separate job: block merge when using a CS3D branch ─────────────
cs3d-branch-merge-guard:
name: 'CS3D Branch Merge Guard'
merge-reports:
if: ${{ !cancelled() }}
needs: [playwright-tests]
runs-on: ubuntu-latest
timeout-minutes: 5
container:
image: mcr.microsoft.com/playwright:v1.48.1-focal
steps:
- uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
- 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:
persist-credentials: false
- name: Check for CS3D branch usage
run: bash .scripts/ci/cs3d-branch-merge-guard.sh
env:
GH_TOKEN: ${{ github.token }}
EVENT_NAME: ${{ github.event_name }}
CS3D_REF_INPUT: ${{ github.event.inputs.cs3d_ref || '4.19+' }}
REPO: ${{ github.repository }}
PR_NUMBER: ${{ github.event.pull_request.number }}
node-version: 20
- name: Install dependencies
run: bun install --frozen-lockfile
- name: Set up Git safe directory
run: git config --global --add safe.directory /__w/Viewers/Viewers
- name: Download blob reports from GitHub Actions Artifacts
uses: actions/download-artifact@v4
with:
path: all-blob-reports
pattern: blob-report-*
merge-multiple: true
- name: Merge into HTML Report
run: bun x playwright merge-reports --reporter html ./all-blob-reports
- name: Upload HTML report
uses: actions/upload-artifact@v4
with:
name: html-report--attempt-${{ github.run_attempt }}
path: playwright-report
retention-days: 14
+1 -18
View File
@@ -1,8 +1,7 @@
# Packages
node_modules
.cursor/
.claude/
.nyc_output/
# Output
build
dist
@@ -14,7 +13,6 @@ coverage/
.yarn/
.nx/
addOns/yarn.lock
playwright-report/
# YALC (for Erik)
.yalc
@@ -45,7 +43,6 @@ videos/
# autogenerated files
platform/app/src/pluginImports.js
CLAUDE.md
/Viewers.iml
platform/app/.recipes/Nginx-Dcm4Chee/logs/*
platform/app/.recipes/OpenResty-Orthanc/logs/*
@@ -60,17 +57,3 @@ tests/test-results/
tests/playwright-report/
/blob-report/
/playwright/.cache/
**/.claude/settings.local.json
# cornerstone3D local linking
libs/
# Backup files
*~
# cornerstone3D local linking
libs/
link-cs3d.js
unlink-cs3d.js
auth.json
+10 -4
View File
@@ -6,21 +6,27 @@ cd "$(dirname "$0")"
cd .. # Up to project root
# Helpful to verify which versions we're using
echo 'My pnpm version is... '
echo 'My yarn version is... '
pnpm -v
yarn -v
node -v
# Build && Move PWA Output
pnpm run build:ci
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)
pnpm --filter ohif-docs run build
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.'
+4 -3
View File
@@ -2,13 +2,14 @@
"name": "root",
"private": true,
"engines": {
"node": ">=24",
"pnpm": ">=11"
"node": ">=14",
"npm": ">=6",
"yarn": ">=1.16.0"
},
"scripts": {
"deploy": "netlify deploy --prod --dir ./../platform/app/dist"
},
"devDependencies": {
"netlify-cli": "2.21.0"
"netlify-cli": "^2.21.0"
}
}
+1 -1
View File
@@ -1 +1 @@
24
20.9.0
-5
View File
@@ -1,5 +0,0 @@
node-linker=hoisted
strict-peer-dependencies=false
link-workspace-packages=true
prefer-workspace-packages=true
manage-package-manager-versions=false
-24
View File
@@ -1,24 +0,0 @@
{
"extends": "@istanbuljs/nyc-config-typescript",
"instrument": true,
"sourceMap": true,
"cache": false,
"all": true,
"include": [
"platform/*/src/**/*.ts",
"platform/*/src/**/*.js",
"extensions/*/src/**/*.ts",
"extensions/*/src/**/*.js",
"modes/*/src/**/*.ts",
"modes/*/src/**/*.js"
],
"exclude": [
"**/*.spec.ts",
"**/*.test.ts",
"**/test/**",
"**/tests/**",
"**/examples/**",
"**/stories/**",
"platform/docs/**"
]
}
-42
View File
@@ -1,42 +0,0 @@
#!/usr/bin/env bash
# CS3D branch merge guard: blocks merge when tests ran against a CS3D branch (not a version).
# Exits 0 when merge is allowed or guard is skipped; exits 1 when merge must be blocked.
#
# Required env: GH_TOKEN, EVENT_NAME, REPO, PR_NUMBER
# Optional env: CS3D_REF_INPUT (for workflow_dispatch, default 4.19+)
set -e
if [[ "$EVENT_NAME" == "workflow_dispatch" ]]; then
echo "::notice::workflow_dispatch — no merge to block, skipping guard."
exit 0
elif [[ "$EVENT_NAME" == "pull_request" ]]; then
LABELS=$(gh api "repos/${REPO}/issues/${PR_NUMBER}/labels" --jq '.[].name')
if echo "$LABELS" | grep -q "ohif-integration"; then
ENABLED=true
CS3D_REF=$(gh api "repos/${REPO}/pulls/${PR_NUMBER}" --jq '.body' \
| sed -n 's/^[[:space:]]*CS3D_REF:[[:space:]]*\([^[:space:]]*\).*/\1/p' | head -1)
if [[ -z "$CS3D_REF" ]]; then
CS3D_REF="4.19+"
fi
else
ENABLED=false
fi
else
ENABLED=false
fi
if [[ "$ENABLED" != "true" ]]; then
echo "::notice::No ohif-integration label — skipping merge guard."
exit 0
fi
# Check if the ref is a branch (not a version)
if [[ "$CS3D_REF" =~ ^[0-9]+\.[0-9x]+\+?(\.[0-9x]+)?(-[a-zA-Z0-9._]+)?$ ]]; then
echo "::notice::CS3D ref '$CS3D_REF' is a version — merge allowed."
exit 0
fi
echo "::error::Tests ran against CS3D branch '${CS3D_REF}' — this build cannot be merged."
echo "::error::Re-run with a published CS3D version (e.g. 4.19+) before merging."
exit 1
-29
View File
@@ -1,29 +0,0 @@
#!/usr/bin/env bash
# CS3D integration check: detects ohif-integration label and parses CS3D_REF.
# Writes to GITHUB_OUTPUT: enabled (true|false), cs3d_ref (when enabled).
#
# Required env: GH_TOKEN, EVENT_NAME, REPO, PR_NUMBER, GITHUB_OUTPUT
# Optional env: CS3D_REF_INPUT (for workflow_dispatch, default 4.19+)
set -e
if [[ "$EVENT_NAME" == "workflow_dispatch" ]]; then
echo "enabled=true" >> "$GITHUB_OUTPUT"
echo "cs3d_ref=${CS3D_REF_INPUT:-4.19+}" >> "$GITHUB_OUTPUT"
elif [[ "$EVENT_NAME" == "pull_request" ]]; then
LABELS=$(gh api "repos/${REPO}/issues/${PR_NUMBER}/labels" --jq '.[].name')
if echo "$LABELS" | grep -q "ohif-integration"; then
echo "enabled=true" >> "$GITHUB_OUTPUT"
REF=$(gh api "repos/${REPO}/pulls/${PR_NUMBER}" --jq '.body' \
| sed -n 's/^[[:space:]]*CS3D_REF:[[:space:]]*\([^[:space:]]*\).*/\1/p' | head -1)
if [[ -z "$REF" ]]; then
REF="4.19+"
fi
echo "cs3d_ref=${REF}" >> "$GITHUB_OUTPUT"
echo "::notice::CS3D ref from PR body: ${REF}"
else
echo "enabled=false" >> "$GITHUB_OUTPUT"
fi
else
echo "enabled=false" >> "$GITHUB_OUTPUT"
fi
-55
View File
@@ -1,55 +0,0 @@
import fs from 'node:fs';
import path from 'node:path';
import { execSync } from 'node:child_process';
const workflowPath = path.resolve(
process.cwd(),
'libs',
'@cornerstonejs',
'.github',
'workflows',
'ohif-downstream.yml'
);
if (!fs.existsSync(workflowPath)) {
console.error(`[cs3d:check] Workflow file not found: ${workflowPath}`);
process.exit(1);
}
const workflowText = fs.readFileSync(workflowPath, 'utf8');
const ohifRefMatch = workflowText.match(/^\s*OHIF_REF:\s*["']?([^"'\r\n]+)["']?\s*$/m);
if (!ohifRefMatch) {
console.error('[cs3d:check] Could not find OHIF_REF in ohif-downstream workflow.');
process.exit(1);
}
const expectedBranch = ohifRefMatch[1].trim();
let currentBranch = '';
try {
currentBranch = execSync('git rev-parse --abbrev-ref HEAD', {
cwd: process.cwd(),
encoding: 'utf8',
}).trim();
} catch (error) {
console.error('[cs3d:check] Failed to determine current git branch.');
process.exit(1);
}
if (currentBranch !== expectedBranch) {
console.error(
`[cs3d:check] Branch mismatch: current='${currentBranch}', expected='${expectedBranch}' from ${path.relative(
process.cwd(),
workflowPath
)}`
);
process.exit(1);
}
console.log(
`[cs3d:check] OK: current branch '${currentBranch}' matches OHIF_REF in ${path.relative(
process.cwd(),
workflowPath
)}`
);
-63
View File
@@ -1,63 +0,0 @@
#!/usr/bin/env node
/**
* Resolves a version pattern to a concrete npm version of @cornerstonejs/core.
*
* Patterns:
* 4.18.2 -> 4.18.2 (exact, returned as-is)
* 4.18.2-beta.3 -> 4.18.2-beta.3 (exact prerelease)
* 4.x -> latest 4.* from npm
* 4.17.x -> latest 4.17.* from npm
* 4.19+ -> latest >=4.19.0 <5.0.0-0 from npm (4.19 and later, same major)
*
* Prints the resolved version to stdout.
*/
import { execSync } from 'child_process';
const pattern = process.argv[2];
if (!pattern) {
console.error('Usage: cs3d-resolve-version.mjs <pattern>');
console.error(' e.g. 4.x, 4.17.x, 4.19+, 4.18.2, 4.18.2-beta.3');
process.exit(1);
}
// Exact version (no wildcard or range) — pass through unchanged
if (!pattern.includes('x') && !pattern.endsWith('+')) {
console.log(pattern);
process.exit(0);
}
// Convert "M.m+" to npm semver range ">=M.m.0 <(M+1).0.0-0"
let npmRange = pattern;
const plusMatch = pattern.match(/^(\d+)\.(\d+)\+$/);
if (plusMatch) {
const major = Number(plusMatch[1]);
const minor = Number(plusMatch[2]);
npmRange = `>=${major}.${minor}.0 <${major + 1}.0.0-0`;
}
try {
// Let npm resolve the range: @package@<range> → concrete version
const raw = execSync(`npm view @cornerstonejs/core@"${npmRange}" version --json`, {
encoding: 'utf8',
timeout: 30_000,
});
const resolved = JSON.parse(raw);
if (!resolved) {
console.error(`npm returned no version when resolving @cornerstonejs/core@${npmRange}`);
process.exit(1);
}
// npm may return an array of versions for ranges; pick the latest (last) one
const version = Array.isArray(resolved) ? resolved[resolved.length - 1] : resolved;
console.log(version);
} catch (err) {
const message =
(err && (err.stderr?.toString() || err.message || String(err))) ||
`Unknown error resolving @cornerstonejs/core@${pattern}`;
console.error(`Failed to resolve @cornerstonejs/core version for pattern "${pattern}":`);
console.error(message);
process.exit(1);
}
-131
View File
@@ -1,131 +0,0 @@
#!/usr/bin/env node
/**
* Updates all @cornerstonejs/* package versions across the OHIF workspace.
*
* Usage: node .scripts/cs3d-set-version.mjs <version>
*
* Only updates the 8 main CS3D packages (not codec packages):
* adapters, ai, core, dicom-image-loader, labelmap-interpolation,
* nifti-volume-loader, polymorphic-segmentation, tools
*/
import { readFileSync, writeFileSync, existsSync, readdirSync } from 'fs';
import { resolve, dirname, join } from 'path';
import { fileURLToPath } from 'url';
const __dirname = dirname(fileURLToPath(import.meta.url));
const rootDir = resolve(__dirname, '..');
const version = process.argv[2];
if (!version) {
console.error('Usage: cs3d-set-version.mjs <version>');
console.error(' e.g. 4.18.2, 4.19.0-beta.1');
process.exit(1);
}
// The 8 CS3D packages that are built from source (not codecs)
const CS3D_PACKAGES = [
'@cornerstonejs/adapters',
'@cornerstonejs/ai',
'@cornerstonejs/core',
'@cornerstonejs/dicom-image-loader',
'@cornerstonejs/labelmap-interpolation',
'@cornerstonejs/nifti-volume-loader',
'@cornerstonejs/polymorphic-segmentation',
'@cornerstonejs/tools',
];
// Read root package.json to get workspace globs
const rootPkgPath = resolve(rootDir, 'package.json');
const rootPkg = JSON.parse(readFileSync(rootPkgPath, 'utf8'));
const workspaceGlobs = rootPkg.workspaces?.packages || rootPkg.workspaces || [];
// Collect all package.json paths from workspace globs
function findWorkspacePackageJsons() {
const paths = [rootPkgPath]; // include root
for (const pattern of workspaceGlobs) {
const parts = pattern.split('/');
let searchDir = rootDir;
let hasWildcard = false;
for (const part of parts) {
if (part === '*') {
hasWildcard = true;
break;
}
searchDir = join(searchDir, part);
}
if (hasWildcard) {
try {
const entries = readdirSync(searchDir, { withFileTypes: true });
for (const entry of entries) {
if (entry.isDirectory()) {
const pkgJson = join(searchDir, entry.name, 'package.json');
if (existsSync(pkgJson)) {
paths.push(pkgJson);
}
}
}
} catch {
// directory doesn't exist, skip
}
} else {
const pkgJson = join(rootDir, pattern, 'package.json');
if (existsSync(pkgJson)) {
paths.push(pkgJson);
}
}
}
return paths;
}
// Update a dependencies object, returning count of changes
function updateDeps(deps, targetVersion) {
let count = 0;
if (!deps) return count;
for (const pkg of CS3D_PACKAGES) {
if (pkg in deps && deps[pkg] !== targetVersion) {
deps[pkg] = targetVersion;
count++;
}
}
return count;
}
const pkgPaths = findWorkspacePackageJsons();
let totalChanges = 0;
for (const pkgPath of pkgPaths) {
const content = readFileSync(pkgPath, 'utf8');
const pkg = JSON.parse(content);
let changes = 0;
changes += updateDeps(pkg.dependencies, version);
changes += updateDeps(pkg.devDependencies, version);
changes += updateDeps(pkg.peerDependencies, version);
changes += updateDeps(pkg.resolutions, version);
if (changes > 0) {
// Preserve original formatting (detect indent — restrict to spaces/tabs so
// we don't accidentally capture a CRLF newline as part of the indent string)
const indent = content.match(/^([ \t]+)/m)?.[1] || ' ';
writeFileSync(pkgPath, JSON.stringify(pkg, null, indent) + '\n');
const rel = pkgPath.replace(rootDir + '/', '').replace(rootDir + '\\', '');
console.log(` Updated ${rel} (${changes} packages)`);
totalChanges += changes;
}
}
console.log(
`\nDone: ${totalChanges} version(s) updated to ${version} across ${pkgPaths.length} package files.`
);
console.log(
'This step changes package.json; the following install must not use a frozen Bun lockfile ' +
'(OHIF+CS3D combined “version” CI does: `bun install --config=./bunfig.update-lockfile.toml`). ' +
'Other installs stay frozen. Locally after this script, use that bun command and/or ' +
'`bun run install:update-lockfile` when you intend to commit lockfile updates.\n'
);
+2 -2
View File
@@ -6,9 +6,9 @@ PROJECT=$1
if [ -z "$PROJECT" ]
then
# Default
pnpm --filter @ohif/app run dev:viewer
npx lerna run dev:viewer
else
pnpm --filter @ohif/app run "dev:$PROJECT"
eval "npx lerna run dev:$PROJECT"
fi
read -p 'Press [Enter] key to continue...'
-108
View File
@@ -1,108 +0,0 @@
#!/usr/bin/env node
/**
* Logs build context (OHIF branch/version, CS3D source) for diagnosing build issues on GitHub.
* Run from repo root. Used by version.mjs and can be invoked from CI workflows.
*/
import { execa } from 'execa';
import fs from 'fs/promises';
import path from 'path';
import { fileURLToPath } from 'url';
const __dirname = path.dirname(fileURLToPath(import.meta.url));
const REPO_ROOT = path.resolve(__dirname, '..');
function log(msg) {
console.log(`[build-context] ${msg}`);
}
async function detectCs3dSource() {
const libsCs3d = path.join(REPO_ROOT, 'libs/@cornerstonejs');
const coreInNodeModules = path.join(REPO_ROOT, 'node_modules/@cornerstonejs/core');
try {
const libsExists = await fs.access(libsCs3d).then(() => true).catch(() => false);
if (!libsExists) {
return { source: 'npm', detail: 'published @cornerstonejs packages (no libs/@cornerstonejs)' };
}
const coreStat = await fs.lstat(coreInNodeModules).catch(() => null);
const isSymlink = coreStat?.isSymbolicLink();
if (isSymlink) {
const target = await fs.readlink(coreInNodeModules);
return { source: 'integrated', detail: `linked from libs/@cornerstonejs (→ ${target})` };
}
return { source: 'npm', detail: 'published @cornerstonejs packages (libs exists but not linked)' };
} catch {
return { source: 'unknown', detail: 'could not detect' };
}
}
async function getCs3dVersion() {
try {
const corePkg = path.join(REPO_ROOT, 'node_modules/@cornerstonejs/core/package.json');
const pkg = JSON.parse(await fs.readFile(corePkg, 'utf-8'));
return pkg.version || 'unknown';
} catch {
return 'unknown';
}
}
async function getCs3dBranchFromLibs() {
try {
const libsCs3d = path.join(REPO_ROOT, 'libs/@cornerstonejs');
const { stdout } = await execa('git', ['rev-parse', '--abbrev-ref', 'HEAD'], {
cwd: libsCs3d,
});
return stdout;
} catch {
return null;
}
}
async function run() {
const inCI = process.env.GITHUB_ACTIONS === 'true';
const buildType = inCI ? (process.env.BUILD_TYPE || 'ohif-upstream') : 'local';
log('═══════════════════════════════════════════════════════════════');
log('Build context (for diagnosing GitHub build issues)');
log('═══════════════════════════════════════════════════════════════');
if (inCI) {
log(`Build type: ${process.env.BUILD_TYPE || 'ohif-upstream'}`);
log(`GitHub repo: ${process.env.GITHUB_REPOSITORY || 'unknown'}`);
log(`GitHub ref: ${process.env.GITHUB_REF || 'unknown'}`);
log(`GitHub SHA: ${process.env.GITHUB_SHA || 'unknown'}`);
log(`Workflow: ${process.env.GITHUB_WORKFLOW || 'unknown'}`);
}
try {
const { stdout: branch } = await execa('git', ['rev-parse', '--abbrev-ref', 'HEAD'], {
cwd: REPO_ROOT,
});
const { stdout: sha } = await execa('git', ['rev-parse', '--short', 'HEAD'], {
cwd: REPO_ROOT,
});
log(`OHIF branch: ${branch} (${sha})`);
} catch {
log('OHIF branch: (not a git repo or error)');
}
const cs3d = await detectCs3dSource();
log(`CS3D source: ${cs3d.source} — ${cs3d.detail}`);
if (cs3d.source === 'integrated') {
const branch = await getCs3dBranchFromLibs();
if (branch) log(`CS3D branch (libs/@cornerstonejs): ${branch}`);
} else {
const ver = await getCs3dVersion();
log(`CS3D version (@cornerstonejs/core): ${ver}`);
}
log('═══════════════════════════════════════════════════════════════');
}
run().catch((err) => {
console.error('[build-context] Error:', err.message);
process.exitCode = 1;
});
+1 -4
View File
@@ -82,7 +82,6 @@
"Reslices",
"roadmap",
"ROADMAPS",
"rtstruct",
"Segmentations",
"semibold",
"sitk",
@@ -110,8 +109,6 @@
"wado",
"wadors",
"wadouri",
"workerpool",
"Colorbar",
"Colorbars"
"workerpool"
]
}
-51
View File
@@ -1,51 +0,0 @@
const path = require('path');
// Shared module-resolution rules (alias + module search paths) used by BOTH
// build pipelines so they cannot drift apart:
// - the webpack/rspack build: webpack.base.js -> webpack.pwa.js, plus every
// per-package webpack.prod.js / webpack.dev.js that merges webpack.base.js
// - the rsbuild build: rsbuild.config.ts (dev:fast)
//
// Plugin aliases (writePluginImportsFile.getPluginResolveAliases) are NOT
// included here: they depend on pluginConfig.json and are merged in separately
// by each config.
//
// All paths are anchored to this file's location (the repo-root `.webpack/`
// directory), so the values are identical regardless of which package's build
// is doing the resolving.
const alias = {
// Some extensions import app-level utilities (e.g. history,
// preserveQueryParameters) from '@ohif/app'. pnpm's isolated layout does not
// expose the top-level app package to those extensions, and adding it as a
// workspace dependency would create an app<->default cycle, so we resolve the
// bare specifier to the app source here ($ = exact match).
'@ohif/app$': path.resolve(__dirname, '../platform/app/src/index.js'),
'@': path.resolve(__dirname, '../platform/app/src'),
'@components': path.resolve(__dirname, '../platform/app/src/components'),
'@hooks': path.resolve(__dirname, '../platform/app/src/hooks'),
'@routes': path.resolve(__dirname, '../platform/app/src/routes'),
'@state': path.resolve(__dirname, '../platform/app/src/state'),
};
// Directories to search when resolving modules. The leading bare 'node_modules'
// preserves the default importer-relative walk-up, which pnpm's isolated layout
// requires so that transitive deps (e.g. react-remove-scroll -> tslib 2.x)
// resolve to the sibling copy inside .pnpm/<pkg>/node_modules rather than a
// hoisted older version.
const moduleSearchPaths = [
'node_modules',
path.resolve(__dirname, '../node_modules'),
path.resolve(__dirname, '../../../node_modules'),
path.resolve(__dirname, '../platform/app/node_modules'),
path.resolve(__dirname, '../platform/ui/node_modules'),
];
// Build the resolve.modules array for a build. `srcDir` is the building
// package's source root; it is appended last (matching the previous inline
// behavior in webpack.base.js). Pass nothing to get just the shared paths.
function getModules(srcDir) {
return srcDir ? [...moduleSearchPaths, srcDir] : [...moduleSearchPaths];
}
module.exports = { alias, moduleSearchPaths, getModules };
+2 -2
View File
@@ -2,14 +2,14 @@ const autoprefixer = require('autoprefixer');
const path = require('path');
const tailwindcss = require('tailwindcss');
const tailwindConfigPath = path.resolve('../../platform/app/tailwind.config.js');
const rspack = require('@rspack/core');
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const devMode = process.env.NODE_ENV !== 'production';
const cssToJavaScript = {
test: /\.css$/,
use: [
//'style-loader',
devMode ? 'style-loader' : rspack.CssExtractRspackPlugin.loader,
devMode ? 'style-loader' : MiniCssExtractPlugin.loader,
{ loader: 'css-loader', options: { importLoaders: 1 } },
{
loader: 'postcss-loader',
-2
View File
@@ -4,8 +4,6 @@ function transpileJavaScript(mode) {
const exclude =
mode === 'production'
? excludeNodeModulesExcept([
// Workspace packages (needed for pnpm shamefully-hoist where they resolve through node_modules)
'@ohif',
// 'dicomweb-client',
// https://github.com/react-dnd/react-dnd/blob/master/babel.config.js
'react-dnd',
+43 -63
View File
@@ -4,10 +4,11 @@ const dotenv = require('dotenv');
const path = require('path');
const fs = require('fs');
const webpack = require('@rspack/core');
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
@@ -17,21 +18,14 @@ const webpack = require('@rspack/core');
const loadWebWorkersRule = require('./rules/loadWebWorkers.js');
const transpileJavaScriptRule = require('./rules/transpileJavaScript.js');
const cssToJavaScript = require('./rules/cssToJavaScript.js');
// Module-resolution rules shared with the rsbuild build (see rsbuild.config.ts).
const resolveConfig = require('./resolveConfig');
// Only uncomment for old v2 stylus
// const stylusToJavaScript = require('./rules/stylusToJavaScript.js');
let ReactRefreshWebpackPlugin;
try {
const mod = require('@rspack/plugin-react-refresh');
ReactRefreshWebpackPlugin = mod.ReactRefreshRspackPlugin || mod.default || mod;
} catch { ReactRefreshWebpackPlugin = null; }
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';
const IS_COVERAGE = process.env.COVERAGE === 'true';
// read from ../version.txt
const VERSION_NUMBER = fs.readFileSync(path.join(__dirname, '../version.txt'), 'utf8') || '';
@@ -71,12 +65,6 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
const config = {
mode: isProdBuild ? 'production' : 'development',
devtool: isProdBuild ? 'source-map' : 'cheap-module-source-map',
// `rspack serve` (@rspack/cli) auto-enables lazyCompilation for web-only
// apps unless the config defines it explicitly. The on-demand proxy chunks
// it produces fail to load in the headless cypress/electron e2e run
// (ChunkLoadError on cornerstone vendor chunks), so disable it here to match
// the rsbuild build (see rsbuild.config.ts `dev.lazyCompilation: false`).
lazyCompilation: false,
entry: ENTRY,
optimization: {
// splitChunks: {
@@ -103,37 +91,23 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
children: false,
warnings: true,
},
cache: isProdBuild ? false : { type: 'filesystem' },
cache: {
type: 'filesystem',
},
module: {
noParse: [/(dicomicc)/],
rules: [
...(isProdBuild
? []
: [
...(IS_COVERAGE
? [
{
test: /\.[jt]sx?$/,
exclude: /node_modules/,
use: {
loader: 'babel-loader',
options: {
presets: ['@babel/preset-typescript', '@babel/preset-react'],
plugins: ['istanbul'],
},
},
},
]
: [
{
test: /\.[jt]sx?$/,
exclude: /node_modules/,
loader: 'babel-loader',
options: {
plugins: isProdBuild ? [] : ['react-refresh/babel'],
},
},
]),
{
test: /\.[jt]sx?$/,
exclude: /node_modules/,
loader: 'babel-loader',
options: {
plugins: isProdBuild ? [] : ['react-refresh/babel'],
},
},
]),
{
test: /\.svg?$/,
@@ -177,6 +151,9 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
},
},
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',
@@ -200,16 +177,29 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
},
resolve: {
mainFields: ['module', 'browser', 'main'],
// alias and modules are shared with the rsbuild build via ./resolveConfig
// so the two pipelines resolve identically.
alias: {
...resolveConfig.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',
},
modules: resolveConfig.getModules(SRC_DIR),
// 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', '*'],
// Workspace packages use relative imports between sibling packages.
