feat: Add DICOM SEG support and MPR, referenceLines and StackSync and…

… more (#3015) * feat: add initial sop class handler for SEG * feat: move segmentation service * update segmentation service methods * fix: viewport data structure * feat: Add initial render for the DICOM SEG for each displaySet * fix: various wrong architectural dependencies between services * feat: initial separate SEG display in each viewport * feat: refactore viewport action bar * initial work for SEG hydration * fix: various bugs regarding drag and dropping different viewports * fix: rendering issues for multiple seg displaysets * fix: bugs for thumbnail and hydration * feat: fix the initial segment color * update after rebase * feat: initial design for the segmentation group table * feat: initial new design for the segmentation panel * feat: segmentation panel * feat: make segmentation appear on all related viewports * fix: segmentation load bug based on functional groups * initial work for segmentation crosshairs * fix: various stylings and functionality * fix: various stylings for the seg panel * fix: overflow styles * feat: add more ui components * feat: added segmentation config * feat: add jump to segment * feat: add jump to segment for DICOM SEG viewport * fix: bugs after rebase * feat: jump in segmentation viewport * fix: mpr support for seg * feat: add more icons * feat: new icons * feat: add new side panel * feat: add segmentation config * feat: add loading indicator to ohif * feat: make hanging protocols follow matching rules for viewports * feat: enhance drag and drop to be hanging protocol aware * fix: mpr restore previous layout * fix: crosshairs toggle * fix: add auth headers to the dicom loader via dicomwebclient * fix: bug for crosshairs toggle in mpr * fix: seg viewport reusing old toolGroup * feat: add loading animation with lottie * fix: various bugs for Segmentation hydration in mpr * feat: change outline alpha to outline opacity * feat: loading indicator for seg viewport * fix: various segmentation group styles * fix: local mode for seg * feat: add animation for the highlight * fix: loading indicatro to show segment indices * feat: enhance modality drop down ui * fix: panels * fix: download form * fix: layout shift in loading indicator * fix: loading indicator to have correct values * fix: update software number * fix: image jump between MPR and default * fix: segmentation cleanup and cine service cleanup * fix: segmentation toolgroup clena up * fix: highlight interval should not trigger again * fix: issue with multiframe sorting * rename: change onSeriesChange to onArrowsClick * fix: buttons for tmtv and layout shift * fix: various bugs wrt crosshairs * fix: crosshairs re init on reset camera * fix: middle slice calculation different from cs middle reset camera * fix: reset camera should reset viewport camera * fix: loading segments in MPR mode * fix: tmtv hp back to before * fix: layout shift * feat: orientation markers for volume viewport * fix: capture for volume viewports * fix: memory leak for back to worklist * fix: loading bar bg color * fix: side panel for only one panel * fix: react select style in production * fix: various styling for segmentation groups * fix: various ui styles * feat: add new segmentation config styles * fix: hover state for segmentation item * fix: side panel layout shift * temp add panels * try to fix scrollbar for thimbnail * fix: scroll not appearing for side panels * feat: changed styles for scrollbar * feat: add cpu fallback warning * fix: webworker destroy * fix: select styles * fix: orientation marker color and position * fix: capture screenshot for volume viewports * fix: hide segment visibility on mpr * fix: reloading an already loaded seg displayset * feat: add is equal * fix: mpr jump to measurements * apply review comments * fix: optimization for the segmentation load * fix: remove unnecessary context menu and hp service reset * fix: segmentation service wrt brush settings * feat: initial work for the stack synchronization * fix: add validateDisplaySetSelectorsForNewDisplaySets to make sure drag and drop can follow requirements * fix: various react proptypes * fix: thumbnails for the tmtv and change default props to default params * feat: make showing loading indicator configurable and add docs * bump versions and add more docs * fix demo * update cornerstone versions * apply review comments * feat: add reference lines * fix build * fix unit tests * add reference lines icon * fix: e2e tests * fix static wado config * docs: add segmentation service docs * fix: docker build * fix: keep camera and bump versions * Try re-enabling minification to fix deploy previews Co-authored-by: Erik Ziegler <[email protected]>
OHIF · Nov 16, 2022 · 83ea228 · 83ea228
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diff --git a/.docker/README.md b/.docker/README.md
@@ -0,0 +1,43 @@
+# Docker compose files
+
+This folder contains docker-compose files used to spin up OHIF-Viewer with
+different options such as locally or with any PAS you desire to
+
+## Public Server
+
+## Local Orthanc
+
+### Build
+
+`$ docker-compose -f docker-compose-orthanc.yml build`
+
+### Run
+
+Starts containers and leaves them running in the background.
+
+`$ docker-compose -f docker-compose-orthanc.yml up -d`
+
+then, access the application at [http://localhost](http://localhost)
+
+**remember that you have to access orthanc application and include your studies
+there**
+
+## Local Dcm4chee
+
+#### build
+
+`$ docker-compose -f docker-compose-dcm4chee.yml build`
+
+#### run
+
+`$ docker-compose -f docker-compose-dcm4chee.yml up -d`
+
+then, access the application at [http://localhost](http://localhost)
+
+**remember that you have to access dcm4chee application and include your studies
+there** You can use the following command to import your studies into dcm4che
+
+`$ docker run -v {YOUR_STUDY_FOLDER}:/tmp --rm --network=docker_dcm4che_default dcm4che/dcm4che-tools:5.14.0 storescu -cDCM4CHEE@arc:11112 /tmp`
+
+**make sure that your Docker network name is docker_dcm4chee_default or change
+it to the right one**
diff --git a/.docker/Viewer-v2.x/default.conf → .docker/Viewer-v3.x/default.conf.template b/.docker/Viewer-v2.x/default.conf → .docker/Viewer-v3.x/default.conf.template
@@ -1,5 +1,6 @@
 server {
-  listen 80;
+  listen ${PORT};
+  # listen 3000;
   location / {
     root   /usr/share/nginx/html;
     index  index.html index.htm;

