chore(release): publish [skip ci]

- @ohif/extension-cornerstone@2.10.8
 - @ohif/extension-dicom-rt@0.6.12
 - @ohif/extension-dicom-segmentation@0.6.9
 - @ohif/extension-vtk@1.11.12
 - @ohif/core@2.13.11
 - @ohif/ui@1.9.2
 - @ohif/viewer@4.9.17

.circleci/config.yml

@@ -13,11 +13,23 @@ version: 2.1
 ##
 orbs:
   codecov: codecov/codecov@1.0.5
-  cypress: cypress-io/cypress@1.13.0
+  cypress: cypress-io/cypress@1.26.0
+executors:
+  # Custom executor to override Cypress config
+  deploy-to-prod-executor:
+    docker:
+      - image: 'cypress/browsers:node14.15.0-chrome86-ff82'
+        environment:
+          CYPRESS_BASE_URL: https://ohif-staging.netlify.com/
+  chrome-and-pacs:
+    docker:
+      # Primary container image where all steps run.
+      - image: 'cypress/browsers:node14.15.0-chrome86-ff82'
+      - image: 'ohif/viewer-testdata:0.1-test'
 
 defaults: &defaults
   docker:
-    - image: circleci/node:12.9.1
+    - image: circleci/node:14.15.0
       environment:
         TERM: xterm # Enable colors in term
         QUICK_BUILD: true
@@ -36,12 +48,12 @@ jobs:
       - checkout:
           post:
             - git fetch --all
-      - restore_cache:
+      # - restore_cache:
-          name: Restore Yarn and Cypress Package Cache
+      #     name: Restore Yarn and Cypress Package Cache
-          keys:
+      #     keys:
-            # when lock file changes, use increasingly general patterns to restore cache
+      #       # when lock file changes, use increasingly general patterns to restore cache
-            - yarn-packages-{{ checksum "yarn.lock" }}
+      #       - yarn-packages-{{ checksum "yarn.lock" }}
-            - yarn-packages-
+      #       - yarn-packages-
       - run:
           name: Install Dependencies
           command: yarn install --frozen-lockfile
@@ -95,12 +107,12 @@ jobs:
           post:
             - git fetch --all
 
-      - restore_cache:
+      # - restore_cache:
-          name: Restore Yarn and Cypress Package Cache
+      #     name: Restore Yarn and Cypress Package Cache
-          keys:
+      #     keys:
-            # when lock file changes, use increasingly general patterns to restore cache
+      #       # when lock file changes, use increasingly general patterns to restore cache
-            - yarn-packages-{{ checksum "yarn.lock" }}
+      #       - yarn-packages-{{ checksum "yarn.lock" }}
-            - yarn-packages-
+      #       - yarn-packages-
 
       - run:
           name: Install Dependencies
@@ -131,12 +143,12 @@ jobs:
       - checkout:
           post:
             - git fetch --all
-      - restore_cache:
+      # - restore_cache:
-          name: Restore Yarn and Cypress Package Cache
+      #     name: Restore Yarn and Cypress Package Cache
-          keys:
+      #     keys:
-            # when lock file changes, use increasingly general patterns to restore cache
+      #       # when lock file changes, use increasingly general patterns to restore cache
-            - yarn-packages-{{ checksum "yarn.lock" }}
+      #       - yarn-packages-{{ checksum "yarn.lock" }}
-            - yarn-packages-
+      #       - yarn-packages-
       - run:
           name: Install Dependencies
           command: yarn install --frozen-lockfile
@@ -170,7 +182,7 @@ jobs:
 
   DEPLOY_TO_DEV:
     docker:
-      - image: circleci/node:12.9.1
+      - image: circleci/node:14.15.0
         environment:
           TERM: xterm
           NETLIFY_SITE_ID: 32708787-c9b0-4634-b50f-7ca41952da77
@@ -185,7 +197,7 @@ jobs:
 
   DEPLOY_TO_STAGING:
     docker:
-      - image: circleci/node:12.9.1
+      - image: circleci/node:14.15.0
         environment:
           TERM: xterm
           NETLIFY_SITE_ID: c7502ae3-b150-493c-8422-05701e44a969
@@ -200,7 +212,7 @@ jobs:
 
   DEPLOY_TO_PRODUCTION:
     docker:
-      - image: circleci/node:12.9.1
+      - image: circleci/node:14.15.0
         environment:
           TERM: xterm
           NETLIFY_SITE_ID: 79c4a5da-5c95-4dc9-84f7-45fd9dfe21b0
@@ -225,11 +237,11 @@ jobs:
           post:
             - git fetch --all
       # Use increasingly general patterns to restore cache
-      - restore_cache:
+      # - restore_cache:
-          name: Restore Yarn and Cypress Package Cache
+      #     name: Restore Yarn and Cypress Package Cache
-          keys:
+      #     keys:
-            - yarn-packages-{{ checksum "yarn.lock" }}
+      #       - yarn-packages-{{ checksum "yarn.lock" }}
-            - yarn-packages-
+      #       - yarn-packages-
       - run:
           name: Install Dependencies
           command: yarn install --frozen-lockfile
@@ -257,7 +269,12 @@ jobs:
           paths: .
 
   DOCS_PUBLISH:
-    <<: *defaults
+    docker:
+      # Gitbook fails due to graceful-fs updates above this node version :-(
+      - image: circleci/node:12.9.1
+        environment:
+          TERM: xterm # Enable colors in term
+    working_directory: ~/repo
     steps:
       - checkout
       - run:
@@ -317,16 +334,21 @@ workflows:
       # E2E: PWA
       - cypress/run:
           name: 'E2E: PWA'
-          executor: cypress/browsers-chrome76
+          executor: chrome-and-pacs
           browser: chrome
           pre-steps:
-            - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v && yarn global
+            - run: |
-                add wait-on' # Use yarn latest
+                # Clear yarn cache; update to latest
+                rm -rf ~/.yarn
+                npm i -g yarn
+                yarn -v
           yarn: true
-          record: false
+          record: true
-          store_artifacts: false
+          store_artifacts: true
           working_directory: platform/viewer
-          build: npx cross-env QUICK_BUILD=true yarn run build
+          build:
+            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            yarn run build
           start: yarn run test:e2e:serve
           spec: 'cypress/integration/common/**/*,cypress/integration/pwa/**/*'
           wait-on: 'http://localhost:3000'
@@ -337,21 +359,24 @@ workflows:
                 path: platform/viewer/cypress/screenshots
             - store_artifacts:
                 path: platform/viewer/cypress/videos
+            - store_test_results:
+                path: platform/viewer/cypress/results
           requires:
             - UNIT_TESTS
       # E2E: script-tag
       - cypress/run:
           name: 'E2E: Script Tag'
-          executor: cypress/browsers-chrome76
+          executor: chrome-and-pacs
           browser: chrome
           pre-steps:
-            - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v && yarn global
+            - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v' # Use yarn latest
-                add wait-on' # Use yarn latest
           yarn: true
-          record: false
+          record: true
-          store_artifacts: false
+          store_artifacts: true
           working_directory: platform/viewer
-          build: npx cross-env QUICK_BUILD=true yarn run build:package
+          build:
+            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            yarn run build:package
           start: yarn run test:e2e:serve
           spec: 'cypress/integration/common/**/*,cypress/integration/script-tag/**/*'
           wait-on: 'http://localhost:3000'
@@ -362,6 +387,8 @@ workflows:
                 path: platform/viewer/cypress/screenshots
             - store_artifacts:
                 path: platform/viewer/cypress/videos
+            - store_test_results:
+                path: platform/viewer/cypress/results
           requires:
             - UNIT_TESTS
 
@@ -372,7 +399,7 @@ workflows:
       # Update hub.docker.org
       - cypress/run:
           name: 'Generate Percy Snapshots'
-          executor: cypress/browsers-chrome76
+          executor: chrome-and-pacs
           browser: chrome
           pre-steps:
             - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v && yarn global
@@ -380,7 +407,9 @@ workflows:
           yarn: true
           store_artifacts: false
           working_directory: platform/viewer
-          build: npx cross-env QUICK_BUILD=true yarn run build
+          build:
+            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            yarn run build
           # start server --> verify running --> percy + chrome + cypress
           command: yarn run test:e2e:dist
           cache-key: 'yarn-packages-{{ checksum "yarn.lock" }}'
@@ -449,7 +478,7 @@ workflows:
       # and record a Cypress dashboard test run
       - cypress/run:
           name: 'Generate Percy Snapshots'
-          executor: cypress/browsers-chrome76
+          executor: chrome-and-pacs
           browser: chrome
           pre-steps:
             - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v && yarn global
@@ -457,7 +486,9 @@ workflows:
           yarn: true
           store_artifacts: false
           working_directory: platform/viewer
-          build: npx cross-env QUICK_BUILD=true yarn run build
+          build:
+            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            yarn run build
           # start server --> verify running --> percy + chrome + cypress
           command: yarn run test:e2e:dist
           cache-key: 'yarn-packages-{{ checksum "yarn.lock" }}'

.github/stale.yml

@@ -2,9 +2,9 @@
 # https://github.com/apps/stale
 #
 # Number of days of inactivity before an issue becomes stale
-daysUntilStale: 21
+daysUntilStale: 180
 # Number of days of inactivity before a stale issue is closed
-daysUntilClose: 7
+daysUntilClose: 9000
 # Issues with these labels will never be considered stale
 exemptLabels:
   - 'Story :raised_hands:'

.webpack/webpack.base.js

@@ -3,7 +3,6 @@ const dotenv = require('dotenv');
 //
 const path = require('path');
 const webpack = require('webpack');
-const PACKAGE = require('../platform/viewer/package.json');
 // ~~ RULES
 const loadShadersRule = require('./rules/loadShaders.js');
 const loadWebWorkersRule = require('./rules/loadWebWorkers.js');
@@ -77,7 +76,10 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => {
         'process.env.DEBUG': JSON.stringify(process.env.DEBUG),
         'process.env.APP_CONFIG': JSON.stringify(process.env.APP_CONFIG || ''),
         'process.env.PUBLIC_URL': JSON.stringify(process.env.PUBLIC_URL || '/'),
-        'process.env.VERSION_NUMBER': JSON.stringify(PACKAGE.version || ''),
+        'process.env.VERSION_NUMBER': webpack.DefinePlugin.runtimeValue(() => {
+          const package = require('../platform/viewer/package.json');
+          return JSON.stringify(package.version || '');
+        }, ['../platform/viewer/package.json']),
         'process.env.BUILD_NUM': JSON.stringify(BUILD_NUM),
         /* i18n */
         'process.env.USE_LOCIZE': JSON.stringify(process.env.USE_LOCIZE || ''),

Dockerfile

@@ -21,7 +21,7 @@
 
 # Stage 1: Build the application
 # docker build -t ohif/viewer:latest .
-FROM node:10.16.3-slim as builder
+FROM node:15.13.0-slim as builder
 
 RUN mkdir /usr/src/app
 WORKDIR /usr/src/app
@@ -39,6 +39,7 @@ COPY package.json /usr/src/app/package.json
 COPY postcss.config.js /usr/src/app/postcss.config.js
 COPY yarn.lock /usr/src/app/yarn.lock
 
+RUN apt-get update && apt-get install -y python make g++
 # Run the install before copying the rest of the files
 RUN yarn config set workspaces-experimental true
 RUN yarn install