// Resolve symlinks to keep those imports anchored at the real package paths.
// symlinked resources are resolved to their real path, not their symlinked location
symlinks: true,
fallback: {
fs: false,
@@ -218,34 +208,24 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
buffer: require.resolve('buffer'),
},
},
node: {
// Leave __filename / __dirname references alone. The previous 'mock'
// value triggers an rspack warning whenever bundled deps reference
// __dirname (e.g. Emscripten-compiled cornerstone codecs). Those refs
// sit inside `if (ENVIRONMENT_IS_NODE)` branches that never execute in
// the browser, so leaving them un-substituted is harmless at runtime.
__filename: false,
__dirname: false,
},
plugins: [
new webpack.DefinePlugin(defineValues),
new webpack.ProvidePlugin({
Buffer: ['buffer', 'Buffer'],
}),
new webpack.IgnorePlugin({
resourceRegExp: /^(fs|path)$/,
contextRegExp: /@cornerstonejs[\\/]codec-/,
}),
...(isProdBuild || IS_COVERAGE || !ReactRefreshWebpackPlugin
? []
: [new ReactRefreshWebpackPlugin({ overlay: false })]),
...(isProdBuild ? [] : [new ReactRefreshWebpackPlugin({ overlay: false })]),
// Uncomment to generate bundle analyzer
// new BundleAnalyzerPlugin(),
],
};
if (isProdBuild) {
config.optimization.minimizer = [new webpack.SwcJsMinimizerRspackPlugin()];
config.optimization.minimizer = [
new TerserJSPlugin({
parallel: true,
terserOptions: {},
}),
];
}
if (isQuickBuild) {
-201
View File
@@ -1,201 +0,0 @@
# AGENTS.md
This file provides guidance to AI coding agents (Claude, Codex, and other LLM tools) when working with code in this repository.
## Project Overview
This is **OHIF** v3 (Open Health Imaging Foundation) - a medical imaging viewer. It's an extensible web imaging platform.
## Development Commands
### Main Development
```bash
# Start development server for all packages
yarn dev
```
### Building
```bash
# Build all packages for production
yarn build
# Build specific packages
cd platform/app && yarn build # Main viewer app
```
## Architecture Overview
### Monorepo Structure
- **`platform/`** - Core OHIF infrastructure
- `app/` - Main viewer application (`@ohif/viewer`)
- `core/` - Core services and utilities
- `ui-next/` - Modern UI component library
- **`extensions/`** - Modular functionality plugins
- **`modes/`** - Application workflow configurations
### Key Extension Architecture
**Extension System**: Each extension exports modules (viewports, tools, panels, commands) that the app dynamically loads. Extensions are self-contained with their own webpack builds.
**Core Extensions:**
- `cornerstone/` - Medical image rendering engine
- `cornerstone-dicom-pmp/` - DICOM PMP support
- `cornerstone-dicom-seg/` - DICOM Segmentation support
- `cornerstone-dicom-sr/` - DICOM SR support
- `dicom-pdf/` - DICOM PDF support
- `dicom-video/` - DICOM Video support
- `measurement-tracking/` - Measurement tracking support
- `default/` - Standard OHIF functionality
### Service-Oriented Design (PUB-SUB)
The app uses a Services Manager pattern with these core services:
- **Display Set Service**: Manages image series organization
- **Measurement Service**: Handles annotations and measurements
- **Hanging Protocol Service**: Controls image layout and display rules
- **UI Service**: Manages panels, modals, and notifications
- **Segmentation Service**: AI/ML powered image segmentation, loading segmentations, etc.
- **Viewport Grid Service**: Manages viewport layout and display rules
- **Viewport Display Set History Service**: Manages viewport display set history
- **Viewport Dialog Service**: Manages viewport dialogs
- **Notification Service**: Manages notifications
- **Modal Service**: Manages modals
- **Dialog Service**: Manages dialogs, more general not just viewport dialogs
- **Customization Service**: Manages customization of the app
- **Toolbar Service**: Manages the toolbar, viewport action corners, tool states
- **User Authentication Service**: Manages user authentication, but used only for injecting tokens in dicomweb requests in our context
- **Panel Service**: Manages side panels
- **Cornerstone Viewport Service**: Manages the cornerstone viewport, rendering engines, presentation states, more tightly coupled to cornerstone than the other services
- **Tool Group Service**: Manages tool groups, creating and managing tool groups, etc.
- **Sync Group Service**: Manages sync groups, syncing zooming, panning, scrolling, etc.
- **Cornerstone Cache Service**: Manages the cornerstone cache, caching images, etc.
Most of the services utilize a pub sub architecture and extend the pub sub service interace at `pubSubServiceInterface.ts`
### Commands Manager
The Commands Manager tracks named commands (or functions) that are scoped to
a context. When we attempt to run a command with a given name, we look for it
in our active contexts, in the order specified.
If found, we run the command, passing in any application
or call specific data specified in the command's definition.
You can call `commandsManager.runCommand` to run a command.
### Extension Manager
Aggregates and exposes extension modules throughout the OHIF application, manages data sources, and provides a centralized registry for accessing extension functionality.
### Build System
**Yarn Workspaces**: Optimized monorepo builds with dependency caching
**Webpack 5**: Module federation for dynamic extension loading
**Plugin Import System**: Extensions auto-register via `writePluginImportsFile.js`
### Key Technologies
- **React 18 + TypeScript**: UI framework
- **Cornerstone.js**: Medical image rendering
- **DICOM**: Medical imaging standard support
- **ONNX Runtime**: AI model inference (SAM segmentation models)
- **Zustand**: State management
- **TailwindCSS**: Styling system
## Development Patterns
### Adding New Tools
1. Create tool class in `extensions/cornerstone/src/tools/`
2. Register in tool module's `toolNames.ts`
3. Add to toolbar via `getToolbarModule.tsx`
4. Add measurement mapping if needed in `measurementServiceMappings/`
### Creating Extensions
Extensions must export:
- `id.js` - Unique extension identifier
- `index.tsx` - Extension registration
- Module functions (`getToolbarModule`, `getViewportModule`, etc.)
### Viewport Customization
Custom viewports extend base Cornerstone viewport:
- Override render methods for custom overlays
- Implement measurement tracking
- Add viewport-specific tools and interactions
### Service Integration
Register services in extension's `servicesManager.registerService` and access via:
```javascript
const { MeasurementService } = servicesManager.services;
```
### Creating stores
To create a store, you can make one in your extension's `stores/` directory, and you can follow the example of an existing store such as `useLutPresentationStore.ts` or `useSynchronizersStore.ts`.
### Creating hooks
To create a hook, you can make one in your extension's `hooks/` directory, and you can follow the example of an existing hook such as `usePatientInfo.tsx`.
### Creating providers
To create a provider, you can make one in your extension's `providers/` or `contexts/` directory, and you can follow the example of an existing provider such as `ViewportGridProvider.tsx`.
### Adding new icons
To add a new icon, you can add it to the `icons/` directory, then register the icon using `import { addIcon } from '@ohif/extension-default/src/utils'`
### Creating synchronizers
You can create custom synchronizers and place them in the `synchronizers/` directory, you can follow the example of `frameViewSynchronizer.ts`
### Utilites
Any new utilites should be placed in the `utils/` directory, and you can follow the example of `formatPN.ts`
### Commands
Commands are created in the commandsModule of the extension, for example the cornerstone extension has `commandsModule.tsx`, sometimes its also named `getCommandsModule.tsx.`
### Overriding OHIF Components
To override an OHIF component, you can create a new component in your extension's `components/` directory, then import it instead of the original ui-next component.
### Mode layout
The layoutTemplate is a function that returns a layout object, you can follow the example of `longitudinal/src/index.ts`. This would be helpful when you need to override a component as you can know where to look for the original component.
### Pub Sub
Always prioritrize pub sub, by calling a services subscribe over useEffects as it's more reliable, for example
```ts
useEffect(() => {
const subscriptions = [
cornerstoneViewportService.subscribe(EVENTS.VIEWPORT_DATA_CHANGED, handleViewportDataChanged),
syncGroupService.subscribe(EVENTS.VIEWPORT_REMOVED, onHotKeyRemoval),
syncGroupService.subscribe(EVENTS.VIEWPORT_ADDED, onHotKeyAddition),
];
return () => {
subscriptions.forEach(({ unsubscribe }) => unsubscribe());
};
}, []);
```
### Never modify core architecture
Do not modify the core and always find a way to implement the solution via the extensions and modes, only modify core as a last resort if all other fail or there's an architectural constraint.
## Configuration
### Plugin Configuration
Extensions are auto-discovered via `pluginConfig.json` and dynamically imported during build.
## Medical Imaging Specifics
### DICOM Support
- Multi-format: CT, MRI, X-Ray, Mammography, Ultrasound
- SOP Class handlers for specialized DICOM types (RT, SEG, SR)
- DICOMweb protocol for web-based image retrieval
### Hanging Protocols
Define how images are arranged and displayed:
- Located in `hps/` directories
- JSON configuration with viewport rules
- Support for priors comparison and multi-monitor layouts
### Measurement Tools
- Cornerstone Tools integration for annotations
- Bidirectional measurements, polylines, annotations
- Export capabilities (DICOM SR, CSV reports)
- AI-assisted measurements via ONNX models
+7 -3518
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+35 -20
View File
@@ -20,33 +20,48 @@
#
# 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:24-slim as builder
FROM node:20.18.1-slim as builder
RUN apt-get update && apt-get install -y --no-install-recommends build-essential python3 \
&& rm -rf /var/lib/apt/lists/*
RUN apt-get update && apt-get install -y build-essential python3
RUN npm install -g pnpm@11
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
# Copy package manifests for install caching. preinstall.js is included because
# the root package.json's "preinstall" lifecycle script (node preinstall.js)
# runs during `pnpm install` below -- before the full source is copied -- so the
# script file must already be present or install fails with MODULE_NOT_FOUND.
COPY package.json pnpm-lock.yaml pnpm-workspace.yaml .npmrc preinstall.js ./
COPY --parents ./extensions/*/package.json ./modes/*/package.json ./platform/*/package.json ./
# Run the install before copying the rest of the files.
# Keep --no-frozen-lockfile here (unlike CI): .dockerignore excludes
# platform/docs, so the lockfile's docs importer has no manifest in the build
# context and a frozen install would fail. pnpm reconciles (drops docs) instead.
RUN pnpm install --no-frozen-lockfile
# 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=pnpm-lock.yaml --exclude=package.json --exclude=Dockerfile . .
COPY --link --exclude=yarn.lock --exclude=package.json --exclude=Dockerfile . .
# Build here
# After install it should hopefully be stable until the local directory changes
@@ -56,14 +71,14 @@ ARG APP_CONFIG=config/default.js
ARG PUBLIC_URL=/
ENV PUBLIC_URL=${PUBLIC_URL}
RUN pnpm run show:config
RUN pnpm run build
RUN bun run show:config
RUN bun run build
# Precompress files
RUN chmod u+x .docker/compressDist.sh
RUN ./.docker/compressDist.sh
# Stage 2: Bundle the built application into a Docker container
# 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
@@ -83,7 +98,7 @@ COPY --from=builder /usr/src/app/platform/app/dist/dicom-microscopy-viewer /usr/
# 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 && chmod -R 777 /usr/share/nginx/html
RUN chown -R nginx:nginx /usr/share/nginx/html
USER nginx
ENTRYPOINT ["/usr/src/entrypoint.sh"]
CMD ["nginx", "-g", "daemon off;"]
+5 -70
View File
@@ -49,12 +49,11 @@ provided by the <a href="https://ohif.org/">Open Health Imaging Foundation (OHIF
| <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) |
| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-ecg.webp?raw=true" alt="ECG" width="350"/> | ECG Waveform | [Demo](https://viewer-dev.ohif.org/viewer?StudyInstanceUIDs=2.25.209974489360710696739324151261716440238) |
## About
The OHIF Viewer can retrieve
and load images from most sources and formats, render sets in 2D, 3D, and
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.
@@ -77,7 +76,7 @@ contributions of individuals, research groups, and commercial organizations.
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 its own extension system. The same extensibility
core features are built using it's own extension system. The same extensibility
that allows us to offer:
- 2D and 3D medical image viewing
@@ -105,6 +104,7 @@ For commercial support, academic collaborations, and answers to common
questions; please use [Get Support](https://ohif.org/get-support/) to contact
us.
## Developing
### Branches
@@ -147,14 +147,7 @@ Here is a schematic representation of our development workflow:
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 --frozen-lockfile` to restore dependencies and link projects
:::danger
In general run `yarn install` with the `--frozen-lockfile` flag to help avoid
supply chain attacks by enforcing reproducible dependencies. That is, if the
`yarn.lock` file is clean and does NOT reference compromised packages, then
no compromised packages should land on your machine by using this flag.
:::
5. `yarn install` to restore dependencies and link projects
#### To Develop
@@ -165,67 +158,9 @@ _From this repository's root directory:_
yarn config set workspaces-experimental true
# Restore dependencies
yarn install --frozen-lockfile
yarn install
```
### Cornerstone3D Integration Testing
OHIF's Playwright end-to-end tests can run against a **CS3D branch** or a
**published CS3D version**, allowing changes that span both repositories to be
validated together before merging.
#### Setting up an integration build
1. Add the **`ohif-integration`** label to your OHIF pull request.
2. In the PR body, add a line specifying the CS3D ref:
```
CS3D_REF: feat/my-feature
```
- **Version ref** (e.g. `4.19+`, `4.18.2`) — the workflow resolves it to an
exact published version and swaps the CS3D dependency via npm.
- **Branch ref** (e.g. `main`, `cornerstonejs:feat/foo`) — the workflow
clones the branch, builds CS3D from source with `bun run build:esm`, and
symlinks the built packages into OHIF's `node_modules`.
- For forks, use the `<owner>:<branch>` format
(e.g. `myGithubUser:feat/foo`).
- If no `CS3D_REF` is specified, the default is `4.19+`.
3. The workflow can also be triggered manually via **workflow_dispatch** with a
`cs3d_ref` input.
#### What happens in CI
The [Playwright workflow](.github/workflows/playwright.yml) runs two jobs:
| Job | Purpose |
|-----|---------|
| **Playwright Tests** | Builds OHIF (with CS3D linked or version-swapped), runs the full Playwright suite, uploads test results and coverage, and deploys a Netlify preview when `ohif-integration` is active. |
| **CS3D Branch Merge Guard** | A lightweight check that **fails** when the `ohif-integration` label is present and `CS3D_REF` points to a branch (not a version). This prevents merging while still letting the Playwright tests show green so you can see whether the code actually works. |
#### Testing changes that span both repos
If a feature requires changes in both Cornerstone3D and OHIF:
1. Create your feature branch in CS3D and push it.
2. Create a matching branch in OHIF.
3. Add the `ohif-integration` label to the OHIF pull request.
4. In the PR body, add: `CS3D_REF: <your-cs3d-branch>`.
5. Playwright tests will build CS3D from source, link it, and run the full
suite. The merge guard will block merge until you switch to a published
version — but you can see the test results and the preview deploy while
iterating.
6. Once the CS3D side is merged and published, update the PR body to reference
the published version (e.g. `CS3D_REF: 4.19+`). The tests will run against
the registry version and the merge guard will pass.
#### Preview deploys
When `ohif-integration` is active, the Playwright workflow also builds the OHIF
viewer and deploys it to Netlify as a preview. This gives you a live URL to
manually test the combined CS3D + OHIF changes without running anything locally.
For details on linking CS3D locally for development, see the
[Cornerstone3D README](libs/@cornerstonejs/README.md#local-development-linking--unlinking).
## Commands
These commands are available from the root directory. Each project directory
+3
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@@ -0,0 +1,3 @@
# 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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+95
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@@ -0,0 +1,95 @@
{
"name": "@externals/devDependencies",
"description": "External dev dependencies - put dev build dependencies here",
"version": "3.10.4",
"license": "MIT",
"private": true,
"engines": {
"node": ">=12",
"yarn": ">=1.19.1"
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@kitware/vtk.js": "32.12.0",
"clsx": "^2.1.1",
"core-js": "^3.2.1",
"moment": "^2.30.1"
},
"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": "5.5.1",
"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": "3.6.2",
"prettier-plugin-tailwindcss": "0.6.9",
"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",
"style-loader": "^1.0.0",
"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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+9
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@@ -0,0 +1,9 @@
{
"name": "@externals/dicom-microscopy-viewer",
"description": "External reference to dicom-microscopy-viewer",
"version": "3.10.4",
"license": "MIT",
"dependencies": {
"dicom-microscopy-viewer": "^0.46.1"
}
}
+51
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@@ -0,0 +1,51 @@
{
"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"
}
}
+4 -11
View File
@@ -3,10 +3,10 @@ module.exports = {
babelrcRoots: ['./platform/*', './extensions/*', './modes/*'],
presets: ['@babel/preset-env', '@babel/preset-react', '@babel/preset-typescript'],
plugins: [
['@babel/plugin-transform-class-properties', { loose: true }],
['@babel/plugin-proposal-class-properties', { loose: true }],
'@babel/plugin-transform-typescript',
['@babel/plugin-transform-private-property-in-object', { loose: true }],
['@babel/plugin-transform-private-methods', { loose: true }],
['@babel/plugin-proposal-private-property-in-object', { loose: true }],
['@babel/plugin-proposal-private-methods', { loose: true }],
'@babel/plugin-transform-class-static-block',
],
env: {
@@ -18,26 +18,19 @@ module.exports = {
{
modules: 'commonjs',
debug: false,
targets: { node: 'current' },
bugfixes: true,
},
],
'@babel/preset-react',
'@babel/preset-typescript',
],
plugins: [
// jest's babel coverage provider injects babel-plugin-istanbul when
// --collectCoverage is set; adding it here too makes babel 7 (pulled in
// by jest 30) throw "Duplicate plugin/preset detected".
'@babel/plugin-transform-object-rest-spread',
'@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',
'@babel/plugin-transform-for-of',
['babel-plugin-transform-import-meta', { module: 'ES6' }],
],
},
production: {
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+1 -1
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@@ -1 +1 @@
6dd150d401ad73d60632a23378b7dfd4b5142690
d383be7c720ec61f5bb1262ebe70893873718951
@@ -1,8 +1,8 @@
const webpack = require('@rspack/core');
const webpack = require('webpack');
const { merge } = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const MiniCssExtractPlugin = webpack.CssExtractRspackPlugin;
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const pkg = require('./../package.json');
@@ -35,11 +35,9 @@ module.exports = (env, argv) => {
sideEffects: true,
},
output: {
library: {
name: 'ohif-extension-cornerstone-dicom-pmap',
type: 'umd',
},
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/],
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@@ -1,5 +1,5 @@
module.exports = {
plugins: ['@babel/plugin-transform-class-properties'],
plugins: ['@babel/plugin-proposal-class-properties'],
env: {
test: {
presets: [
@@ -15,7 +15,7 @@ module.exports = {
'@babel/preset-react',
],
plugins: [
'@babel/plugin-transform-object-rest-spread',
'@babel/plugin-proposal-object-rest-spread',
'@babel/plugin-syntax-dynamic-import',
'@babel/plugin-transform-regenerator',
'@babel/plugin-transform-runtime',
+32 -32
View File
@@ -1,54 +1,54 @@
{
"name": "@ohif/extension-cornerstone-dicom-pmap",
"version": "3.13.0-beta.97",
"version": "3.10.4",
"description": "DICOM Parametric Map read workflow",
"author": "OHIF",
"license": "MIT",
"repository": "OHIF/Viewers",
"main": "dist/ohif-extension-cornerstone-dicom-pmap.umd.js",
"module": "src/index.tsx",
"engines": {
"node": ">=24"
},
"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": "pnpm run clean && shx rm -rf node_modules",
"dev": "cross-env NODE_ENV=development rspack build --config .webpack/webpack.dev.js --watch",
"dev:dicom-pmap": "pnpm run dev",
"build": "cross-env NODE_ENV=production rspack build --config .webpack/webpack.prod.js",
"build:package-1": "pnpm run build",
"start": "pnpm run dev"
"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": "workspace:*",
"@ohif/extension-cornerstone": "workspace:*",
"@ohif/extension-default": "workspace:*",
"@ohif/i18n": "workspace:*",
"prop-types": "15.8.1",
"react": "18.3.1",
"react-dom": "18.3.1",
"react-i18next": "12.3.1",
"react-router": "6.30.3",
"react-router-dom": "6.30.3"
"@ohif/core": "3.10.4",
"@ohif/extension-cornerstone": "3.10.4",
"@ohif/extension-default": "3.10.4",
"@ohif/i18n": "3.10.4",
"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": "7.29.7",
"@cornerstonejs/adapters": "5.0.2",
"@cornerstonejs/core": "5.0.2",
"@kitware/vtk.js": "35.5.3"
},
"devDependencies": {
"cross-env": "7.0.3"
},
"keywords": [
"ohif-extension"
]
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^3.11.6",
"@cornerstonejs/core": "^3.11.6",
"@kitware/vtk.js": "32.12.0",
"react-color": "^2.19.3"
}
}
@@ -1,9 +1,10 @@
import { utils, Types as OhifTypes } from '@ohif/core';
import i18n from '@ohif/i18n';
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, VOLUME_LOADER_SCHEME } from '@ohif/extension-cornerstone';
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(
@@ -56,8 +57,7 @@ function _getDisplaySetsFromSeries(
wadoRoot,
wadoUriRoot,
wadoUri,
supportsWindowLevel: true,
label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('PMAP')}`,
isOverlayDisplaySet: true,
};
const referencedSeriesSequence = instance.ReferencedSeriesSequence;
@@ -227,8 +227,7 @@ async function _loadParametricMap({ displaySet, headers }: withAppTypes) {
return derivedVolume;
}
function getSopClassHandlerModule(params: OhifTypes.Extensions.ExtensionParams) {
const { servicesManager, extensionManager } = params;
function getSopClassHandlerModule({ servicesManager, extensionManager }) {
const getDisplaySetsFromSeries = instances => {
return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
};
@@ -1,10 +1,16 @@
import PropTypes from 'prop-types';
import React, { useCallback, useEffect, useRef, useState } from 'react';
import { useViewportGrid } from '@ohif/ui-next';
import { OHIFCornerstoneViewport } from '@ohif/extension-cornerstone';
function OHIFCornerstonePMAPViewport(props: withAppTypes) {
const { displaySets, children, viewportOptions, displaySetOptions, servicesManager } = props;
const {
displaySets,
children,
viewportOptions,
displaySetOptions,
servicesManager,
extensionManager,
} = props;
const viewportId = viewportOptions.viewportId;
const { displaySetService, segmentationService, uiNotificationService, customizationService } =
servicesManager.services;
@@ -53,6 +59,9 @@ function OHIFCornerstonePMAPViewport(props: withAppTypes) {
const getCornerstoneViewport = useCallback(() => {
const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
const { component: Component } = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.viewportModule.cornerstone'
);
displaySetOptions.unshift({});
const [pmapDisplaySetOptions] = displaySetOptions;
@@ -84,7 +93,7 @@ function OHIFCornerstonePMAPViewport(props: withAppTypes) {
});
return (
<OHIFCornerstoneViewport
<Component
{...props}
// Referenced + PMAP displaySets must be passed as parameter in this order
displaySets={[referencedDisplaySet, pmapDisplaySet]}
@@ -95,16 +104,15 @@ function OHIFCornerstonePMAPViewport(props: withAppTypes) {
presentationIds: viewportOptions.presentationIds,
}}
displaySetOptions={[{}, pmapDisplaySetOptions]}
/>
></Component>
);
}, [
extensionManager,
displaySetOptions,
props,
pmapDisplaySet,
viewportOptions.orientation,
viewportOptions.viewportId,
viewportOptions.presentationIds,
uiNotificationService,
]);
// Cleanup the PMAP viewport when the viewport is destroyed
@@ -1,4 +1,4 @@
const webpack = require('@rspack/core');
const webpack = require('webpack');
const { merge } = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
@@ -32,11 +32,9 @@ module.exports = (env, argv) => {
sideEffects: false,
},
output: {
library: {
name: 'ohif-extension-cornerstone-dicom-rt',
type: 'umd',
},
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/],
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@@ -1,5 +1,5 @@
module.exports = {
plugins: ['@babel/plugin-transform-class-properties'],
plugins: ['@babel/plugin-proposal-class-properties'],
env: {
test: {
presets: [
@@ -15,7 +15,7 @@ module.exports = {
'@babel/preset-react',
],
plugins: [
'@babel/plugin-transform-object-rest-spread',
'@babel/plugin-proposal-object-rest-spread',
'@babel/plugin-syntax-dynamic-import',
'@babel/plugin-transform-regenerator',
'@babel/plugin-transform-runtime',
+33 -33
View File
@@ -1,15 +1,11 @@
{
"name": "@ohif/extension-cornerstone-dicom-rt",
"version": "3.13.0-beta.97",
"version": "3.10.4",
"description": "DICOM RT read workflow",
"author": "OHIF",
"license": "MIT",
"repository": "OHIF/Viewers",
"main": "dist/ohif-extension-cornerstone-dicom-rt.umd.js",
"module": "src/index.tsx",
"engines": {
"node": ">=24"
},
"files": [
"dist/**",
"public/**",
@@ -18,34 +14,38 @@
"publishConfig": {
"access": "public"
},
"scripts": {
"clean": "shx rm -rf dist",
"clean:deep": "pnpm run clean && shx rm -rf node_modules",
"dev": "cross-env NODE_ENV=development rspack build --config .webpack/webpack.dev.js --watch",
"dev:dicom-seg": "pnpm run dev",
"build": "cross-env NODE_ENV=production rspack build --config .webpack/webpack.prod.js",
"build:package-1": "pnpm run build",
"start": "pnpm run dev"
},
"peerDependencies": {
"@ohif/core": "workspace:*",
"@ohif/extension-cornerstone": "workspace:*",
"@ohif/extension-default": "workspace:*",
"@ohif/i18n": "workspace:*",
"prop-types": "15.8.1",
"react": "18.3.1",
"react-dom": "18.3.1",
"react-i18next": "12.3.1",
"react-router": "6.30.3",
"react-router-dom": "6.30.3"
},
"dependencies": {
"@babel/runtime": "7.29.7"
},
"devDependencies": {
"cross-env": "7.0.3"
},
"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": "3.10.4",
"@ohif/extension-cornerstone": "3.10.4",
"@ohif/extension-default": "3.10.4",
"@ohif/i18n": "3.10.4",
"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"
}
}
@@ -27,7 +27,7 @@ const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
// it will be in the correct position zoom and pan
commandsManager.runCommand('updateStoredPositionPresentation', {
viewportId,
displaySetInstanceUIDs: [referencedDisplaySet.displaySetInstanceUID],
displaySetInstanceUID: referencedDisplaySet.displaySetInstanceUID,
});
viewportGridService.setDisplaySetsForViewport({
@@ -1,13 +1,9 @@
import { utils, Types as OhifTypes } from '@ohif/core';
import i18n from '@ohif/i18n';
import { segmentation as cstSegmentation } from '@cornerstonejs/tools';
import { utils } from '@ohif/core';
import { SOPClassHandlerId } from './id';
import loadRTStruct from './loadRTStruct';
const { sopClassDictionary } = utils;
const sopClassUids = [sopClassDictionary.RTStructureSetStorage];
const sopClassUids = ['1.2.840.10008.5.1.4.1.1.481.3'];
const loadPromises = {};
@@ -16,47 +12,34 @@ function _getDisplaySetsFromSeries(
servicesManager: AppTypes.ServicesManager,
extensionManager
) {
utils.sortStudyInstances(instances);
// Choose the LAST instance in the list as the most recently created one.
const instance = instances[instances.length - 1];
const instance = instances[0];
const {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
SeriesDescription = '',
SeriesDescription,
SeriesNumber,
SeriesDate,
SeriesTime,
StructureSetDate,
StructureSetTime,
SOPClassUID,
wadoRoot,
wadoUri,
wadoUriRoot,
imageId: predecessorImageId,
} = instance;
const displaySet = {
Modality: 'RTSTRUCT',
loading: false,
isReconstructable: false,
isReconstructable: false, // by default for now since it is a volumetric SEG currently
displaySetInstanceUID: utils.guid(),
SeriesDescription,
SeriesNumber,
/**
* The "SeriesDate" for a display set is really the display set date, which
* should be the date of the instance being used, which will be the structure
* set date in this case.