diff --git a/.docker/Viewer-v2.x/entrypoint.sh → .docker/Viewer-v3.x/entrypoint.sh b/.docker/Viewer-v2.x/entrypoint.sh → .docker/Viewer-v3.x/entrypoint.sh
@@ -1,4 +1,6 @@
-#!/bin/bash
+#!/bin/sh
+
+envsubst `${PORT}` < /usr/src/default.conf.template > /etc/nginx/conf.d/default.conf
 
 if [ -n "$CLIENT_ID" ] || [ -n "$HEALTHCARE_API_ENDPOINT" ]
   then

diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,5 @@
+# Set the default behavior,
+# in case people don't have core.autocrlf set.
+* text=auto
+# Declares that files will always have CRLF line ends
+*.sh text eol=lf
diff --git a/.gitignore b/.gitignore
@@ -40,3 +40,5 @@ screenshots/
 # autogenerated files
 platform/viewer/src/pluginImports.js
 /Viewers.iml
+platform/viewer/.recipes/Nginx-Dcm4Che/dcm4che/dcm4che-arc/*
+platform/viewer/.recipes/OpenResty-Orthanc/logs/*
diff --git a/Dockerfile b/Dockerfile
@@ -1,3 +1,23 @@
+# This dockerfile is used to publish the `ohif/viewer` image on dockerhub.
+#
+# It's a good example of how to build our static application and package it
+# with a web server capable of hosting it as static content.
+#
+# docker build
+# --------------
+# If you would like to use this dockerfile to build and tag an image, make sure
+# you set the context to the project's root directory:
+# https://docs.docker.com/engine/reference/commandline/build/
+#
+#
+# SUMMARY
+# --------------
+# This dockerfile has two stages:
+#
+# 1. Building the React application for production
+# 2. Setting up our Nginx (Alpine Linux) image w/ step one's output
+#
+
 
 # Stage 1: Build the application
 # docker build -t ohif/viewer:latest .
@@ -34,10 +54,21 @@ RUN yarn install --frozen-lockfile --verbose
 
 ENV PATH /usr/src/app/node_modules/.bin:$PATH
 ENV QUICK_BUILD true
+# ENV GENERATE_SOURCEMAP=false
+# ENV REACT_APP_CONFIG=config/default.js
+
+RUN yarn run build
 