README.md

@@ -121,8 +121,7 @@ window.config = {
 };
 ```
 
-- Install the viewer:
+- Install the viewer: `window.OHIFViewer.installViewer(window.config);`
-  `window.OHIFViewer.installViewer(window.config);`
 
 This exact setup is demonstrated in this
 [CodeSandbox](https://codesandbox.io/s/viewer-script-tag-tprch) and in our
@@ -259,6 +258,22 @@ Cancer Institute, Informatics Technology for Cancer Research (ITCR) program,
 under a
 [grant to Dr. Gordon Harris at Massachusetts General Hospital (U24 CA199460)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8971104).
 
+## Projects that contributed to OHIF Viewer
+
+The following is a (partial) list of projects that contributed resources towards
+development of OHIF Viewer:
+
+- [NCI Imaging Data Commons (IDC) project](https://imaging.datacommons.cancer.gov/)
+  supported development of new features and bug fixes marked with
+  ["IDC:priority"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Apriority),
+  ["IDC:candidate"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Acandidate)
+  or
+  ["IDC:collaboration"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Acollaboration).
+  NCI Imaging Data Commons is supported by the contract number 19X037Q from
+  Leidos Biomedical Research under Task Order HHSN26100071 from NCI.
+  [IDC Viewer](https://learn.canceridc.dev/portal/visualization) is a customized
+  version of the OHIF Viewer.
+
 ## License
 
 MIT © [OHIF](https://github.com/OHIF)

docs/latest/book.json

@@ -8,7 +8,6 @@
     "-fontsettings",
     "github",
     "ga",
-    "sitemap",
     "anchors",
     "versions"
   ],
@@ -24,7 +23,8 @@
       "token": "UA-110573590-2"
     },
     "sitemap": {
-      "hostname": "https://docs.ohif.org"
+      "hostname": "https://docs.ohif.org",
+      "todo": "sitemap plugin removed; causing build errors"
     },
     "versions": {
       "gitbookConfigURL": "https://raw.githubusercontent.com/OHIF/Viewers/master/docs/book.json",

docs/v1/book.json

@@ -8,7 +8,6 @@
     "-fontsettings",
     "github",
     "ga",
-    "sitemap",
     "anchors",
     "versions"
   ],
@@ -24,7 +23,8 @@
       "token": "UA-110573590-2"
     },
     "sitemap": {
-      "hostname": "https://docs.ohif.org"
+      "hostname": "https://docs.ohif.org",
+      "todo": "sitemap plugin removed; causing build errors"
     },
     "versions": {
       "gitbookConfigURL": "https://raw.githubusercontent.com/OHIF/Viewers/master/docs/book.json",

extensions/cornerstone/CHANGELOG.md

@@ -3,6 +3,81 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.10.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.7...@ohif/extension-cornerstone@2.10.8) (2021-05-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.6...@ohif/extension-cornerstone@2.10.7) (2021-04-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.5...@ohif/extension-cornerstone@2.10.6) (2021-03-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.4...@ohif/extension-cornerstone@2.10.5) (2021-03-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.3...@ohif/extension-cornerstone@2.10.4) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.2...@ohif/extension-cornerstone@2.10.3) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.1...@ohif/extension-cornerstone@2.10.2) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.0...@ohif/extension-cornerstone@2.10.1) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [2.10.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.6...@ohif/extension-cornerstone@2.10.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
 ## [2.9.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.5...@ohif/extension-cornerstone@2.9.6) (2020-10-07)
 
 **Note:** Version bump only for package @ohif/extension-cornerstone

extensions/cornerstone/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone",
-  "version": "2.9.6",
+  "version": "2.10.8",
   "description": "OHIF extension for Cornerstone",
   "author": "OHIF",
   "license": "MIT",
@@ -36,7 +36,7 @@
     "cornerstone-math": "^0.1.8",
     "cornerstone-tools": "^4.20.1",
     "cornerstone-wado-image-loader": "^3.1.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.18.4",
     "dicom-parser": "^1.8.3",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",
@@ -51,6 +51,6 @@
     "classnames": "^2.2.6",
     "lodash.merge": "^4.6.2",
     "lodash.throttle": "^4.1.1",
-    "react-cornerstone-viewport": "4.0.4"
+    "react-cornerstone-viewport": "4.0.5"
   }
 }

extensions/cornerstone/src/OHIFCornerstoneViewport.js

@@ -1,5 +1,6 @@
 import React, { Component } from 'react';
 
+import OHIFCornerstoneViewportOverlay from './components/OHIFCornerstoneViewportOverlay'
 import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
 import OHIF from '@ohif/core';
 import PropTypes from 'prop-types';
@@ -179,7 +180,7 @@ class OHIFCornerstoneViewport extends Component {
 
     if (
       displaySet.displaySetInstanceUID !==
-      prevDisplaySet.displaySetInstanceUID ||
+        prevDisplaySet.displaySetInstanceUID ||
       displaySet.SOPInstanceUID !== prevDisplaySet.SOPInstanceUID ||
       displaySet.frameIndex !== prevDisplaySet.frameIndex
     ) {
@@ -194,6 +195,7 @@ class OHIFCornerstoneViewport extends Component {
       return null;
     }
     const { viewportIndex } = this.props;
+    const { inconsistencyWarnings } = this.props.viewportData.displaySet;
     const {
       imageIds,
       currentImageIdIndex,
@@ -229,14 +231,19 @@ class OHIFCornerstoneViewport extends Component {
       }
     };
 
+    const warningsOverlay = props => {
+      return <OHIFCornerstoneViewportOverlay {...props} inconsistencyWarnings={inconsistencyWarnings} />
+    };
+
     return (
       <>
         <ConnectedCornerstoneViewport
           viewportIndex={viewportIndex}
           imageIds={imageIds}
           imageIdIndex={currentImageIdIndex}
-          onNewImage={newImageHandler}
+          onNewImageDebounced={newImageHandler}
-          onNewImageDebounceTime={700}
+          onNewImageDebounceTime={300}
+          viewportOverlayComponent={warningsOverlay}
           // ~~ Connected (From REDUX)
           // frameRate={frameRate}
           // isPlaying={false}

extensions/cornerstone/src/commandsModule.js

@@ -268,6 +268,7 @@ const commandsModule = ({ servicesManager }) => {
       SOPInstanceUID,
       frameIndex,
       activeViewportIndex,
+      refreshViewports = true,
     }) => {
       const study = studyMetadataManager.get(StudyInstanceUID);
 
@@ -278,6 +279,10 @@ const commandsModule = ({ servicesManager }) => {
         );
       });
 
+      if (!displaySet) {
+        return;
+      }
+
       displaySet.SOPInstanceUID = SOPInstanceUID;
       displaySet.frameIndex = frameIndex;
 
@@ -285,7 +290,9 @@ const commandsModule = ({ servicesManager }) => {
         setViewportSpecificData(activeViewportIndex, displaySet)
       );
 
-      refreshCornerstoneViewports();
+      if (refreshViewports) {
+        refreshCornerstoneViewports();
+      }
     },
   };
 

extensions/cornerstone/src/components/OHIFCornerstoneViewportOverlay.css

@@ -0,0 +1,69 @@
+.imageViewerViewport.empty ~ .OHIFCornerstoneViewportOverlay {
+  display: none;
+}
+.OHIFCornerstoneViewportOverlay {
+  color: #9ccef9;
+}
+.OHIFCornerstoneViewportOverlay .overlay-element {
+  position: absolute;
+  font-weight: 400;
+  text-shadow: 1px 1px #000;
+  pointer-events: none;
+}
+.OHIFCornerstoneViewportOverlay .top-left {
+  top: 20px;
+  left: 20px;
+}
+.OHIFCornerstoneViewportOverlay .top-center {
+  top: 20px;
+  padding-top: 20px;
+  width: 100%;
+  text-align: center;
+}
+.OHIFCornerstoneViewportOverlay .top-right {
+  top: 20px;
+  right: 20px;
+  text-align: right;
+}
+.OHIFCornerstoneViewportOverlay .bottom-left {
+  bottom: 20px;
+  left: 20px;
+}
+.OHIFCornerstoneViewportOverlay .bottom-left2 {
+  bottom: 140px;
+  left: 20px;
+}
+.OHIFCornerstoneViewportOverlay .bottom-right {
+  bottom: 20px;
+  right: 20px;
+  text-align: right;
+}
+.OHIFCornerstoneViewportOverlay.controlsVisible .topright,
+.OHIFCornerstoneViewportOverlay.controlsVisible .bottomright {
+  right: calc(20px + 19px);
+}
+.OHIFCornerstoneViewportOverlay .warning {
+  position: absolute;
+  font-weight: 400;
+  text-shadow: 1px 1px #000;
+  pointer-events: inherit;
+}
+
+.OHIFCornerstoneViewportOverlay .warning svg {
+  opacity: 1;
+  color: #e29e4a;
+  fill: #e29e4a;
+  stroke: #e29e4a;
+  width: 32px;
+  height: 28px;
+}
+
+.OHIFCornerstoneViewportOverlay svg {
+  color: #9ccef9;
+  fill: #9ccef9;
+  stroke: #9ccef9;
+  background-color: transparent;
+  margin: 2px;
+  width: 18px;
+  height: 18px;
+}

extensions/cornerstone/src/components/OHIFCornerstoneViewportOverlay.js

@@ -0,0 +1,167 @@
+import { PureComponent } from 'react';
+import React from 'react';
+import PropTypes from 'prop-types';
+import cornerstone from 'cornerstone-core';
+import './OHIFCornerstoneViewportOverlay.css';
+import {
+  isValidNumber,
+  formatNumberPrecision,
+  formatDICOMDate,
+  formatDICOMTime,
+  formatPN,
+  getCompression
+} from '../utils/formatStudy';
+import classNames from 'classnames';
+import { Icon } from '@ohif/ui/src/elements/Icon';
+import { Tooltip } from '@ohif/ui/src/components/tooltip';
+import { OverlayTrigger } from '@ohif/ui/src/components/overlayTrigger';
+
+class OHIFCornerstoneViewportOverlay extends PureComponent {
+  static propTypes = {
+    scale: PropTypes.number.isRequired,
+    windowWidth: PropTypes.oneOfType([
+      PropTypes.number.isRequired,
+      PropTypes.string.isRequired,
+    ]),
+    windowCenter: PropTypes.oneOfType([
+      PropTypes.number.isRequired,
+      PropTypes.string.isRequired,
+    ]),
+    imageId: PropTypes.string.isRequired,
+    imageIndex: PropTypes.number.isRequired,
+    stackSize: PropTypes.number.isRequired,
+    inconsistencyWarnings: PropTypes.array.isRequired
+  };
+
+  render() {
+    const { imageId, scale, windowWidth, windowCenter, inconsistencyWarnings } = this.props;
+
+    if (!imageId) {
+      return null;
+    }
+
+    const zoomPercentage = formatNumberPrecision(scale * 100, 0);
+    const seriesMetadata =
+      cornerstone.metaData.get('generalSeriesModule', imageId) || {};
+    const imagePlaneModule =
+      cornerstone.metaData.get('imagePlaneModule', imageId) || {};
+    const { rows, columns, sliceThickness, sliceLocation } = imagePlaneModule;
+    const { seriesNumber, seriesDescription } = seriesMetadata;
+
+    const generalStudyModule =
+      cornerstone.metaData.get('generalStudyModule', imageId) || {};
+    const { studyDate, studyTime, studyDescription } = generalStudyModule;
+
+    const patientModule =
+      cornerstone.metaData.get('patientModule', imageId) || {};
+    const { patientId, patientName } = patientModule;
+
+    const generalImageModule =
+      cornerstone.metaData.get('generalImageModule', imageId) || {};
+    const { instanceNumber } = generalImageModule;
+
+    const cineModule = cornerstone.metaData.get('cineModule', imageId) || {};
+    const { frameTime } = cineModule;
+
+    const frameRate = formatNumberPrecision(1000 / frameTime, 1);
+    const compression = getCompression(imageId);
+    const wwwc = `W: ${
+      windowWidth.toFixed ? windowWidth.toFixed(0) : windowWidth
+    } L: ${windowWidth.toFixed ? windowCenter.toFixed(0) : windowCenter}`;
+    const imageDimensions = `${columns} x ${rows}`;
+
+    const { imageIndex, stackSize } = this.props;
+
+    const inconsistencyWarningsOn = inconsistencyWarnings && inconsistencyWarnings.length !== 0 ? true : false;
+    const getWarningContent = (warningList) => {
+      if (Array.isArray(warningList)) {
+        const listedWarnings = warningList.map((warn, index) => {
+          return <li key={index}>{warn}</li>;
+        });
+
+        return <ol>{listedWarnings}</ol>;
+      } else {
+        return <React.Fragment>{warningList}</React.Fragment>;
+      }
+    };
+
+    const getWarningInfo = (seriesNumber, inconsistencyWarnings) => {
+      return(
+        <React.Fragment>
+        {inconsistencyWarnings.length != 0 ? (
+          <OverlayTrigger
+            key={seriesNumber}
+            placement="left"
+            overlay={
+              <Tooltip
+                placement="left"
+                className="in tooltip-warning"
+                id="tooltip-left"
+              >
+                <div className="warningTitle">Series Inconsistencies</div>
+                <div className="warningContent">{getWarningContent(inconsistencyWarnings)}</div>
+              </Tooltip>
+            }
+          >
+            <div className={classNames('warning')}>
+              <span className="warning-icon">
+                <Icon name="exclamation-triangle" />
+              </span>
+            </div>
+          </OverlayTrigger>
+        ) : (
+          <React.Fragment></React.Fragment>
+          )}
+      </React.Fragment>
+      );
+    };
+
+    const normal = (
+      <React.Fragment>
+        <div className="top-left overlay-element">
+          <div>{formatPN(patientName)}</div>
+          <div>{patientId}</div>
+        </div>
+        <div className="top-right overlay-element">
+          <div>{studyDescription}</div>
+          <div>
+            {formatDICOMDate(studyDate)} {formatDICOMTime(studyTime)}
+          </div>
+        </div>
+        <div className="bottom-right overlay-element">
+          <div>Zoom: {zoomPercentage}%</div>
+          <div>{wwwc}</div>
+          <div className="compressionIndicator">{compression}</div>
+        </div>
+        <div className="bottom-left2 warning">
+          <div>{inconsistencyWarningsOn ? getWarningInfo(seriesNumber, inconsistencyWarnings) : ''}</div>
+        </div>
+        <div className="bottom-left overlay-element">
+          <div>{seriesNumber >= 0 ? `Ser: ${seriesNumber}` : ''}</div>
+          <div>
+            {stackSize > 1
+              ? `Img: ${instanceNumber} ${imageIndex}/${stackSize}`
+              : ''}
+          </div>
+          <div>
+            {frameRate >= 0 ? `${formatNumberPrecision(frameRate, 2)} FPS` : ''}
+            <div>{imageDimensions}</div>
+            <div>
+              {isValidNumber(sliceLocation)
+                ? `Loc: ${formatNumberPrecision(sliceLocation, 2)} mm `
+                : ''}
+              {sliceThickness
+                ? `Thick: ${formatNumberPrecision(sliceThickness, 2)} mm`
+                : ''}
+            </div>
+            <div>{seriesDescription}</div>
+          </div>
+        </div>
+      </React.Fragment>
+    );
+
+    return <div className="OHIFCornerstoneViewportOverlay">{normal}</div>;
+  }
+}
+
+export default OHIFCornerstoneViewportOverlay;

extensions/cornerstone/src/index.js

@@ -38,7 +38,14 @@ export default {
   },
   getViewportModule({ commandsManager }) {
     const ExtendedOHIFCornerstoneViewport = props => {
+      /**
+       * TODO: This appears to be used to set the redux parameters for
+       * the viewport when new images are loaded. It's very ugly
+       * and we should remove it.
+       */
       const onNewImageHandler = jumpData => {
+        /** Do not trigger all viewports to render unnecessarily */
+        jumpData.refreshViewports = false;
         commandsManager.runCommand('jumpToImage', jumpData);
       };
       return (

extensions/cornerstone/src/utils/formatStudy.js

@@ -0,0 +1,109 @@
+import moment from 'moment';
+
+/**
+ * Checks if value is valid.
+ *
+ * @param {number} value
+ * @returns {boolean} is valid.
+ */
+function isValidNumber(value) {
+  return typeof value === 'number' && !isNaN(value);
+}
+
+/**
+ * Formats number precision.
+ *
+ * @param {number} number
+ * @param {number} precision
+ * @returns {number} formatted number.
+ */
+function formatNumberPrecision(number, precision) {
+  if (number !== null) {
+    return parseFloat(number).toFixed(precision);
+  }
+}
+
+/**
+ * Formats DICOM date.
+ *
+ * @param {string} date
+ * @param {string} strFormat
+ * @returns {string} formatted date.
+ */
+function formatDICOMDate(date, strFormat = 'MMM D, YYYY') {
+  return moment(date, 'YYYYMMDD').format(strFormat);
+}
+
+/**
+ *    DICOM Time is stored as HHmmss.SSS, where:
+ *      HH 24 hour time:
+ *        m mm        0..59   Minutes
+ *        s ss        0..59   Seconds
+ *        S SS SSS    0..999  Fractional seconds
+ *
+ *        Goal: '24:12:12'
+ *
+ * @param {*} time
+ * @param {string} strFormat
+ * @returns {string} formatted name.
+ */
+function formatDICOMTime(time, strFormat = 'HH:mm:ss') {
+  return moment(time, 'HH:mm:ss').format(strFormat);
+}
+
+/**
+ * Formats a patient name for display purposes
+ *
+ * @param {string} name
+ * @returns {string} formatted name.
+ */
+function formatPN(name) {
+  if (!name) {
+    return;
+  }
+