*/
SeriesDate: StructureSetDate || SeriesDate,
SeriesTime: StructureSetTime || SeriesTime,
SeriesDate,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
SOPClassHandlerId,
SOPClassUID,
FrameOfReferenceUID: null,
referencedImages: null,
referencedSeriesInstanceUID: null,
referencedDisplaySetInstanceUID: null,
@@ -66,20 +49,14 @@ function _getDisplaySetsFromSeries(
structureSet: null,
sopClassUids,
instance,
instances,
predecessorImageId,
wadoRoot,
wadoUriRoot,
wadoUri,
isOverlayDisplaySet: true,
label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('RTSTRUCT')}`,
};
let referencedSeriesSequence = instance.ReferencedSeriesSequence;
if (
instance.ReferencedFrameOfReferenceSequence?.RTReferencedStudySequence &&
!instance.ReferencedSeriesSequence
) {
if (instance.ReferencedFrameOfReferenceSequence && !instance.ReferencedSeriesSequence) {
instance.ReferencedSeriesSequence = _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
instance.ReferencedFrameOfReferenceSequence
);
@@ -87,8 +64,7 @@ function _getDisplaySetsFromSeries(
}
if (!referencedSeriesSequence) {
console.error('ReferencedSeriesSequence is missing for the RTSTRUCT');
return;
throw new Error('ReferencedSeriesSequence is missing for the RTSTRUCT');
}
const referencedSeries = referencedSeriesSequence[0];
@@ -96,17 +72,10 @@ function _getDisplaySetsFromSeries(
displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
displaySet.FrameOfReferenceUID =
instance.ReferencedFrameOfReferenceSequence?.[0]?.FrameOfReferenceUID;
const { displaySetService } = servicesManager.services;
const referencedDisplaySets =
displaySetService.getDisplaySetsForReferences(referencedSeriesSequence);
if (referencedDisplaySets?.length > 1) {
console.warn(
'Reference applies to more than 1 display set for Contours, applying only to first display set'
);
}
const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
displaySet.referencedSeriesInstanceUID
);
if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
// Instead of throwing error, subscribe to display sets added
@@ -116,39 +85,27 @@ function _getDisplaySetsFromSeries(
const addedDisplaySet = displaySetsAdded[0];
if (addedDisplaySet.SeriesInstanceUID === displaySet.referencedSeriesInstanceUID) {
displaySet.referencedDisplaySetInstanceUID = addedDisplaySet.displaySetInstanceUID;
displaySet.isReconstructable = addedDisplaySet.isReconstructable;
displaySet.FrameOfReferenceUID = addedDisplaySet.FrameOfReferenceUID;
unsubscribe();
}
}
);
} else {
const [referencedDisplaySet] = referencedDisplaySets;
const referencedDisplaySet = referencedDisplaySets[0];
displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
displaySet.isReconstructable = referencedDisplaySet.isReconstructable;
displaySet.FrameOfReferenceUID = referencedDisplaySet.FrameOfReferenceUID;
}
displaySet.load = ({ headers, createSegmentation = true }) =>
_load(displaySet, servicesManager, extensionManager, headers, createSegmentation);
displaySet.load = ({ headers }) => _load(displaySet, servicesManager, extensionManager, headers);
return [displaySet];
}
function _load(
rtDisplaySet,
servicesManager: AppTypes.ServicesManager,
extensionManager,
headers,
createSegmentation = true
) {
function _load(rtDisplaySet, servicesManager: AppTypes.ServicesManager, extensionManager, headers) {
const { SOPInstanceUID } = rtDisplaySet;
const { segmentationService } = servicesManager.services;
if (
(rtDisplaySet.loading || rtDisplaySet.isLoaded) &&
loadPromises[SOPInstanceUID] &&
_segmentationExists(rtDisplaySet)
_segmentationExistsInCache(rtDisplaySet, segmentationService)
) {
return loadPromises[SOPInstanceUID];
}
@@ -157,23 +114,23 @@ function _load(
// 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<void>(async (resolve, reject) => {
try {
if (!rtDisplaySet.structureSet) {
const structureSet = await loadRTStruct(extensionManager, rtDisplaySet, headers);
rtDisplaySet.structureSet = structureSet;
}
loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => {
if (!rtDisplaySet.structureSet) {
const structureSet = await loadRTStruct(extensionManager, rtDisplaySet, headers);
if (createSegmentation) {
await segmentationService.createSegmentationForRTDisplaySet(rtDisplaySet);
}
resolve();
} catch (error) {
reject(error);
} finally {
rtDisplaySet.loading = false;
rtDisplaySet.structureSet = structureSet;
}
segmentationService
.createSegmentationForRTDisplaySet(rtDisplaySet)
.then(() => {
rtDisplaySet.loading = false;
resolve();
})
.catch(error => {
rtDisplaySet.loading = false;
reject(error);
});
});
return loadPromises[SOPInstanceUID];
@@ -214,13 +171,20 @@ function _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
return ReferencedSeriesSequence;
}
function _segmentationExists(segDisplaySet) {
return !!cstSegmentation.state.getSegmentation(segDisplaySet.displaySetInstanceUID);
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(params: OhifTypes.Extensions.ExtensionParams) {
const { servicesManager, extensionManager } = params;
function getSopClassHandlerModule({ servicesManager, extensionManager }) {
return [
{
name: 'dicom-rt',
@@ -2,34 +2,9 @@ import dcmjs from 'dcmjs';
const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
const dicomlab2RGB = dcmjs.data.Colors.dicomlab2RGB;
/**
* Checks and loads contour data for RT Structure Set, handling both inline and bulk data URIs.
* Processes ROIContourSequence to extract contour data and resolve any bulk data references.
*
* @async
* @function checkAndLoadContourData
* @param {Object} params - Parameters object
* @param {Object} params.instance - Initial RT Structure instance
* @param {Object} params.dataSource - Data source for retrieving bulk data
* @param {Object} params.extensionManager - OHIF extension manager
* @param {Object} params.rtStructDisplaySet - RT Structure display set
* @param {Object} params.headers - HTTP headers for requests
* @returns {Promise<Object>} Promise that resolves to the processed RT Structure instance with loaded contour data
* @throws {Promise<string>} Rejects with error message if instance is invalid or data retrieval fails
*/
async function checkAndLoadContourData({
instance: initialInstance,
dataSource,
extensionManager,
rtStructDisplaySet,
headers,
}) {
let instance = initialInstance;
async function checkAndLoadContourData(instance, datasource) {
if (!instance || !instance.ROIContourSequence) {
instance = await getRTStructInstance({ extensionManager, rtStructDisplaySet, headers });
if (!instance || !instance.ROIContourSequence) {
return Promise.reject('Invalid instance object or ROIContourSequence');
}
return Promise.reject('Invalid instance object or ROIContourSequence');
}
const promisesMap = new Map();
@@ -55,11 +30,11 @@ async function checkAndLoadContourData({
} 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');
if (!datasource || !datasource.retrieve || !datasource.retrieve.bulkDataURI) {
return Promise.reject('Invalid datasource object or retrieve function');
}
const bulkDataPromise = dataSource.retrieve.bulkDataURI({
const bulkDataPromise = datasource.retrieve.bulkDataURI({
BulkDataURI: bulkDataURI,
StudyInstanceUID: instance.StudyInstanceUID,
SeriesInstanceUID: instance.SeriesInstanceUID,
@@ -69,40 +44,6 @@ async function checkAndLoadContourData({
promisesMap.has(referencedROINumber)
? promisesMap.get(referencedROINumber).push(bulkDataPromise)
: promisesMap.set(referencedROINumber, [bulkDataPromise]);
} else if (contourData && contourData.InlineBinary) {
// Contour data is still in binary format, conversion needed
const base64String = contourData.InlineBinary;
const decodedText = atob(base64String);
const rawValues = decodedText.split('\\');
const result = [];
// Ensure strictly that we have a full set of 3 coordinates
if (rawValues.length % 3 !== 0) {
return Promise.reject('ContourData raw values not divisible by 3');
}
for (let i = 0; i < rawValues.length; i += 3) {
if (i + 2 < rawValues.length) {
const x = parseFloat(rawValues[i]);
const y = parseFloat(rawValues[i + 1]);
const z = parseFloat(rawValues[i + 2]);
// Only push if all three are valid numbers (filters out trailing empty splits)
if (!isNaN(x) && !isNaN(y) && !isNaN(z)) {
result.push(x);
result.push(y);
result.push(z);
} else {
return Promise.reject('Error parsing contourData from InlineBinary format');
}
}
}
promisesMap.has(referencedROINumber)
? promisesMap.get(referencedROINumber).push(result)
: promisesMap.set(referencedROINumber, [result]);
} else {
return Promise.reject(`Invalid ContourData: ${contourData}`);
}
@@ -123,12 +64,9 @@ async function checkAndLoadContourData({
ROIContour.ContourSequence.forEach((Contour, index) => {
const promise = resolvedPromises[index];
if (promise.status === 'fulfilled') {
if (
Array.isArray(promise.value) &&
promise.value.every(it => Number.isFinite(Number(it)))
) {
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.map(Number);
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);
@@ -149,74 +87,35 @@ async function checkAndLoadContourData({
console.error(error);
}
});
return instance;
}
/**
* Retrieves and parses RT Structure Set instance from DICOM data.
* Uses the cornerstone utility module to load DICOM data and converts it to a naturalized dataset.
*
* @async
* @function getRTStructInstance
* @param {Object} params - Parameters object
* @param {Object} params.extensionManager - OHIF extension manager
* @param {Object} params.rtStructDisplaySet - RT Structure display set
* @param {Object} params.headers - HTTP headers for requests
* @returns {Promise<Object>} Promise that resolves to the parsed RT Structure dataset
*/
const getRTStructInstance = async ({ extensionManager, rtStructDisplaySet, headers }) => {
export default async function loadRTStruct(extensionManager, rtStructDisplaySet, headers) {
const utilityModule = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.utilityModule.common'
);
const { dicomLoaderService } = utilityModule.exports;
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);
return rtStructDataset;
};
/**
* Main function to load and process RT Structure Set data.
* Creates a structure set object with ROI contours, metadata, and visualization properties.
* Handles both bulk data URI and inline contour data scenarios.
*
* @async
* @function loadRTStruct
* @param {Object} extensionManager - OHIF extension manager
* @param {Object} rtStructDisplaySet - RT Structure display set to process
* @param {Object} headers - HTTP headers for data requests
* @returns {Promise<Object>} Promise that resolves to a structure set object containing:
* - StructureSetLabel: Label of the structure set
* - SeriesInstanceUID: Series instance UID
* - ROIContours: Array of ROI contour data with points and metadata
* - visible: Visibility state
* - ReferencedSOPInstanceUIDsSet: Set of referenced SOP instance UIDs
*/
export default async function loadRTStruct(extensionManager, rtStructDisplaySet, headers) {
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) {
instance = await getRTStructInstance({ extensionManager, rtStructDisplaySet, headers });
} else {
instance = await checkAndLoadContourData({
instance,
dataSource,
extensionManager,
const segArrayBuffer = await dicomLoaderService.findDicomDataPromise(
rtStructDisplaySet,
headers,
});
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;
@@ -233,16 +132,21 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
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 (const ContourSequenceItem of ContourSequenceArray) {
for (let c = 0; c < ContourSequenceArray.length; c++) {
const { ContourData, NumberOfContourPoints, ContourGeometricType, ContourImageSequence } =
ContourSequenceItem;
ContourSequenceArray[c];
let isSupported = false;
const points = [];
for (let p = 0; p < NumberOfContourPoints * 3; p += 3) {
@@ -253,18 +157,22 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
});
}
const supportedContourTypesMap = new Map([
['CLOSED_PLANAR', false],
['OPEN_NONPLANAR', false],
['OPEN_PLANAR', false],
['POINT', true],
]);
switch (ContourGeometricType) {
case 'CLOSED_PLANAR':
case 'OPEN_PLANAR':
case 'POINT':
isSupported = true;
break;
default:
continue;
}
contourPoints.push({
numberOfPoints: NumberOfContourPoints,
points,
type: ContourGeometricType,
isSupported: supportedContourTypesMap.get(ContourGeometricType) ?? false,
isSupported,
});
if (ContourImageSequence?.ReferencedSOPInstanceUID) {
@@ -279,30 +187,20 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
StructureSetROISequence,
RTROIObservationsSequence,
ROIContour,
contourPoints
contourPoints,
isSupported
);
}
return structureSet;
}
/**
* Sets metadata for ROI contour data and adds it to the structure set.
* Extracts ROI information from StructureSetROISequence and RTROIObservationsSequence,
* then creates a complete ROI contour data object with visualization properties.
*
* @function _setROIContourMetadata
* @param {Object} structureSet - The structure set object to add ROI contour to
* @param {Array} StructureSetROISequence - Array of structure set ROI definitions
* @param {Array} RTROIObservationsSequence - Array of RT ROI observations
* @param {Object} ROIContour - ROI contour object containing contour data
* @param {Array} contourPoints - Array of processed contour points
*/
function _setROIContourMetadata(
structureSet,
StructureSetROISequence,
RTROIObservationsSequence,
ROIContour,
contourPoints
contourPoints,
isSupported
) {
const StructureSetROI = StructureSetROISequence.find(
structureSetROI => structureSetROI.ROINumber === ROIContour.ReferencedROINumber
@@ -313,9 +211,9 @@ function _setROIContourMetadata(
ROIName: StructureSetROI.ROIName,
ROIGenerationAlgorithm: StructureSetROI.ROIGenerationAlgorithm,
ROIDescription: StructureSetROI.ROIDescription,
isSupported,
contourPoints,
visible: true,
colorArray: [],
};
_setROIContourDataColor(ROIContour, ROIContourData);
@@ -332,14 +230,6 @@ function _setROIContourMetadata(
structureSet.ROIContours.push(ROIContourData);
}
/**
* Sets the display color for ROI contour data.
* Uses ROIDisplayColor if available, otherwise converts RecommendedDisplayCIELabValue to RGB.
*
* @function _setROIContourDataColor
* @param {Object} ROIContour - ROI contour object containing color information
* @param {Object} ROIContourData - ROI contour data object to set color on
*/
function _setROIContourDataColor(ROIContour, ROIContourData) {
let { ROIDisplayColor, RecommendedDisplayCIELabValue } = ROIContour;
@@ -353,15 +243,6 @@ function _setROIContourDataColor(ROIContour, ROIContourData) {
}
}
/**
* Sets RT ROI observations metadata for ROI contour data.
* Finds matching RTROIObservations by ROINumber and adds observation details to contour data.
*
* @function _setROIContourRTROIObservations
* @param {Object} ROIContourData - ROI contour data object to add observations to
* @param {Array} RTROIObservationsSequence - Array of RT ROI observations
* @param {number} ROINumber - ROI number to match observations
*/
function _setROIContourRTROIObservations(ROIContourData, RTROIObservationsSequence, ROINumber) {
const RTROIObservations = RTROIObservationsSequence.find(
RTROIObservations => RTROIObservations.ReferencedROINumber === ROINumber
@@ -381,14 +262,6 @@ function _setROIContourRTROIObservations(ROIContourData, RTROIObservationsSequen
}
}
/**
* Converts a single object or array to an array.
* Utility function to ensure consistent array handling for DICOM sequences.
*
* @function _toArray
* @param {*} objOrArray - Object or array to convert
* @returns {Array} Array containing the input (if already array) or wrapped in array
*/
function _toArray(objOrArray) {
return Array.isArray(objOrArray) ? objOrArray : [objOrArray];
}
@@ -1,4 +1,8 @@
import { utils, Types } from '@ohif/extension-cornerstone';
const RESPONSE = {
NO_NEVER: -1,
CANCEL: 0,
HYDRATE_SEG: 5,
};
function promptHydrateRT({
servicesManager,
@@ -6,20 +10,74 @@ function promptHydrateRT({
viewportId,
preHydrateCallbacks,
hydrateRTDisplaySet,
}: {
servicesManager: AppTypes.ServicesManager;
rtDisplaySet: AppTypes.DisplaySet;
viewportId: string;
preHydrateCallbacks?: Types.HydrationCallback[];
hydrateRTDisplaySet: Types.HydrationCallback;
}) {
return utils.promptHydrationDialog({
servicesManager,
viewportId,
displaySet: rtDisplaySet,
preHydrateCallbacks,
hydrateCallback: hydrateRTDisplaySet,
type: 'RTSTRUCT',
}: withAppTypes) {
const { uiViewportDialogService, customizationService } = 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, customizationService, viewportId);
if (promptResult === RESPONSE.HYDRATE_SEG) {
preHydrateCallbacks?.forEach(callback => {
callback();
});
const isHydrated = await hydrateRTDisplaySet({
rtDisplaySet,
viewportId,
servicesManager,
});
resolve(isHydrated);
}
});
}
function _askHydrate(
uiViewportDialogService: AppTypes.UIViewportDialogService,
customizationService: AppTypes.CustomizationService,
viewportId
) {
return new Promise(function (resolve, reject) {
const message = customizationService.getCustomization('viewportNotification.hydrateRTMessage');
const actions = [
{
id: 'no-hydrate',
type: 'secondary',
text: 'No',
value: RESPONSE.CANCEL,
},
{
id: 'yes-hydrate',
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);
}
},
});
});
}
@@ -1,27 +1,35 @@
import React, { Component, useCallback, useEffect, useRef, useState } from 'react';
import React, { useCallback, useEffect, useRef, useState } from 'react';
import PropTypes from 'prop-types';
import { ViewportActionArrows } from '@ohif/ui-next';
import { useViewportGrid } from '@ohif/ui-next';
import {
utils,
usePositionPresentationStore,
OHIFCornerstoneViewport,
} from '@ohif/extension-cornerstone';
import { utils } from '@ohif/extension-cornerstone';
import promptHydrateRT from '../utils/promptHydrateRT';
import _getStatusComponent from './_getStatusComponent';
import createRTToolGroupAndAddTools from '../utils/initRTToolGroup';
import { useSystem } from '@ohif/core/src';
import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
const RT_TOOLGROUP_BASE_NAME = 'RTToolGroup';
function OHIFCornerstoneRTViewport(props: withAppTypes) {
const { servicesManager, commandsManager } = useSystem();
const { children, displaySets, viewportOptions } = props as {
children: React.ReactNode;
displaySets: AppTypes.DisplaySet[];
viewportOptions: AppTypes.ViewportOptions;
};
const {
children,
displaySets,
viewportOptions,
servicesManager,
extensionManager,
commandsManager,
} = props;
const { displaySetService, toolGroupService, segmentationService, customizationService } =
servicesManager.services;
const {
displaySetService,
toolGroupService,
segmentationService,
uiNotificationService,
customizationService,
viewportActionCornersService,
} = servicesManager.services;
const viewportId = viewportOptions.viewportId;
@@ -38,34 +46,31 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
const rtDisplaySet = displaySets[0];
const [{ viewports, activeViewportId }, viewportGridService] = useViewportGrid();
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;
// If the referencedDisplaySetInstanceUID is not found, it means the RTStruct series is being
// launched without its corresponding referenced display set (e.g., the RTStruct series is launched using
// series launch /mode?StudyInstanceUIDs=&SeriesInstanceUID).
// In such cases, we attempt to handle this scenario gracefully by
// invoking a custom handler. Ideally, if a user tries to launch a series that isn't viewable,
// (eg.: we can prompt them with an explanation and provide a link to the full study).
if (!referencedDisplaySetInstanceUID) {
const missingReferenceDisplaySetHandler = customizationService.getCustomization(
'missingReferenceDisplaySetHandler'
);
const { handled } = missingReferenceDisplaySetHandler();
if (handled) {
return;
}
}
const referencedDisplaySet = displaySetService.getDisplaySetByUID(
referencedDisplaySetInstanceUID
);
@@ -75,35 +80,104 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
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;
}
// if not active viewport, return
if (viewportId !== activeViewportId) {
return;
}
promptHydrateRT({
servicesManager,
viewportId,
rtDisplaySet,
hydrateRTDisplaySet: async () => {
return commandsManager.runCommand('hydrateSecondaryDisplaySet', {
displaySet: rtDisplaySet,
viewportId,
});
},
preHydrateCallbacks: [storePresentationState],
hydrateRTDisplaySet,
}).then(isHydrated => {
if (isHydrated) {
setIsHydrated(true);
}
});
}, [servicesManager, viewportId, rtDisplaySet, rtIsLoading, commandsManager, activeViewportId]);
}, [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) {
if (evt.rtDisplaySet.displaySetInstanceUID === rtDisplaySet.displaySetInstanceUID) {
setRtIsLoading(false);
}
@@ -119,6 +193,14 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
viewPresentation: {},
});
}
if (evt.overlappingSegments) {
uiNotificationService.show({
title: 'Overlapping Segments',
message: 'Overlapping segments detected which is not currently supported',
type: 'warning',
});
}
}
);
@@ -128,7 +210,7 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
}, [rtDisplaySet]);
useEffect(() => {
const segmentLoadingSubscription = segmentationService.subscribe(
const { unsubscribe } = segmentationService.subscribe(
segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE,
({ percentComplete, numSegments }) => {
setProcessingProgress({
@@ -138,7 +220,16 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
}
);
const displaySetsRemovedSubscription = displaySetService.subscribe(
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);
@@ -152,10 +243,9 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
);
return () => {
segmentLoadingSubscription.unsubscribe();
displaySetsRemovedSubscription.unsubscribe();
onDisplaySetsRemovedSubscription.unsubscribe();
};
}, [rtDisplaySet, displaySetService, viewports, activeViewportId, viewportGridService]);
}, []);
useEffect(() => {
let toolGroup = toolGroupService.getToolGroup(toolGroupId);
@@ -168,34 +258,39 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
return () => {
// remove the segmentation representations if seg displayset changed
segmentationService.removeRepresentationsFromViewport(viewportId);
referencedDisplaySetRef.current = null;
segmentationService.removeSegmentationRepresentations(viewportId);
toolGroupService.destroyToolGroup(toolGroupId);
};
}, []);
const getCornerstoneViewport = useCallback(() => {
const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
useEffect(() => {
setIsHydrated(rtDisplaySet.isHydrated);
// Todo: jump to the center of the first segment
return (
<OHIFCornerstoneViewport
{...props}
displaySets={[referencedDisplaySet, rtDisplaySet]}
viewportOptions={{
viewportType: viewportOptions.viewportType,
toolGroupId: toolGroupId,
orientation: viewportOptions.orientation,
viewportId: viewportOptions.viewportId,
presentationIds: viewportOptions.presentationIds,
}}
onElementEnabled={evt => {
props.onElementEnabled?.(evt);
}}
/>
);
}, [viewportId, rtDisplaySet, toolGroupId]);
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 (
@@ -218,6 +313,43 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
});
}
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">
@@ -0,0 +1,59 @@
import React from 'react';
import { useTranslation } from 'react-i18next';
import { ViewportActionButton } from '@ohif/ui-next';
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-muted-foreground h-4 w-4"
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 />}
</>
);
}
@@ -1,8 +1,8 @@
const webpack = require('@rspack/core');
const webpack = require('webpack');
const { merge } = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const MiniCssExtractPlugin = webpack.CssExtractRspackPlugin;
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const pkg = require('./../package.json');
@@ -35,11 +35,9 @@ module.exports = (env, argv) => {
sideEffects: true,
},
output: {
library: {
name: 'ohif-extension-cornerstone-dicom-seg',
type: 'umd',
},
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/],
File diff suppressed because it is too large. Load diff
@@ -1,5 +1,5 @@
module.exports = {
plugins: ['@babel/plugin-transform-class-properties'],
plugins: ['@babel/plugin-proposal-class-properties'],
env: {
test: {
presets: [
@@ -15,7 +15,7 @@ module.exports = {
'@babel/preset-react',
],
plugins: [
'@babel/plugin-transform-object-rest-spread',
'@babel/plugin-proposal-object-rest-spread',
'@babel/plugin-syntax-dynamic-import',
'@babel/plugin-transform-regenerator',
'@babel/plugin-transform-runtime',
+32 -32
View File
@@ -1,54 +1,54 @@
{
"name": "@ohif/extension-cornerstone-dicom-seg",
"version": "3.13.0-beta.97",
"version": "3.10.4",
"description": "DICOM SEG read workflow",
"author": "OHIF",
"license": "MIT",
"repository": "OHIF/Viewers",
"main": "dist/ohif-extension-cornerstone-dicom-seg.umd.js",
"module": "src/index.tsx",
"engines": {
"node": ">=24"
},
"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": "pnpm run clean && shx rm -rf node_modules",
"dev": "cross-env NODE_ENV=development rspack build --config .webpack/webpack.dev.js --watch",
"dev:dicom-seg": "pnpm run dev",
"build": "cross-env NODE_ENV=production rspack build --config .webpack/webpack.prod.js",
"build:package-1": "pnpm run build",
"start": "pnpm run dev"
"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": "workspace:*",
"@ohif/extension-cornerstone": "workspace:*",
"@ohif/extension-default": "workspace:*",
"@ohif/i18n": "workspace:*",
"prop-types": "15.8.1",
"react": "18.3.1",
"react-dom": "18.3.1",
"react-i18next": "12.3.1",
"react-router": "6.30.3",
"react-router-dom": "6.30.3"
"@ohif/core": "3.10.4",
"@ohif/extension-cornerstone": "3.10.4",
"@ohif/extension-default": "3.10.4",
"@ohif/i18n": "3.10.4",
"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": "7.29.7",
"@cornerstonejs/adapters": "5.0.2",
"@cornerstonejs/core": "5.0.2",
"@kitware/vtk.js": "35.5.3"
},
"devDependencies": {
"cross-env": "7.0.3"
},
"keywords": [
"ohif-extension"
]
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^3.11.6",
"@cornerstonejs/core": "^3.11.6",
"@kitware/vtk.js": "32.12.0",
"react-color": "^2.19.3"
}
}
@@ -1,12 +1,15 @@
import dcmjs from 'dcmjs';
import { classes, Types, utils } from '@ohif/core';
import { classes, Types } from '@ohif/core';
import { cache, metaData } from '@cornerstonejs/core';
import { segmentation as cornerstoneToolsSegmentation } from '@cornerstonejs/tools';
import { adaptersRT, adaptersSEG } from '@cornerstonejs/adapters';
import { createReportDialogPrompt, useUIStateStore } from '@ohif/extension-default';
import { adaptersRT, helpers, adaptersSEG } from '@cornerstonejs/adapters';
import { createReportDialogPrompt } from '@ohif/extension-default';
import { DicomMetadataStore } from '@ohif/core';
import PROMPT_RESPONSES from '../../default/src/utils/_shared/PROMPT_RESPONSES';
const { datasetToBlob } = dcmjs.data;
const getTargetViewport = ({ viewportId, viewportGridService }) => {
const { viewports, activeViewportId } = viewportGridService.getState();
const targetViewportId = viewportId || activeViewportId;
@@ -24,17 +27,17 @@ const {
const {
Cornerstone3D: {
RTSS: { generateRTSSFromRepresentation },
RTSS: { generateRTSSFromSegmentations },
},
} = adaptersRT;
const { downloadDICOMData } = helpers;
const commandsModule = ({
servicesManager,
extensionManager,
commandsManager,
}: Types.Extensions.ExtensionParams): Types.Extensions.CommandsModule => {
const { segmentationService, displaySetService, viewportGridService } =
const { segmentationService, displaySetService, viewportGridService, toolGroupService } =
servicesManager.services as AppTypes.Services;
const actions = {
@@ -89,7 +92,6 @@ const commandsModule = ({
*/
generateSegmentation: ({ segmentationId, options = {} }) => {
const segmentation = cornerstoneToolsSegmentation.state.getSegmentation(segmentationId);
const predecessorImageId = options.predecessorImageId ?? segmentation.predecessorImageId;
const { imageIds } = segmentation.representationData.Labelmap;
@@ -171,10 +173,12 @@ const commandsModule = ({
labelmap3D.metadata[segmentIndex] = segmentMetadata;
});
const generatedSegmentation = generateSegmentation(referencedImages, labelmap3D, metaData, {
predecessorImageId,
...options,
});
const generatedSegmentation = generateSegmentation(
referencedImages,
labelmap3D,
metaData,
options
);
return generatedSegmentation;
},
@@ -193,11 +197,8 @@ const commandsModule = ({
const generatedSegmentation = actions.generateSegmentation({
segmentationId,
});
const storeFn = commandsManager.runCommand('createStoreFunction', {
dataSource: 'download',
defaultFileName: `${segmentationInOHIF.label}.dcm`,
});
storeFn(generatedSegmentation.dataset);
downloadDICOMData(generatedSegmentation.dataset, `${segmentationInOHIF.label}`);
},
/**
* Stores a segmentation based on the provided segmentationId into a specified data source.