 # Stage 3: Bundle the built application into a Docker container
 # which runs Nginx using Alpine Linux
-FROM nginx:1.15.5-alpine as final
-RUN apk add --no-cache bash
-RUN rm -rf /etc/nginx/conf.d
-COPY .docker/Viewer-v2.x /etc/nginx/conf.d
+FROM nginxinc/nginx-unprivileged:1.23.1-alpine as final
+#RUN apk add --no-cache bash
+ENV PORT=3000
+RUN rm /etc/nginx/conf.d/default.conf
+USER nginx
+COPY --chown=nginx:nginx .docker/Viewer-v3.x /usr/src
+RUN envsubst `${PORT}` < /usr/src/default.conf.template > /etc/nginx/conf.d/default.conf
+RUN chmod 777 /usr/src/entrypoint.sh
+COPY --from=builder /usr/src/app/platform/viewer/dist /usr/share/nginx/html
+ENTRYPOINT ["/usr/src/entrypoint.sh"]
+CMD ["nginx", "-g", "daemon off;"]
diff --git a/extensions/cornerstone-dicom-seg/.webpack/webpack.dev.js b/extensions/cornerstone-dicom-seg/.webpack/webpack.dev.js
@@ -0,0 +1,8 @@
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+};
diff --git a/extensions/cornerstone-dicom-seg/.webpack/webpack.prod.js b/extensions/cornerstone-dicom-seg/.webpack/webpack.prod.js
@@ -0,0 +1,63 @@
+const path = require('path');
+const pkg = require('../package.json');
+
+const outputFile = 'index.umd.js';
+const rootDir = path.resolve(__dirname, '../');
+const outputFolder = path.join(__dirname, `../dist/umd/${pkg.name}/`);
+
+// Todo: add ESM build for the extension in addition to umd build
+
+const config = {
+  mode: 'production',
+  entry: rootDir + '/' + pkg.module,
+  devtool: 'source-map',
+  output: {
+    path: outputFolder,
+    filename: outputFile,
+    library: pkg.name,
+    libraryTarget: 'umd',
+    chunkFilename: '[name].chunk.js',
+    umdNamedDefine: true,
+    globalObject: "typeof self !== 'undefined' ? self : this",
+  },
+  externals: [
+    {
+      react: {
+        root: 'React',
+        commonjs2: 'react',
+        commonjs: 'react',
+        amd: 'react',
+      },
+      '@ohif/core': {
+        commonjs2: '@ohif/core',
+        commonjs: '@ohif/core',
+        amd: '@ohif/core',
+        root: '@ohif/core',
+      },
+      '@ohif/ui': {
+        commonjs2: '@ohif/ui',
+        commonjs: '@ohif/ui',
+        amd: '@ohif/ui',
+        root: '@ohif/ui',
+      },
+    },
+  ],
+  module: {
+    rules: [
+      {
+        test: /(\.jsx|\.js|\.tsx|\.ts)$/,
+        loader: 'babel-loader',
+        exclude: /(node_modules|bower_components)/,
+        resolve: {
+          extensions: ['.js', '.jsx', '.ts', '.tsx'],
+        },
+      },
+    ],
+  },
+  resolve: {
+    modules: [path.resolve('./node_modules'), path.resolve('./src')],
+    extensions: ['.json', '.js', '.jsx', '.tsx', '.ts'],
+  },
+};
+
+module.exports = config;
diff --git a/extensions/cornerstone-dicom-seg/LICENSE b/extensions/cornerstone-dicom-seg/LICENSE
@@ -0,0 +1,20 @@
+MIT License
+
+Copyright (c) 2022 Open Health Imaging Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/extensions/cornerstone-dicom-seg/README.md b/extensions/cornerstone-dicom-seg/README.md
@@ -0,0 +1,18 @@
+# dicom-seg
+## Description
+
+DICOM SEG read workflow. This extension will allow you to load a DICOM SEG image
+and display it on OHIF. Currently Segmentations are loaded as a volumetric labelmap
+and displayed as a 3D volume.
+
+This extension provides a SEG viewport, which enables rendering and reviewing
+of the DICOM SEG images. However, in order to fully load all the segments
+you will need to click on the SEG Pill button on the viewport action bar
+to fully load the segments.
+
+## Author
+
+OHIF
+
+## License
+MIT
diff --git a/extensions/cornerstone-dicom-seg/babel.config.js b/extensions/cornerstone-dicom-seg/babel.config.js