+  // Convert the first ^ to a ', '. String.replace() only affects
+  // the first appearance of the character.
+  const commaBetweenFirstAndLast = name.replace('^', ', ');
+
+  // Replace any remaining '^' characters with spaces
+  const cleaned = commaBetweenFirstAndLast.replace(/\^/g, ' ');
+
+  // Trim any extraneous whitespace
+  return cleaned.trim();
+}
+
+/**
+ * Gets compression type
+ *
+ * @param {number} imageId
+ * @returns {string} comrpession type.
+ */
+function getCompression(imageId) {
+  const generalImageModule =
+    cornerstone.metaData.get('generalImageModule', imageId) || {};
+  const {
+    lossyImageCompression,
+    lossyImageCompressionRatio,
+    lossyImageCompressionMethod,
+  } = generalImageModule;
+
+  if (lossyImageCompression === '01' && lossyImageCompressionRatio !== '') {
+    const compressionMethod = lossyImageCompressionMethod || 'Lossy: ';
+    const compressionRatio = formatNumberPrecision(
+      lossyImageCompressionRatio,
+      2
+    );
+    return compressionMethod + compressionRatio + ' : 1';
+  }
+
+  return 'Lossless / Uncompressed';
+}
+
+export { isValidNumber,
+  formatNumberPrecision,
+  formatDICOMDate,
+  formatDICOMTime,
+  formatPN,
+  getCompression
+};

extensions/debugging/CHANGELOG.md

@@ -3,6 +3,25 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.2.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.2.0...@ohif/extension-debugging@0.2.1) (2021-03-19)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+# [0.2.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.1.6...@ohif/extension-debugging@0.2.0) (2021-03-04)
+
+
+### Features
+
+* **log:** add new log service ([14d6454](https://github.com/OHIF/Viewers/commit/14d6454eafaa2ccb50e133c2945c9558052ea27e))
+
+
+
+
+
 ## [0.1.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.1.5...@ohif/extension-debugging@0.1.6) (2020-10-06)
 
 **Note:** Version bump only for package @ohif/extension-debugging

extensions/debugging/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-debugging",
-  "version": "0.1.6",
+  "version": "0.2.1",
   "description": "OHIF extension for debugging.",
   "author": "OHIF",
   "license": "MIT",

extensions/debugging/src/DebugReportModal.css

@@ -12,3 +12,15 @@
   display: flex;
   flex-direction: row;
 }
+
+.debug-report-modal-container .errors {
+  margin-top: 10px;
+}
+
+.debug-report-modal-container .errors-container {
+  border: 1px solid var(--active-color);
+  border-radius: 5px;
+  padding: 10px;
+  overflow: scroll;
+  max-height: 300px;
+}

extensions/debugging/src/DebugReportModal.js

@@ -10,6 +10,7 @@ const DubugReportModal = ({
   extensionManager,
   mailTo,
   debugModalMessage,
+  errors = [],
 }) => {
   const copyDebugDataToClipboard = () => {
     const body = getEmailBody();
@@ -131,6 +132,19 @@ const DubugReportModal = ({
           {getLayout(viewports)}
         </table>
       </div>
+      <div className="errors">
+        <h3>Errors ({errors.length})</h3>
+        <div className="errors-container">
+          {errors.map(error => {
+            return (
+              <div>
+                <pre>Message: {error.message}</pre>
+                {error.error && <pre>Stack: {error.error.stack}</pre>}
+              </div>
+            );
+          })}
+        </div>
+      </div>
     </div>
   );
 };

extensions/debugging/src/commandsModule.js

@@ -1,4 +1,6 @@
 import OHIF from '@ohif/core';
+import { useLogger } from '@ohif/ui';
+
 import {
   save,
   upload,
@@ -95,6 +97,7 @@ export function getCommands(context, servicesManager, extensionManager) {
       const { UIModalService } = servicesManager.services;
 
       const WrappedDebugReportModal = function() {
+        const { state: loggerState } = useLogger();
         return (
           <DebugReportModal
             viewports={viewports}
@@ -103,6 +106,7 @@ export function getCommands(context, servicesManager, extensionManager) {
             extensionManager={extensionManager}
             mailTo={state.mailTo}
             debugModalMessage={state.debugModalMessage}
+            errors={loggerState.errors}
           />
         );
       };

extensions/debugging/src/state.js

@@ -1,3 +1,3 @@
-const state = { mailTo: undefined, message: undefined };
+const state = { mailTo: undefined, debugModalMessage: undefined };
 
 export default state;

extensions/dicom-html/CHANGELOG.md

@@ -3,6 +3,89 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.3.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.8...@ohif/extension-dicom-html@1.3.9) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.7...@ohif/extension-dicom-html@1.3.8) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.6...@ohif/extension-dicom-html@1.3.7) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.5...@ohif/extension-dicom-html@1.3.6) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.4...@ohif/extension-dicom-html@1.3.5) (2021-04-15)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.3...@ohif/extension-dicom-html@1.3.4) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.2...@ohif/extension-dicom-html@1.3.3) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.1...@ohif/extension-dicom-html@1.3.2) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.0...@ohif/extension-dicom-html@1.3.1) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+# [1.3.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.9...@ohif/extension-dicom-html@1.3.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
 ## [1.2.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.8...@ohif/extension-dicom-html@1.2.9) (2020-10-07)
 
 **Note:** Version bump only for package @ohif/extension-dicom-html

extensions/dicom-html/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-html",
-  "version": "1.2.9",
+  "version": "1.3.9",
   "description": "OHIF extension for rendering structured reports to HTML",
   "author": "OHIF",
   "license": "MIT",
@@ -29,7 +29,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.18.5",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-html/src/OHIFDicomHtmlSopClassHandler.js

@@ -9,6 +9,7 @@ const SOP_CLASS_UIDS = {
   MAMMOGRAPHY_CAD_SR: '1.2.840.10008.5.1.4.1.1.88.50',
   CHEST_CAD_SR: '1.2.840.10008.5.1.4.1.1.88.65',
   X_RAY_RADIATION_DOSE_SR: '1.2.840.10008.5.1.4.1.1.88.67',
+  ACQUISITION_CONTEXT_SR_STORAGE: '1.2.840.10008.5.1.4.1.1.88.71',
 };
 
 const sopClassUIDs = Object.values(SOP_CLASS_UIDS);

extensions/dicom-microscopy/CHANGELOG.md

@@ -3,6 +3,25 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+# [0.52.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.4...@ohif/extension-dicom-microscopy@0.52.0) (2021-03-04)
+
+
+### Features
+
+* **log:** add new log service ([14d6454](https://github.com/OHIF/Viewers/commit/14d6454eafaa2ccb50e133c2945c9558052ea27e))
+
+
+
+
+
+## [0.51.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.3...@ohif/extension-dicom-microscopy@0.51.4) (2021-01-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
 ## [0.51.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.2...@ohif/extension-dicom-microscopy@0.51.3) (2020-09-10)
 
 **Note:** Version bump only for package @ohif/extension-dicom-microscopy

extensions/dicom-microscopy/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-microscopy",
-  "version": "0.51.3",
+  "version": "0.52.0",
   "description": "OHIF extension for Dicom Microscopy",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-microscopy/src/DicomMicroscopyViewport.js

@@ -62,11 +62,30 @@ class DicomMicroscopyViewport extends Component {
         );
         const microscopyViewer = api.VLWholeSlideMicroscopyImageViewer;
 
-        this.viewer = new microscopyViewer({
+        try {
-          client: dicomWebClient,
+          this.viewer = new microscopyViewer({
-          metadata,
+            client: dicomWebClient,
-          retrieveRendered: false,
+            metadata,
-        });
+            retrieveRendered: false,
+          });
+        } catch (error) {
+          console.error('[Microscopy Viewer] Failed to load:', error);
+          const {
+            UINotificationService,
+            LoggerService,
+          } = this.props.servicesManager.services;
+          if (UINotificationService) {
+            const message =
+              'Failed to load viewport. Please check that you have hardware acceleration enabled.';
+            LoggerService.error({ error, message });
+            UINotificationService.show({
+              autoClose: false,
+              title: 'Microscopy Viewport',
+              message,
+              type: 'error',
+            });
+          }
+        }
 
         this.viewer.render({ container });
       });
@@ -92,8 +111,8 @@ class DicomMicroscopyViewport extends Component {
         {this.state.error ? (
           <h2>{JSON.stringify(this.state.error)}</h2>
         ) : (
-            <div style={style} ref={this.container} />
+          <div style={style} ref={this.container} />
-          )}
+        )}
       </div>
     );
   }

extensions/dicom-microscopy/src/index.js

@@ -6,14 +6,6 @@ const Component = React.lazy(() => {
   return import('./DicomMicroscopyViewport');
 });
 
-const DicomMicroscopyViewport = props => {
-  return (
-    <React.Suspense fallback={<div>Loading...</div>}>
-      <Component {...props} />
-    </React.Suspense>
-  );
-};
-
 export default {
   /**
    * Only required property. Should be a unique value across all extensions.
@@ -21,8 +13,14 @@ export default {
   id: 'microscopy',
   version,
 
-  getViewportModule() {
+  getViewportModule({ servicesManager }) {
-    return DicomMicroscopyViewport;
+    return props => {
+      return (
+        <React.Suspense fallback={<div>Loading...</div>}>
+          <Component {...props} servicesManager={servicesManager} />
+        </React.Suspense>
+      );
+    };
   },
   getSopClassHandlerModule() {
     return DicomMicroscopySopClassHandler;

extensions/dicom-rt/CHANGELOG.md

@@ -3,6 +3,127 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.6.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.11...@ohif/extension-dicom-rt@0.6.12) (2021-05-17)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.10...@ohif/extension-dicom-rt@0.6.11) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.9...@ohif/extension-dicom-rt@0.6.10) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.8...@ohif/extension-dicom-rt@0.6.9) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.7...@ohif/extension-dicom-rt@0.6.8) (2021-04-15)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.6...@ohif/extension-dicom-rt@0.6.7) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.5...@ohif/extension-dicom-rt@0.6.6) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.4...@ohif/extension-dicom-rt@0.6.5) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.3...@ohif/extension-dicom-rt@0.6.4) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.2...@ohif/extension-dicom-rt@0.6.3) (2021-01-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.1...@ohif/extension-dicom-rt@0.6.2) (2021-01-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.0...@ohif/extension-dicom-rt@0.6.1) (2020-12-10)
+
+
+### Bug Fixes
+
+* panel issues and mpr button (IDC2122-IDC2117) ([32022f5](https://github.com/OHIF/Viewers/commit/32022f51f2d24f53f4c98188980db038a6dfe76c))
+
+
+
+
+
+# [0.6.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.5.0...@ohif/extension-dicom-rt@0.6.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
+# [0.5.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.9...@ohif/extension-dicom-rt@0.5.0) (2020-12-03)
+
+
+### Features
+
+* Update approach to better handle rtdose instead of disabling panel ([f3cecf1](https://github.com/OHIF/Viewers/commit/f3cecf129b16f8d24d239aa44fdff7f46e6ba683))
+
+
+
+
+
 ## [0.4.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.8...@ohif/extension-dicom-rt@0.4.9) (2020-10-12)
 
 **Note:** Version bump only for package @ohif/extension-dicom-rt

extensions/dicom-rt/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-rt",
-  "version": "0.4.9",
+  "version": "0.6.12",
   "description": "OHIF extension for rendering DICOM RTSTRUCTs on top of cornerstone images.",
   "author": "OHIF",
   "license": "MIT",
@@ -31,7 +31,7 @@
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "^4.20.1",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.18.5",
     "gl-matrix": "^3.3.0",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",

extensions/dicom-rt/src/OHIFDicomRTStructSopClassHandler.js

@@ -15,7 +15,7 @@ const OHIFDicomRTStructSopClassHandler = {
   id: 'OHIFDicomRTStructSopClassHandler',
   type: MODULE_TYPES.SOP_CLASS_HANDLER,
   sopClassUIDs,
-  getDisplaySetFromSeries: function(
+  getDisplaySetFromSeries: function (
     series,
     study,
     dicomWebClient,
@@ -71,11 +71,11 @@ const OHIFDicomRTStructSopClassHandler = {
       }
     }
 
-    rtStructDisplaySet.getSourceDisplaySet = function(studies) {
+    rtStructDisplaySet.getSourceDisplaySet = function (studies, activateLabelMap = true) {
-      return getSourceDisplaySet(studies, rtStructDisplaySet);
+      return getSourceDisplaySet(studies, rtStructDisplaySet, activateLabelMap);
     };
 
-    rtStructDisplaySet.load = function(referencedDisplaySet, studies) {
+    rtStructDisplaySet.load = function (referencedDisplaySet, studies) {
       return loadRTStruct(
         rtStructDisplaySet,
         referencedDisplaySet,

extensions/dicom-rt/src/components/PanelSection/PanelSection.css

@@ -39,6 +39,8 @@
   border-radius: 5px;
 }
 
-.icons .angle-double-down, .icons .angle-double-up {
+.icons .angle-double-down,
+.icons .angle-double-up {
   margin-left: 15px;
+  margin-right: -5px;
 }

extensions/dicom-rt/src/components/RTPanel/RTPanel.css

@@ -9,16 +9,21 @@
 
 .dcmrt-panel .dcmrt-panel-header {
   display: flex;
-  flex-direction: row;
+  flex-direction: column;
   justify-content: space-between;
   color: white;
 }
 
+.dcmrt-panel .dcmrt-panel-header h3 {
+  margin-top: 0;
+}
+
 .dcmrt-panel .dcmrt-panel-header .cog-icon {
   align-self: flex-end;
   color: var(--default-color);
   cursor: pointer;
-  margin-bottom: 20px;
+  min-height: 23px;
+  max-height: 23px;
 }
 
 .dcmrt-panel .dcmrt-panel-header .cog-icon:hover {

extensions/dicom-rt/src/components/RTPanel/RTPanel.js

@@ -1,4 +1,4 @@
-import React, { useState, useEffect } from 'react';
+import React, { useState, useEffect, useCallback } from 'react';
 import PropTypes from 'prop-types';
 import cornerstoneTools from 'cornerstone-tools';
 import cornerstone from 'cornerstone-core';
@@ -31,19 +31,20 @@ const refreshViewport = () => {
  *
  * @param {Object} props
  * @param {Array} props.studies
- * @param {Array} props.viewports - viewportSpecificData
+ * @param {Array} props.getActiveViewport - get active viewport data
  * @param {number} props.activeIndex - activeViewportIndex
  * @param {number} props.isOpen - isOpen
  * @returns component
  */
 const RTPanel = ({
   studies,
-  viewports,
   activeIndex,
   isOpen,
   onContourItemClick,
   activeContexts = [],
   contexts = {},
+  activeViewport,
+  getActiveViewport,
 }) => {
   const isVTK = () => activeContexts.includes(contexts.VTK);
   const isCornerstone = () => activeContexts.includes(contexts.CORNERSTONE);
@@ -54,11 +55,11 @@ const RTPanel = ({
     referencedDisplaysets: [],
     sets: [],
     selectedSet: null,
+    isLocked: false,
   };
 
   const [state, setState] = useState(DEFAULT_STATE);
   const [showSettings, setShowSettings] = useState(false);
-  const activeViewport = viewports[activeIndex];
 
   /*
    * TODO: Improve the way we notify parts of the app that depends on rts to be loaded.
@@ -78,6 +79,8 @@ const RTPanel = ({
    * without subscribing to external events.
    */
   useEffect(() => {
+    updateStructureSets();
+
     document.addEventListener('extensiondicomrtrtloaded', updateStructureSets);
 
     return () => {
@@ -88,20 +91,30 @@ const RTPanel = ({
     };
   }, []);
 
+  useEffect(() => {
+    const studyMetadata = studyMetadataManager.get(
+      activeViewport.StudyInstanceUID
+    );
+    const referencedDisplaysets = studyMetadata.getDerivedDatasets({
+      referencedSeriesInstanceUID: activeViewport.SeriesInstanceUID,
+      Modality: 'RTSTRUCT',
+    });
+    setState(state => ({ ...state, isLocked: !referencedDisplaysets.length }));
+  }, [activeViewport]);
+
   const updateStructureSets = () => {
+    const viewport = getActiveViewport();
     const module = cornerstoneTools.getModule('rtstruct');
     const StructureSets = module.state.StructureSets;
 
     if (StructureSets && StructureSets.length) {
       const viewportSets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
-        activeViewport.SeriesInstanceUID