@@ -211,84 +212,67 @@ const commandsModule = ({
* @returns {Object|void} Returns the naturalized report if successfully stored,
* otherwise throws an error.
*/
storeSegmentation: async ({ segmentationId, dataSource, modality = 'SEG' }) => {
storeSegmentation: async ({ segmentationId, dataSource }) => {
const segmentation = segmentationService.getSegmentation(segmentationId);
if (!segmentation) {
throw new Error('No segmentation found');
}
const { label, predecessorImageId } = segmentation;
const { label } = segmentation;
const defaultDataSource = dataSource ?? extensionManager.getActiveDataSource();
const {
value: reportName,
dataSourceName,
series,
priorSeriesNumber,
dataSourceName: selectedDataSource,
action,
} = await createReportDialogPrompt({
servicesManager,
extensionManager,
predecessorImageId,
title: 'Store Segmentation',
modality,
enableDownload: true,
});
if (action !== PROMPT_RESPONSES.CREATE_REPORT) {
return;
}
if (action === PROMPT_RESPONSES.CREATE_REPORT) {
try {
const selectedDataSourceConfig = selectedDataSource
? extensionManager.getDataSources(selectedDataSource)[0]
: defaultDataSource;
const defaultFileName =
modality === 'RTSTRUCT'
? `rtss-${segmentationId}.dcm`
: `${label || 'segmentation'}.dcm`;
const generatedData = actions.generateSegmentation({
segmentationId,
options: {
SeriesDescription: reportName || label || 'Research Derived Series',
},
});
const storeFn = commandsManager.runCommand('createStoreFunction', {
dataSource: dataSourceName,
defaultFileName,
});
if (!generatedData || !generatedData.dataset) {
throw new Error('Error during segmentation generation');
}
if (!storeFn) {
throw new Error(`No valid store for dataSource: ${dataSourceName}`);
}
const { dataset: naturalizedReport } = generatedData;
try {
const args = {
segmentationId,
options: {
SeriesDescription: series ? undefined : reportName || label || 'Contour Series',
SeriesNumber: series ? undefined : 1 + priorSeriesNumber,
predecessorImageId: series,
},
};
const generatedDataAsync =
(modality === 'SEG' && actions.generateSegmentation(args)) ||
(modality === 'RTSTRUCT' && actions.generateContour(args));
const generatedData = await generatedDataAsync;
await selectedDataSourceConfig.store.dicom(naturalizedReport);
if (!generatedData?.dataset) {
throw new Error('Error during segmentation generation');
// add the information for where we stored it to the instance as well
naturalizedReport.wadoRoot = selectedDataSourceConfig.getConfig().wadoRoot;
DicomMetadataStore.addInstances([naturalizedReport], true);
return naturalizedReport;
} catch (error) {
console.debug('Error storing segmentation:', error);
throw error;
}
const { dataset: naturalizedReport } = generatedData;
// DCMJS assigns a dummy study id during creation, and this can cause problems, so clearing it out
if (naturalizedReport.StudyID === 'No Study ID') {
naturalizedReport.StudyID = '';
}
await storeFn(naturalizedReport, {});
return naturalizedReport;
} catch (error) {
console.debug('Error storing segmentation:', error);
throw error;
}
},
generateContour: async args => {
const { segmentationId, options } = args;
/**
* 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: async ({ segmentationId }) => {
const segmentations = segmentationService.getSegmentation(segmentationId);
// inject colors to the segmentIndex
@@ -298,51 +282,45 @@ const commandsModule = ({
segment.color = segmentationService.getSegmentColor(
firstRepresentation.viewportId,
segmentationId,
Number(segmentIndex)
segmentIndex
);
});
const predecessorImageId = options?.predecessorImageId ?? segmentations.predecessorImageId;
const dataset = await generateRTSSFromRepresentation(segmentations, {
predecessorImageId,
...options,
});
return { dataset };
},
/**
* Downloads an RTSS instance from a segmentation or contour
* representation.
*/
downloadRTSS: async args => {
const { dataset } = await actions.generateContour(args);
const { InstanceNumber: instanceNumber = 1, SeriesInstanceUID: seriesUID } = dataset;
const storeFn = commandsManager.runCommand('createStoreFunction', {
dataSource: 'download',
defaultFileName: `rtss-${seriesUID}-${instanceNumber}.dcm`,
});
await storeFn(dataset);
},
const RTSS = await generateRTSSFromSegmentations(
segmentations,
classes.MetadataProvider,
DicomMetadataStore
);
toggleActiveSegmentationUtility: ({ itemId: buttonId }) => {
const { uiState, setUIState } = useUIStateStore.getState();
const isButtonActive = uiState['activeSegmentationUtility'] === buttonId;
console.log('toggleActiveSegmentationUtility', isButtonActive, buttonId);
// if the button is active, clear the active segmentation utility
if (isButtonActive) {
setUIState('activeSegmentationUtility', null);
} else {
setUIState('activeSegmentationUtility', buttonId);
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);
}
},
};
const definitions = {
loadSegmentationsForViewport: actions.loadSegmentationsForViewport,
generateSegmentation: actions.generateSegmentation,
downloadSegmentation: actions.downloadSegmentation,
storeSegmentation: actions.storeSegmentation,
downloadRTSS: actions.downloadRTSS,
toggleActiveSegmentationUtility: actions.toggleActiveSegmentationUtility,
loadSegmentationsForViewport: {
commandFn: actions.loadSegmentationsForViewport,
},
generateSegmentation: {
commandFn: actions.generateSegmentation,
},
downloadSegmentation: {
commandFn: actions.downloadSegmentation,
},
storeSegmentation: {
commandFn: actions.storeSegmentation,
},
downloadRTSS: {
commandFn: actions.downloadRTSS,
},
};
return {
@@ -1,246 +0,0 @@
import React, { useCallback, useEffect, useState } from 'react';
import { useRunCommand, useSystem } from '@ohif/core';
import { useActiveViewportSegmentationRepresentations } from '@ohif/extension-cornerstone';
import {
Button,
cn,
Input,
Label,
Select,
SelectContent,
SelectItem,
SelectTrigger,
SelectValue,
Separator,
Switch,
Tabs,
TabsList,
TabsTrigger,
} from '@ohif/ui-next';
import { Icons } from '@ohif/ui-next';
import { contourSegmentation } from '@cornerstonejs/tools/utilities';
import { useTranslation } from 'react-i18next';
import { Segment } from '@cornerstonejs/tools/types';
const { LogicalOperation } = contourSegmentation;
const options = [
{
value: 'merge',
logicalOperation: LogicalOperation.Union,
label: 'Merge',
icon: 'actions-combine-merge',
helperIcon: 'helper-combine-merge',
},
{
value: 'intersect',
logicalOperation: LogicalOperation.Intersect,
label: 'Intersect',
icon: 'actions-combine-intersect',
helperIcon: 'helper-combine-intersect',
},
{
value: 'subtract',
logicalOperation: LogicalOperation.Subtract,
label: 'Subtract',
icon: 'actions-combine-subtract',
helperIcon: 'helper-combine-subtract',
},
];
// Shared component for segment selection
function SegmentSelector({
label,
value,
onValueChange,
segments,
placeholder = 'Select a segment',
}: {
label: string;
value: string;
onValueChange: (value: string) => void;
segments: Segment[];
placeholder?: string;
}) {
const { t } = useTranslation('SegmentationPanel');
return (
<div className="flex justify-between gap-6">
<div>{label}</div>
<Select
key={`select-segment-${label}`}
onValueChange={onValueChange}
value={value}
>
<SelectTrigger className="overflow-hidden">
<SelectValue placeholder={t(placeholder)} />
</SelectTrigger>
<SelectContent>
{segments.map(segment => (
<SelectItem
key={segment.segmentIndex}
value={segment.segmentIndex.toString()}
>
{segment.label}
</SelectItem>
))}
</SelectContent>
</Select>
</div>
);
}
function LogicalContourOperationOptions() {
const { servicesManager } = useSystem();
const { segmentationService } = servicesManager.services;
const { t } = useTranslation('SegmentationPanel');
const { segmentationsWithRepresentations } = useActiveViewportSegmentationRepresentations();
const activeRepresentation = segmentationsWithRepresentations?.find(
({ representation }) => representation?.active
);
const segments = activeRepresentation
? Object.values(activeRepresentation.segmentation.segments)
: [];
// Calculate the next available segment index
const nextSegmentIndex = activeRepresentation
? segmentationService.getNextAvailableSegmentIndex(
activeRepresentation.segmentation.segmentationId
)
: 1;
const activeSegment = segments.find(segment => segment.active);
const activeSegmentIndex = activeSegment?.segmentIndex || 0;
const [operation, setOperation] = useState(options[0]);
const [segmentA, setSegmentA] = useState<string>(activeSegmentIndex?.toString() || '');
const [segmentB, setSegmentB] = useState<string>('');
const [createNewSegment, setCreateNewSegment] = useState<boolean>(false);
const [newSegmentName, setNewSegmentName] = useState<string>('');
useEffect(() => {
setSegmentA(activeSegmentIndex?.toString() || null);
}, [activeSegmentIndex]);
useEffect(() => {
setNewSegmentName(`Segment ${nextSegmentIndex}`);
}, [nextSegmentIndex]);
const runCommand = useRunCommand();
const applyLogicalContourOperation = useCallback(() => {
let resultSegmentIndex = segmentA;
if (createNewSegment) {
resultSegmentIndex = nextSegmentIndex.toString();
runCommand('addSegment', {
segmentationId: activeRepresentation.segmentation.segmentationId,
config: {
label: newSegmentName,
segmentIndex: nextSegmentIndex,
},
});
}
runCommand('applyLogicalContourOperation', {
segmentAInfo: {
segmentationId: activeRepresentation.segmentation.segmentationId,
segmentIndex: parseInt(segmentA),
},
segmentBInfo: {
segmentationId: activeRepresentation.segmentation.segmentationId,
segmentIndex: parseInt(segmentB),
},
resultSegmentInfo: {
segmentationId: activeRepresentation.segmentation.segmentationId,
segmentIndex: parseInt(resultSegmentIndex),
},
logicalOperation: operation.logicalOperation,
});
}, [
activeRepresentation?.segmentation?.segmentationId,
createNewSegment,
newSegmentName,
nextSegmentIndex,
operation.logicalOperation,
runCommand,
segmentA,
segmentB,
]);
return (
<div className="flex w-[245px] flex-col gap-4">
<div className="flex items-start justify-between">
<div className="flex w-auto flex-col items-center gap-2 text-base font-normal leading-none">
<Tabs value={operation.value}>
<TabsList className="inline-flex space-x-1">
{options.map(option => {
const { value, icon } = option;
return (
<TabsTrigger
value={value}
key={`logical-contour-operation-${value}`}
onClick={() => setOperation(option)}
>
<Icons.ByName name={icon}></Icons.ByName>
</TabsTrigger>
);
})}
</TabsList>
</Tabs>
<div>{t(operation.label)}</div>
</div>
<div className="bg-muted flex h-[62px] w-[88px] items-center justify-center rounded-lg">
<Icons.ByName name={operation.helperIcon}></Icons.ByName>
</div>
</div>
<SegmentSelector
label="A"
value={segmentA}
onValueChange={setSegmentA}
segments={segments}
/>
<SegmentSelector
label="B"
value={segmentB}
onValueChange={setSegmentB}
segments={segments}
/>
<div className="flex justify-end pl-[34px]">
<Button
className="border-primary/60 grow border"
variant="ghost"
onClick={() => {
applyLogicalContourOperation();
}}
>
{t(operation.label)}
</Button>
</div>
<Separator className="bg-input mt-2 h-[1px]" />
<div className="flex flex-col gap-2">
<div className="flex items-center justify-start gap-2">
<Switch
id="logical-contour-operations-create-new-segment-switch"
onCheckedChange={setCreateNewSegment}
></Switch>
<Label htmlFor="logical-contour-operations-create-new-segment-switch">
{t('Create a new segment')}
</Label>
</div>
<div className="pl-9">
<Input
className={cn(createNewSegment ? 'visible' : 'hidden')}
disabled={!createNewSegment}
id="logical-contour-operations-create-new-segment-input"
type="text"
placeholder={t('New segment name')}
value={newSegmentName}
onChange={e => setNewSegmentName(e.target.value)}
/>
</div>
</div>
</div>
);
}
export default LogicalContourOperationOptions;
@@ -1,73 +0,0 @@
import React, { useState } from 'react';
import { Button, Input, Label, Separator } from '@ohif/ui-next';
import { useRunCommand } from '@ohif/core';
import { useTranslation } from 'react-i18next';
function SimplifyContourOptions() {
const [areaThreshold, setAreaThreshold] = useState(10);
const runCommand = useRunCommand();
const { t } = useTranslation('SegmentationPanel');
return (
<div className="flex w-auto w-[252px] flex-col gap-[8px] text-base font-normal leading-none">
<div className="flex w-auto flex-col gap-[10px] text-base font-normal leading-none">
<div>{t('Fill contour holes')}</div>
<Button
className="border-primary/60 border"
variant="ghost"
onClick={() => {
runCommand('removeContourHoles');
}}
>
{t('Fill Holes')}
</Button>
<Separator className="bg-input mt-[20px] h-[1px]" />
</div>
<div className="flex w-auto flex-col gap-[10px] text-base font-normal leading-none">
<div>{t('Remove Small Contours')}</div>
<div className="flex items-center gap-2 self-end">
<Label
htmlFor="simplify-contour-options"
className="text-muted-foreground"
>
{t('Area Threshold')}
</Label>
<Input
id="simplify-contour-options"
className="w-20"
type="number"
value={areaThreshold}
onChange={e => setAreaThreshold(Number(e.target.value))}
/>
</div>
<Button
className="border-primary/60 border"
variant="ghost"
onClick={() => {
runCommand('removeSmallContours', {
areaThreshold,
});
}}
>
{t('Remove Small Contours')}
</Button>
<Separator className="bg-input mt-[20px] h-[1px]" />
</div>
<div className="flex w-auto flex-col gap-[10px] text-base font-normal leading-none">
<div>{t('Create New Segment from Holes')}</div>
<Button
className="border-primary/60 border"
variant="ghost"
onClick={() => {
runCommand('convertContourHoles');
}}
>
{t('Create New Segment')}
</Button>
</div>
</div>
);
}
export default SimplifyContourOptions;
@@ -1,41 +0,0 @@
import React from 'react';
import { Button, Separator } from '@ohif/ui-next';
import { useRunCommand } from '@ohif/core';
import { useTranslation } from 'react-i18next';
function SmoothContoursOptions() {
const runCommand = useRunCommand();
const { t } = useTranslation('SegmentationPanel');
return (
<div className="flex w-auto w-[245px] flex-col gap-[8px] text-base font-normal leading-none">
<div className="flex w-auto flex-col gap-[10px] text-base font-normal leading-none">
<div>{t('Smooth all edges')}</div>
<Button
className="border-primary/60 border"
variant="ghost"
onClick={() => {
runCommand('smoothContours');
}}
>
{t('Smooth Edges')}
</Button>
<Separator className="bg-input mt-[20px] h-[1px]" />
</div>
<div className="flex w-auto flex-col gap-[10px] text-base font-normal leading-none">
<div>{t('Remove extra points')}</div>
<Button
className="border-primary/60 border"
variant="ghost"
onClick={() => {
runCommand('decimateContours');
}}
>
{t('Remove Points')}
</Button>
</div>
</div>
);
}
export default SmoothContoursOptions;
@@ -1,13 +1,12 @@
import { utils, Types as OhifTypes } from '@ohif/core';
import i18n from '@ohif/i18n';
import { metaData, eventTarget } from '@cornerstonejs/core';
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', '1.2.840.10008.5.1.4.1.1.66.7'];
const sopClassUids = ['1.2.840.10008.5.1.4.1.1.66.4'];
const loadPromises = {};
@@ -16,41 +15,34 @@ function _getDisplaySetsFromSeries(
servicesManager: AppTypes.ServicesManager,
extensionManager
) {
utils.sortStudyInstances(instances);
// Choose the LAST instance in the list as the most recently created one.
const instance = instances[instances.length - 1];
const instance = instances[0];
const {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
SeriesDescription = '',
SeriesDescription,
SeriesNumber,
SeriesDate,
StructureSetDate,
SOPClassUID,
FrameOfReferenceUID,
wadoRoot,
wadoUri,
wadoUriRoot,
imageId: predecessorImageId,
} = instance;
const displaySet = {
Modality: 'SEG',
loading: false,
isReconstructable: false,
isReconstructable: true, // by default for now since it is a volumetric SEG currently
displaySetInstanceUID: utils.guid(),
SeriesDescription,
SeriesNumber,
SeriesDate: SeriesDate || StructureSetDate || '',
SeriesDate,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
SOPClassHandlerId,
SOPClassUID,
FrameOfReferenceUID,
referencedImages: null,
referencedSeriesInstanceUID: null,
referencedDisplaySetInstanceUID: null,
@@ -60,13 +52,11 @@ function _getDisplaySetsFromSeries(
segments: {},
sopClassUids,
instance,
predecessorImageId,
instances: [instance],
wadoRoot,
wadoUriRoot,
wadoUri,
isOverlayDisplaySet: true,
label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('SEG')}`,
};
const referencedSeriesSequence = instance.ReferencedSeriesSequence;
@@ -81,16 +71,10 @@ function _getDisplaySetsFromSeries(
displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
const { displaySetService } = servicesManager.services;
const referencedDisplaySets = displaySetService.getDisplaySetsForReferences(
instance.ReferencedSeriesSequence
const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
displaySet.referencedSeriesInstanceUID
);
if (referencedDisplaySets?.length > 1) {
console.warn(
'Segmentation does not currently handle references to multiple series, defaulting to first series'
);
}
const referencedDisplaySet = referencedDisplaySets[0];
if (!referencedDisplaySet) {
@@ -105,16 +89,12 @@ function _getDisplaySetsFromSeries(
const addedDisplaySet = displaySetsAdded[0];
if (addedDisplaySet.SeriesInstanceUID === displaySet.referencedSeriesInstanceUID) {
displaySet.referencedDisplaySetInstanceUID = addedDisplaySet.displaySetInstanceUID;
displaySet.isReconstructable = addedDisplaySet.isReconstructable;
displaySet.FrameOfReferenceUID = addedDisplaySet.FrameOfReferenceUID;
unsubscribe();
}
}
);
} else {
displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
displaySet.isReconstructable = referencedDisplaySet.isReconstructable;
displaySet.FrameOfReferenceUID = referencedDisplaySet.FrameOfReferenceUID;
}
displaySet.load = async ({ headers }) =>
@@ -252,8 +232,7 @@ function _segmentationExists(segDisplaySet) {
return cstSegmentation.state.getSegmentation(segDisplaySet.displaySetInstanceUID);
}
function getSopClassHandlerModule(params: OhifTypes.Extensions.ExtensionParams) {
const { servicesManager, extensionManager } = params;
function getSopClassHandlerModule({ servicesManager, extensionManager }) {
const getDisplaySetsFromSeries = instances => {
return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
};
@@ -1,35 +1,6 @@
import { utilities as cstUtils } from '@cornerstonejs/tools';
import i18n from '@ohif/i18n';
import { useUIStateStore } from '@ohif/extension-default';
import LogicalContourOperationsOptions from './components/LogicalContourOperationsOptions';
import SimplifyContourOptions from './components/SimplifyContourOptions';
import SmoothContoursOptions from './components/SmoothContoursOptions';
export function getToolbarModule({ servicesManager }: withAppTypes) {
const { segmentationService, toolbarService, toolGroupService } = servicesManager.services;
return [
{
name: 'cornerstone.SimplifyContourOptions',
defaultComponent: SimplifyContourOptions,
},
{
name: 'cornerstone.LogicalContourOperationsOptions',
defaultComponent: LogicalContourOperationsOptions,
},
{
name: 'cornerstone.SmoothContoursOptions',
defaultComponent: SmoothContoursOptions,
},
{
name: 'cornerstone.isActiveSegmentationUtility',
evaluate: ({ button }) => {
const { uiState } = useUIStateStore.getState();
return {
isActive: uiState[`activeSegmentationUtility`] === button.id,
};
},
},
{
name: 'evaluate.cornerstone.hasSegmentation',
evaluate: ({ viewportId }) => {
@@ -39,30 +10,6 @@ export function getToolbarModule({ servicesManager }: withAppTypes) {
};
},
},
{
name: 'evaluate.cornerstone.hasSegmentationOfType',
evaluate: ({ viewportId, segmentationRepresentationType }) => {
const segmentations = segmentationService.getSegmentationRepresentations(viewportId);
if (!segmentations?.length) {
return {
disabled: true,
disabledText: i18n.t('SegmentationPanel:No segmentations available'),
};
}
if (
!segmentations.some(segmentation =>
Boolean(segmentation.type === segmentationRepresentationType)
)
) {
return {
disabled: true,
disabledText: `No ${segmentationRepresentationType} segmentations available`,
};
}
},
},
{
name: 'evaluate.cornerstone.segmentation',
evaluate: ({ viewportId, button, toolNames, disabledText }) => {
@@ -74,7 +21,7 @@ export function getToolbarModule({ servicesManager }: withAppTypes) {
if (!segmentations?.length) {
return {
disabled: true,
disabledText: disabledText ?? i18n.t('SegmentationPanel:No segmentations available'),
disabledText: disabledText ?? 'No segmentations available',
};
}
@@ -82,7 +29,7 @@ export function getToolbarModule({ servicesManager }: withAppTypes) {
if (!Object.keys(activeSegmentation.segments).length) {
return {
disabled: true,
disabledText: i18n.t('SegmentationPanel:Add segment to enable this tool'),
disabledText: 'Add segment to enable this tool',
};
}
@@ -91,7 +38,7 @@ export function getToolbarModule({ servicesManager }: withAppTypes) {
if (!toolGroup) {
return {
disabled: true,
disabledText: disabledText ?? i18n.t('SegmentationPanel:Not available on the current viewport'),
disabledText: disabledText ?? 'Not available on the current viewport',
};
}
@@ -107,7 +54,7 @@ export function getToolbarModule({ servicesManager }: withAppTypes) {
if (!toolGroup.hasTool(toolName) && !toolNames) {
return {
disabled: true,
disabledText: disabledText ?? i18n.t('SegmentationPanel:Not available on the current viewport'),
disabledText: disabledText ?? 'Not available on the current viewport',
};
}
@@ -121,23 +68,5 @@ export function getToolbarModule({ servicesManager }: withAppTypes) {
};
},
},
{
name: 'evaluate.cornerstone.segmentation.synchronizeDrawingRadius',
evaluate: ({ button, radiusOptionId }) => {
const toolGroupIds = toolGroupService.getToolGroupIds();
if (!toolGroupIds?.length) {
return;
}
for (const toolGroupId of toolGroupIds) {
const brushSize = cstUtils.segmentation.getBrushSizeForToolGroup(toolGroupId);
if (brushSize) {
const option = toolbarService.getOptionById(button, radiusOptionId);
option.value = brushSize;
}
}
},
},
];
}
@@ -1,14 +1,7 @@
function createSEGToolGroupAndAddTools({
commandsManager,
toolGroupService,
customizationService,
toolGroupId,
}) {
function createSEGToolGroupAndAddTools(ToolGroupService, customizationService, toolGroupId) {
const tools = customizationService.getCustomization('cornerstone.overlayViewportTools');
const updatedTools = commandsManager.run('initializeSegmentLabelTool', { tools });
return toolGroupService.createToolGroupAndAddTools(toolGroupId, updatedTools);
return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools);
}
export default createSEGToolGroupAndAddTools;
@@ -1,4 +1,8 @@
import { utils, Types } from '@ohif/extension-cornerstone';
const RESPONSE = {
NO_NEVER: -1,
CANCEL: 0,
HYDRATE_SEG: 5,
};
function promptHydrateSEG({
servicesManager,
@@ -6,20 +10,75 @@ function promptHydrateSEG({
viewportId,
preHydrateCallbacks,
hydrateCallback,
}: {
servicesManager: AppTypes.ServicesManager;
segDisplaySet: AppTypes.DisplaySet;
viewportId: string;
preHydrateCallbacks?: Types.HydrationCallback[];
hydrateCallback: Types.HydrationCallback;
}) {
return utils.promptHydrationDialog({
servicesManager,
viewportId,
displaySet: segDisplaySet as AppTypes.DisplaySet,
preHydrateCallbacks,
hydrateCallback,
type: 'SEG',
}: withAppTypes) {
const { uiViewportDialogService, customizationService } = 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, customizationService, viewportId);
if (promptResult === RESPONSE.HYDRATE_SEG) {
preHydrateCallbacks?.forEach(callback => {
callback();
});
window.setTimeout(async () => {
const isHydrated = await hydrateCallback({
segDisplaySet,
viewportId,
});
resolve(isHydrated);
}, 0);
}
});
}
function _askHydrate(
uiViewportDialogService: AppTypes.UIViewportDialogService,
customizationService: AppTypes.CustomizationService,
viewportId
) {
return new Promise(function (resolve, reject) {
const message = customizationService.getCustomization('viewportNotification.hydrateSEGMessage');
const actions = [
{
id: 'no-hydrate',
type: 'secondary',
text: 'No',
value: RESPONSE.CANCEL,
},
{
id: 'yes-hydrate',
type: 'primary',
text: 'Yes',
value: RESPONSE.HYDRATE_SEG,
},
];
const onSubmit = result => {
uiViewportDialogService.hide();
resolve(result);
};
uiViewportDialogService.show({
viewportId,
type: 'info',
message,
actions,
onSubmit,
onOutsideClick: () => {
uiViewportDialogService.hide();
resolve(RESPONSE.CANCEL);
},
onKeyPress: event => {
if (event.key === 'Enter') {
onSubmit(RESPONSE.HYDRATE_SEG);
}
},
});
});
}
@@ -1,24 +1,36 @@
import React, { useCallback, useEffect, useRef, useState } from 'react';
import { useTranslation } from 'react-i18next';
import { ViewportActionArrows } from '@ohif/ui-next';
import { useViewportGrid } from '@ohif/ui-next';
import createSEGToolGroupAndAddTools from '../utils/initSEGToolGroup';
import promptHydrateSEG from '../utils/promptHydrateSEG';
import { usePositionPresentationStore, OHIFCornerstoneViewport } from '@ohif/extension-cornerstone';
import _getStatusComponent from './_getStatusComponent';
import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
import { SegmentationRepresentations } from '@cornerstonejs/tools/enums';
import { useSystem } from '@ohif/core/src/contextProviders/SystemProvider';
import { utils } from '@ohif/extension-cornerstone';
const SEG_TOOLGROUP_BASE_NAME = 'SEGToolGroup';
function OHIFCornerstoneSEGViewport(props: withAppTypes) {
const { servicesManager, commandsManager } = useSystem();
const { children, displaySets, viewportOptions } = props as {
children: React.ReactNode;
displaySets: AppTypes.DisplaySet[];
viewportOptions: AppTypes.ViewportOptions;
};
const {
children,
displaySets,
viewportOptions,
servicesManager,
extensionManager,
commandsManager,
} = props;
const { t } = useTranslation('SEGViewport');
const viewportId = viewportOptions.viewportId;
const { displaySetService, toolGroupService, segmentationService, customizationService } =
servicesManager.services;
const {
displaySetService,
toolGroupService,
segmentationService,
customizationService,
viewportActionCornersService,
} = servicesManager.services;
const LoadingIndicatorTotalPercent = customizationService.getCustomization(
'ui.loadingIndicatorTotalPercent'
@@ -35,6 +47,7 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
const [viewportGrid, viewportGridService] = useViewportGrid();
// States
const selectedSegmentObjectIndex: number = 0;
const { setPositionPresentation } = usePositionPresentationStore();
// Hydration means that the SEG is opened and segments are loaded into the
@@ -42,7 +55,9 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
// same frameOfReferenceUID as the referencedSeriesUID of the SEG. However,
// loading basically means SEG loading over network and bit unpacking of the
// SEG data.