@@ -0,0 +1,44 @@
+module.exports = {
+  plugins: ['inline-react-svg', '@babel/plugin-proposal-class-properties'],
+  env: {
+    test: {
+      presets: [
+        [
+          // TODO: https://babeljs.io/blog/2019/03/19/7.4.0#migration-from-core-js-2
+          '@babel/preset-env',
+          {
+            modules: 'commonjs',
+            debug: false,
+          },
+          "@babel/preset-typescript",
+        ],
+        '@babel/preset-react',
+      ],
+      plugins: [
+        '@babel/plugin-proposal-object-rest-spread',
+        '@babel/plugin-syntax-dynamic-import',
+        '@babel/plugin-transform-regenerator',
+        '@babel/plugin-transform-runtime',
+      ],
+    },
+    production: {
+      presets: [
+        // WebPack handles ES6 --> Target Syntax
+        ['@babel/preset-env', { modules: false }],
+        '@babel/preset-react',
+        "@babel/preset-typescript",
+      ],
+      ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
+    },
+    development: {
+      presets: [
+        // WebPack handles ES6 --> Target Syntax
+        ['@babel/preset-env', { modules: false }],
+        '@babel/preset-react',
+        "@babel/preset-typescript",
+      ],
+      plugins: ['react-hot-loader/babel'],
+      ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
+    },
+  },
+};
diff --git a/extensions/cornerstone-dicom-seg/package.json b/extensions/cornerstone-dicom-seg/package.json
@@ -0,0 +1,71 @@
+{
+  "name": "@ohif/extension-cornerstone-dicom-seg",
+  "version": "3.0.0",
+  "description": "DICOM SEG read workflow",
+  "author": "OHIF",
+  "license": "MIT",
+  "main": "dist/umd/@ohif/dicom-seg/index.umd.js",
+  "module": "src/index.tsx",
+  "files": [
+    "dist/**",
+    "public/**",
+    "README.md"
+  ],
+  "repository": "OHIF/Viewers",
+  "keywords": [
+    "ohif-extension"
+  ],
+  "engines": {
+    "node": ">=14",
+    "npm": ">=6",
+    "yarn": ">=1.18.0"
+  },
+  "scripts": {
+    "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
+    "dev:dicom-seg": "yarn run dev",
+    "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
+    "build:package": "yarn run build",
+    "start": "yarn run dev"
+  },
+  "peerDependencies": {
+    "@ohif/core": "^3.0.0",
+    "@ohif/extension-default": "^3.0.0",
+    "@ohif/extension-cornerstone": "^3.0.0",
+    "@ohif/i18n": "^1.0.0",
+    "prop-types": "^15.6.2",
+    "react": "^17.0.2",
+    "react-dom": "^17.0.2",
+    "react-i18next": "^10.11.0",
+    "react-router": "^6.3.0",
+    "react-router-dom": "^6.3.0",
+    "webpack": "^5.50.0",
+    "webpack-merge": "^5.7.3"
+  },
+  "dependencies": {
+    "@babel/runtime": "7.7.6",
+    "react-color": "^2.19.3"
+  },
+  "devDependencies": {
+    "@babel/core": "^7.5.0",
+    "@babel/plugin-proposal-class-properties": "^7.5.0",
+    "@babel/plugin-proposal-object-rest-spread": "^7.5.5",
+    "@babel/plugin-syntax-dynamic-import": "^7.2.0",
+    "@babel/plugin-transform-arrow-functions": "^7.2.0",
+    "@babel/plugin-transform-regenerator": "^7.4.5",
+    "@babel/plugin-transform-runtime": "^7.5.0",
+    "babel-plugin-inline-react-svg": "^2.0.1",
+    "@babel/preset-env": "^7.5.0",
+    "@babel/preset-react": "^7.0.0",
+    "babel-eslint": "^8.0.3",
+    "babel-loader": "^8.0.0-beta.4",
+    "clean-webpack-plugin": "^4.0.0",
+    "copy-webpack-plugin": "^10.2.0",
+    "cross-env": "^7.0.3",
+    "dotenv": "^14.1.0",
+    "eslint": "^5.0.1",
+    "eslint-loader": "^2.0.0",
+    "webpack": "^5.50.0",
+    "webpack-merge": "^5.7.3",
+    "webpack-cli": "^4.7.2"
+  }
+}