+        viewport.SeriesInstanceUID
       );
 
-      const studyMetadata = studyMetadataManager.get(
+      const studyMetadata = studyMetadataManager.get(viewport.StudyInstanceUID);
-        activeViewport.StudyInstanceUID
-      );
       const referencedDisplaysets = studyMetadata.getDerivedDatasets({
-        referencedSeriesInstanceUID: activeViewport.SeriesInstanceUID,
+        referencedSeriesInstanceUID: viewport.SeriesInstanceUID,
         Modality: 'RTSTRUCT',
       });
 
@@ -118,10 +131,6 @@ const RTPanel = ({
     }
   };
 
-  useEffect(() => {
-    updateStructureSets();
-  }, [studies, viewports, activeIndex]);
-
   useEffect(() => {
     setShowSettings(showSettings && !isOpen);
   }, [isOpen]);
@@ -231,16 +240,19 @@ const RTPanel = ({
   return (
     <div className="dcmrt-panel">
       <div className="dcmrt-panel-header">
+        {' '}
+        {!state.isLocked && (
+          <Icon
+            className="cog-icon"
+            name="cog"
+            width="25px"
+            height="25px"
+            onClick={() => setShowSettings(true)}
+          />
+        )}
         <h3>RT Structure Sets</h3>
-        <Icon
-          className="cog-icon"
-          name="cog"
-          width="25px"
-          height="25px"
-          onClick={() => setShowSettings(true)}
-        />
       </div>
-      {!state.referencedDisplaysets.length && (
+      {!state.isLocked && !state.referencedDisplaysets.length && (
         <LoadingIndicator expand height="70px" width="70px" />
       )}
       {state.sets &&
@@ -249,12 +261,15 @@ const RTPanel = ({
 
           const module = cornerstoneTools.getModule('rtstruct');
           const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
-            viewports[activeIndex].SeriesInstanceUID
+            activeViewport.SeriesInstanceUID
           );
 
           const loadedSet = sets.find(
             set => set.SeriesInstanceUID === SeriesInstanceUID
           );
+
+          if (!loadedSet) return null;
+
           return (
             <PanelSection
               key={SeriesInstanceUID}
@@ -276,17 +291,17 @@ const RTPanel = ({
                   module.setters.hideStructureSet(loadedSet.SeriesInstanceUID);
                 }
                 const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
-                  viewports[activeIndex].SeriesInstanceUID
+                  activeViewport.SeriesInstanceUID
                 );
                 setState(state => ({ ...state, sets }));
                 refreshViewport();
               }}
               onExpandChange={async () => {
                 if (!isLoaded) {
-                  await displaySet.load(viewports[activeIndex], studies);
+                  await displaySet.load(activeViewport, studies);
                   const module = cornerstoneTools.getModule('rtstruct');
                   const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
-                    viewports[activeIndex].SeriesInstanceUID
+                    activeViewport.SeriesInstanceUID
                   );
                   const selectedSet = sets.find(
                     set => set.SeriesInstanceUID === SeriesInstanceUID

extensions/dicom-rt/src/getSourceDisplaySet.js

@@ -1,38 +1,14 @@
-export default function getSourceDisplaySet(studies, rtStructDisplaySet) {
+import { metadata } from '@ohif/core';
-  const referencedDisplaySet = _getReferencedDisplaySet(
+
+export default function getSourceDisplaySet(studies, rtStructDisplaySet, activateLabelMap = true) {
+  const referencedDisplaySet = metadata.StudyMetadata.getReferencedDisplaySet(
     rtStructDisplaySet,
     studies
   );
 
-  rtStructDisplaySet.load(referencedDisplaySet, studies);
+  if (activateLabelMap) {
+    rtStructDisplaySet.load(referencedDisplaySet, studies);
+  }
 
   return referencedDisplaySet;
 }
-
-const _getReferencedDisplaySet = (rtStructDisplaySet, studies) => {
-  let allDisplaySets = [];
-
-  studies.forEach(study => {
-    allDisplaySets = allDisplaySets.concat(study.displaySets);
-  });
-
-  const otherDisplaySets = allDisplaySets.filter(
-    ds => ds.displaySetInstanceUID !== rtStructDisplaySet.displaySetInstanceUID
-  );
-
-  const ReferencedSeriesSequence = Array.isArray(
-    rtStructDisplaySet.metadata.ReferencedSeriesSequence
-  )
-    ? rtStructDisplaySet.metadata.ReferencedSeriesSequence
-    : [rtStructDisplaySet.metadata.ReferencedSeriesSequence];
-
-  const referencedSeriesInstanceUIDs = ReferencedSeriesSequence.map(
-    ReferencedSeries => ReferencedSeries.SeriesInstanceUID
-  );
-
-  const referencedDisplaySet = otherDisplaySets.find(ds =>
-    referencedSeriesInstanceUIDs.includes(ds.SeriesInstanceUID)
-  );
-
-  return referencedDisplaySet;
-};

extensions/dicom-rt/src/index.js

@@ -5,6 +5,9 @@ import id from './id.js';
 import RTPanel from './components/RTPanel/RTPanel';
 import { version } from '../package.json';
 
+import { utils } from '@ohif/core';
+const { studyMetadataManager } = utils;
+
 export default {
   /**
    * Only required property. Should be a unique value across all extensions.
@@ -45,24 +48,34 @@ export default {
           icon: 'list',
           label: 'RTSTRUCT',
           target: 'rt-panel',
-          isDisabled: studies => {
+          isDisabled: (studies, activeViewport) => {
             if (!studies) {
               return true;
             }
 
-            for (let i = 0; i < studies.length; i++) {
+            if (activeViewport) {
-              const study = studies[i];
+              const study = studies.find(
-
+                s => s.StudyInstanceUID === activeViewport.StudyInstanceUID
-              if (study && study.series) {
+              );
-                for (let j = 0; j < study.series.length; j++) {
+              const ds = study.displaySets.find(
-                  const series = study.series[j];
+                ds =>
-                  if (
+                  ds.displaySetInstanceUID ===
-                    /* Could be expanded to contain RTPLAN and RTDOSE information in the future */
+                  activeViewport.displaySetInstanceUID
-                    ['RTSTRUCT'].includes(series.Modality)
+              );
-                  ) {
+              const studyMetadata = studyMetadataManager.get(
-                    return false;
+                activeViewport.StudyInstanceUID
-                  }
+              );
-                }
+              const referencedDisplaySets = studyMetadata.getDerivedDatasets({
+                referencedSeriesInstanceUID: activeViewport.SeriesInstanceUID,
+                Modality: 'RTSTRUCT',
+              });
+              if (
+                referencedDisplaySets &&
+                referencedDisplaySets.some(ds =>
+                  ['RTSTRUCT'].includes(ds.Modality)
+                )
+              ) {
+                return false;
               }
             }
 

extensions/dicom-rt/src/loadRTStruct.js

@@ -90,12 +90,17 @@ export default async function loadRTStruct(
       const sopInstanceUID = ContourImageSequence
         ? ContourImageSequence.ReferencedSOPInstanceUID
         : _getClosestSOPInstanceUID(
-            ContourData,
+          ContourData,
-            ContourGeometricType,
+          ContourGeometricType,
-            NumberOfContourPoints,
+          NumberOfContourPoints,
-            imageIdSopInstanceUidPairs
+          imageIdSopInstanceUidPairs
-          );
+        );
       const imageId = _getImageId(imageIdSopInstanceUidPairs, sopInstanceUID);
+
+      if (!imageId) {
+        continue;
+      }
+
       const imageIdSpecificToolData = _getOrCreateImageIdSpecificToolData(
         toolState,
         imageId,
@@ -294,7 +299,7 @@ const _getImageId = (imageIdSopInstanceUidPairs, sopInstanceUID) => {
       imageIdSopInstanceUidPairsEntry.sopInstanceUID === sopInstanceUID
   );
 
-  return imageIdSopInstanceUidPairsEntry.imageId;
+  return imageIdSopInstanceUidPairsEntry ? imageIdSopInstanceUidPairsEntry.imageId : null;
 };
 
 function _getImageIdSopInstanceUidPairsForDisplaySet(

extensions/dicom-segmentation/CHANGELOG.md

@@ -3,6 +3,132 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.6.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.8...@ohif/extension-dicom-segmentation@0.6.9) (2021-05-17)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.7...@ohif/extension-dicom-segmentation@0.6.8) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.6...@ohif/extension-dicom-segmentation@0.6.7) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.5...@ohif/extension-dicom-segmentation@0.6.6) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.4...@ohif/extension-dicom-segmentation@0.6.5) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.3...@ohif/extension-dicom-segmentation@0.6.4) (2021-04-16)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.2...@ohif/extension-dicom-segmentation@0.6.3) (2021-04-15)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.1...@ohif/extension-dicom-segmentation@0.6.2) (2021-03-31)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.0...@ohif/extension-dicom-segmentation@0.6.1) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+# [0.6.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.5.4...@ohif/extension-dicom-segmentation@0.6.0) (2021-03-04)
+
+
+### Features
+
+* **log:** add new log service ([14d6454](https://github.com/OHIF/Viewers/commit/14d6454eafaa2ccb50e133c2945c9558052ea27e))
+
+
+
+
+
+## [0.5.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.5.3...@ohif/extension-dicom-segmentation@0.5.4) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.5.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.5.2...@ohif/extension-dicom-segmentation@0.5.3) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.5.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.5.1...@ohif/extension-dicom-segmentation@0.5.2) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.5.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.5.0...@ohif/extension-dicom-segmentation@0.5.1) (2021-01-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+# [0.5.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.7...@ohif/extension-dicom-segmentation@0.5.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
 ## [0.4.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.6...@ohif/extension-dicom-segmentation@0.4.7) (2020-10-07)
 
 **Note:** Version bump only for package @ohif/extension-dicom-segmentation

extensions/dicom-segmentation/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-segmentation",
-  "version": "0.4.7",
+  "version": "0.6.9",
   "description": "OHIF extension for viewing segmentations in the 2D MPR view",
   "author": "OHIF",
   "license": "MIT",
@@ -31,7 +31,7 @@
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "^4.20.1",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.18.5",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-segmentation/src/components/SegmentItem/SegmentItem.js

@@ -24,7 +24,7 @@ const SegmentItem = ({
   onClick,
   itemClass,
   color,
-  visible = true,
+  visible,
   onVisibilityChange,
 }) => {
   const [isVisible, setIsVisible] = useState(visible);
@@ -33,6 +33,15 @@ const SegmentItem = ({
     setIsVisible(visible);
   }, [visible]);
 
+  const onClickHandler = () => onClick(index);
+
+  const onVisibilityChangeHandler = event => {
+    event.stopPropagation();
+    const newVisibility = !isVisible;
+    setIsVisible(newVisibility);
+    onVisibilityChange(newVisibility, index);
+  };
+
   return (
     <div className="dcmseg-segment-item">
       <TableListItem
@@ -42,7 +51,7 @@ const SegmentItem = ({
         itemClass={itemClass}
         itemMeta={<ColoredCircle color={color} />}
         itemMetaClass="segment-color-section"
-        onItemClick={onClick}
+        onItemClick={onClickHandler}
       >
         <div>
           <div className="segment-label" style={{ marginBottom: 4 }}>
@@ -63,12 +72,7 @@ const SegmentItem = ({
               name={isVisible ? 'eye' : 'eye-closed'}
               width="20px"
               height="20px"
-              onClick={event => {
+              onClick={onVisibilityChangeHandler}
-                event.stopPropagation();
-                const newVisibility = !isVisible;
-                setIsVisible(newVisibility);
-                onVisibilityChange(newVisibility);
-              }}
             />
           </div>
           {false && <div className="segment-info">{'...'}</div>}

extensions/dicom-segmentation/src/components/SegmentationPanel/SegmentationPanel.css

@@ -6,6 +6,7 @@
   width: 100%;
   display: flex;
   flex-direction: column;
+  padding: 20px;
 }
 
 .dcmseg-segmentation-panel.disabled {
@@ -14,19 +15,19 @@
 }
 
 .dcmseg-segmentation-panel h3 {
-  padding-left: 20px;
   margin-top: 0;
 }
 
 .dcmseg-segmentation-panel .segmentations {
-  padding: 0 20px 20px 20px;
+  padding-bottom: 10px;
 }
 
 .dcmseg-segmentation-panel .cog-icon {
-  margin: 20px 20px 0 0;
   align-self: flex-end;
   color: var(--default-color);
   cursor: pointer;
+  min-height: 23px;
+  max-height: 23px;
 }
 
 .dcmseg-segmentation-panel .cog-icon:hover {
@@ -48,11 +49,11 @@
   height: 150px;
 }
 
-.dcmseg-segmentation-panel .selector-form>div {
+.dcmseg-segmentation-panel .selector-form > div {
   width: 100%;
 }
 
-.dcmseg-segmentation-panel .selector-form>div:first-of-type {
+.dcmseg-segmentation-panel .selector-form > div:first-of-type {
   display: flex;
   flex-direction: row;
   justify-content: center;
@@ -64,3 +65,61 @@
   flex: unset;
   margin-right: 16px;
 }
+
+.SegmentsSection {
+  display: flex;
+  flex-direction: column;
+  color: var(--text-primary-color);
+  font-size: 12px;
+  margin-bottom: 0px;
+  height: 100%;
+}
+
+.SegmentsSection .header {
+  display: flex;
+  flex-direction: row;
+  align-items: center;
+  justify-content: space-between;
+  background-color: var(--ui-gray-dark);
+  border-radius: 5px;
+  font-weight: bold;
+  padding: 10px 15px;
+}
+
+.SegmentsSection .count {
+  font-size: 15px;
+  color: var(--active-color);
+  margin-left: 15px;
+  border-radius: 5px;
+  background-color: var(--ui-gray-darker);
+  text-align: center;
+  min-width: 25px;
+}
+
+.SegmentsSection .header .eye-icon,
+.SegmentsSection .header .angle-double-down,
+.SegmentsSection .header .angle-double-up {
+  cursor: pointer;
+  color: var(--active-color);
+}
+
+.SegmentsSection .header .eye-icon:hover,
+.SegmentsSection .header .angle-double-down:hover,
+.SegmentsSection .header .angle-double-up:hover {
+  color: var(--hover-color);
+}
+
+.SegmentsSection .header .eye-icon.expanded {
+  color: var(--default-color);
+}
+
+.SegmentsSection .header .icons {
+  display: flex;
+  align-items: center;
+  border-radius: 5px;
+}
+
+.SegmentsSection .header .icons .angle-double-down,
+.SegmentsSection .header .icons .angle-double-up {
+  margin-left: 15px;
+}

extensions/dicom-segmentation/src/components/SegmentationPanel/SegmentationPanel.js

@@ -1,8 +1,9 @@
-import React, { useState, useEffect, useCallback } from 'react';
+import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
 import cornerstoneTools from 'cornerstone-tools';
 import cornerstone from 'cornerstone-core';
 import moment from 'moment';
+import classNames from 'classnames';
 import { utils, log } from '@ohif/core';
 import { ScrollableArea, TableList, Icon } from '@ohif/ui';
 import DICOMSegTempCrosshairsTool from '../../tools/DICOMSegTempCrosshairsTool';
@@ -67,29 +68,106 @@ const SegmentationPanel = ({
   const [state, setState] = useState({
     brushRadius: DEFAULT_BRUSH_RADIUS,
     brushColor: 'rgba(221, 85, 85, 1)',
-    selectedSegment: null,
+    selectedSegment: 0,
-    selectedSegmentation: null,
+    selectedSegmentation: 0,
-    showSegmentationSettings: false,
+    showSettings: false,
-    brushStackState: null,
+    labelMapList: [],
-    labelmapList: [],
     segmentList: [],
-    cachedSegmentsProperties: [],
+    segmentsHidden: [],
+    segmentNumbers: [],
     isLoading: false,
     isDisabled: true,
   });
 
+  const getActiveViewport = () => viewports[activeIndex];
+
+  const getFirstImageId = () => {
+    const { StudyInstanceUID, displaySetInstanceUID } = getActiveViewport();
+    const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+    return studyMetadata.getFirstImageId(displaySetInstanceUID);
+  };
+
+  const getActiveLabelMaps3D = () => {
+    const { labelmaps3D, activeLabelmapIndex } = getBrushStackState();
+    return labelmaps3D[activeLabelmapIndex];
+  };
+
+  const getActiveLabelMapIndex = () => {
+    const { activeLabelmapIndex } = getBrushStackState();
+    return activeLabelmapIndex;
+  };
+
+  const getActiveSegmentIndex = () => {
+    const { activeSegmentIndex } = getActiveLabelMaps3D();