const [isHydrated, setIsHydrated] = useState(segDisplaySet.isHydrated);
const [segIsLoading, setSegIsLoading] = useState(!segDisplaySet.isLoaded);
const [element, setElement] = useState(null);
const [processingProgress, setProcessingProgress] = useState({
percentComplete: null,
totalSegments: null,
@@ -54,32 +69,6 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
const { viewports, activeViewportId } = viewportGrid;
const referencedDisplaySetInstanceUID = segDisplaySet.referencedDisplaySetInstanceUID;
// If the referencedDisplaySetInstanceUID is not found, it means the SEG series is being
// launched without its corresponding referenced display set (e.g., the SEG series is launched using
// series launch /mode?StudyInstanceUIDs=&SeriesInstanceUID).
// In such cases, we attempt to handle this scenario gracefully by
// invoking a custom handler. Ideally, if a user tries to launch a series that isn't viewable,
// (eg.: we can prompt them with an explanation and provide a link to the full study).
// Additional guard: If no customization handler is registered for missing
// referenced display sets, skip SEG rendering to avoid a viewport crash.
if (!referencedDisplaySetInstanceUID) {
const missingReferenceDisplaySetHandler = customizationService.getCustomization(
'missingReferenceDisplaySetHandler'
);
if (typeof missingReferenceDisplaySetHandler === 'function') {
const { handled } = missingReferenceDisplaySetHandler();
if (handled) {
return;
}
} else {
console.log(
"No customization 'missingReferenceDisplaySetHandler' registered. Skipping SEG rendering."
);
return;
}
}
const referencedDisplaySet = displaySetService.getDisplaySetByUID(
referencedDisplaySetInstanceUID
);
@@ -93,10 +82,36 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
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 getCornerstoneViewport = useCallback(() => {
const { component: Component } = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.viewportModule.cornerstone'
);
// Todo: jump to the center of the first segment
return (
<OHIFCornerstoneViewport
<Component
{...props}
displaySets={[segDisplaySet]}
viewportOptions={{
@@ -108,35 +123,66 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
}}
onElementEnabled={evt => {
props.onElementEnabled?.(evt);
onElementEnabled(evt);
}}
/>
onElementDisabled={onElementDisabled}
></Component>
);
}, [viewportId, segDisplaySet, toolGroupId, props, viewportOptions]);
}, [viewportId, segDisplaySet, toolGroupId]);
const onSegmentChange = useCallback(
direction => {
utils.handleSegmentChange({
direction,
segDisplaySet: segDisplaySet,
viewportId,
selectedSegmentObjectIndex,
segmentationService,
});
},
[selectedSegmentObjectIndex]
);
const hydrateSEG = useCallback(() => {
// 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: segDisplaySet,
type: SegmentationRepresentations.Labelmap,
});
// 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,
});
commandsManager.runCommand('loadSegmentationDisplaySetsForViewport', {
viewportId,
displaySetInstanceUIDs: [referencedDisplaySet.displaySetInstanceUID],
});
}, [commandsManager, viewportId, referencedDisplaySet, segDisplaySet]);
useEffect(() => {
if (segIsLoading) {
return;
}
// if not active viewport, return
if (viewportId !== activeViewportId) {
return;
}
promptHydrateSEG({
servicesManager,
viewportId,
segDisplaySet,
hydrateCallback: async () => {
await commandsManager.runCommand('hydrateSecondaryDisplaySet', {
displaySet: segDisplaySet,
viewportId,
});
return true;
},
preHydrateCallbacks: [storePresentationState],
hydrateCallback: hydrateSEG,
}).then(isHydrated => {
if (isHydrated) {
setIsHydrated(true);
}
});
}, [servicesManager, viewportId, segDisplaySet, segIsLoading, commandsManager, activeViewportId]);
}, [servicesManager, viewportId, segDisplaySet, segIsLoading, hydrateSEG]);
useEffect(() => {
// on new seg display set, remove all segmentations from all viewports
@@ -145,7 +191,7 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
const { unsubscribe } = segmentationService.subscribe(
segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
evt => {
if (evt.segDisplaySet?.displaySetInstanceUID === segDisplaySet?.displaySetInstanceUID) {
if (evt.segDisplaySet.displaySetInstanceUID === segDisplaySet.displaySetInstanceUID) {
setSegIsLoading(false);
}
@@ -225,12 +271,7 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
// This creates a custom tool group which has the lifetime of this view
// only, and does NOT interfere with currently displayed segmentations.
toolGroup = createSEGToolGroupAndAddTools({
commandsManager,
toolGroupService,
customizationService,
toolGroupId,
});
toolGroup = createSEGToolGroupAndAddTools(toolGroupService, customizationService, toolGroupId);
return () => {
// remove the segmentation representations if seg displayset changed
@@ -242,6 +283,54 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
};
}, []);
const onStatusClick = useCallback(async () => {
// Before hydrating a SEG 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 SEG. This is
// required if the user has changed the viewport (other viewport than SEG viewport)
// presentation state (w/l and invert) and then opens the SEG. If we don't store
// the presentation state, the viewport will be reset to the default presentation
storePresentationState();
hydrateSEG();
}, [storePresentationState, hydrateSEG]);
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,
]);
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
let childrenWithProps = null;
@@ -0,0 +1,59 @@
import React from 'react';
import { useTranslation } from 'react-i18next';
import { ViewportActionButton } from '@ohif/ui-next';
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-muted-foreground h-4 w-4"
name="status-untracked"
/>
);
ToolTipMessage = () => <div>Click LOAD to load segmentation.</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">SEG</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 />}
</>
);
}
@@ -1,8 +1,8 @@
const webpack = require('@rspack/core');
const webpack = require('webpack');
const { merge } = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const MiniCssExtractPlugin = webpack.CssExtractRspackPlugin;
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const pkg = require('./../package.json');
@@ -36,11 +36,9 @@ module.exports = (env, argv) => {
sideEffects: true,
},
output: {
library: {
name: 'ohif-extension-cornerstone-dicom-sr',
type: 'umd',
},
path: ROOT_DIR,
library: 'ohif-extension-cornerstone-dicom-sr',
libraryTarget: 'umd',
filename: pkg.main,
},
externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
File diff suppressed because it is too large. Load diff
+28 -28
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-cornerstone-dicom-sr",
"version": "3.13.0-beta.97",
"version": "3.10.4",
"description": "OHIF extension for an SR Cornerstone Viewport",
"author": "OHIF",
"license": "MIT",
@@ -8,7 +8,9 @@
"main": "dist/ohif-extension-cornerstone-dicom-sr.umd.js",
"module": "src/index.tsx",
"engines": {
"node": ">=24"
"node": ">=14",
"npm": ">=6",
"yarn": ">=1.16.0"
},
"files": [
"dist",
@@ -17,38 +19,36 @@
"publishConfig": {
"access": "public"
},
"keywords": [
"ohif-extension"
],
"scripts": {
"clean": "shx rm -rf dist",
"clean:deep": "pnpm run clean && shx rm -rf node_modules",
"dev": "cross-env NODE_ENV=development rspack build --config .webpack/webpack.dev.js --watch",
"dev:cornerstone": "pnpm run dev",
"build": "cross-env NODE_ENV=production rspack build --config .webpack/webpack.prod.js",
"build:package-1": "pnpm run build",
"start": "pnpm run dev",
"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:cornerstone": "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",
"test:unit": "jest --watchAll",
"test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
},
"peerDependencies": {
"@ohif/core": "workspace:*",
"@ohif/extension-cornerstone": "workspace:*",
"@ohif/ui": "workspace:*",
"dcmjs": "0.49.4",
"dicom-parser": "1.8.21",
"hammerjs": "2.0.8",
"prop-types": "15.8.1",
"react": "18.3.1"
"@ohif/core": "3.10.4",
"@ohif/extension-cornerstone": "3.10.4",
"@ohif/extension-measurement-tracking": "3.10.4",
"@ohif/ui": "3.10.4",
"dcmjs": "*",
"dicom-parser": "^1.8.9",
"hammerjs": "^2.0.8",
"prop-types": "^15.6.2",
"react": "^18.3.1"
},
"dependencies": {
"@babel/runtime": "7.29.7",
"@cornerstonejs/adapters": "5.0.2",
"@cornerstonejs/core": "5.0.2",
"@cornerstonejs/tools": "5.0.2",
"classnames": "2.5.1"
},
"devDependencies": {
"cross-env": "7.0.3"
},
"keywords": [
"ohif-extension"
]
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^3.11.6",
"@cornerstonejs/core": "^3.11.6",
"@cornerstonejs/tools": "^3.11.6",
"classnames": "^2.3.2"
}
}
@@ -1,6 +1,7 @@
import { metaData } from '@cornerstonejs/core';
import { metaData, utilities } from '@cornerstonejs/core';
import OHIF from '@ohif/core';
import OHIF, { DicomMetadataStore } from '@ohif/core';
import dcmjs from 'dcmjs';
import { adaptersSR } from '@cornerstonejs/adapters';
import getFilteredCornerstoneToolState from './utils/getFilteredCornerstoneToolState';
@@ -31,7 +32,12 @@ const _generateReport = (measurementData, additionalFindingTypes, options: Optio
additionalFindingTypes
);
const report = MeasurementReport.generateReport(filteredToolState, metaData, options);
const report = MeasurementReport.generateReport(
filteredToolState,
metaData,
utilities.worldToImageCoords,
options
);
const { dataset } = report;
@@ -41,12 +47,14 @@ const _generateReport = (measurementData, additionalFindingTypes, options: Optio
dataset.SpecificCharacterSet = 'ISO_IR 192';
}
dataset.InstanceNumber = options.InstanceNumber ?? 1;
return dataset;
};
const commandsModule = (props: withAppTypes) => {
const { servicesManager, extensionManager, commandsManager } = props;
const { customizationService } = servicesManager.services;
const { customizationService, viewportGridService, displaySetService } = servicesManager.services;
const actions = {
changeColorMeasurement: ({ uid }) => {
@@ -72,8 +80,25 @@ const commandsModule = (props: withAppTypes) => {
/**
*
* @param measurementData An array of measurements from the measurements service
* @param additionalFindingTypes toolTypes that should be stored with labels as Findings
* @param options Naturalized DICOM JSON headers to merge into the displaySet.
* as opposed to Finding Sites.
* that you wish to serialize.
* @param dataSource The data source name ('download', 'copyToClipboard', or a named data source).
*/
downloadReport: ({ measurementData, additionalFindingTypes, options = {} }) => {
const srDataset = _generateReport(measurementData, additionalFindingTypes, options);
const reportBlob = dcmjs.data.datasetToBlob(srDataset);
//Create a URL for the binary.
const objectUrl = URL.createObjectURL(reportBlob);
window.location.assign(objectUrl);
},
/**
*
* @param measurementData An array of measurements from the measurements service
* that you wish to serialize.
* @param dataSource The dataSource that you wish to use to persist the data.
* @param additionalFindingTypes toolTypes that should be stored with labels as Findings
* @param options Naturalized DICOM JSON headers to merge into the displaySet.
* @return The naturalized report
@@ -84,44 +109,44 @@ const commandsModule = (props: withAppTypes) => {
additionalFindingTypes,
options = {},
}) => {
// Use the @cornerstonejs adapter for converting to/from DICOM
// But it is good enough for now whilst we only have cornerstone as a datasource.
log.info('[DICOMSR] storeMeasurements');
const storeFn = commandsManager.runCommand('createStoreFunction', {
dataSource,
defaultFileName: 'dicom-sr.dcm',
});
if (!storeFn) {
log.error('[DICOMSR] No valid store for dataSource:', dataSource);
if (!dataSource || !dataSource.store || !dataSource.store.dicom) {
log.error('[DICOMSR] datasource has no dataSource.store.dicom endpoint!');
return Promise.reject({});
}
try {
const naturalizedReport = _generateReport(
measurementData,
additionalFindingTypes,
options
);
const naturalizedReport = _generateReport(measurementData, additionalFindingTypes, options);
const { ContentSequence } = naturalizedReport;
const { StudyInstanceUID, ContentSequence } = naturalizedReport;
// The content sequence has 5 or more elements, of which
// the `[4]` element contains the annotation data, so this is
// checking that there is some annotation data present.
if (!ContentSequence?.[4]?.ContentSequence?.length) {
if (!ContentSequence?.[4].ContentSequence?.length) {
console.log('naturalizedReport missing imaging content', naturalizedReport);
throw new Error('Invalid report, no content');
}
if (!naturalizedReport.SOPClassUID) {
throw new Error('No sop class uid');
}
const onBeforeDicomStore = customizationService.getCustomization('onBeforeDicomStore');
let dicomDict;
if (typeof onBeforeDicomStore === 'function') {
dicomDict = onBeforeDicomStore({ dicomDict, measurementData, naturalizedReport });
}
await storeFn(naturalizedReport, { measurementData, dicomDict });
await dataSource.store.dicom(naturalizedReport, null, dicomDict);
if (StudyInstanceUID) {
dataSource.deleteStudyMetadataPromise(StudyInstanceUID);
}
// The "Mode" route listens for DicomMetadataStore changes
// When a new instance is added, it listens and
// automatically calls makeDisplaySets
DicomMetadataStore.addInstances([naturalizedReport], true);
return naturalizedReport;
} catch (error) {
@@ -135,17 +160,36 @@ const commandsModule = (props: withAppTypes) => {
* Loads measurements by hydrating and loading the SR for the given display set instance UID
* and displays it in the active viewport.
*/
hydrateStructuredReport: ({ displaySetInstanceUID }) => {
return hydrateStructuredReport(
loadSRMeasurements: ({ displaySetInstanceUID }) => {
const { SeriesInstanceUIDs } = hydrateStructuredReport(
{ servicesManager, extensionManager, commandsManager },
displaySetInstanceUID
);
const displaySets = displaySetService.getDisplaySetsForSeries(SeriesInstanceUIDs[0]);
if (displaySets.length) {
commandsManager.run('setDisplaySetsForViewports', {
viewportsToUpdate: [
{
viewportId: viewportGridService.getActiveViewportId(),
displaySetInstanceUIDs: [displaySets[0].displaySetInstanceUID],
},
],
});
}
},
};
const definitions = {
storeMeasurements: actions.storeMeasurements,
hydrateStructuredReport: actions.hydrateStructuredReport,
downloadReport: {
commandFn: actions.downloadReport,
},
storeMeasurements: {
commandFn: actions.storeMeasurements,
},
loadSRMeasurements: {
commandFn: actions.loadSRMeasurements,
},
};
return {
@@ -1,24 +1,25 @@
import PropTypes from 'prop-types';
import React, { useCallback, useEffect, useState } from 'react';
import React, { useCallback, useContext, useEffect, useState } from 'react';
import { useTranslation } from 'react-i18next';
import { ExtensionManager, useToolbar } from '@ohif/core';
import { setTrackingUniqueIdentifiersForElement } from '../tools/modules/dicomSRModule';
import { ViewportActionArrows } from '@ohif/ui-next';
import createReferencedImageDisplaySet from '../utils/createReferencedImageDisplaySet';
import { usePositionPresentationStore, OHIFCornerstoneViewport } from '@ohif/extension-cornerstone';
import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
import { useViewportGrid } from '@ohif/ui-next';
import { useSystem } from '@ohif/core/src/contextProviders/SystemProvider';
import { Icons, Tooltip, TooltipTrigger, TooltipContent } from '@ohif/ui-next';
const MEASUREMENT_TRACKING_EXTENSION_ID = '@ohif/extension-measurement-tracking';
const SR_TOOLGROUP_BASE_NAME = 'SRToolGroup';
function OHIFCornerstoneSRMeasurementViewport(props) {
const { servicesManager } = useSystem();
const { children, dataSource, displaySets, viewportOptions } = props as {
children: React.ReactNode;
dataSource: unknown;
displaySets: AppTypes.DisplaySet[];
viewportOptions: AppTypes.ViewportOptions;
};
function OHIFCornerstoneSRMeasurementViewport(props: withAppTypes) {
const { children, dataSource, displaySets, viewportOptions, servicesManager, extensionManager } =
props;
const { displaySetService } = servicesManager.services;
const { displaySetService, viewportActionCornersService } = servicesManager.services;
const viewportId = viewportOptions.viewportId;
@@ -33,11 +34,40 @@ function OHIFCornerstoneSRMeasurementViewport(props) {
const [viewportGrid, viewportGridService] = useViewportGrid();
const [measurementSelected, setMeasurementSelected] = useState(0);
const [measurementCount, setMeasurementCount] = useState(1);
const [activeImageDisplaySetData, setActiveImageDisplaySetData] = useState(null);
const [referencedDisplaySetMetadata, setReferencedDisplaySetMetadata] = useState(null);
const [element, setElement] = useState(null);
const { viewports, activeViewportId } = viewportGrid;
const { t } = useTranslation('Common');
// Optional hook into tracking extension, if present.
let trackedMeasurements;
const hasMeasurementTrackingExtension = extensionManager.registeredExtensionIds.includes(
MEASUREMENT_TRACKING_EXTENSION_ID
);
if (hasMeasurementTrackingExtension) {
const contextModule = extensionManager.getModuleEntry(
'@ohif/extension-measurement-tracking.contextModule.TrackedMeasurementsContext'
);
const tracked = useContext(contextModule.context);
trackedMeasurements = tracked?.[0];
}
/**
* Todo: what is this, not sure what it does regarding the react aspect,
* it is updating a local variable? which is not state.
*/
const [isLocked, setIsLocked] = useState(trackedMeasurements?.context?.trackedSeries?.length > 0);
/**
* Store the tracking identifiers per viewport in order to be able to
* show the SR measurements on the referenced image on the correct viewport,
* when multiple viewports are used.
*/
const setTrackingIdentifiers = useCallback(
measurementSelected => {
const { measurements } = srDisplaySet;
@@ -63,12 +93,22 @@ function OHIFCornerstoneSRMeasurementViewport(props) {
const updateViewport = useCallback(
newMeasurementSelected => {
const { StudyInstanceUID, displaySetInstanceUID } = srDisplaySet;
const { StudyInstanceUID, displaySetInstanceUID, sopClassUids } = srDisplaySet;
if (!StudyInstanceUID || !displaySetInstanceUID) {
return;
}
if (sopClassUids && sopClassUids.length > 1) {
// Todo: what happens if there are multiple SOP Classes? Why we are
// not throwing an error?
console.warn('More than one SOPClassUID in the same series is not yet supported.');
}
// if (!srDisplaySet.measurements || !srDisplaySet.measurements.length) {
// return;
// }
_getViewportReferencedDisplaySetData(
srDisplaySet,
newMeasurementSelected,
@@ -86,7 +126,7 @@ function OHIFCornerstoneSRMeasurementViewport(props) {
const { presentationIds } = viewportOptions;
const measurement = srDisplaySet.measurements[newMeasurementSelected];
setPositionPresentation(presentationIds.positionPresentationId, {
viewReference: measurement.viewReference || {
viewReference: {
referencedImageId: measurement.imageId,
},
});
@@ -100,6 +140,10 @@ function OHIFCornerstoneSRMeasurementViewport(props) {
return null;
}
const { component: Component } = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.viewportModule.cornerstone'
);
const { measurements } = srDisplaySet;
const measurement = measurements[measurementSelected];
@@ -108,7 +152,7 @@ function OHIFCornerstoneSRMeasurementViewport(props) {
}
return (
<OHIFCornerstoneViewport
<Component
{...props}
// should be passed second since we don't want SR displaySet to
// override the activeImageDisplaySetData
@@ -132,10 +176,27 @@ function OHIFCornerstoneSRMeasurementViewport(props) {
onElementEnabled(evt);
}}
isJumpToMeasurementDisabled={true}
/>
></Component>
);
}, [activeImageDisplaySetData, viewportId, measurementSelected]);
const onMeasurementChange = useCallback(
direction => {
let newMeasurementSelected = measurementSelected;
newMeasurementSelected += direction;
if (newMeasurementSelected >= measurementCount) {
newMeasurementSelected = 0;
} else if (newMeasurementSelected < 0) {
newMeasurementSelected = measurementCount - 1;
}
setTrackingIdentifiers(newMeasurementSelected);
updateViewport(newMeasurementSelected);
},
[measurementSelected, measurementCount, updateViewport, setTrackingIdentifiers]
);
/**
Cleanup the SR viewport when the viewport is destroyed
*/
@@ -170,6 +231,8 @@ function OHIFCornerstoneSRMeasurementViewport(props) {
if (!srDisplaySet.isLoaded) {
await srDisplaySet.load();
}
const numMeasurements = srDisplaySet.measurements.length;
setMeasurementCount(numMeasurements);
updateViewport(measurementSelected);
};
loadSR();
@@ -192,6 +255,42 @@ function OHIFCornerstoneSRMeasurementViewport(props) {
updateSR();
}, [measurementSelected, element, setTrackingIdentifiers, srDisplaySet]);
useEffect(() => {
setIsLocked(trackedMeasurements?.context?.trackedSeries?.length > 0);
}, [trackedMeasurements]);
useEffect(() => {
viewportActionCornersService.addComponents([
{
viewportId,
id: 'viewportStatusComponent',
component: _getStatusComponent({
srDisplaySet,
viewportId,
isRehydratable: srDisplaySet.isRehydratable,
isLocked,
t,
servicesManager,
}),
indexPriority: -100,
location: viewportActionCornersService.LOCATIONS.topLeft,
},
{
viewportId,
id: 'viewportActionArrowsComponent',
index: 0,
component: (
<ViewportActionArrows
key="actionArrows"
onArrowsClick={onMeasurementChange}
></ViewportActionArrows>
),
indexPriority: 0,
location: viewportActionCornersService.LOCATIONS.topRight,
},
]);
}, [isLocked, onMeasurementChange, srDisplaySet, t, viewportActionCornersService, viewportId]);
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
let childrenWithProps = null;
@@ -228,6 +327,8 @@ OHIFCornerstoneSRMeasurementViewport.propTypes = {
children: PropTypes.node,
viewportLabel: PropTypes.string,
viewportOptions: PropTypes.object,
servicesManager: PropTypes.object.isRequired,
extensionManager: PropTypes.instanceOf(ExtensionManager).isRequired,
};
async function _getViewportReferencedDisplaySetData(
@@ -252,9 +353,6 @@ async function _getViewportReferencedDisplaySetData(
}
const referencedDisplaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
if (!referencedDisplaySet?.images) {
return { referencedDisplaySetMetadata: null, referencedDisplaySet: null };
}
const image0 = referencedDisplaySet.images[0];
const referencedDisplaySetMetadata = {
@@ -274,4 +372,130 @@ async function _getViewportReferencedDisplaySetData(
return { referencedDisplaySetMetadata, referencedDisplaySet };
}
function _getStatusComponent({
srDisplaySet,
viewportId,
isRehydratable,
isLocked,
t,
servicesManager,
}) {
const loadStr = t('LOAD');
// 1 - Incompatible
// 2 - Locked
// 3 - Rehydratable / Open
const state = isRehydratable && !isLocked ? 3 : isRehydratable && isLocked ? 2 : 1;
let ToolTipMessage = null;
let StatusIcon = null;
switch (state) {
case 1:
StatusIcon = () => (
<Icons.ByName
name="status-alert"
className="h-4 w-4"
/>
);
ToolTipMessage = () => (
<div>
This structured report is not compatible
<br />
with this application.