+    return activeSegmentIndex;
+  };
+
+  const getActiveLabelMaps2D = () => {
+    const { labelmaps2D } = getActiveLabelMaps3D();
+    return labelmaps2D;
+  };
+
+  const getCurrentDisplaySet = () => {
+    const { StudyInstanceUID, displaySetInstanceUID } = getActiveViewport();
+    const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+    const allDisplaySets = studyMetadata.getDisplaySets();
+    return allDisplaySets.find(
+      ds => ds.displaySetInstanceUID === displaySetInstanceUID
+    );
+  };
+
+  const setActiveSegment = segmentIndex => {
+    const activeSegmentIndex = getActiveSegmentIndex();
+    const activeViewport = getActiveViewport();
+
+    if (segmentIndex === activeSegmentIndex) {
+      log.info(`${activeSegmentIndex} is already the active segment`);
+      return;
+    }
+
+    const labelmap3D = getActiveLabelMaps3D();
+    labelmap3D.activeSegmentIndex = segmentIndex;
+
+    /**
+     * Activates the correct label map if clicked segment
+     * does not belong to the active labelmap
+     */
+    const { StudyInstanceUID } = activeViewport;
+    const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+    const allDisplaySets = studyMetadata.getDisplaySets();
+    let selectedSegmentation;
+    let newLabelmapIndex = getActiveLabelMapIndex();
+    allDisplaySets.forEach(displaySet => {
+      if (displaySet.labelmapSegments) {
+        Object.keys(displaySet.labelmapSegments).forEach(labelmapIndex => {
+          if (
+            displaySet.labelmapSegments[labelmapIndex].includes(segmentIndex)
+          ) {
+            newLabelmapIndex = labelmapIndex;
+            selectedSegmentation =
+              displaySet.hasOverlapping === true
+                ? displaySet.originLabelMapIndex
+                : labelmapIndex;
+          }
+        });
+      }
+    });
+
+    const brushStackState = getBrushStackState();
+    brushStackState.activeLabelmapIndex = newLabelmapIndex;
+    if (selectedSegmentation) {
+      setState(state => ({ ...state, selectedSegmentation }));
+    }
+
+    refreshViewports();
+
+    return segmentIndex;
+  };
+
   useEffect(() => {
     const labelmapModifiedHandler = event => {
       log.warn('Segmentation Panel: labelmap modified', event);
-      const module = cornerstoneTools.getModule('segmentation');
+      refreshSegmentations();
-      const activeViewport = viewports[activeIndex];
-      const studyMetadata = studyMetadataManager.get(
-        activeViewport.StudyInstanceUID
-      );
-      const firstImageId = studyMetadata.getFirstImageId(
-        activeViewport.displaySetInstanceUID
-      );
-      updateState('brushStackState', module.state.series[firstImageId]);
     };
 
     /*
@@ -113,6 +191,10 @@ const SegmentationPanel = ({
       'extensiondicomsegmentationsegloaded',
       refreshSegmentations
     );
+    document.addEventListener(
+      'extensiondicomsegmentationsegselected',
+      updateSegmentationComboBox
+    );
 
     /*
      * These are specific to each element;
@@ -131,6 +213,10 @@ const SegmentationPanel = ({
         'extensiondicomsegmentationsegloaded',
         refreshSegmentations
       );
+      document.removeEventListener(
+        'extensiondicomsegmentationsegselected',
+        updateSegmentationComboBox
+      );
       cornerstoneTools.store.state.enabledElements.forEach(enabledElement =>
         enabledElement.removeEventListener(
           'cornerstonetoolslabelmapmodified',
@@ -140,50 +226,59 @@ const SegmentationPanel = ({
     };
   }, [activeIndex, viewports]);
 
-  const refreshSegmentations = useCallback(() => {
+  const updateSegmentationComboBox = (e) => {
-    const module = cornerstoneTools.getModule('segmentation');
+    const index = e.detail.activatedLabelmapIndex;
-    const activeViewport = viewports[activeIndex];
+    if (index !== -1) {
+      setState(state => ({ ...state, selectedSegmentation: index }));
+    } else {
+      cleanSegmentationComboBox();
+    }
+  }
 
+  const cleanSegmentationComboBox = () => {
+    setState(state => ({
+      ...state,
+      segmentsHidden: [],
+      segmentNumbers: [],
+      labelMapList: [],
+      segmentList: [],
+      isDisabled: true,
+      selectedSegmentation: -1,
+    }));
+  }
+
+  const refreshSegmentations = () => {
+    const activeViewport = getActiveViewport();
     const isDisabled = !activeViewport || !activeViewport.StudyInstanceUID;
     if (!isDisabled) {
-      const studyMetadata = studyMetadataManager.get(
+      const brushStackState = getBrushStackState();
-        activeViewport.StudyInstanceUID
-      );
-      const firstImageId = studyMetadata.getFirstImageId(
-        activeViewport.displaySetInstanceUID
-      );
-      const brushStackState = module.state.series[firstImageId];
       if (brushStackState) {
-        const labelmap3D =
+        const labelMapList = getLabelMapList();
-          brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
+        const {
-        const labelmapList = getLabelmapList(
+          items: segmentList,
-          brushStackState,
+          numbers: segmentNumbers,
-          firstImageId,
+          segmentsHidden,
-          activeViewport
+        } = getSegmentList();
-        );
-        const segmentList = getSegmentList(
-          labelmap3D,
-          firstImageId,
-          brushStackState
-        );
         setState(state => ({
           ...state,
-          brushStackState,
+          segmentsHidden,
-          selectedSegmentation: brushStackState.activeLabelmapIndex,
+          segmentNumbers,
-          labelmapList,
+          labelMapList,
           segmentList,
           isDisabled,
         }));
       } else {
         setState(state => ({
           ...state,
-          labelmapList: [],
+          segmentsHidden: [],
+          segmentNumbers: [],
+          labelMapList: [],
           segmentList: [],
           isDisabled,
         }));
       }
     }
-  }, [viewports, activeIndex, state.isLoading]);
+  };
 
   useEffect(() => {
     refreshSegmentations();
@@ -200,306 +295,288 @@ const SegmentationPanel = ({
   useEffect(() => {
     setState(state => ({
       ...state,
-      showSegmentationSettings: state.showSegmentationSettings && !isOpen,
+      showSettings: state.showSettings && !isOpen,
     }));
   }, [isOpen]);
 
-  const getLabelmapList = useCallback(
+  const getLabelMapList = () => {
-    (brushStackState, firstImageId, activeViewport) => {
+    const activeViewport = getActiveViewport();
-      /* Get list of SEG labelmaps specific to active viewport (reference series) */
-      const referencedSegDisplaysets = _getReferencedSegDisplaysets(
-        activeViewport.StudyInstanceUID,
-        activeViewport.SeriesInstanceUID
-      );
 
-      return referencedSegDisplaysets.map((displaySet, index) => {
+    /* Get list of SEG labelmaps specific to active viewport (reference series) */
-        const { labelmapIndex, SeriesDate, SeriesTime } = displaySet;
+    const referencedSegDisplaysets = _getReferencedSegDisplaysets(
+      activeViewport.StudyInstanceUID,
+      activeViewport.SeriesInstanceUID
+    );
 
-        /* Map to display representation */
+    const filteredReferencedSegDisplaysets = referencedSegDisplaysets.filter(
-        const dateStr = `${SeriesDate}:${SeriesTime}`.split('.')[0];
+      (segDisplay => segDisplay.loadError !== true));
-        const date = moment(dateStr, 'YYYYMMDD:HHmmss');
-        const isActiveLabelmap =
-          labelmapIndex === brushStackState.activeLabelmapIndex;
-        const displayDate = date.format('ddd, MMM Do YYYY');
-        const displayTime = date.format('h:mm:ss a');
-        const displayDescription = displaySet.SeriesDescription;
 
-        return {
+    return filteredReferencedSegDisplaysets.map((displaySet, index) => {
-          value: labelmapIndex,
+      const {
-          title: displayDescription,
+        labelmapIndex,
-          description: displayDate,
+        originLabelMapIndex,
-          onClick: async () => {
+        hasOverlapping,
-            const activatedLabelmapIndex = await setActiveLabelmap(
+        SeriesDate,
-              activeViewport,
+        SeriesTime,
-              studies,
+      } = displaySet;
-              displaySet,
-              () => onSelectedSegmentationChange(),
-              onDisplaySetLoadFailure
-            );
-            updateState('selectedSegmentation', activatedLabelmapIndex);
-          },
-        };
-      });
-    },
-    [studies]
-  );
 
-  const getSegmentList = useCallback(
+      /* Map to display representation */
-    (labelmap3D, firstImageId, brushStackState) => {
+      const dateStr = `${SeriesDate}:${SeriesTime}`.split('.')[0];
-      /*
+      const date = moment(dateStr, 'YYYYMMDD:HHmmss');
-       * Newly created segments have no `meta`
+      const displayDate = date.format('ddd, MMM Do YYYY, h:mm:ss a');
-       * So we instead build a list of all segment indexes in use
+      const displayDescription = displaySet.SeriesDescription;
-       * Then find any associated metadata
-       */
-      const uniqueSegmentIndexes = labelmap3D.labelmaps2D
-        .reduce((acc, labelmap2D) => {
-          if (labelmap2D) {
-            const segmentIndexes = labelmap2D.segmentsOnLabelmap;
 
-            for (let i = 0; i < segmentIndexes.length; i++) {
+      return {
-              if (!acc.includes(segmentIndexes[i]) && segmentIndexes[i] !== 0) {
+        value: hasOverlapping === true ? originLabelMapIndex : labelmapIndex,
-                acc.push(segmentIndexes[i]);
+        title: displayDescription,
-              }
+        description: displayDate,
-            }
+        onClick: async () => {
-          }
+          const activatedLabelmapIndex = await setActiveLabelmap(
-
+            activeViewport,
-          return acc;
+            studies,
-        }, [])
+            displaySet,
-        .sort((a, b) => a - b);
+            onSelectedSegmentationChange,
-
+            onDisplaySetLoadFailure
-      const module = cornerstoneTools.getModule('segmentation');
-      const colorLutTable =
-        module.state.colorLutTables[labelmap3D.colorLUTIndex];
-      const hasLabelmapMeta = labelmap3D.metadata && labelmap3D.metadata.data;
-
-      const segmentList = [];
-      for (let i = 0; i < uniqueSegmentIndexes.length; i++) {
-        const segmentIndex = uniqueSegmentIndexes[i];
-
-        const color = colorLutTable[segmentIndex];
-        let segmentLabel = '(unlabeled)';
-        let segmentNumber = segmentIndex;
-
-        /* Meta */
-        if (hasLabelmapMeta) {
-          const segmentMeta = labelmap3D.metadata.data[segmentIndex];
-
-          if (segmentMeta) {
-            segmentNumber = segmentMeta.SegmentNumber;
-            segmentLabel = segmentMeta.SegmentLabel;
-          }
-        }
-
-        const sameSegment = state.selectedSegment === segmentNumber;
-        const setCurrentSelectedSegment = () => {
-          _setActiveSegment(
-            firstImageId,
-            segmentNumber,
-            labelmap3D.activeSegmentIndex
           );
-          updateState('selectedSegment', sameSegment ? null : segmentNumber);
+          setState(state => ({
-
+            ...state,
-          const validIndexList = [];
+            selectedSegmentation: activatedLabelmapIndex,
-          labelmap3D.labelmaps2D.forEach((labelMap2D, index) => {
+          }));
-            if (labelMap2D.segmentsOnLabelmap.includes(segmentNumber)) {
+        },
-              validIndexList.push(index);
+      };
-            }
+    });
-          });
-          const avg = array => array.reduce((a, b) => a + b) / array.length;
-          const average = avg(validIndexList);
-          const closest = validIndexList.reduce((prev, curr) => {
-            return Math.abs(curr - average) < Math.abs(prev - average)
-              ? curr
-              : prev;
-          });
-
-          if (isCornerstone()) {
-            const enabledElements = cornerstone.getEnabledElements();
-            const element = enabledElements[activeIndex].element;
-            const toolState = cornerstoneTools.getToolState(element, 'stack');
-
-            if (!toolState) {
-              return;
-            }
-
-            const imageIds = toolState.data[0].imageIds;
-            const imageId = imageIds[closest];
-            const frameIndex = imageIds.indexOf(imageId);
-
-            const SOPInstanceUID = cornerstone.metaData.get(
-              'SOPInstanceUID',
-              imageId
-            );
-            const StudyInstanceUID = cornerstone.metaData.get(
-              'StudyInstanceUID',
-              imageId
-            );
-
-            DICOMSegTempCrosshairsTool.addCrosshair(
-              element,
-              imageId,
-              segmentNumber
-            );
-
-            onSegmentItemClick({
-              StudyInstanceUID,
-              SOPInstanceUID,
-              frameIndex,
-              activeViewportIndex: activeIndex,
-            });
-          }
-
-          if (isVTK()) {
-            const activeViewport = viewports[activeIndex];
-            const studyMetadata = studyMetadataManager.get(
-              activeViewport.StudyInstanceUID
-            );
-            const allDisplaySets = studyMetadata.getDisplaySets();
-            const currentDisplaySet = allDisplaySets.find(
-              displaySet =>
-                displaySet.displaySetInstanceUID ===
-                activeViewport.displaySetInstanceUID
-            );
-
-            const frame = labelmap3D.labelmaps2D[closest];
-
-            onSegmentItemClick({
-              studies,
-              StudyInstanceUID: currentDisplaySet.StudyInstanceUID,
-              displaySetInstanceUID: currentDisplaySet.displaySetInstanceUID,
-              SOPClassUID: viewports[activeIndex].sopClassUIDs[0],
-              SOPInstanceUID: currentDisplaySet.SOPInstanceUID,
-              segmentNumber,
-              frameIndex: closest,
-              frame,
-            });
-          }
-        };
-
-        const isSegmentVisible = () => {
-          return !labelmap3D.segmentsHidden[segmentIndex];
-        };
-
-        const toggleSegmentVisibility = () => {
-          const segmentsHidden = labelmap3D.segmentsHidden;
-          segmentsHidden[segmentIndex] = !segmentsHidden[segmentIndex];
-          return !segmentsHidden[segmentIndex];
-        };
-
-        const cachedSegmentProperties =
-          state.cachedSegmentsProperties[segmentNumber];
-        let visible = isSegmentVisible();
-        if (
-          cachedSegmentProperties &&
-          cachedSegmentProperties.visible !== visible
-        ) {
-          toggleSegmentVisibility();
-        }
-
-        segmentList.push(
-          <SegmentItem
-            key={segmentNumber}
-            itemClass={`segment-item ${sameSegment && 'selected'}`}
-            onClick={() => setCurrentSelectedSegment()}
-            label={segmentLabel}
-            index={segmentNumber}
-            color={color}
-            visible={visible}
-            onVisibilityChange={newVisibility => {
-              if (isCornerstone()) {
-                const enabledElements = cornerstone.getEnabledElements();
-                const element = enabledElements[activeIndex].element;
-                module.setters.toggleSegmentVisibility(
-                  element,
-                  segmentNumber,
-                  brushStackState.activeLabelmapIndex
-                );
-              }
-
-              if (isVTK()) {
-                onSegmentVisibilityChange(segmentNumber, newVisibility);
-              }
-
-              updateCachedSegmentsProperties(segmentNumber, {
-                visible: newVisibility,
-              });
-              refreshViewports();
-            }}
-          />
-        );
-      }
-
-      return segmentList;
-
-      /*
-       * Let's iterate over segmentIndexes ^ above
-       * If meta has a match, use it to show info
-       * If now, add "no-meta" class
-       * Show default name
-       */
-    },
-    [activeIndex, onSegmentItemClick, state.selectedSegment, state.isLoading]
-  );
-
-  const updateCachedSegmentsProperties = (segmentNumber, properties) => {
-    const segmentsProperties = state.cachedSegmentsProperties;
-    const segmentProperties = state.cachedSegmentsProperties[segmentNumber];
-
-    segmentsProperties[segmentNumber] = segmentProperties
-      ? { ...segmentProperties, ...properties }
-      : properties;
-
-    updateState('cachedSegmentsProperties', segmentsProperties);
   };
 
-  useEffect(() => {
+  const setCurrentSelectedSegment = segmentNumber => {
-    updateState('cachedSegmentsProperties', []);
+    setActiveSegment(segmentNumber);