</div>
);
break;
case 2:
StatusIcon = () => (
<Icons.ByName
name="status-locked"
className="h-4 w-4"
/>
);
ToolTipMessage = () => (
<div>
This structured report is currently read-only
<br />
because you are tracking measurements in
<br />
another viewport.
</div>
);
break;
case 3:
StatusIcon = () => (
<Icons.ByName
className="text-muted-foreground h-4 w-4"
name="status-untracked"
/>
);
ToolTipMessage = () => <div>{`Click ${loadStr} to restore measurements.`}</div>;
}
const StatusArea = () => {
const { toolbarButtons: loadSRMeasurementsButtons, onInteraction } = useToolbar({
servicesManager,
buttonSection: 'loadSRMeasurements',
});
const commandOptions = {
displaySetInstanceUID: srDisplaySet.displaySetInstanceUID,
viewportId,
};
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 className="h-4 w-4" />
<span className="ml-1">SR</span>
</div>
{state === 3 && (
<>
{loadSRMeasurementsButtons.map(toolDef => {
if (!toolDef) {
return null;
}
const { id, Component, componentProps } = toolDef;
const tool = (
<Component
key={id}
id={id}
onInteraction={args => onInteraction({ ...args, ...commandOptions })}
{...componentProps}
/>
);
return <div key={id}>{tool}</div>;
})}
</>
)}
</div>
);
};
return (
<>
{ToolTipMessage && (
<Tooltip>
<TooltipTrigger asChild>
<span>
<StatusArea />
</span>
</TooltipTrigger>
<TooltipContent
side="bottom"
align="start"
>
<ToolTipMessage />
</TooltipContent>
</Tooltip>
)}
{!ToolTipMessage && <StatusArea />}
</>
);
}
export default OHIFCornerstoneSRMeasurementViewport;
@@ -9,7 +9,7 @@ function OHIFCornerstoneSRTextViewport(props: withAppTypes) {
const instance = displaySet.instances[0];
return (
<div className="text-foreground relative flex h-full w-full flex-col overflow-auto p-4">
<div className="relative flex h-full w-full flex-col overflow-auto p-4 text-white">
<div>
{/* The root level is always a container */}
<OHIFCornerstoneSRContainer container={instance} />
@@ -1,5 +1,4 @@
import { utils, classes, DisplaySetService, Types as OhifTypes } from '@ohif/core';
import i18n from '@ohif/i18n';
import { utils, classes, DisplaySetService, Types } from '@ohif/core';
import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
import { adaptersSR } from '@cornerstonejs/adapters';
@@ -15,14 +14,10 @@ import { CodeNameCodeSequenceValues, CodingSchemeDesignators } from './enums';
const { sopClassDictionary } = utils;
const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
const { MetadataProvider: metadataProvider } = classes;
const {
TEXT_ANNOTATION_POSITION,
COMMENT_CODE,
CodeScheme: Cornerstone3DCodeScheme,
} = adaptersSR.Cornerstone3D;
const { ImageSet, MetadataProvider: metadataProvider } = classes;
const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
type InstanceMetadata = OhifTypes.InstanceMetadata;
type InstanceMetadata = Types.InstanceMetadata;
/**
* TODO
@@ -35,7 +30,6 @@ const sopClassUids = [
sopClassDictionary.BasicTextSR,
sopClassDictionary.EnhancedSR,
sopClassDictionary.ComprehensiveSR,
sopClassDictionary.Comprehensive3DSR,
];
const validateSameStudyUID = (uid: string, instances): void => {
@@ -54,7 +48,7 @@ const validateSameStudyUID = (uid: string, instances): void => {
* @param instances is a list of instances from THIS series that are not
* in this DICOM SR Display Set already.
*/
function addInstances(instances: InstanceMetadata[], _displaySetService: DisplaySetService) {
function addInstances(instances: InstanceMetadata[], displaySetService: DisplaySetService) {
this.instances.push(...instances);
utils.sortStudyInstances(this.instances);
// The last instance is the newest one, so is the one most interesting.
@@ -69,10 +63,9 @@ function addInstances(instances: InstanceMetadata[], _displaySetService: Display
* DICOM SR SOP Class Handler
* For all referenced images in the TID 1500/300 sections, add an image to the
* display.
* @param {InstanceMetadata[]} instances - A set of instances all from the same series
* @param {AppTypes.ServicesManager} servicesManager - The services that can be used for creating
* @param {AppTypes.ExtensionManager} extensionManager - The extension manager
* @returns {Types.DisplaySet[]} The list of display sets created for the given instances object
* @param instances is a set of instances all from the same series
* @param servicesManager is the services that can be used for creating
* @returns The list of display sets created for the given instances object
*/
function _getDisplaySetsFromSeries(
instances,
@@ -100,7 +93,6 @@ function _getDisplaySetsFromSeries(
SeriesTime,
ConceptNameCodeSequence,
SOPClassUID,
imageId: predecessorImageId,
} = instance;
validateSameStudyUID(instance.StudyInstanceUID, instances);
@@ -129,9 +121,7 @@ function _getDisplaySetsFromSeries(
isImagingMeasurementReport,
sopClassUids,
instance,
predecessorImageId,
addInstances,
label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('SR')}`,
};
displaySet.load = () => _load(displaySet, servicesManager, extensionManager);
@@ -146,7 +136,7 @@ function _getDisplaySetsFromSeries(
* @param extensionManager - The extension manager containing data sources.
*/
async function _load(
srDisplaySet: OhifTypes.DisplaySet,
srDisplaySet: Types.DisplaySet,
servicesManager: AppTypes.ServicesManager,
extensionManager: AppTypes.ExtensionManager
) {
@@ -186,10 +176,6 @@ async function _load(
srDisplaySet.referencedImages = [];
srDisplaySet.measurements = [];
}
const { predecessorImageId } = srDisplaySet;
for (const measurement of srDisplaySet.measurements) {
measurement.predecessorImageId = predecessorImageId;
}
const mappings = measurementService.getSourceMappings(
CORNERSTONE_3D_TOOLS_SOURCE_NAME,
@@ -200,13 +186,8 @@ async function _load(
srDisplaySet.isRehydratable = isRehydratable(srDisplaySet, mappings);
srDisplaySet.isLoaded = true;
/** Check currently added displaySets and add measurements if the sources exist.
* Walk the SR's study first in default series order (not load order) so SCOORD3D
* FrameOfReference matching picks a stable series when several share FOR. */
const displaySetsForSRPass = utils.sortDisplaySetsCopy(displaySetService.activeDisplaySets, {
studyInstanceUIDFirst: srDisplaySet.StudyInstanceUID,
});
displaySetsForSRPass.forEach(activeDisplaySet => {
/** Check currently added displaySets and add measurements if the sources exist */
displaySetService.activeDisplaySets.forEach(activeDisplaySet => {
_checkIfCanAddMeasurementsToDisplaySet(
srDisplaySet,
activeDisplaySet,
@@ -233,15 +214,17 @@ async function _load(
});
}
function _measurementBelongsToDisplaySet({ measurement, displaySet }) {
return (
measurement.coords[0].ReferencedFrameOfReferenceSequence === displaySet.FrameOfReferenceUID
);
}
/**
* Checks if measurements can be added to a display set.
*
* @param srDisplaySet - The source display set containing measurements.
* @param newDisplaySet - The new display set to check if measurements can be added.
* @param dataSource - The data source used to retrieve image IDs.
* @param servicesManager - The services manager.
*/
function _checkIfCanAddMeasurementsToDisplaySet(
srDisplaySet: OhifTypes.DisplaySet,
newDisplaySet: OhifTypes.DisplaySet,
srDisplaySet,
newDisplaySet,
dataSource,
servicesManager: AppTypes.ServicesManager
) {
@@ -251,10 +234,18 @@ function _checkIfCanAddMeasurementsToDisplaySet(
measurement => measurement.loaded === false
);
if (!unloadedMeasurements.length || newDisplaySet.unsupported) {
if (
unloadedMeasurements.length === 0 ||
!(newDisplaySet instanceof ImageSet) ||
newDisplaySet.unsupported
) {
return;
}
// const { sopClassUids } = newDisplaySet;
// Create a Set for faster lookups
// const sopClassUidSet = new Set(sopClassUids);
// Create a Map to efficiently look up ImageIds by SOPInstanceUID and frame number
const imageIdMap = new Map<string, string>();
const imageIds = dataSource.getImageIdsForDisplaySet(newDisplaySet);
@@ -273,7 +264,6 @@ function _checkIfCanAddMeasurementsToDisplaySet(
for (let j = unloadedMeasurements.length - 1; j >= 0; j--) {
let measurement = unloadedMeasurements[j];
const is3DMeasurement = measurement.coords?.[0]?.ValueType === 'SCOORD3D';
const onBeforeSRAddMeasurement = customizationService.getCustomization(
'onBeforeSRAddMeasurement'
@@ -288,15 +278,9 @@ function _checkIfCanAddMeasurementsToDisplaySet(
}
// if it is 3d SR we can just add the SR annotation
if (
is3DSR &&
is3DMeasurement &&
_measurementBelongsToDisplaySet({ measurement, displaySet: newDisplaySet })
) {
addSRAnnotation({ measurement, displaySet: newDisplaySet });
if (is3DSR) {
addSRAnnotation(measurement, null, null);
measurement.loaded = true;
measurement.displaySetInstanceUID = newDisplaySet.displaySetInstanceUID;
unloadedMeasurements.splice(j, 1);
continue;
}
@@ -314,12 +298,15 @@ function _checkIfCanAddMeasurementsToDisplaySet(
imageId &&
_measurementReferencesSOPInstanceUID(measurement, ReferencedSOPInstanceUID, frame)
) {
addSRAnnotation({ measurement, imageId, frameNumber: frame, displaySet: newDisplaySet });
addSRAnnotation(measurement, imageId, frame);
// Update measurement properties
measurement.loaded = true;
measurement.imageId = imageId;
measurement.displaySetInstanceUID = newDisplaySet.displaySetInstanceUID;
measurement.ReferencedSOPInstanceUID = ReferencedSOPInstanceUID;
measurement.frameNumber = frame;
unloadedMeasurements.splice(j, 1);
}
}
@@ -327,10 +314,10 @@ function _checkIfCanAddMeasurementsToDisplaySet(
/**
* Checks if a measurement references a specific SOP Instance UID.
* @param {any} measurement - The measurement object.
* @param {string} sopInstanceUID - The SOP Instance UID to check against.
* @param {number} frameNumber - The frame number to check against (optional).
* @returns {boolean} True if the measurement references the specified SOP Instance UID, false otherwise.
* @param measurement - The measurement object.
* @param SOPInstanceUID - The SOP Instance UID to check against.
* @param frameNumber - The frame number to check against (optional).
* @returns True if the measurement references the specified SOP Instance UID, false otherwise.
*/
function _measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frameNumber) {
const { coords } = measurement;
@@ -362,11 +349,12 @@ function _measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frame
/**
* Retrieves the SOP class handler module.
*
* @param {OhifTypes.Extensions.ExtensionParams} params - The extension parameters.
* @returns {Array} An array containing the SOP class handler modules.
* @param {Object} options - The options for retrieving the SOP class handler module.
* @param {Object} options.servicesManager - The services manager.
* @param {Object} options.extensionManager - The extension manager.
* @returns {Array} An array containing the SOP class handler module.
*/
function getSopClassHandlerModule(params: OhifTypes.Extensions.ExtensionParams) {
const { servicesManager, extensionManager } = params;
function getSopClassHandlerModule({ servicesManager, extensionManager }) {
const getDisplaySetsFromSeries = instances => {
return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
};
@@ -387,8 +375,8 @@ function getSopClassHandlerModule(params: OhifTypes.Extensions.ExtensionParams)
/**
* Retrieves the measurements from the ImagingMeasurementReportContentSequence.
*
* @param {any[]} imagingMeasurementReportContentSequence - The ImagingMeasurementReportContentSequence array.
* @returns {any[]} The array of measurements.
* @param {Array} ImagingMeasurementReportContentSequence - The ImagingMeasurementReportContentSequence array.
* @returns {Array} - The array of measurements.
*/
function _getMeasurements(ImagingMeasurementReportContentSequence) {
const ImagingMeasurements = ImagingMeasurementReportContentSequence.find(
@@ -426,8 +414,8 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) {
/**
* Retrieves merged content sequences by tracking unique identifiers.
*
* @param {any[]} measurementGroups - The measurement groups.
* @returns {Object} The merged content sequences by tracking unique identifiers.
* @param {Array} MeasurementGroups - The measurement groups.
* @returns {Object} - The merged content sequences by tracking unique identifiers.
*/
function _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups) {
const mergedContentSequencesByTrackingUniqueIdentifiers = {};
@@ -474,11 +462,15 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups
* it calls the _processTID1410Measurement function.
* Otherwise, it calls the _processNonGeometricallyDefinedMeasurement function.
*
* @param {any[]} mergedContentSequence - The merged content sequence to process.
* @returns {any} The processed measurement result.
* @param {Array<Object>} mergedContentSequence - The merged content sequence to process.
* @returns {any} - The processed measurement result.
*/
function _processMeasurement(mergedContentSequence) {
if (mergedContentSequence.some(group => isScoordOr3d(group) && !isTextPosition(group))) {
if (
mergedContentSequence.some(
group => group.ValueType === 'SCOORD' || group.ValueType === 'SCOORD3D'
)
) {
return _processTID1410Measurement(mergedContentSequence);
}
@@ -490,8 +482,8 @@ function _processMeasurement(mergedContentSequence) {
* TID 1410 style measurements have a SCOORD or SCOORD3D at the top level,
* and non-geometric representations where each NUM has "INFERRED FROM" SCOORD/SCOORD3D.
*
* @param {any[]} mergedContentSequence - The merged content sequence containing the measurements.
* @returns {any} The measurement object containing the loaded status, labels, coordinates, tracking unique identifier, and tracking identifier.
* @param mergedContentSequence - The merged content sequence containing the measurements.
* @returns The measurement object containing the loaded status, labels, coordinates, tracking unique identifier, and tracking identifier.
*/
function _processTID1410Measurement(mergedContentSequence) {
// Need to deal with TID 1410 style measurements, which will have a SCOORD or SCOORD3D at the top level,
@@ -516,25 +508,12 @@ function _processTID1410Measurement(mergedContentSequence) {
const NUMContentItems = mergedContentSequence.filter(group => group.ValueType === 'NUM');
const { ConceptNameCodeSequence: conceptNameItem } = graphicItem;
const { CodeValue: graphicValue, CodingSchemeDesignator: graphicDesignator } = conceptNameItem;
const graphicCode = `${graphicDesignator}:${graphicValue}`;
const pointDataItem = _getCoordsFromSCOORDOrSCOORD3D(graphicItem);
const is3DMeasurement = pointDataItem.ValueType === 'SCOORD3D';
const pointLength = is3DMeasurement ? 3 : 2;
const pointsLength = pointDataItem.GraphicData.length / pointLength;
const measurement = {
loaded: false,
labels: [],
coords: [pointDataItem],
coords: [_getCoordsFromSCOORDOrSCOORD3D(graphicItem)],
TrackingUniqueIdentifier: UIDREFContentItem.UID,
TrackingIdentifier: TrackingIdentifierContentItem.TextValue,
graphicCode,
is3DMeasurement,
pointsLength,
graphicType: pointDataItem.GraphicType,
};
NUMContentItems.forEach(item => {
@@ -564,8 +543,8 @@ function _processTID1410Measurement(mergedContentSequence) {
/**
* Processes the non-geometrically defined measurement from the merged content sequence.
*
* @param {any[]} mergedContentSequence The merged content sequence containing the measurement data.
* @returns {any} The processed measurement object.
* @param mergedContentSequence The merged content sequence containing the measurement data.
* @returns The processed measurement object.
*/
function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
const NUMContentItems = mergedContentSequence.filter(group => group.ValueType === 'NUM');
@@ -585,12 +564,6 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.FindingSite
);
const commentSites = mergedContentSequence.filter(
item =>
item.ConceptNameCodeSequence.CodingSchemeDesignator === COMMENT_CODE.schemeDesignator &&
item.ConceptNameCodeSequence.CodeValue === COMMENT_CODE.value
);
const measurement = {
loaded: false,
labels: [],
@@ -599,14 +572,6 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
TrackingIdentifier: TrackingIdentifierContentItem.TextValue,
};
if (commentSites) {
for (const group of commentSites) {
if (group.TextValue) {
measurement.labels.push({ label: group.TextValue, value: '' });
}
}
}
if (
finding &&
CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
@@ -642,39 +607,15 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
NUMContentItems.forEach(item => {
const { ConceptNameCodeSequence, ContentSequence, MeasuredValueSequence } = item;
// Handle spatial reference ONLY if ContentSequence exists.
// ContentSequence may be a scalar SCOORD or an array when additional named
// SCOORDs (e.g. control points) are nested alongside the primary geometry.
// Pick the primary geometry entry: prefer the SCOORD without a
// ConceptNameCodeSequence (plain polyline), falling back to the first SCOORD.
if (ContentSequence) {
const scoordItem = Array.isArray(ContentSequence)
? (ContentSequence.find(
cs =>
(cs.ValueType === 'SCOORD' || cs.ValueType === 'SCOORD3D') &&
!cs.ConceptNameCodeSequence
) ?? ContentSequence.find(cs => cs.ValueType === 'SCOORD' || cs.ValueType === 'SCOORD3D'))
: ContentSequence;
const { ValueType } = ContentSequence;
if (!ValueType === 'SCOORD') {
console.warn(`Graphic ${ValueType} not currently supported, skipping annotation.`);
return;
}
if (!scoordItem) {
console.warn(
'ContentSequence array contains no SCOORD or SCOORD3D entry, skipping annotation.'
);
return;
}
const { ValueType } = scoordItem;
if (ValueType !== 'SCOORD' && ValueType !== 'SCOORD3D') {
console.warn(`Graphic ${ValueType} not currently supported, skipping annotation.`);
return;
}
const coords = _getCoordsFromSCOORDOrSCOORD3D(scoordItem);
if (coords) {
measurement.coords.push(coords);
}
const coords = _getCoordsFromSCOORDOrSCOORD3D(ContentSequence);
if (coords) {
measurement.coords.push(coords);
}
if (MeasuredValueSequence) {
@@ -689,8 +630,8 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
/**
* Extracts coordinates from a graphic item of type SCOORD or SCOORD3D.
* @param {any} graphicItem - The graphic item containing the coordinates.
* @returns {any} The extracted coordinates.
* @param {object} graphicItem - The graphic item containing the coordinates.
* @returns {object} - The extracted coordinates.
*/
const _getCoordsFromSCOORDOrSCOORD3D = graphicItem => {
const { ValueType, GraphicType, GraphicData } = graphicItem;
@@ -704,9 +645,9 @@ const _getCoordsFromSCOORDOrSCOORD3D = graphicItem => {
/**
* Retrieves the label and value from the provided ConceptNameCodeSequence and MeasuredValueSequence.
* @param {any} conceptNameCodeSequence - The ConceptNameCodeSequence object.
* @param {any} measuredValueSequence - The MeasuredValueSequence object.
* @returns {Object} An object containing the label and value.
* @param {Object} ConceptNameCodeSequence - The ConceptNameCodeSequence object.
* @param {Object} MeasuredValueSequence - The MeasuredValueSequence object.
* @returns {Object} - An object containing the label and value.
* The label represents the CodeMeaning from the ConceptNameCodeSequence.
* The value represents the formatted NumericValue and CodeValue from the MeasuredValueSequence.
* Example: { label: 'Long Axis', value: '31.00 mm' }
@@ -725,8 +666,8 @@ function _getLabelFromMeasuredValueSequence(ConceptNameCodeSequence, MeasuredVal
/**
* Retrieves a list of referenced images from the Imaging Measurement Report Content Sequence.
*
* @param {any[]} imagingMeasurementReportContentSequence - The Imaging Measurement Report Content Sequence.
* @returns {any[]} The list of referenced images.
* @param {Array} ImagingMeasurementReportContentSequence - The Imaging Measurement Report Content Sequence.
* @returns {Array} - The list of referenced images.
*/
function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
const ImageLibrary = ImagingMeasurementReportContentSequence.find(
@@ -773,7 +714,7 @@ function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
* Otherwise, the sequence is wrapped in an array and returned.
*
* @param {any} sequence - The DICOM sequence to convert.
* @returns {any[]} The converted array.
* @returns {any[]} - The converted array.
*/
function _getSequenceAsArray(sequence) {
if (!sequence) {
@@ -782,17 +723,4 @@ function _getSequenceAsArray(sequence) {
return Array.isArray(sequence) ? sequence : [sequence];
}
function isScoordOr3d(group) {
return group.ValueType === 'SCOORD' || group.ValueType === 'SCOORD3D';
}
function isTextPosition(group) {
const concept = group.ConceptNameCodeSequence[0];
return (
concept &&
concept.CodeValue === TEXT_ANNOTATION_POSITION.value &&
concept.CodingSchemeDesignator === TEXT_ANNOTATION_POSITION.schemeDesignator
);
}
export default getSopClassHandlerModule;
+26 -2
View File
@@ -9,13 +9,19 @@ import {
LengthTool,
PlanarFreehandROITool,
RectangleROITool,
utilities as csToolsUtils,
} from '@cornerstonejs/tools';
import { Types } from '@ohif/core';
import { Types, MeasurementService } from '@ohif/core';
import { StackViewport, utilities as csUtils } from '@cornerstonejs/core';
import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
import DICOMSRDisplayTool from './tools/DICOMSRDisplayTool';
import SCOORD3DPointTool from './tools/SCOORD3DPointTool';
import SRSCOOR3DProbeMapper from './utils/SRSCOOR3DProbeMapper';
import addToolInstance from './utils/addToolInstance';
import toolNames from './tools/toolNames';
const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
/**
* @param {object} configuration
*/
@@ -23,6 +29,8 @@ export default function init({
configuration = {},
servicesManager,
}: Types.Extensions.ExtensionParams): void {
const { measurementService, cornerstoneViewportService } = servicesManager.services;
addToolInstance(toolNames.DICOMSRDisplay, DICOMSRDisplayTool);
addToolInstance(toolNames.SRLength, LengthTool);
addToolInstance(toolNames.SRBidirectional, BidirectionalTool);
@@ -32,10 +40,26 @@ export default function init({
addToolInstance(toolNames.SRAngle, AngleTool);
addToolInstance(toolNames.SRPlanarFreehandROI, PlanarFreehandROITool);
addToolInstance(toolNames.SRRectangleROI, RectangleROITool);
addToolInstance(toolNames.SRSCOORD3DPoint, SCOORD3DPointTool);
// TODO - fix the SR display of Cobb Angle, as it joins the two lines
addToolInstance(toolNames.SRCobbAngle, CobbAngleTool);
const csTools3DVer1MeasurementSource = measurementService.getSource(
CORNERSTONE_3D_TOOLS_SOURCE_NAME,
CORNERSTONE_3D_TOOLS_SOURCE_VERSION
);
const { POINT } = measurementService.VALUE_TYPES;
measurementService.addMapping(
csTools3DVer1MeasurementSource,
'SRSCOORD3DPoint',
POINT,
SRSCOOR3DProbeMapper.toAnnotation,
SRSCOOR3DProbeMapper.toMeasurement
);
// Modify annotation tools to use dashed lines on SR
const dashedLine = {
lineDash: '4,4',
@@ -1,7 +1,11 @@
import React from 'react';
import { SOPClassHandlerId, SOPClassHandlerId3D } from './id';
import { ViewportActionButton } from '@ohif/ui-next';
import i18n from '@ohif/i18n';
export default function onModeEnter({ servicesManager }) {
const { displaySetService } = servicesManager.services;
const { displaySetService, toolbarService } = servicesManager.services;
const displaySetCache = displaySetService.getDisplaySetCache();
const srDisplaySets = [...displaySetCache.values()].filter(
@@ -12,4 +16,24 @@ export default function onModeEnter({ servicesManager }) {
// New mode route, allow SRs to be hydrated again
ds.isHydrated = false;
});
toolbarService.addButtons([
{
// A base/default button for loading measurements. It is added to the toolbar below.
// Customizations to this button can be made in the mode or by another extension.