-  }, [activeContexts]);
 
-  const updateState = (field, value) => {
+    const sameSegment = state.selectedSegment === segmentNumber;
-    setState(state => ({ ...state, [field]: value }));
+    if (!sameSegment) {
+      setState(state => ({ ...state, selectedSegment: segmentNumber }));
+    }
+
+    const validIndexList = [];
+    getActiveLabelMaps2D().forEach((labelMap2D, index) => {
+      if (labelMap2D.segmentsOnLabelmap.includes(segmentNumber)) {
+        validIndexList.push(index);
+      }
+    });
+
+    const avg = array => array.reduce((a, b) => a + b) / array.length;
+    const average = avg(validIndexList);
+    const closest = validIndexList.reduce((prev, curr) => {
+      return Math.abs(curr - average) < Math.abs(prev - average) ? curr : prev;
+    });
+
+    if (isCornerstone()) {
+      const element = getEnabledElement();
+      const toolState = cornerstoneTools.getToolState(element, 'stack');
+
+      if (!toolState) return;
+
+      const imageIds = toolState.data[0].imageIds;
+      const imageId = imageIds[closest];
+      const frameIndex = imageIds.indexOf(imageId);
+
+      const SOPInstanceUID = cornerstone.metaData.get(
+        'SOPInstanceUID',
+        imageId
+      );
+      const StudyInstanceUID = cornerstone.metaData.get(
+        'StudyInstanceUID',
+        imageId
+      );
+
+      DICOMSegTempCrosshairsTool.addCrosshair(element, imageId, segmentNumber);
+
+      onSegmentItemClick({
+        StudyInstanceUID,
+        SOPInstanceUID,
+        frameIndex,
+        activeViewportIndex: activeIndex,
+      });
+    }
+
+    if (isVTK()) {
+      const labelMaps3D = getActiveLabelMaps3D();
+      const currentDisplaySet = getCurrentDisplaySet();
+      const frame = labelMaps3D.labelmaps2D[closest];
+
+      onSegmentItemClick({
+        studies,
+        StudyInstanceUID: currentDisplaySet.StudyInstanceUID,
+        displaySetInstanceUID: currentDisplaySet.displaySetInstanceUID,
+        SOPClassUID: getActiveViewport().sopClassUIDs[0],
+        SOPInstanceUID: currentDisplaySet.SOPInstanceUID,
+        segmentNumber,
+        frameIndex: closest,
+        frame,
+      });
+    }
+  };
+
+  const getColorLUTTable = () => {
+    const { state } = cornerstoneTools.getModule('segmentation');
+    const { colorLUTIndex } = getActiveLabelMaps3D();
+    return state.colorLutTables[colorLUTIndex];
+  };
+
+  const getEnabledElement = () => {
+    const enabledElements = cornerstone.getEnabledElements();
+    return enabledElements[activeIndex].element;
+  };
+
+  const onSegmentVisibilityChangeHandler = (isVisible, segmentNumber) => {
+    /** Get all labelmaps with this segmentNumber (overlapping segments) */
+    const { labelmaps3D } = getBrushStackState();
+    const possibleLabelMaps3D = labelmaps3D.filter(({ labelmaps2D }) => {
+      return labelmaps2D.some(({ segmentsOnLabelmap }) =>
+        segmentsOnLabelmap.includes(segmentNumber)
+      );
+    });
+
+    let segmentsHidden = [];
+    possibleLabelMaps3D.forEach(labelmap3D => {
+      labelmap3D.segmentsHidden[segmentNumber] = !isVisible;
+
+      segmentsHidden = [
+        ...new Set([...segmentsHidden, ...labelmap3D.segmentsHidden]),
+      ];
+    });
+
+    setState(state => ({ ...state, segmentsHidden }));
+
+    refreshSegmentations();
+    refreshViewports();
+
+    if (isVTK()) {
+      onSegmentVisibilityChange(segmentNumber, isVisible);
+    }
+  };
+
+  const getSegmentList = () => {
+    /*
+     * Newly created segments have no `meta`
+     * So we instead build a list of all segment indexes in use
+     * Then find any associated metadata
+     */
+    const uniqueSegmentIndexes = getActiveLabelMaps2D()
+      .reduce((acc, labelmap2D) => {
+        if (labelmap2D) {
+          const segmentIndexes = labelmap2D.segmentsOnLabelmap;
+
+          for (let i = 0; i < segmentIndexes.length; i++) {
+            if (!acc.includes(segmentIndexes[i]) && segmentIndexes[i] !== 0) {
+              acc.push(segmentIndexes[i]);
+            }
+          }
+        }
+
+        return acc;
+      }, [])
+      .sort((a, b) => a - b);
+
+    const labelmap3D = getActiveLabelMaps3D();
+    const colorLutTable = getColorLUTTable();
+    const hasLabelmapMeta = labelmap3D.metadata && labelmap3D.metadata.data;
+
+    const segmentList = [];
+    const segmentNumbers = [];
+    for (let i = 0; i < uniqueSegmentIndexes.length; i++) {
+      const segmentIndex = uniqueSegmentIndexes[i];
+
+      const color = colorLutTable[segmentIndex];
+      let segmentLabel = '(unlabeled)';
+      let segmentNumber = segmentIndex;
+
+      /* Meta */
+      if (hasLabelmapMeta) {
+        const segmentMeta = labelmap3D.metadata.data[segmentIndex];
+        if (segmentMeta) {
+          segmentNumber = segmentMeta.SegmentNumber;
+          segmentLabel = segmentMeta.SegmentLabel;
+        }
+      }
+
+      const sameSegment = state.selectedSegment === segmentNumber;
+
+      segmentNumbers.push(segmentNumber);
+      segmentList.push(
+        <SegmentItem
+          key={segmentNumber}
+          itemClass={`segment-item ${sameSegment && 'selected'}`}
+          onClick={setCurrentSelectedSegment}
+          label={segmentLabel}
+          index={segmentNumber}
+          color={color}
+          visible={!labelmap3D.segmentsHidden[segmentIndex]}
+          onVisibilityChange={onSegmentVisibilityChangeHandler}
+        />
+      );
+    }
+
+    return {
+      items: segmentList,
+      numbers: segmentNumbers,
+      segmentsHidden: labelmap3D.segmentsHidden,
+    };
+
+    /*
+     * Let's iterate over segmentIndexes ^ above
+     * If meta has a match, use it to show info
+     * If now, add "no-meta" class
+     * Show default name
+     */
   };
 
   const updateBrushSize = evt => {
     const updatedRadius = Number(evt.target.value);
 
     if (updatedRadius !== brushRadius) {
-      updateState('brushRadius', updatedRadius);
+      setState(state => ({ ...state, brushRadius: updatedRadius }));
       const module = cornerstoneTools.getModule('segmentation');
       module.setters.radius(updatedRadius);
     }
   };
 
   const decrementSegment = event => {
+    const activeSegmentIndex = getActiveSegmentIndex();
     event.preventDefault();
-    if (labelmap3D.activeSegmentIndex > 1) {
+    if (activeSegmentIndex > 1) {
-      labelmap3D.activeSegmentIndex--;
+      activeSegmentIndex--;
     }
-    updateState('selectedSegment', labelmap3D.activeSegmentIndex);
+    setState(state => ({ ...state, selectedSegment: activeSegmentIndex }));
     updateActiveSegmentColor();
   };
 
   const incrementSegment = event => {
+    const activeSegmentIndex = getActiveSegmentIndex();
     event.preventDefault();
-    labelmap3D.activeSegmentIndex++;
+    activeSegmentIndex++;
-    updateState('selectedSegment', labelmap3D.activeSegmentIndex);
+    setState(state => ({ ...state, selectedSegment: activeSegmentIndex }));
     updateActiveSegmentColor();
   };
 
   const updateActiveSegmentColor = () => {
     const color = getActiveSegmentColor();
-    updateState('brushColor', color);
+    setState(state => ({ ...state, brushColor: color }));
+  };
+
+  const getBrushStackState = () => {
+    const module = cornerstoneTools.getModule('segmentation');
+    const firstImageId = getFirstImageId();
+    const brushStackState = module.state.series[firstImageId];
+    return brushStackState;
   };
 
   const getActiveSegmentColor = () => {
-    if (!state.brushStackState) {
+    const brushStackState = getBrushStackState();
+    if (!brushStackState) {
       return 'rgba(255, 255, 255, 1)';
     }
 
-    const module = cornerstoneTools.getModule('segmentation');
+    const colorLutTable = getColorLUTTable();
-    const colorLutTable = module.state.colorLutTables[labelmap3D.colorLUTIndex];
     const color = colorLutTable[labelmap3D.activeSegmentIndex];
-
     return `rgba(${color.join(',')})`;
   };
 
@@ -517,65 +594,103 @@ const SegmentationPanel = ({
     refreshViewports();
   };
 
+  const onVisibilityChangeHandler = isVisible => {
+    let segmentsHidden = [];
+    state.segmentNumbers.forEach(segmentNumber => {
+      if (isVTK()) {
+        onSegmentVisibilityChange(segmentNumber, isVisible);
+      }
+
+      /** Get all labelmaps with this segmentNumber (overlapping segments) */
+      const { labelmaps3D } = getBrushStackState();
+      const possibleLabelMaps3D = labelmaps3D.filter(({ labelmaps2D }) => {
+        return labelmaps2D.some(({ segmentsOnLabelmap }) =>
+          segmentsOnLabelmap.includes(segmentNumber)
+        );
+      });
+
+      possibleLabelMaps3D.forEach(labelmap3D => {
+        labelmap3D.segmentsHidden[segmentNumber] = !isVisible;
+        segmentsHidden = [
+          ...new Set([...segmentsHidden, ...labelmap3D.segmentsHidden]),
+        ];
+      });
+    });
+
+    setState(state => ({ ...state, segmentsHidden }));
+
+    refreshSegmentations();
+    refreshViewports();
+  };
+
   const disabledConfigurationFields = [
     'outlineAlpha',
     'shouldRenderInactiveLabelmaps',
   ];
-  if (state.showSegmentationSettings) {
+
+  const selectedSegmentationOption = state.labelMapList.find(
+    i => i.value === state.selectedSegmentation
+  );
+
+  if (state.showSettings) {
     return (
       <SegmentationSettings
         disabledFields={isVTK() ? disabledConfigurationFields : []}
         configuration={configuration}
-        onBack={() => updateState('showSegmentationSettings', false)}
+        onBack={() => setState(state => ({ ...state, showSettings: false }))}
         onChange={updateConfiguration}
       />
     );
   } else {
     return (
       <div
-        className={`dcmseg-segmentation-panel ${state.isDisabled &&
+        className={classNames('dcmseg-segmentation-panel', {
-          'disabled'}`}
+          disabled: state.isDisabled,
+        })}
       >
-        <Icon
-          className="cog-icon"
-          name="cog"
-          width="25px"
-          height="25px"
-          onClick={() => updateState('showSegmentationSettings', true)}
-        />
         {false && (
           <form className="selector-form">
             <BrushColorSelector
-              defaultColor={brushColor}
+              defaultColor={state.brushColor}
               index={state.selectedSegment}
               onNext={incrementSegment}
               onPrev={decrementSegment}
             />
             <BrushRadius
-              value={brushRadius}
+              value={state.brushRadius}
               onChange={updateBrushSize}
               min={configuration.minRadius}
               max={configuration.maxRadius}
             />
           </form>
         )}
+        <Icon
+          className="cog-icon"
+          name="cog"
+          width="25px"
+          height="25px"
+          onClick={() => setState(state => ({ ...state, showSettings: true }))}
+        />
         <h3>Segmentations</h3>
         <div className="segmentations">
           <SegmentationSelect
-            value={state.labelmapList.find(
+            value={selectedSegmentationOption}
-              i => i.value === state.selectedSegmentation
-            )}
             formatOptionLabel={SegmentationItem}
-            options={state.labelmapList}
+            options={state.labelMapList}
           />
         </div>
-        <ScrollableArea>
+        <SegmentsSection
-          <TableList
+          count={state.segmentList.length}
-            customHeader={<SegmentsHeader count={state.segmentList.length} />}
+          isVisible={
-          >
+            state.segmentsHidden.filter(isHidden => isHidden === true).length <
-            {state.segmentList}
+            state.segmentNumbers.length
-          </TableList>
+          }
-        </ScrollableArea>
+          onVisibilityChange={onVisibilityChangeHandler}
+        >
+          <ScrollableArea>
+            <TableList headless>{state.segmentList}</TableList>
+          </ScrollableArea>
+        </SegmentsSection>
       </div>
     );
   }
@@ -610,7 +725,7 @@ SegmentationPanel.propTypes = {
 SegmentationPanel.defaultProps = {};
 
 /**
- * Returns SEG Displaysets that reference the target series, sorted by dateTime
+ * Returns SEG DisplaySets that reference the target series, sorted by dateTime
  *
  * @param {string} StudyInstanceUID
  * @param {string} SeriesInstanceUID
@@ -628,43 +743,54 @@ const _getReferencedSegDisplaysets = (StudyInstanceUID, SeriesInstanceUID) => {
   referencedDisplaysets.sort((a, b) => {
     const aNumber = Number(`${a.SeriesDate}${a.SeriesTime}`);
     const bNumber = Number(`${b.SeriesDate}${b.SeriesTime}`);
-    return aNumber - bNumber;
+    return bNumber - aNumber;
   });
 
   return referencedDisplaysets;
 };
 
-/**
+const SegmentsSection = ({
- *
+  count,
- * @param {*} firstImageId
+  children,
- * @param {*} activeSegmentIndex
+  isVisible: defaultVisibility,
- * @returns
+  onVisibilityChange,
- */
+}) => {
-const _setActiveSegment = (firstImageId, segmentIndex, activeSegmentIndex) => {
+  const [isVisible, setIsVisible] = useState(defaultVisibility);
-  if (segmentIndex === activeSegmentIndex) {
-    log.info(`${activeSegmentIndex} is already the active segment`);
-    return;
-  }
 
-  const { state } = cornerstoneTools.getModule('segmentation');
+  const onVisibilityChangeHandler = () => {
-  const brushStackState = state.series[firstImageId];
+    const newVisibility = !isVisible;
+    setIsVisible(newVisibility);
+    onVisibilityChange(newVisibility);
+  };
 
-  const labelmap3D =
+  useEffect(() => {
-    brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
+    setIsVisible(defaultVisibility);
-  labelmap3D.activeSegmentIndex = segmentIndex;
+  }, [defaultVisibility]);
 
-  refreshViewports();
-
-  return segmentIndex;
-};
-
-const SegmentsHeader = ({ count }) => {
   return (
-    <React.Fragment>
+    <div className="SegmentsSection">
-      <div className="tableListHeaderTitle">Segments</div>
+      <div className="header">
-      <div className="numberOfItems">{count}</div>
+        <div>Segments</div>
-    </React.Fragment>
+        <div className="icons">
+          <Icon
+            className={`eye-icon ${isVisible && 'expanded'}`}
+            name={isVisible ? 'eye' : 'eye-closed'}
+            width="20px"
+            height="20px"
+            onClick={onVisibilityChangeHandler}
+          />
+          <div className="count">{count}</div>
+        </div>
+      </div>
+      {children}
+    </div>
   );
 };
 
+const noop = () => {};
+
+SegmentsSection.defaultProps = {
+  onVisibilityChange: noop,
+};
+
 export default SegmentationPanel;

extensions/dicom-segmentation/src/components/SegmentationSelect.js

@@ -3,7 +3,7 @@ import Select from 'react-select';
 
 const SegmentationSelect = ({ value, formatOptionLabel, options }) => (
   <Select
-    value={value}
+    value={value === undefined ? null : value}
     formatOptionLabel={formatOptionLabel}
     styles={segmentationSelectStyles}
     options={options}

extensions/dicom-segmentation/src/getOHIFDicomSegSopClassHandler.js

@@ -1,6 +1,11 @@
 import { MODULE_TYPES, utils } from '@ohif/core';
 import loadSegmentation from './loadSegmentation';
 import getSourceDisplaySet from './getSourceDisplaySet';
+import OHIF from '@ohif/core';
+import dcmjs from 'dcmjs';
+
+const { DicomLoaderService } = OHIF.utils;
+const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
 
 // TODO: Should probably use dcmjs for this
 const SOP_CLASS_UIDS = {
@@ -46,11 +51,12 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         StudyInstanceUID,
         FrameOfReferenceUID,
         authorizationHeaders,
-        metadata,
         isDerived: true,
         referencedDisplaySetUID: null, // Assigned when loaded.
         labelmapIndex: null, // Assigned when loaded.
         isLoaded: false,
+        loadError: false,
+        hasOverlapping: false,
         SeriesDate,
         SeriesTime,
         SeriesNumber,
@@ -58,15 +64,107 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         metadata,
       };
 
-      segDisplaySet.getSourceDisplaySet = function(studies) {
+      segDisplaySet.getSourceDisplaySet = function(studies, activateLabelMap = true, onDisplaySetLoadFailureHandler) {
-        return getSourceDisplaySet(studies, segDisplaySet);
+        return getSourceDisplaySet(studies, segDisplaySet, activateLabelMap, onDisplaySetLoadFailureHandler);
       };
 
-      segDisplaySet.load = function(referencedDisplaySet, studies) {
+      segDisplaySet.load = async function(referencedDisplaySet, studies) {
-        return loadSegmentation(segDisplaySet, referencedDisplaySet, studies);
+        segDisplaySet.isLoaded = true;
+        const { StudyInstanceUID } = referencedDisplaySet;