// For example, the button label can be changed and/or the command to clear
// the measurements can be dropped.
id: 'loadSRMeasurements',
component: props => (
<ViewportActionButton {...props}>{i18n.t('Common:LOAD')}</ViewportActionButton>
),
props: {
commands: ['clearMeasurements', 'loadSRMeasurements'],
},
},
]);
// The toolbar used in the viewport's status bar. Modes and extensions can further customize
// it to optionally add other buttons.
toolbarService.createButtonSection('loadSRMeasurements', ['loadSRMeasurements']);
}
@@ -69,12 +69,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
trackingUniqueIdentifiers.includes(annotation.data?.TrackingUniqueIdentifier)
);
const hasActors =
typeof viewport.getActors === 'function'
? viewport.getActors().length > 0
: Boolean(viewport._actors?.size);
if (!hasActors) {
if (!viewport._actors?.size) {
return;
}
@@ -0,0 +1,203 @@
import { Types, metaData, utilities as csUtils } from '@cornerstonejs/core';
import {
annotation,
drawing,
utilities,
Types as cs3DToolsTypes,
AnnotationDisplayTool,
} from '@cornerstonejs/tools';
import toolNames from './toolNames';
import { Annotation } from '@cornerstonejs/tools/dist/types/types';
export default class SCOORD3DPointTool extends AnnotationDisplayTool {
static toolName = toolNames.SRSCOORD3DPoint;
constructor(
toolProps = {},
defaultToolProps = {
configuration: {},
}
) {
super(toolProps, defaultToolProps);
}
_getTextBoxLinesFromLabels(labels) {
// TODO -> max 5 for now (label + shortAxis + longAxis), need a generic solution for this!
const labelLength = Math.min(labels.length, 5);
const lines = [];
return lines;
}
// This tool should not inherit from AnnotationTool and we should not need
// to add the following lines.
isPointNearTool = () => null;
getHandleNearImagePoint = () => null;
renderAnnotation = (enabledElement: Types.IEnabledElement, svgDrawingHelper: any): void => {
const { viewport } = enabledElement;
const { element } = viewport;
const annotations = annotation.state.getAnnotations(this.getToolName(), element);
// Todo: We don't need this anymore, filtering happens in triggerAnnotationRender
if (!annotations?.length) {
return;
}
// Filter toolData to only render the data for the active SR.
const filteredAnnotations = annotations;
if (!viewport._actors?.size) {
return;
}
const styleSpecifier: cs3DToolsTypes.AnnotationStyle.StyleSpecifier = {
toolGroupId: this.toolGroupId,
toolName: this.getToolName(),
viewportId: enabledElement.viewport.id,
};
for (let i = 0; i < filteredAnnotations.length; i++) {
const annotation = filteredAnnotations[i];
const annotationUID = annotation.annotationUID;
const { renderableData } = annotation.data;
const { POINT: points } = renderableData;
styleSpecifier.annotationUID = annotationUID;
const lineWidth = this.getStyle('lineWidth', styleSpecifier, annotation);
const lineDash = this.getStyle('lineDash', styleSpecifier, annotation);
const color = this.getStyle('color', styleSpecifier, annotation);
const options = {
color,
lineDash,
lineWidth,
};
const point = points[0][0];
// check if viewport can render it
const viewable = viewport.isReferenceViewable(
{ FrameOfReferenceUID: annotation.metadata.FrameOfReferenceUID, cameraFocalPoint: point },
{ asNearbyProjection: true }
);
if (!viewable) {
continue;
}
// render the point
const arrowPointCanvas = viewport.worldToCanvas(point);
// Todo: configure this
const arrowEndCanvas = [arrowPointCanvas[0] + 20, arrowPointCanvas[1] + 20];
const canvasCoordinates = [arrowPointCanvas, arrowEndCanvas];
drawing.drawArrow(
svgDrawingHelper,
annotationUID,
'1',
canvasCoordinates[1],
canvasCoordinates[0],
{
color: options.color,
width: options.lineWidth,
}
);
this.renderTextBox(
svgDrawingHelper,
viewport,
canvasCoordinates,
annotation,
styleSpecifier,
options
);
}
};
renderTextBox(
svgDrawingHelper,
viewport,
canvasCoordinates,
annotation,
styleSpecifier,
options = {}
) {
if (!canvasCoordinates || !annotation) {
return;
}
const { annotationUID, data = {} } = annotation;
const { labels } = data;
const textLines = [];
for (const label of labels) {
// make this generic
// fix this
if (label.label === '363698007') {
textLines.push(`Finding Site: ${label.value}`);
}
}
const { color } = options;
const adaptedCanvasCoordinates = canvasCoordinates;
// adapt coordinates if there is an adapter
const canvasTextBoxCoords = utilities.drawing.getTextBoxCoordsCanvas(adaptedCanvasCoordinates);
if (!annotation.data?.handles?.textBox?.worldPosition) {
annotation.data.handles.textBox.worldPosition = viewport.canvasToWorld(canvasTextBoxCoords);
}
const textBoxPosition = viewport.worldToCanvas(annotation.data.handles.textBox.worldPosition);
const textBoxUID = '1';
const textBoxOptions = this.getLinkedTextBoxStyle(styleSpecifier, annotation);
const boundingBox = drawing.drawLinkedTextBox(
svgDrawingHelper,
annotationUID,
textBoxUID,
textLines,
textBoxPosition,
canvasCoordinates,
{},
{
...textBoxOptions,
color,
}
);
const { x: left, y: top, width, height } = boundingBox;
annotation.data.handles.textBox.worldBoundingBox = {
topLeft: viewport.canvasToWorld([left, top]),
topRight: viewport.canvasToWorld([left + width, top]),
bottomLeft: viewport.canvasToWorld([left, top + height]),
bottomRight: viewport.canvasToWorld([left + width, top + height]),
};
}
public getLinkedTextBoxStyle(
specifications: cs3DToolsTypes.AnnotationStyle.StyleSpecifier,
annotation?: Annotation
): Record<string, unknown> {
// Todo: this function can be used to set different styles for different toolMode
// for the textBox.
return {
visibility: this.getStyle('textBoxVisibility', specifications, annotation),
fontFamily: this.getStyle('textBoxFontFamily', specifications, annotation),
fontSize: this.getStyle('textBoxFontSize', specifications, annotation),
color: this.getStyle('textBoxColor', specifications, annotation),
shadow: this.getStyle('textBoxShadow', specifications, annotation),
background: this.getStyle('textBoxBackground', specifications, annotation),
lineWidth: this.getStyle('textBoxLinkLineWidth', specifications, annotation),
lineDash: this.getStyle('textBoxLinkLineDash', specifications, annotation),
};
}
}
@@ -9,6 +9,7 @@ const toolNames = {
SRCobbAngle: 'SRCobbAngle',
SRRectangleROI: 'SRRectangleROI',
SRPlanarFreehandROI: 'SRPlanarFreehandROI',
SRSCOORD3DPoint: 'SRSCOORD3DPoint',
};
export default toolNames;
@@ -0,0 +1,62 @@
const SRSCOOR3DProbe = {
toAnnotation: measurement => {},
/**
* Maps cornerstone annotation event data to measurement service format.
*
* @param {Object} cornerstone Cornerstone event data
* @return {Measurement} Measurement instance
*/
toMeasurement: (
csToolsEventDetail,
displaySetService,
CornerstoneViewportService,
getValueTypeFromToolType,
customizationService
) => {
const { annotation } = csToolsEventDetail;
const { metadata, data, annotationUID } = annotation;
if (!metadata || !data) {
console.warn('Probe tool: Missing metadata or data');
return null;
}
const { toolName } = metadata;
const { points } = data.handles;
const displayText = getDisplayText(annotation);
return {
uid: annotationUID,
points,
metadata,
toolName: metadata.toolName,
label: data.label,
displayText: displayText,
data: data.cachedStats,
type: getValueTypeFromToolType?.(toolName) ?? null,
};
},
};
function getDisplayText(annotation) {
const { data } = annotation;
if (!data) {
return [''];
}
const { labels } = data;
const displayText = [];
for (const label of labels) {
// make this generic
if (label.label === '33636980076') {
displayText.push(`Finding Site: ${label.value}`);
}
}
return displayText;
}
export default SRSCOOR3DProbe;
@@ -1,59 +1,11 @@
import { Types, annotation } from '@cornerstonejs/tools';
import { metaData } from '@cornerstonejs/core';
import { adaptersSR } from '@cornerstonejs/adapters';
import getRenderableData from './getRenderableData';
import toolNames from '../tools/toolNames';
const { MeasurementReport } = adaptersSR.Cornerstone3D;
/**
* Adds a DICOM SR (Structured Report) annotation to the annotation manager.
* This function processes measurement data from DICOM SR and converts it into
* a format suitable for display in the Cornerstone3D viewer.
*
* @param {Object} params - The parameters object
* @param {Object} params.measurement - The DICOM SR measurement data containing coordinates, labels, and metadata
* @param {Array} params.measurement.coords - Array of coordinate objects with GraphicType, ValueType, and other properties
* @param {string} params.measurement.TrackingUniqueIdentifier - Unique identifier for the measurement
* @param {string} params.measurement.TrackingIdentifier - Tracking identifier for adapter lookup
* @param {Array} [params.measurement.labels] - Optional array of label objects
* @param {string} [params.measurement.displayText] - Optional display text for the annotation
* @param {Object} [params.measurement.textBox] - Optional text box configuration
* @param {string|null} [params.imageId] - Optional image ID for the referenced image (defaults to null)
* @param {number|null} [params.frameNumber] - Optional frame number for multi-frame images (defaults to null)
* @param {Object} params.displaySet - The display set containing the image
* @param {string} params.displaySet.displaySetInstanceUID - Unique identifier for the display set
* @returns {void}
*
* @example
* ```typescript
* addSRAnnotation({
* measurement: {
* TrackingUniqueIdentifier: '1.2.3.4.5',
* TrackingIdentifier: 'POINT',
* coords: [{
* GraphicType: 'POINT',
* ValueType: 'SCOORD',
* // ... other coordinate properties
* }],
* labels: [{ value: 'Measurement Point' }],
* displayText: 'Point measurement'
* },
* imageId: 'wadouri:file://path/to/image.dcm', // Optional
* frameNumber: 0, // Optional
* displaySet: { displaySetInstanceUID: '1.2.3.4' }
* });
* ```
*/
export default function addSRAnnotation({ measurement, imageId = null, frameNumber = null, displaySet }) {
/** @type {string} The tool name to use for the annotation, defaults to DICOMSRDisplay */
export default function addSRAnnotation(measurement, imageId, frameNumber) {
let toolName = toolNames.DICOMSRDisplay;
/**
* @type {Object} Renderable data organized by graphic type
* Groups coordinate data by GraphicType for efficient rendering
*/
const renderableData = measurement.coords.reduce((acc, coordProps) => {
acc[coordProps.GraphicType] = acc[coordProps.GraphicType] || [];
acc[coordProps.GraphicType].push(getRenderableData({ ...coordProps, imageId }));
@@ -64,58 +16,32 @@ export default function addSRAnnotation({ measurement, imageId = null, frameNumb
const { ValueType: valueType, GraphicType: graphicType } = measurement.coords[0];
const graphicTypePoints = renderableData[graphicType];
/**
* TODO: Read the tool name from the DICOM SR identification type in the future.
*/
/** TODO: Read the tool name from the DICOM SR identification type in the future. */
let frameOfReferenceUID = null;
let planeRestriction = null;
/**
* Store the view reference for use in initial navigation
*/
if (imageId) {
const imagePlaneModule = metaData.get('imagePlaneModule', imageId);
frameOfReferenceUID = imagePlaneModule?.frameOfReferenceUID;
}
/**
* Store the view reference for use in initial navigation
*/
if (valueType === 'SCOORD3D') {
toolName = toolNames.SRSCOORD3DPoint;
// get the ReferencedFrameOfReferenceUID from the measurement
frameOfReferenceUID = measurement.coords[0].ReferencedFrameOfReferenceSequence;
planeRestriction = {
FrameOfReferenceUID: frameOfReferenceUID,
point: graphicTypePoints[0][0],
};
}
/**
* Store the view reference for use in initial navigation
*/
measurement.viewReference = {
planeRestriction,
FrameOfReferenceUID: frameOfReferenceUID,
referencedImageId: imageId,
};
/**
* @type {Types.Annotation} The annotation object to be added to the annotation manager
* Contains all necessary metadata and data for rendering the DICOM SR measurement
*/
const SRAnnotation: Types.Annotation = {
annotationUID: TrackingUniqueIdentifier,
highlighted: false,
isLocked: false,
isPreview: toolName === toolNames.DICOMSRDisplay,
invalidated: false,
metadata: {
toolName,
planeRestriction,
valueType,
graphicType,
FrameOfReferenceUID: frameOfReferenceUID,
referencedImageId: imageId,
displaySetInstanceUID: displaySet.displaySetInstanceUID,
},
data: {
label: measurement.labels?.[0]?.value || undefined,
@@ -133,11 +59,9 @@ export default function addSRAnnotation({ measurement, imageId = null, frameNumb
};
/**
* Add the annotation to the annotation state manager.
* Note: Using annotation.state.addAnnotation() instead of annotationManager.addAnnotation()
* because the latter was not triggering annotation_added events properly.
*
* @param {Types.Annotation} SRAnnotation - The annotation to add
* const annotationManager = annotation.annotationState.getAnnotationManager();
* was not triggering annotation_added events.
*/
annotation.state.addAnnotation(SRAnnotation);
console.debug('Adding SR annotation:', SRAnnotation);
}
@@ -1,11 +1,17 @@
import OHIF from '@ohif/core';
import { annotation } from '@cornerstonejs/tools';
import { NO_IMAGE_ID } from '@cornerstonejs/adapters';
const { log } = OHIF;
function getFilteredCornerstoneToolState(measurementData, additionalFindingTypes) {
const filteredToolState = {};
function addToFilteredToolState(annotation, toolType) {
const imageId = annotation.metadata?.referencedImageId ?? NO_IMAGE_ID;
if (!annotation.metadata?.referencedImageId) {
log.warn(`[DICOMSR] No referencedImageId found for ${toolType} ${annotation.id}`);
return;
}
const imageId = annotation.metadata.referencedImageId;
if (!filteredToolState[imageId]) {
filteredToolState[imageId] = {};
@@ -11,11 +11,7 @@ const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
* @returns {string} The extracted label.
*/
export default function getLabelFromDCMJSImportedToolData(toolData) {
const { findingSites = [], finding, annotation } = toolData;
if (annotation.data.label) {
return annotation.data.label;
}
const { findingSites = [], finding } = toolData;
let freeTextLabel = findingSites.find(
fs => fs.CodeValue === Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT
@@ -36,14 +36,6 @@ function getRenderableData({ GraphicType, GraphicData, ValueType, imageId }) {
ValueType,
imageId,
});
if (!imageId) {
// without the image id it's not possible to perform the calculations below
// these calculations also do not seem to be needed, since everything works
// just fine when we skip them. At least for SCOORD3D annotations.
return pointsWorld;
}
// We do not have an explicit draw circle svg helper in Cornerstone3D at
// this time, but we can use the ellipse svg helper to draw a circle, so
// here we reshape the data for that purpose.
@@ -98,13 +90,6 @@ function getRenderableData({ GraphicType, GraphicData, ValueType, imageId }) {
imageId,
});
if (!imageId) {
// without the image id it's not possible to perform the calculations below
// these calculations also do not seem to be needed, since everything works
// just fine when we skip them. At least for SCOORD3D annotations.
return pointsWorld;
}
const majorAxisStart = vec3.fromValues(...pointsWorld[0]);
const majorAxisEnd = vec3.fromValues(...pointsWorld[1]);
const minorAxisStart = vec3.fromValues(...pointsWorld[2]);
@@ -1,16 +1,15 @@
import { utilities, metaData, type Types } from '@cornerstonejs/core';
import { utilities, metaData } from '@cornerstonejs/core';
import OHIF, { DicomMetadataStore } from '@ohif/core';
import { vec3 } from 'gl-matrix';
import getLabelFromDCMJSImportedToolData from './getLabelFromDCMJSImportedToolData';
import { adaptersSR } from '@cornerstonejs/adapters';
import { annotation as CsAnnotation, type Types as ToolTypes } from '@cornerstonejs/tools';
import { annotation as CsAnnotation } from '@cornerstonejs/tools';
import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
const { locking } = CsAnnotation;
const { guid } = OHIF.utils;
const { MeasurementReport } = adaptersSR.Cornerstone3D;
const { MeasurementReport, CORNERSTONE_3D_TAG } = adaptersSR.Cornerstone3D;
const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
const convertCode = (codingValues, code) => {
if (!code || code.CodingSchemeDesignator === 'CORNERSTONEJS') {
@@ -38,10 +37,8 @@ const convertSites = (codingValues, sites) => {
};
/**
* Hydrates a structured report
* Handles 2d and 3d hydration from SCOORD and SCOORD3D points
* For 3D hydration, chooses a volume display set to display with
* FOr 2D hydration, chooses the (first) display set containing the referenced image.
* Hydrates a structured report, for default viewports.
*
*/
export default function hydrateStructuredReport(
{ servicesManager, extensionManager, commandsManager }: withAppTypes,
@@ -54,11 +51,6 @@ export default function hydrateStructuredReport(
const disableEditing = customizationService.getCustomization('panelMeasurement.disableEditing');
const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
const {
StudyInstanceUID: studyUID,
SeriesInstanceUID: seriesUID,
instance: { SOPInstanceUID: sopUID },
} = displaySet;
// TODO -> We should define a strict versioning somewhere.
const mappings = measurementService.getSourceMappings(
@@ -72,23 +64,31 @@ export default function hydrateStructuredReport(
);
}
const instance = DicomMetadataStore.getInstance(studyUID, seriesUID, sopUID);
const instance = DicomMetadataStore.getInstance(
displaySet.StudyInstanceUID,
displaySet.SeriesInstanceUID,
displaySet.SOPInstanceUID
);
const sopInstanceUIDToImageId = {};
const imageIdsForToolState = {};
displaySet.measurements.forEach(measurement => {
const { ReferencedSOPInstanceUID, imageId, frameNumber = 1 } = measurement;
const key = `${ReferencedSOPInstanceUID}:${frameNumber}`;
const { ReferencedSOPInstanceUID, imageId, frameNumber } = measurement;
if (imageId && !sopInstanceUIDToImageId[key]) {
sopInstanceUIDToImageId[key] = imageId;
if (!sopInstanceUIDToImageId[ReferencedSOPInstanceUID]) {
sopInstanceUIDToImageId[ReferencedSOPInstanceUID] = imageId;
imageIdsForToolState[ReferencedSOPInstanceUID] = [];
}
if (!imageIdsForToolState[ReferencedSOPInstanceUID][frameNumber]) {
imageIdsForToolState[ReferencedSOPInstanceUID][frameNumber] = imageId;
}
});
// Mapping of legacy datasets is now directly handled by adapters module
const datasetToUse = instance;
// Use CS3D adapters to generate toolState.
// Use dcmjs to generate toolState.
let storedMeasurementByAnnotationType = MeasurementReport.generateToolState(
datasetToUse,
// NOTE: we need to pass in the imageIds to dcmjs since the we use them
@@ -96,6 +96,7 @@ export default function hydrateStructuredReport(
// that measurements were added to the display set are the same order as
// the measurementGroups in the instance.
sopInstanceUIDToImageId,
utilities.imageToWorldCoords,
metaData
);
@@ -118,17 +119,40 @@ export default function hydrateStructuredReport(
}
});
// Set the series touched as tracked.
const imageIds = [];
// TODO: notification if no hydratable?
Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
toolDataForAnnotationType.forEach(toolData => {
// Add the measurement to toolState
// dcmjs and Cornerstone3D has structural defect in supporting multi-frame
// files, and looking up the imageId from sopInstanceUIDToImageId results
// in the wrong value.
const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
const imageId =
imageIdsForToolState[toolData.sopInstanceUid][frameNumber] ||
sopInstanceUIDToImageId[toolData.sopInstanceUid];
if (!imageIds.includes(imageId)) {
imageIds.push(imageId);
}
});
});
let targetStudyInstanceUID;
const SeriesInstanceUIDs = [];
// Set the series touched as tracked.
const imageIds = getImageIds(hydratableMeasurementsInSR, sopInstanceUIDToImageId);
for (const imageId of imageIds) {
for (let i = 0; i < imageIds.length; i++) {
const imageId = imageIds[i];
const { SeriesInstanceUID, StudyInstanceUID } = metaData.get('instance', imageId);
if (!SeriesInstanceUIDs.includes(SeriesInstanceUID)) {
SeriesInstanceUIDs.push(SeriesInstanceUID);
}
if (!targetStudyInstanceUID) {
targetStudyInstanceUID = StudyInstanceUID;
} else if (targetStudyInstanceUID !== StudyInstanceUID) {
@@ -136,79 +160,38 @@ export default function hydrateStructuredReport(
}
}
// For 3d annotations there are no image IDs,
// so we need to find the display sets by frame of reference to get the SeriesInstanceUIDs
const frameOfReferenceUIDs = getFrameOfReferenceUIDs(
hydratableMeasurementsInSR,
sopInstanceUIDToImageId
);
for (const FrameOfReferenceUID of frameOfReferenceUIDs) {
const displaySetsFOR = displaySetService.getDisplaySetsBy(
ds => ds.FrameOfReferenceUID === FrameOfReferenceUID && !ds.isDerivedDisplaySet
);
const ds = chooseDisplaySet(displaySetsFOR, FrameOfReferenceUID);
if (!ds) {
continue;
}
if (!SeriesInstanceUIDs.includes(ds.SeriesInstanceUID)) {
SeriesInstanceUIDs.push(ds.SeriesInstanceUID);
}
if (!targetStudyInstanceUID) {
targetStudyInstanceUID = ds.StudyInstanceUID;
} else if (targetStudyInstanceUID !== ds.StudyInstanceUID) {
console.warn('NO SUPPORT FOR SRs THAT HAVE MEASUREMENTS FROM MULTIPLE STUDIES.');
}
}
/**
* Gets reference data for what frame of reference and the referenced
* image id, or for 3d measurements, the volumeId to apply this annotation to.
*/
function getReferenceData(toolData): ToolTypes.AnnotationMetadata {
// Add the measurement to toolState
// dcmjs and Cornerstone3D has structural defect in supporting multi-frame
// files, and looking up the imageId from sopInstanceUIDToImageId results
// in the wrong value.
const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
const imageId = sopInstanceUIDToImageId[`${toolData.sopInstanceUid}:${frameNumber}`];
if (!imageId) {
return getReferenceData3D(toolData, servicesManager);
}
const instance = metaData.get('instance', imageId);
const {
FrameOfReferenceUID,
// SOPInstanceUID,
// SeriesInstanceUID,
// StudyInstanceUID,
} = instance;
return {
referencedImageId: imageId,
FrameOfReferenceUID,
};
}
Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
toolDataForAnnotationType.forEach(toolData => {
// Add the measurement to toolState
// dcmjs and Cornerstone3D has structural defect in supporting multi-frame
// files, and looking up the imageId from sopInstanceUIDToImageId results
// in the wrong value.
const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
const imageId =
imageIdsForToolState[toolData.sopInstanceUid][frameNumber] ||
sopInstanceUIDToImageId[toolData.sopInstanceUid];
toolData.uid = guid();
const referenceData = getReferenceData(toolData);
const { referencedImageId } = referenceData;
const instance = metaData.get('instance', imageId);
const {
FrameOfReferenceUID,
// SOPInstanceUID,
// SeriesInstanceUID,
// StudyInstanceUID,
} = instance;
const annotation = {
annotationUID: toolData.annotation.annotationUID,
data: toolData.annotation.data,
predecessorImageId: toolData.predecessorImageId,
metadata: {
...referenceData,
toolName: annotationType,
referencedImageId: imageId,
FrameOfReferenceUID,
},
};
utilities.updatePlaneRestriction(annotation.data.handles.points, annotation.metadata);
const source = measurementService.getSource(
CORNERSTONE_3D_TOOLS_SOURCE_NAME,
@@ -242,8 +225,8 @@ export default function hydrateStructuredReport(
locking.setAnnotationLocked(newAnnotationUID, true);
}
if (referencedImageId && !imageIds.includes(referencedImageId)) {
imageIds.push(referencedImageId);
if (!imageIds.includes(imageId)) {
imageIds.push(imageId);
}
});
});
@@ -255,141 +238,3 @@ export default function hydrateStructuredReport(
SeriesInstanceUIDs,
};
}
/**
* Gets the unique imageIds from hydratable measurements that have an imageId reference
* (i.e., 2D/SCOORD annotations).
*/
function getImageIds(hydratableMeasurementsInSR, sopInstanceUIDToImageId): string[] {
const imageIds: string[] = [];
Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
toolDataForAnnotationType.forEach(toolData => {
// Add the measurement to toolState
// dcmjs and Cornerstone3D has structural defect in supporting multi-frame
// files, and looking up the imageId from sopInstanceUIDToImageId results
// in the wrong value.
const frameNumber = toolData.annotation.data?.frameNumber || 1;
const imageId = sopInstanceUIDToImageId[`${toolData.sopInstanceUid}:${frameNumber}`];
if (imageId && !imageIds.includes(imageId)) {
imageIds.push(imageId);
}
});
});
return imageIds;
}
/**
* Gets the unique FrameOfReferenceUIDs from hydratable measurements that have no imageId reference
* (i.e., 3D/SCOORD3D annotations). This excludes annotations handled by the getImageIds function.
*/
function getFrameOfReferenceUIDs(hydratableMeasurementsInSR, sopInstanceUIDToImageId): string[] {
const frameOfReferenceUIDs: string[] = [];
Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
toolDataForAnnotationType.forEach(toolData => {
const frameNumber = toolData.annotation.data?.frameNumber || 1;
const imageId = sopInstanceUIDToImageId[`${toolData.sopInstanceUid}:${frameNumber}`];
if (!imageId) {
const { FrameOfReferenceUID } = toolData.annotation.metadata;
if (FrameOfReferenceUID && !frameOfReferenceUIDs.includes(FrameOfReferenceUID)) {
frameOfReferenceUIDs.push(FrameOfReferenceUID);
}
}
});
});
return frameOfReferenceUIDs;
}
/**
* For 3d annotations, there are often several display sets which could
* be used to display the annotation. Choose the first annotation with the
* same frame of reference that is reconstructable, or the first display set
* otherwise.
*/
function chooseDisplaySet(displaySets, reference) {
if (!displaySets?.length) {
console.warn('No display set found for', reference);
return;
}
if (displaySets.length === 1) {
return displaySets[0];
}
const volumeDs = displaySets.find(ds => ds.isReconstructable);
if (volumeDs) {
return volumeDs;
}
return displaySets[0];
}
/**
* Gets the additional reference data appropriate for a 3d reference.
* This will choose a volume id, frame of reference and a plane restriction.
*/
function getReferenceData3D(toolData, servicesManager: Types.ServicesManager) {
const { FrameOfReferenceUID } = toolData.annotation.metadata;
const { points } = toolData.annotation.data.handles;
const { displaySetService } = servicesManager.services;
const displaySetsFOR = displaySetService.getDisplaySetsBy(
ds => ds.FrameOfReferenceUID === FrameOfReferenceUID
);
if (!displaySetsFOR.length || !points?.length) {
return {
FrameOfReferenceUID,
};
}
const ds = chooseDisplaySet(displaySetsFOR, toolData.annotation);
const cameraView = chooseCameraView(ds, points);
const viewReference = {
...cameraView,
volumeId: ds.displaySetInstanceUID,
FrameOfReferenceUID,
};
utilities.updatePlaneRestriction(points, viewReference);
return viewReference;
}
/**
* Chooses a possible camera view - right now this is fairly basic,
* just setting the unknowns to null.