+        const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
+          segDisplaySet,
+          studies
+        );
+        const dicomData = DicomMessage.readFile(segArrayBuffer);
+        const dataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
+        dataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
+        const imageIds = _getImageIdsForDisplaySet(
+          studies,
+          StudyInstanceUID,
+          referencedDisplaySet.SeriesInstanceUID
+        );
+
+        const results = await _parseSeg(segArrayBuffer, imageIds);
+        if (results === undefined) {
+          return;
+        }
+        const {
+          labelmapBufferArray,
+          segMetadata,
+          segmentsOnFrame,
+          segmentsOnFrameArray,
+        } = results;
+        let labelmapIndex;
+        if (labelmapBufferArray.length > 1) {
+          let labelmapIndexes = [];
+          for (let i = 0; i < labelmapBufferArray.length; ++i) {
+            labelmapIndexes.push(
+              await loadSegmentation(
+                imageIds,
+                segDisplaySet,
+                labelmapBufferArray[i],
+                segMetadata,
+                segmentsOnFrame,
+                segmentsOnFrameArray[i]
+              )
+            );
+          }
+          /**
+           * Since overlapping segments have virtual labelmaps,
+           * originLabelMapIndex is used in the panel to select the correct dropdown value.
+           */
+          segDisplaySet.hasOverlapping = true;
+          segDisplaySet.originLabelMapIndex = labelmapIndexes[0];
+          labelmapIndex = labelmapIndexes[0];
+          console.warn('Overlapping segments!');
+        } else {
+          labelmapIndex = await loadSegmentation(
+            imageIds,
+            segDisplaySet,
+            labelmapBufferArray[0],
+            segMetadata,
+            segmentsOnFrame,
+            []
+          );
+        }
       };
 
       return segDisplaySet;
     },
   };
 }
+
+function _parseSeg(arrayBuffer, imageIds) {
+  return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
+    imageIds,
+    arrayBuffer,
+    cornerstone.metaData
+  );
+}
+
+function _getImageIdsForDisplaySet(
+  studies,
+  StudyInstanceUID,
+  SeriesInstanceUID
+) {
+  const study = studies.find(
+    study => study.StudyInstanceUID === StudyInstanceUID
+  );
+
+  const displaySets = study.displaySets.filter(displaySet => {
+    return displaySet.SeriesInstanceUID === SeriesInstanceUID;
+  });
+
+  if (displaySets.length > 1) {
+    console.warn(
+      'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
+    );
+    // TODO -> We could make check the instance list and see if any match?
+    // Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
+    // ^ Will that even happen?
+  }
+
+  const referencedDisplaySet = displaySets[0];
+
+  return referencedDisplaySet.images.map(image => image.getImageId());
+}

extensions/dicom-segmentation/src/getSourceDisplaySet.js

@@ -1,88 +1,16 @@
 import setActiveLabelmap from './utils/setActiveLabelMap';
-import { classes } from '@ohif/core';
+import { metadata } from '@ohif/core';
 
-const { ImageSet } = classes;
+export default function getSourceDisplaySet(studies, segDisplaySet, activateLabelMap = true, onDisplaySetLoadFailureHandler) {
+  const referencedDisplaySet = metadata.StudyMetadata.getReferencedDisplaySet(segDisplaySet, studies);
 
-export default function getSourceDisplaySet(studies, segDisplaySet) {
+  let activatedLabelmapPromise;
-  const referencedDisplaySet = _getReferencedDisplaySet(segDisplaySet, studies);
+  if (activateLabelMap) {
-
+    activatedLabelmapPromise = setActiveLabelmap(referencedDisplaySet, studies, segDisplaySet, undefined, onDisplaySetLoadFailureHandler);
-  setActiveLabelmap(referencedDisplaySet, studies, segDisplaySet);
-
-  return referencedDisplaySet;
-}
-
-const _getReferencedDisplaySet = (segDisplaySet, studies) => {
-  let allDisplaySets = [];
-
-  studies.forEach(study => {
-    allDisplaySets = allDisplaySets.concat(study.displaySets);
-  });
-
-  const otherDisplaySets = allDisplaySets.filter(
-    ds => ds.displaySetInstanceUID !== segDisplaySet.displaySetInstanceUID
-  );
-
-  const { metadata } = segDisplaySet;
-
-  let referencedSeriesInstanceUIDs;
-
-  if (metadata.ReferencedSeriesSequence) {
-    const ReferencedSeriesSequence = _toArray(
-      metadata.ReferencedSeriesSequence
-    );
-
-    referencedSeriesInstanceUIDs = ReferencedSeriesSequence.map(
-      ReferencedSeries => ReferencedSeries.SeriesInstanceUID
-    );
-  } else {
-    const { PerFrameFunctionalGroupsSequence } = metadata;
-
-    let SourceImageSequence;
-
-    if (metadata.SourceImageSequence) {
-      SourceImageSequence = metadata.SourceImageSequence;
-    } else {
-      const firstFunctionalGroups = _toArray(
-        PerFrameFunctionalGroupsSequence
-      )[0];
-      const { DerivationImageSequence } = firstFunctionalGroups;
-
-      SourceImageSequence = DerivationImageSequence;
-    }
-
-    const firstSourceImage = _toArray(SourceImageSequence)[0];
-
-    const { ReferencedSOPInstanceUID } = firstSourceImage;
-
-    referencedSeriesInstanceUIDs = _findReferencedSeriesInstanceUIDsFromSOPInstanceUID(
-      otherDisplaySets,
-      ReferencedSOPInstanceUID
-    );
   }
 
-  const referencedDisplaySet = otherDisplaySets.find(ds =>
+  return {
-    referencedSeriesInstanceUIDs.includes(ds.SeriesInstanceUID)
+    referencedDisplaySet : referencedDisplaySet,
-  );
+    activatedLabelmapPromise : activatedLabelmapPromise
-
-  return referencedDisplaySet;
-};
-
-const _findReferencedSeriesInstanceUIDsFromSOPInstanceUID = (
-  displaySets,
-  SOPInstanceUID
-) => {
-  const imageSets = displaySets.filter(ds => ds instanceof ImageSet);
-
-  for (let i = 0; i < imageSets.length; i++) {
-    const { images } = imageSets[i];
-    for (let j = 0; j < images.length; j++) {
-      if (images[j].SOPInstanceUID === SOPInstanceUID) {
-        return [images[j].getData().metadata.SeriesInstanceUID];
-      }
-    }
   }
-};
-
-function _toArray(arrayOrObject) {
-  return Array.isArray(arrayOrObject) ? arrayOrObject : [arrayOrObject];
 }

extensions/dicom-segmentation/src/index.js

@@ -25,12 +25,13 @@ export default {
     return toolbarModule;
   },
   getPanelModule({ commandsManager, api, servicesManager }) {
-    const { UINotificationService } = servicesManager.services;
+    const { UINotificationService, LoggerService } = servicesManager.services;
 
     const ExtendedSegmentationPanel = props => {
       const { activeContexts } = api.hooks.useAppContext();
 
       const onDisplaySetLoadFailureHandler = error => {
+        LoggerService.error({ error, message: error.message });
         UINotificationService.show({
           title: 'DICOM Segmentation Loader',
           message: error.message,

extensions/dicom-segmentation/src/loadSegmentation.js

@@ -1,92 +1,68 @@
-import OHIF from '@ohif/core';
 import dcmjs from 'dcmjs';
 import cornerstone from 'cornerstone-core';
 import cornerstoneTools from 'cornerstone-tools';
 
-const { DicomLoaderService } = OHIF.utils;
-
 export default async function loadSegmentation(
+  imageIds,
   segDisplaySet,
-  referencedDisplaySet,
+  labelmapBuffer,
-  studies
+  segMetadata,
+  segmentsOnFrame,
+  labelmapSegments
 ) {
-  const { StudyInstanceUID } = referencedDisplaySet;
+  const { setters } = cornerstoneTools.getModule('segmentation');
 
-  // Set here is loading is asynchronous.
+  // TODO: Could define a color LUT based on colors in the SEG.
-  // If this function throws its set back to false.
+  const labelmapIndex = _getNextLabelmapIndex(imageIds[0]);
-  segDisplaySet.isLoaded = true;
+  const colorLUTIndex = _makeColorLUTAndGetIndex(segMetadata);
 
-  const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
+  setters.labelmap3DByFirstImageId(
-    segDisplaySet,
+    imageIds[0],
-    studies
+    labelmapBuffer,
+    labelmapIndex,
+    segMetadata,
+    imageIds.length,
+    segmentsOnFrame,
+    colorLUTIndex
   );
 
-  const dicomData = dcmjs.data.DicomMessage.readFile(segArrayBuffer);
+  if (!segDisplaySet.labelmapSegments) {
-  const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
+    segDisplaySet.labelmapSegments = {};
-    dicomData.dict
+  }
-  );
 
-  dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
+  /**
+   * Cache each labelmap segments.
+   * This data is used to determine the active label map when a given segment is activated/clicked.
+   */
+  segDisplaySet.labelmapSegments[labelmapIndex] = labelmapSegments.length
+    ? Array.from(
+        new Set(labelmapSegments.filter(a => !!a).reduce((a, b) => a.concat(b)))
+      )
+    : [];
+  segDisplaySet.labelmapIndex = labelmapIndex;
 
-  const imageIds = _getImageIdsForDisplaySet(
+  /*
-    studies,
+   * TODO: Improve the way we notify parts of the app that depends on segs to be loaded.
-    StudyInstanceUID,
+   *
-    referencedDisplaySet.SeriesInstanceUID
+   * Currently we are using a non-ideal implementation through a custom event to notify the segmentation panel
-  );
+   * or other components that could rely on loaded segmentations that
+   * the segments were loaded so that e.g. when the user opens the panel
+   * before the segments are fully loaded, the panel can subscribe to this custom event
+   * and update itself with the new segments.
+   *
+   * This limitation is due to the fact that the cs segmentation module is an object (which will be
+   * updated after the segments are loaded) that React its not aware of its changes
+   * because the module object its not passed in to the panel component as prop but accessed externally.
+   *
+   * Improving this event approach to something reactive that can be tracked inside the react lifecycle,
+   * allows us to easily watch the module or the segmentations loading process in any other component
+   * without subscribing to external events.
+   */
+  console.log('Segmentation loaded.');
+  const event = new CustomEvent('extensiondicomsegmentationsegloaded');
+  document.dispatchEvent(event);
 
-  return new Promise((resolve, reject) => {
+  return labelmapIndex;
-    let results;
-
-    try {
-      results = _parseSeg(segArrayBuffer, imageIds);
-    } catch (error) {
-      segDisplaySet.isLoaded = false;
-      segDisplaySet.loadError = true;
-      reject(error);
-    }
-
-    const { labelmapBuffer, segMetadata, segmentsOnFrame } = results;
-    const { setters } = cornerstoneTools.getModule('segmentation');
-
-    // TODO: Could define a color LUT based on colors in the SEG.
-    const labelmapIndex = _getNextLabelmapIndex(imageIds[0]);
-    const colorLUTIndex = _makeColorLUTAndGetIndex(segMetadata);
-
-    setters.labelmap3DByFirstImageId(
-      imageIds[0],
-      labelmapBuffer,
-      labelmapIndex,
-      segMetadata,
-      imageIds.length,
-      segmentsOnFrame,
-      colorLUTIndex
-    );
-
-    segDisplaySet.labelmapIndex = labelmapIndex;
-
-    /*
-     * TODO: Improve the way we notify parts of the app that depends on segs to be loaded.
-     *
-     * Currently we are using a non-ideal implementation through a custom event to notify the segmentation panel
-     * or other components that could rely on loaded segmentations that
-     * the segments were loaded so that e.g. when the user opens the panel
-     * before the segments are fully loaded, the panel can subscribe to this custom event
-     * and update itself with the new segments.
-     *
-     * This limitation is due to the fact that the cs segmentation module is an object (which will be
-     * updated after the segments are loaded) that React its not aware of its changes
-     * because the module object its not passed in to the panel component as prop but accessed externally.
-     *
-     * Improving this event approach to something reactive that can be tracked inside the react lifecycle,
-     * allows us to easily watch the module or the segmentations loading process in any other component
-     * without subscribing to external events.
-     */
-    console.log('Segmentation loaded.');
-    const event = new CustomEvent('extensiondicomsegmentationsegloaded');
-    document.dispatchEvent(event);
-
-    resolve(labelmapIndex);
-  });
 }
 
 function _getNextLabelmapIndex(firstImageId) {
@@ -172,38 +148,3 @@ function _getNextColorLUTIndex() {
 
   return colorLUTIndex;
 }
-
-function _parseSeg(arrayBuffer, imageIds) {
-  return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
-    imageIds,
-    arrayBuffer,
-    cornerstone.metaData
-  );
-}
-
-function _getImageIdsForDisplaySet(
-  studies,
-  StudyInstanceUID,
-  SeriesInstanceUID
-) {
-  const study = studies.find(
-    study => study.StudyInstanceUID === StudyInstanceUID
-  );
-
-  const displaySets = study.displaySets.filter(displaySet => {
-    return displaySet.SeriesInstanceUID === SeriesInstanceUID;
-  });
-
-  if (displaySets.length > 1) {
-    console.warn(
-      'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
-    );
-    // TODO -> We could make check the instance list and see if any match?
-    // Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
-    // ^ Will that even happen?
-  }
-
-  const referencedDisplaySet = displaySets[0];
-
-  return referencedDisplaySet.images.map(image => image.getImageId());
-}

extensions/dicom-segmentation/src/utils/setActiveLabelMap.js

@@ -20,7 +20,7 @@ export default async function setActiveLabelmap(
   displaySet,
   callback = () => {},
   onDisplaySetLoadFailure = err => {
-    throw new Error(err.message);
+    console.error(err.message);
   }
 ) {
   const studyMetadata = studyMetadataManager.get(
@@ -37,31 +37,43 @@ export default async function setActiveLabelmap(
     ? brushStackState.activeLabelmapIndex
     : undefined;
 
-  if (displaySet.labelmapIndex === activeLabelmapIndex) {
+  let labelmapIndex =
+    displaySet.hasOverlapping === true
+      ? displaySet.originLabelMapIndex
+      : displaySet.labelmapIndex;
+
+  if (labelmapIndex === activeLabelmapIndex) {
     log.warn(`${activeLabelmapIndex} is already the active labelmap`);
-    return displaySet.labelmapIndex;
+    return labelmapIndex;
   }
 
   if (!displaySet.isLoaded) {
-    const loadPromise = displaySet.load(referencedDisplaySet, studies);
+    try {
-
+      await displaySet.load(referencedDisplaySet, studies);
-    loadPromise.catch(error => {
+    } catch (error) {
+      displaySet.isLoaded = false;
+      displaySet.loadError = true;
       onDisplaySetLoadFailure(error);
 
-      // Return old index.
+      return -1;
-      return activeLabelmapIndex;
+    }
-    });
-
-    await loadPromise;
   }
 
+  labelmapIndex =
+    displaySet.hasOverlapping === true
+      ? displaySet.originLabelMapIndex
+      : displaySet.labelmapIndex;
+
   // This might have just been created, so need to use the non-cached value.
   state = cornerstoneTools.getModule('segmentation').state;
+
   brushStackState = state.series[firstImageId];
-  brushStackState.activeLabelmapIndex = displaySet.labelmapIndex;
+  if (brushStackState) {
+    brushStackState.activeLabelmapIndex = labelmapIndex;
+  }
 
   refreshViewports();
   callback();
 
-  return displaySet.labelmapIndex;
+  return labelmapIndex;
 }

extensions/dicom-tag-browser/CHANGELOG.md

@@ -3,6 +3,119 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.2.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.8...@ohif/extension-dicom-tag-browser@0.2.9) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.7...@ohif/extension-dicom-tag-browser@0.2.8) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.6...@ohif/extension-dicom-tag-browser@0.2.7) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.5...@ohif/extension-dicom-tag-browser@0.2.6) (2021-04-15)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.4...@ohif/extension-dicom-tag-browser@0.2.5) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.3...@ohif/extension-dicom-tag-browser@0.2.4) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.2...@ohif/extension-dicom-tag-browser@0.2.3) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.1...@ohif/extension-dicom-tag-browser@0.2.2) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.0...@ohif/extension-dicom-tag-browser@0.2.1) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+# [0.2.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.1.1...@ohif/extension-dicom-tag-browser@0.2.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
+## [0.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.1.0...@ohif/extension-dicom-tag-browser@0.1.1) (2020-12-03)
+
+
+### Bug Fixes
+
+* fallback to original dataset VR for XS ([f57725a](https://github.com/OHIF/Viewers/commit/f57725ac8bfd59ea46ab334a1823882afadefba1))
+
+
+