*/
function chooseCameraView(_ds, points) {
const selectedPoints = choosePoints(points);
const cameraFocalPoint = <Point3>centerOf(selectedPoints);
// These are sufficient to be null for now and can be set on first view
let viewPlaneNormal: Types.Point3 = null;
let viewUp: Types.Point3 = null;
return {
cameraFocalPoint,
viewPlaneNormal,
viewUp,
};
}
function centerOf(points) {
const scale = 1 / points.length;
const center = vec3.create();
for (const point of points) {
vec3.scaleAndAdd(center, center, point, scale);
}
return center;
}
function choosePoints(points) {
if (points.length === 1 || points.length === 2) {
return points;
}
const firstIndex = 0;
const secondIndex = Math.ceil(points.length / 4);
const thirdIndex = Math.ceil(points.length / 2);
// TODO - check if colinear, if so try to find another 3 points.
const newPoints = [points[firstIndex], points[secondIndex], points[thirdIndex]];
return newPoints;
}
@@ -22,20 +22,13 @@ export default function isRehydratable(displaySet, mappings) {
const { measurements } = displaySet;
for (let i = 0; i < measurements.length; i++) {
const measurement = measurements[i];
if (!measurement) {
continue;
}
const { TrackingIdentifier = '', graphicType, graphicCode, pointsLength } = measurement;
if (!TrackingIdentifier && !graphicType) {
console.warn('No tracking identifier or graphicType for measurement ', measurement);
const { TrackingIdentifier } = measurements[i] || {};
if (!TrackingIdentifier) {
console.warn('No tracking identifier for measurement ', measurements[i]);
continue;
}
const adapter = MeasurementReport.getAdapterForTrackingIdentifier(TrackingIdentifier);
const adapters = MeasurementReport.getAdaptersForTypes(graphicCode, graphicType, pointsLength);
const hydratable =
(adapter && mappingDefinitions.has(adapter.toolType)) ||
(adapters && adapters.some(adapter => mappingDefinitions.has(adapter.toolType)));
const hydratable = adapter && mappingDefinitions.has(adapter.toolType);
if (hydratable) {
return true;
@@ -1,8 +1,8 @@
const webpack = require('@rspack/core');
const webpack = require('webpack');
const { merge } = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const MiniCssExtractPlugin = webpack.CssExtractRspackPlugin;
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const pkg = require('./../package.json');
@@ -35,11 +35,9 @@ module.exports = (env, argv) => {
sideEffects: true,
},
output: {
library: {
name: 'ohif-extension-cornerstone',
type: 'umd',
},
path: ROOT_DIR,
library: 'ohif-extension-cornerstone',
libraryTarget: 'umd',
filename: pkg.main,
},
externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
File diff suppressed because it is too large. Load diff
@@ -1,15 +1,12 @@
{
"name": "@ohif/extension-cornerstone-dynamic-volume",
"version": "3.13.0-beta.97",
"version": "3.10.4",
"description": "OHIF extension for 4D volumes data",
"author": "OHIF",
"license": "MIT",
"repository": "OHIF/Viewers",
"main": "dist/ohif-extension-cornerstone-dynamic-volume.umd.js",
"module": "src/index.ts",
"engines": {
"node": ">=24"
},
"exports": {
".": "./src/index.ts",
"./types": "./src/types/index.ts"
@@ -22,34 +19,31 @@
"access": "public"
},
"scripts": {
"dev": "cross-env NODE_ENV=development rspack build --config .webpack/webpack.dev.js --watch",
"build": "cross-env NODE_ENV=production rspack build --config .webpack/webpack.prod.js",
"build:package": "pnpm run build",
"dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --output-pathinfo",
"build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
"build:package": "yarn run build",
"clean": "shx rm -rf dist",
"clean:deep": "pnpm run clean && shx rm -rf node_modules",
"start": "pnpm run dev",
"clean:deep": "yarn run clean && shx rm -rf node_modules",
"start": "yarn run dev",
"test:unit": "jest --watchAll",
"test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
},
"peerDependencies": {
"@ohif/core": "workspace:*",
"@ohif/extension-cornerstone": "workspace:*",
"@ohif/extension-default": "workspace:*",
"@ohif/i18n": "workspace:*",
"@ohif/ui": "workspace:*",
"dcmjs": "0.49.4",
"dicom-parser": "1.8.21",
"hammerjs": "2.0.8",
"prop-types": "15.8.1",
"react": "18.3.1"
"@ohif/core": "3.10.4",
"@ohif/extension-cornerstone": "3.10.4",
"@ohif/extension-default": "3.10.4",
"@ohif/i18n": "3.10.4",
"@ohif/ui": "3.10.4",
"dcmjs": "*",
"dicom-parser": "^1.8.21",
"hammerjs": "^2.0.8",
"prop-types": "^15.6.2",
"react": "^18.3.1"
},
"dependencies": {
"@babel/runtime": "7.29.7",
"@cornerstonejs/core": "5.0.2",
"@cornerstonejs/tools": "5.0.2",
"classnames": "2.5.1"
},
"devDependencies": {
"cross-env": "7.0.3"
"@babel/runtime": "^7.20.13",
"@cornerstonejs/core": "^3.11.6",
"@cornerstonejs/tools": "^3.11.6",
"classnames": "^2.3.2"
}
}
@@ -1,10 +1,8 @@
import * as importedActions from './actions';
import { utilities, Enums } from '@cornerstonejs/tools';
import { cache } from '@cornerstonejs/core';
import { utils } from '@ohif/core';
import * as importedActions from './actions';
const { downloadCsv } = utils;
const LABELMAP = Enums.SegmentationRepresentations.Labelmap;
const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
const services = servicesManager.services;
@@ -39,7 +37,7 @@ const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
});
return computedDisplaySets;
},
exportTimeReportCSV: ({ segmentations, summaryStats }) => {
exportTimeReportCSV: ({ segmentations, config, options, summaryStats }) => {
const dynamic4DDisplaySet = actions.getDynamic4DDisplaySet();
const volumeId = dynamic4DDisplaySet?.displaySetInstanceUID;
@@ -205,7 +203,15 @@ const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
// Generate filename and trigger download
const filename = `${instance.PatientID}.csv`;
downloadCsv(csvContent, { filename });
const blob = new Blob([csvContent], { type: 'text/csv;charset=utf-8;' });
const link = document.createElement('a');
const url = URL.createObjectURL(blob);
link.setAttribute('href', url);
link.setAttribute('download', filename);
link.style.visibility = 'hidden';
document.body.appendChild(link);
link.click();
document.body.removeChild(link);
},
swapDynamicWithComputedDisplaySet: ({ displaySet }) => {
const computedDisplaySet = displaySet;
@@ -5,8 +5,6 @@ import { PanelSegmentation } from '@ohif/extension-cornerstone';
import DynamicExport from './panels/DynamicExport';
function getPanelModule({ commandsManager, extensionManager, servicesManager, configuration }) {
const { toolbarService } = servicesManager.services;
const wrappedDynamicDataPanel = () => {
return (
<DynamicDataPanel
@@ -21,8 +19,8 @@ function getPanelModule({ commandsManager, extensionManager, servicesManager, co
return (
<>
<Toolbox
buttonSectionId={toolbarService.sections.dynamicToolbox}
title="Buttons:Threshold Tools"
buttonSectionId="dynamic-toolbox"
title="Threshold Tools"
/>
<PanelSegmentation
servicesManager={servicesManager}
@@ -5,7 +5,7 @@ function DynamicDataPanel({ servicesManager, commandsManager, tab }: withAppType
return (
<>
<div
className="text-foreground flex flex-col"
className="flex flex-col text-white"
data-cy={'dynamic-volume-panel'}
>
<PanelGenerateImage
@@ -10,7 +10,7 @@ function WorkflowPanel({ servicesManager }: { servicesManager: ServicesManager }
return (
<div
data-cy={'workflow-panel'}
className="bg-popover mb-1 px-3 py-4"
className="bg-secondary-dark mb-1 px-3 py-4"
>
<div className="mb-1">Workflow</div>
<div>
@@ -1,8 +1,8 @@
const webpack = require('@rspack/core');
const webpack = require('webpack');
const { merge } = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.base.js');
const MiniCssExtractPlugin = webpack.CssExtractRspackPlugin;
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const pkg = require('./../package.json');
@@ -35,11 +35,9 @@ module.exports = (env, argv) => {
sideEffects: true,
},
output: {
library: {
name: 'ohif-extension-cornerstone',
type: 'umd',
},
path: ROOT_DIR,
library: 'ohif-extension-cornerstone',
libraryTarget: 'umd',
filename: pkg.main,
},
externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
File diff suppressed because it is too large. Load diff
+2 -4
View File
@@ -1,11 +1,9 @@
const base = require('../../jest.config.base.js');
const pkg = require('./package');
module.exports = {
...base,
moduleNameMapper: {
...base.moduleNameMapper,
'@ohif/(.*)': '<rootDir>/../../platform/$1/src',
},
displayName: pkg.name,
// rootDir: "../.."
// testMatch: [
// //`<rootDir>/platform/${pack.name}/**/*.spec.js`
+40 -46
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-cornerstone",
"version": "3.13.0-beta.97",
"version": "3.10.4",
"description": "OHIF extension for Cornerstone",
"author": "OHIF",
"license": "MIT",
@@ -13,7 +13,9 @@
"./types": "./src/types/index.ts"
},
"engines": {
"node": ">=24"
"node": ">=10",
"npm": ">=6",
"yarn": ">=1.16.0"
},
"files": [
"dist",
@@ -24,54 +26,46 @@
},
"scripts": {
"clean": "shx rm -rf dist",
"clean:deep": "pnpm run clean && shx rm -rf node_modules",
"dev": "cross-env NODE_ENV=development rspack build --config .webpack/webpack.dev.js --watch",
"dev:cornerstone": "pnpm run dev",
"build": "cross-env NODE_ENV=production rspack build --config .webpack/webpack.prod.js",
"build:package-1": "pnpm run build",
"start": "pnpm run dev",
"test:unit": "jest --watchAll",
"test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
"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:cornerstone": "yarn run dev",
"build": "cross-env NODE_ENV=production webpack --progress --config .webpack/webpack.prod.js",
"build:package-1": "yarn run build",
"start": "yarn run dev"
},
"peerDependencies": {
"@cornerstonejs/codec-charls": "1.2.3",
"@cornerstonejs/codec-libjpeg-turbo-8bit": "1.2.2",
"@cornerstonejs/codec-openjpeg": "1.3.0",
"@cornerstonejs/codec-openjph": "2.4.7",
"@cornerstonejs/dicom-image-loader": "5.0.2",
"@ohif/core": "workspace:*",
"@ohif/extension-default": "workspace:*",
"@ohif/ui": "workspace:*",
"dcmjs": "0.49.4",
"dicom-parser": "1.8.21",
"hammerjs": "2.0.8",
"prop-types": "15.8.1",
"react": "18.3.1",
"react-dom": "18.3.1",
"react-resize-detector": "10.0.1"
"@cornerstonejs/codec-charls": "^1.2.3",
"@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
"@cornerstonejs/codec-openjpeg": "^1.2.4",
"@cornerstonejs/codec-openjph": "^2.4.5",
"@cornerstonejs/dicom-image-loader": "^3.11.6",
"@ohif/core": "3.10.4",
"@ohif/ui": "3.10.4",
"dcmjs": "*",
"dicom-parser": "^1.8.21",
"hammerjs": "^2.0.8",
"prop-types": "^15.6.2",
"react": "^18.3.1",
"react-dom": "^18.3.1",
"react-resize-detector": "^10.0.1"
},
"dependencies": {
"@babel/runtime": "7.29.7",
"@cornerstonejs/adapters": "5.0.2",
"@cornerstonejs/ai": "5.0.2",
"@cornerstonejs/core": "5.0.2",
"@cornerstonejs/labelmap-interpolation": "5.0.2",
"@cornerstonejs/metadata": "5.0.2",
"@cornerstonejs/polymorphic-segmentation": "5.0.2",
"@cornerstonejs/tools": "5.0.2",
"@icr/polyseg-wasm": "0.4.0",
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^3.11.6",
"@cornerstonejs/ai": "^3.11.6",
"@cornerstonejs/core": "^3.11.6",
"@cornerstonejs/labelmap-interpolation": "^3.11.6",
"@cornerstonejs/polymorphic-segmentation": "^3.11.6",
"@cornerstonejs/tools": "^3.11.6",
"@itk-wasm/morphological-contour-interpolation": "1.1.0",
"@kitware/vtk.js": "35.5.3",
"html2canvas": "1.4.1",
"immutability-helper": "3.1.1",
"lodash.compact": "3.0.1",
"lodash.debounce": "4.0.8",
"lodash.flatten": "4.4.0",
"lodash.zip": "4.2.0",
"shader-loader": "1.3.1",
"worker-loader": "3.0.8"
},
"devDependencies": {
"cross-env": "7.0.3"
"@kitware/vtk.js": "32.12.0",
"html2canvas": "^1.4.1",
"lodash.compact": "^3.0.1",
"lodash.debounce": "^4.0.8",
"lodash.flatten": "^4.4.0",
"lodash.merge": "^4.6.2",
"lodash.zip": "^4.2.0",
"shader-loader": "^1.3.1",
"worker-loader": "^3.0.8"
}
}
@@ -2,11 +2,6 @@
width: 100%;
height: 100%; /* MUST have `height` to prevent resize infinite loop */
position: relative;
/* Prevent text selection on the entire viewport wrapper */
user-select: none;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
}
.cornerstone-viewport-element {
@@ -21,26 +16,4 @@
/* Prevents the entire page from getting larger
when the magnify tool is near the sides/corners of the page */
overflow: hidden;
/* Prevent text selection on the viewport element */
user-select: none;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
}
/* Prevent text selection on overlay elements */
.noselect {
user-select: none;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
}
/* Ensure all elements within viewport wrapper prevent text selection */
.viewport-wrapper * {
user-select: none;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
}
@@ -1,7 +1,9 @@
import React, { useEffect, useRef, useCallback, useState } from 'react';
import { useResizeDetector } from 'react-resize-detector';
import * as cs3DTools from '@cornerstonejs/tools';
import { Enums, eventTarget, getEnabledElement } from '@cornerstonejs/core';
import { MeasurementService, useViewportRef } from '@ohif/core';
import { MeasurementService } from '@ohif/core';
import { AllInOneMenu } from '@ohif/ui-next';
import { useViewportDialog } from '@ohif/ui-next';
import type { Types as csTypes } from '@cornerstonejs/core';
@@ -13,6 +15,8 @@ import CinePlayer from '../components/CinePlayer';
import type { Types } from '@ohif/core';
import OHIFViewportActionCorners from '../components/OHIFViewportActionCorners';
import { getWindowLevelActionMenu } from '../components/WindowLevelActionMenu/getWindowLevelActionMenu';
import { getViewportDataOverlaySettingsMenu } from '../components/ViewportDataOverlaySettingMenu';
import { getViewportPresentations } from '../utils/presentations/getViewportPresentations';
import { useSynchronizersStore } from '../stores/useSynchronizersStore';
import ActiveViewportBehavior from '../utils/ActiveViewportBehavior';
@@ -20,9 +24,6 @@ import { WITH_NAVIGATION } from '../services/ViewportService/CornerstoneViewport
const STACK = 'stack';
// Cache for viewport dimensions, persists across component remounts
const viewportDimensions = new Map<string, { width: number; height: number }>();
// Todo: This should be done with expose of internal API similar to react-vtkjs-viewport
// Then we don't need to worry about the re-renders if the props change.
const OHIFCornerstoneViewport = React.memo(
@@ -40,6 +41,7 @@ const OHIFCornerstoneViewport = React.memo(
viewportOptions,
displaySetOptions,
servicesManager,
commandsManager,
onElementEnabled,
// eslint-disable-next-line react/prop-types
onElementDisabled,
@@ -81,7 +83,6 @@ const OHIFCornerstoneViewport = React.memo(
const [scrollbarHeight, setScrollbarHeight] = useState('100px');
const [enabledVPElement, setEnabledVPElement] = useState(null);
const elementRef = useRef() as React.MutableRefObject<HTMLDivElement>;
const viewportRef = useViewportRef(viewportId);
const {
displaySetService,
@@ -91,6 +92,7 @@ const OHIFCornerstoneViewport = React.memo(
cornerstoneViewportService,
segmentationService,
cornerstoneCacheService,
viewportActionCornersService,
customizationService,
measurementService,
} = servicesManager.services;
@@ -103,44 +105,12 @@ const OHIFCornerstoneViewport = React.memo(
}, [elementRef]);
// useCallback for onResize
const onResize = useCallback(
(entries: ResizeObserverEntry[]) => {
if (elementRef.current && entries?.length) {
const entry = entries[0];
const { width, height } = entry.contentRect;
const prevDimensions = viewportDimensions.get(viewportId) || { width: 0, height: 0 };
// Check if dimensions actually changed and then only resize if they have changed
const hasDimensionsChanged =
prevDimensions.width !== width || prevDimensions.height !== height;
if (width > 0 && height > 0 && hasDimensionsChanged) {
viewportDimensions.set(viewportId, { width, height });
// Perform resize operations
cornerstoneViewportService.resize();
setImageScrollBarHeight();
}
}
},
[viewportId, elementRef, cornerstoneViewportService, setImageScrollBarHeight]
);
useEffect(() => {
const element = elementRef.current;
if (!element) {
return;
const onResize = useCallback(() => {
if (elementRef.current) {
cornerstoneViewportService.resize();
setImageScrollBarHeight();
}
const resizeObserver = new ResizeObserver(onResize);
resizeObserver.observe(element);
// Cleanup function
return () => {
resizeObserver.unobserve(element);
resizeObserver.disconnect();
};
}, [onResize]);
}, [elementRef]);
const cleanUpServices = useCallback(
viewportInfo => {
@@ -151,8 +121,16 @@ const OHIFCornerstoneViewport = React.memo(
syncGroupService.removeViewportFromSyncGroup(viewportId, renderingEngineId, syncGroups);
segmentationService.clearSegmentationRepresentations(viewportId);
viewportActionCornersService.clear(viewportId);
},
[viewportId, segmentationService, syncGroupService, toolGroupService]
[
viewportId,
segmentationService,
syncGroupService,
toolGroupService,
viewportActionCornersService,
]
);
const elementEnabledHandler = useCallback(
@@ -220,7 +198,6 @@ const OHIFCornerstoneViewport = React.memo(
}
cornerstoneViewportService.disableElement(viewportId);
viewportRef.unregister();
eventTarget.removeEventListener(Enums.Events.ELEMENT_ENABLED, elementEnabledHandler);
};
@@ -304,6 +281,79 @@ const OHIFCornerstoneViewport = React.memo(
loadViewportData();
}, [viewportOptions, displaySets, dataSource]);
/**
* There are two scenarios for jump to click
* 1. Current viewports contain the displaySet that the annotation was drawn on
* 2. Current viewports don't contain the displaySet that the annotation was drawn on
* and we need to change the viewports displaySet for jumping.
* Since measurement_jump happens via events and listeners, the former case is handled
* by the measurement_jump direct callback, but the latter case is handled first by
* the viewportGrid to set the correct displaySet on the viewport, AND THEN we check
* the cache for jumping to see if there is any jump queued, then we jump to the correct slice.
*/
useEffect(() => {
if (isJumpToMeasurementDisabled) {
return;
}
const { unsubscribe } = measurementService.subscribe(
MeasurementService.EVENTS.JUMP_TO_MEASUREMENT_VIEWPORT,
event => handleJumpToMeasurement(event, elementRef, viewportId, cornerstoneViewportService)
);
return () => {
unsubscribe();
};
}, [displaySets, elementRef, viewportId, isJumpToMeasurementDisabled, servicesManager]);
// Set up the window level action menu in the viewport action corners.
useEffect(() => {
const windowLevelActionMenu = customizationService.getCustomization(
'viewportActionMenu.windowLevelActionMenu'
);
const segmentationOverlay = customizationService.getCustomization(
'viewportActionMenu.segmentationOverlay'
);
if (windowLevelActionMenu?.enabled) {
viewportActionCornersService.addComponent({
viewportId,
id: 'windowLevelActionMenu',
component: getWindowLevelActionMenu({
viewportId,
element: elementRef.current,
displaySets,
servicesManager,
commandsManager,
location: windowLevelActionMenu.location,
verticalDirection: AllInOneMenu.VerticalDirection.TopToBottom,
horizontalDirection: AllInOneMenu.HorizontalDirection.RightToLeft,
}),
location: windowLevelActionMenu.location,
});
}
if (segmentationOverlay?.enabled) {
viewportActionCornersService.addComponent({
viewportId,
id: 'segmentation',
component: getViewportDataOverlaySettingsMenu({
viewportId,
element: elementRef.current,
displaySets,
servicesManager,
commandsManager,
location: segmentationOverlay.location,
}),
location: segmentationOverlay.location,
});
}
}, [displaySets, viewportId, viewportActionCornersService, servicesManager, commandsManager]);
const { ref: resizeRef } = useResizeDetector({
onResize,
});
const Notification = customizationService.getCustomization('ui.notificationComponent');
return (
@@ -314,12 +364,9 @@ const OHIFCornerstoneViewport = React.memo(
style={{ height: '100%', width: '100%' }}
onContextMenu={e => e.preventDefault()}
onMouseDown={e => e.preventDefault()}
data-viewportid={viewportId}
ref={el => {
resizeRef.current = el;
elementRef.current = el;
if (el) {
viewportRef.register(el);
}
}}
></div>
<CornerstoneOverlays
@@ -361,6 +408,54 @@ const OHIFCornerstoneViewport = React.memo(
areEqual
);
// Helper function to handle jumping to measurements
function handleJumpToMeasurement(event, elementRef, viewportId, cornerstoneViewportService) {
const { measurement, isConsumed } = event;
if (!measurement || isConsumed) {
return;
}
const enabledElement = getEnabledElement(elementRef.current);
if (!enabledElement) {
return;
}
const viewport = enabledElement.viewport as csTypes.IStackViewport | csTypes.IVolumeViewport;
const { metadata, displaySetInstanceUID } = measurement;
const viewportDisplaySets = cornerstoneViewportService.getViewportDisplaySets(viewportId);
const showingDisplaySet = viewportDisplaySets.find(
ds => ds.displaySetInstanceUID === displaySetInstanceUID
);
let metadataToUse = metadata;
// if it is not showing the displaySet we need to remove the FOR from the metadata
if (!showingDisplaySet) {
metadataToUse = {
...metadata,
FrameOfReferenceUID: undefined,
};
}
// Todo: make it work with cases where we want to define FOR based measurements too
if (!viewport.isReferenceViewable(metadataToUse, WITH_NAVIGATION)) {
return;
}
try {
viewport.setViewReference(metadata);
viewport.render();
} catch (e) {
console.warn('Unable to apply', metadata, e);
}
cs3DTools.annotation.selection.setAnnotationSelected(measurement.uid);
event?.consume?.();
}
function _rehydrateSynchronizers(viewportId: string, syncGroupService: any) {
const { synchronizersStore } = useSynchronizersStore.getState();
const synchronizers = synchronizersStore[viewportId];
@@ -421,18 +516,22 @@ OHIFCornerstoneViewport.displayName = 'OHIFCornerstoneViewport';
function areEqual(prevProps, nextProps) {
if (nextProps.needsRerendering) {
console.debug('OHIFCornerstoneViewport: Rerender caused by: needsRerendering');
return false;
}
if (prevProps.displaySets.length !== nextProps.displaySets.length) {
console.debug('OHIFCornerstoneViewport: Rerender caused by: displaySets length change');
return false;
}
if (prevProps.viewportOptions.orientation !== nextProps.viewportOptions.orientation) {
console.debug('OHIFCornerstoneViewport: Rerender caused by: orientation change');
return false;
}
if (prevProps.viewportOptions.toolGroupId !== nextProps.viewportOptions.toolGroupId) {
console.debug('OHIFCornerstoneViewport: Rerender caused by: toolGroupId change');
return false;
}
@@ -440,10 +539,12 @@ function areEqual(prevProps, nextProps) {
nextProps.viewportOptions.viewportType &&
prevProps.viewportOptions.viewportType !== nextProps.viewportOptions.viewportType
) {
console.debug('OHIFCornerstoneViewport: Rerender caused by: viewportType change');
return false;
}
if (nextProps.viewportOptions.needsRerendering) {
console.debug('OHIFCornerstoneViewport: Rerender caused by: viewportOptions.needsRerendering');
return false;
}
@@ -451,6 +552,7 @@ function areEqual(prevProps, nextProps) {
const nextDisplaySets = nextProps.displaySets;
if (prevDisplaySets.length !== nextDisplaySets.length) {
console.debug('OHIFCornerstoneViewport: Rerender caused by: displaySets length mismatch');
return false;
}
@@ -463,11 +565,13 @@ function areEqual(prevProps, nextProps) {
);
if (!foundDisplaySet) {
console.debug('OHIFCornerstoneViewport: Rerender caused by: displaySet not found');
return false;
}
// check they contain the same image
if (foundDisplaySet.images?.length !== prevDisplaySet.images?.length) {
console.debug('OHIFCornerstoneViewport: Rerender caused by: images length mismatch');
return false;
}
@@ -475,6 +579,7 @@ function areEqual(prevProps, nextProps) {
if (foundDisplaySet.images?.length) {
for (let j = 0; j < foundDisplaySet.images.length; j++) {
if (foundDisplaySet.images[j].imageId !== prevDisplaySet.images[j].imageId) {
console.debug('OHIFCornerstoneViewport: Rerender caused by: imageId mismatch');
return false;
}
}
@@ -484,4 +589,16 @@ function areEqual(prevProps, nextProps) {
return true;
}
// Helper function to check if display sets have changed
function haveDisplaySetsChanged(prevDisplaySets, currentDisplaySets) {
if (prevDisplaySets.length !== currentDisplaySets.length) {
return true;
}
return currentDisplaySets.some((currentDS, index) => {
const prevDS = prevDisplaySets[index];
return currentDS.displaySetInstanceUID !== prevDS.displaySetInstanceUID;
});
}
export default OHIFCornerstoneViewport;
@@ -1,14 +1,13 @@
import React, { useEffect, useState } from 'react';
import ViewportImageScrollbar from './ViewportImageScrollbar';
import ViewportSliceProgressScrollbar from './ViewportSliceProgressScrollbar/ViewportSliceProgressScrollbar';
import CustomizableViewportOverlay from './CustomizableViewportOverlay';
import ViewportOrientationMarkers from './ViewportOrientationMarkers';
import ViewportImageSliceLoadingIndicator from './ViewportImageSliceLoadingIndicator';
function CornerstoneOverlays(props: withAppTypes) {
const { viewportId, element, scrollbarHeight, servicesManager } = props;
const { cornerstoneViewportService, customizationService } = servicesManager.services;
const { cornerstoneViewportService } = servicesManager.services;
const [imageSliceData, setImageSliceData] = useState({
imageIndex: 0,
numberOfSlices: 0,
@@ -44,31 +43,17 @@ function CornerstoneOverlays(props: withAppTypes) {
}
}
const viewportScrollbarVariant = customizationService.getCustomization('viewportScrollbar.variant');
const useProgressScrollbar = viewportScrollbarVariant !== 'legacy';
return (
<div className="noselect">
{useProgressScrollbar ? (
<ViewportSliceProgressScrollbar
viewportId={viewportId}
viewportData={viewportData}
element={element}
imageSliceData={imageSliceData}
setImageSliceData={setImageSliceData}
servicesManager={servicesManager}
/>
) : (
<ViewportImageScrollbar
viewportId={viewportId}
viewportData={viewportData}
element={element}
imageSliceData={imageSliceData}
setImageSliceData={setImageSliceData}
scrollbarHeight={scrollbarHeight}
servicesManager={servicesManager}
/>
)}
<ViewportImageScrollbar
viewportId={viewportId}
viewportData={viewportData}
element={element}
imageSliceData={imageSliceData}
setImageSliceData={setImageSliceData}
scrollbarHeight={scrollbarHeight}
servicesManager={servicesManager}
/>
<CustomizableViewportOverlay
imageSliceData={imageSliceData}
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