+
+
+# [0.1.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.0.5...@ohif/extension-dicom-tag-browser@0.1.0) (2020-12-03)
+
+
+### Features
+
+* add show scroll option to modal ([be494a7](https://github.com/OHIF/Viewers/commit/be494a7376d15777dbe598289c4ecdb9f48a6a48))
+
+
+
+
+
+## [0.0.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.0.4...@ohif/extension-dicom-tag-browser@0.0.5) (2020-12-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
 ## [0.0.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.0.3...@ohif/extension-dicom-tag-browser@0.0.4) (2020-10-07)
 
 **Note:** Version bump only for package @ohif/extension-dicom-tag-browser

extensions/dicom-tag-browser/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-tag-browser",
-  "version": "0.0.4",
+  "version": "0.2.9",
   "description": "OHIF extension for checking DICOM headers.",
   "author": "OHIF",
   "license": "MIT",
@@ -28,7 +28,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^2.6.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.18.5",
     "react": "^16.8.6"
   },
   "dependencies": {

extensions/dicom-tag-browser/src/components/DicomTagBrowser.css

@@ -3,6 +3,11 @@
   margin-left: auto;
 }
 
+.dicom-tag-browser-table-wrapper {
+  height: 500px;
+  overflow-y: scroll;
+}
+
 .dicom-tag-browser-table tr {
   padding-left: 10px;
   padding-right: 10px;
@@ -11,6 +16,20 @@
   white-space: nowrap;
 }
 
+.dicom-tag-browser-content {
+  overflow: hidden;
+  width: 100%;
+  padding-bottom: 50px;
+}
+
+.dicom-tag-browser-instance-range .range {
+  height: 20px;
+}
+
+.dicom-tag-browser-instance-range {
+  padding: 20px 0 20px 0;
+}
+
 .dicom-tag-browser-table td.dicom-tag-browser-table-center {
   text-align: center;
 }

extensions/dicom-tag-browser/src/components/DicomTagBrowser.js

@@ -1,5 +1,6 @@
 import React, { useState, useEffect } from 'react';
-import { classes } from '@ohif/core';
+import { classes, cornerstone as OHIFCornerstone } from '@ohif/core';
+import { Range } from '@ohif/ui';
 import dcmjs from 'dcmjs';
 import DicomBrowserSelect from './DicomBrowserSelect';
 import moment from 'moment';
@@ -10,6 +11,8 @@ const { ImageSet } = classes;
 const { DicomMetaDictionary } = dcmjs.data;
 const { nameMap } = DicomMetaDictionary;
 
+const { metadataProvider } = OHIFCornerstone;
+
 const DicomTagBrowser = ({ displaySets, displaySetInstanceUID }) => {
   const [
     activeDisplaySetInstanceUID,
@@ -17,6 +20,7 @@ const DicomTagBrowser = ({ displaySets, displaySetInstanceUID }) => {
   ] = useState(displaySetInstanceUID);
   const [activeInstance, setActiveInstance] = useState(0);
   const [tags, setTags] = useState([]);
+  const [meta, setMeta] = useState('');
   const [instanceList, setInstanceList] = useState([]);
   const [displaySetList, setDisplaySetList] = useState([]);
   const [isImageStack, setIsImageStack] = useState(false);
@@ -83,6 +87,7 @@ const DicomTagBrowser = ({ displaySets, displaySetInstanceUID }) => {
     }
 
     setTags(getSortedTags(metadata));
+    setMeta(metadata);
     setInstanceList(instanceList);
     setDisplaySetList(newDisplaySetList);
     setIsImageStack(isImageStack);
@@ -95,47 +100,56 @@ const DicomTagBrowser = ({ displaySets, displaySetInstanceUID }) => {
   let instanceSelectList = null;
 
   if (isImageStack) {
-    const selectedInstanceValue = instanceList[activeInstance];
-
     instanceSelectList = (
-      <DicomBrowserSelect
+      <div className="dicom-tag-browser-instance-range">
-        value={selectedInstanceValue}
+        <Range
-        formatOptionLabel={DicomBrowserSelectItem}
+          showValue
-        options={instanceList}
+          step={1}
-      />
+          min={1}
+          max={instanceList.length - 1}
+          value={activeInstance}
+          valueRenderer={value => <p>Instance Number: {value}</p>}
+          onChange={({ target }) => {
+            const instanceIndex = parseInt(target.value);
+            setActiveInstance(instanceIndex);
+          }}
+        />
+      </div>
     );
   }
 
   return (
-    <div>
+    <div className="dicom-tag-browser-content">
       <DicomBrowserSelect
         value={selectedDisplaySetValue}
         formatOptionLabel={DicomBrowserSelectItem}
         options={displaySetList}
       />
       {instanceSelectList}
-      <DicomTagTable tags={tags}></DicomTagTable>
+      <div className="dicom-tag-browser-table-wrapper">
+        <DicomTagTable tags={tags} meta={meta}></DicomTagTable>
+      </div>
     </div>
   );
 };
 
-function DicomTagTable({ tags }) {
+function DicomTagTable({ tags, meta }) {
-  const rows = getFormattedRowsFromTags(tags);
+  const rows = getFormattedRowsFromTags(tags, meta);
 
   return (
-    <div>
+    <table className="dicom-tag-browser-table">
-      <table className="dicom-tag-browser-table">
+      <tbody>
         <tr>
           <th className="dicom-tag-browser-table-left">Tag</th>
           <th className="dicom-tag-browser-table-left">Value Representation</th>
           <th className="dicom-tag-browser-table-left">Keyword</th>
           <th className="dicom-tag-browser-table-left">Value</th>
         </tr>
-        {rows.map(row => {
+        {rows.map((row, index) => {
           const className = row.className ? row.className : null;
 
           return (
-            <tr className={className}>
+            <tr className={className} key={`DICOMTagRow-${index}`}>
               <td>{row[0]}</td>
               <td className="dicom-tag-browser-table-center">{row[1]}</td>
               <td>{row[2]}</td>
@@ -143,12 +157,12 @@ function DicomTagTable({ tags }) {
             </tr>
           );
         })}
-      </table>
+      </tbody>
-    </div>
+    </table>
   );
 }
 
-function getFormattedRowsFromTags(tags) {
+function getFormattedRowsFromTags(tags, meta) {
   const rows = [];
 
   tags.forEach(tagInfo => {
@@ -175,6 +189,21 @@ function getFormattedRowsFromTags(tags) {
         rows.push(...formatedRowsFromTags);
       });
     } else {
+      if (tagInfo.vr === 'xs') {
+        try {
+          const dataset = metadataProvider.getStudyDataset(
+            meta.StudyInstanceUID
+          );
+          const tag = dcmjs.data.Tag.fromPString(tagInfo.tag).toCleanString();
+          const originalTagInfo = dataset[tag];
+          tagInfo.vr = originalTagInfo.vr;
+        } catch (error) {
+          console.error(
+            `Failed to parse value representation for tag '${tagInfo.keyword}'`
+          );
+        }
+      }
+
       rows.push([
         `${tagInfo.tagIndent}${tagInfo.tag}`,
         tagInfo.vr,
@@ -247,10 +276,11 @@ function getRows(metadata, depth = 0) {
       sequenceAsArray.forEach(item => {
         const sequenceRows = getRows(item, depth + 1);
 
-        // Sort the sequence group.
+        if (sequenceRows.length) {
-        _sortTagList(sequenceRows);
+          // Sort the sequence group.
-
+          _sortTagList(sequenceRows);
-        sequence.values.push(sequenceRows);
+          sequence.values.push(sequenceRows);
+        }
       });
 
       continue;
@@ -276,13 +306,12 @@ function getRows(metadata, depth = 0) {
           } else if (value.Alphabetic) {
             value = value.Alphabetic;
           } else {
-            console.error('Unrecognised Value for element:');
+            console.warn(`Unrecognised Value: ${value} for ${keyword}:`);
-            console.error(value);
+            console.warn(value);
             value = ' ';
           }
         } else {
-          console.error('Unrecognised Value for element:');
+          console.warn(`Unrecognised Value: ${value} for ${keyword}:`);
-          console.error(value);
           value = ' ';
         }
       }

extensions/dicom-tag-browser/src/getCommandsModule.js

@@ -34,6 +34,7 @@ export default function getCommandsModule(servicesManager) {
         content: WrappedDicomTagBrowser,
         title: `DICOM Tag Browser`,
         fullscreen: true,
+        noScroll: true,
       });
     },
   };

extensions/vtk/CHANGELOG.md

@@ -3,6 +3,232 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.11.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.11...@ohif/extension-vtk@1.11.12) (2021-05-17)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.10...@ohif/extension-vtk@1.11.11) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.9...@ohif/extension-vtk@1.11.10) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.8...@ohif/extension-vtk@1.11.9) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.7...@ohif/extension-vtk@1.11.8) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.6...@ohif/extension-vtk@1.11.7) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.5...@ohif/extension-vtk@1.11.6) (2021-04-16)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.4...@ohif/extension-vtk@1.11.5) (2021-04-15)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.3...@ohif/extension-vtk@1.11.4) (2021-03-26)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.2...@ohif/extension-vtk@1.11.3) (2021-03-25)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.1...@ohif/extension-vtk@1.11.2) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.0...@ohif/extension-vtk@1.11.1) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+# [1.11.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.10.6...@ohif/extension-vtk@1.11.0) (2021-03-04)
+
+
+### Features
+
+* **log:** add new log service ([14d6454](https://github.com/OHIF/Viewers/commit/14d6454eafaa2ccb50e133c2945c9558052ea27e))
+
+
+
+
+
+## [1.10.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.10.5...@ohif/extension-vtk@1.10.6) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.10.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.10.4...@ohif/extension-vtk@1.10.5) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.10.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.10.3...@ohif/extension-vtk@1.10.4) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.10.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.10.2...@ohif/extension-vtk@1.10.3) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.10.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.10.1...@ohif/extension-vtk@1.10.2) (2021-01-21)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.10.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.10.0...@ohif/extension-vtk@1.10.1) (2020-12-10)
+
+
+### Bug Fixes
+
+* panel issues and mpr button (IDC2122-IDC2117) ([32022f5](https://github.com/OHIF/Viewers/commit/32022f51f2d24f53f4c98188980db038a6dfe76c))
+
+
+
+
+
+# [1.10.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.9.4...@ohif/extension-vtk@1.10.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
+## [1.9.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.9.3...@ohif/extension-vtk@1.9.4) (2020-12-03)
+
+
+### Bug Fixes
+
+* reset VOI on mpr reset ([#2115](https://github.com/OHIF/Viewers/issues/2115)) ([0baf18d](https://github.com/OHIF/Viewers/commit/0baf18dcb2985378016236b735329346a851e14f))
+
+
+
+
+
+## [1.9.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.9.2...@ohif/extension-vtk@1.9.3) (2020-12-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.9.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.9.1...@ohif/extension-vtk@1.9.2) (2020-12-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.9.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.9.0...@ohif/extension-vtk@1.9.1) (2020-12-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+# [1.9.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.8.0...@ohif/extension-vtk@1.9.0) (2020-12-03)
+
+
+### Features
+
+* Add error boundary and retry logic for network failures during dynamic imports ([#2145](https://github.com/OHIF/Viewers/issues/2145)) ([4c07904](https://github.com/OHIF/Viewers/commit/4c079044f6ae2381c6054d8d77414100152d1d19))
+
+
+
+
+
+# [1.8.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.16...@ohif/extension-vtk@1.8.0) (2020-11-30)
+
+
+### Features
+
+* **i18n:** Added de (German) translations ([2fff2d5](https://github.com/OHIF/Viewers/commit/2fff2d511fa1d36bdd6476da4ffa5684bf55374f))
+
+
+
+
+
 ## [1.7.16](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.15...@ohif/extension-vtk@1.7.16) (2020-11-19)
 
 **Note:** Version bump only for package @ohif/extension-vtk

extensions/vtk/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-vtk",
-  "version": "1.7.16",
+  "version": "1.11.12",
   "description": "OHIF extension for VTK.js",
   "author": "OHIF",
   "license": "MIT",
@@ -35,7 +35,7 @@
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "^4.20.1",
     "cornerstone-wado-image-loader": "^3.1.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.18.5",
     "dicom-parser": "^1.8.3",
     "i18next": "^17.0.3",
     "i18next-browser-languagedetector": "^3.0.1",
@@ -53,8 +53,8 @@
     "react-vtkjs-viewport": "^0.14.2"
   },
   "devDependencies": {
-    "@ohif/core": "^2.10.7",
+    "@ohif/core": "^2.13.11",
-    "@ohif/ui": "^1.5.7",
+    "@ohif/ui": "^1.9.2",
     "cornerstone-tools": "^4.20.1",
     "cornerstone-wado-image-loader": "^3.1.0",
     "dicom-parser": "^1.8.3",

extensions/vtk/src/OHIFVTKViewport.js

@@ -138,6 +138,8 @@ class OHIFVTKViewport extends Component {
     SOPInstanceUID,
     frameIndex
   ) => {
+    const { UINotificationService } = this.props.servicesManager.services;
+
     const stack = OHIFVTKViewport.getCornerstoneStack(
       studies,
       StudyInstanceUID,
@@ -159,6 +161,18 @@ class OHIFVTKViewport extends Component {
       const { activeLabelmapIndex } = brushStackState;
       const labelmap3D = brushStackState.labelmaps3D[activeLabelmapIndex];
 
+      if (
+        brushStackState.labelmaps3D.length > 1 &&
+        this.props.viewportIndex === 0
+      ) {
+        UINotificationService.show({
+          title: 'Overlapping Segmentation Found',
+          message:
+            'Overlapping segmentations cannot be displayed when in MPR mode',
+          type: 'info',
+        });
+      }
+
       this.segmentsDefaultProperties = labelmap3D.segmentsHidden.map(
         isHidden => {
           return { visible: !isHidden };
@@ -296,52 +310,82 @@ class OHIFVTKViewport extends Component {
       seriesDescription: displaySet.seriesDescription,
     };
 
-    const {
+    try {
-      imageDataObject,
+      const {
-      labelmapDataObject,
+        imageDataObject,
-      labelmapColorLUT,
+        labelmapDataObject,
-    } = this.getViewportData(
+        labelmapColorLUT,
-      studies,
+      } = this.getViewportData(
-      StudyInstanceUID,
+        studies,
-      displaySetInstanceUID,
+        StudyInstanceUID,
-      SOPInstanceUID,
+        displaySetInstanceUID,
-      frameIndex
+        SOPInstanceUID,
-    );
+        frameIndex
+      );
 
-    this.imageDataObject = imageDataObject;
+      this.imageDataObject = imageDataObject;
 
-    /* TODO: Not currently used until we have drawing tools in vtkjs.
+      /* TODO: Not currently used until we have drawing tools in vtkjs.
-    if (!labelmap) {
+      if (!labelmap) {
-      labelmap = createLabelMapImageData(data);
+        labelmap = createLabelMapImageData(data);
-    } */
+      } */
 
-    const volumeActor = this.getOrCreateVolume(
+      const volumeActor = this.getOrCreateVolume(
-      imageDataObject,
+        imageDataObject,
-      displaySetInstanceUID
+        displaySetInstanceUID
-    );
+      );
 
-    this.setState(
+      this.setState(
-      {
+        {
-        percentComplete: 0,
+          percentComplete: 0,
-        dataDetails,
+          dataDetails,
-      },
+        },
-      () => {
+        () => {
-        this.loadProgressively(imageDataObject);
+          this.loadProgressively(imageDataObject);
 
-        // TODO: There must be a better way to do this.
+          // TODO: There must be a better way to do this.
-        // We do this so that if all the data is available the react-vtkjs-viewport
+          // We do this so that if all the data is available the react-vtkjs-viewport
-        // Will render _something_ before the volumes are set and the volume
+          // Will render _something_ before the volumes are set and the volume
-        // Construction that happens in react-vtkjs-viewport locks up the CPU.
+          // Construction that happens in react-vtkjs-viewport locks up the CPU.
-        setTimeout(() => {
+          setTimeout(() => {
-          this.setState({
+            this.setState({
-            volumes: [volumeActor],
+              volumes: [volumeActor],
-            paintFilterLabelMapImageData: labelmapDataObject,
+              paintFilterLabelMapImageData: labelmapDataObject,
-            paintFilterBackgroundImageData: imageDataObject.vtkImageData,
+              paintFilterBackgroundImageData: imageDataObject.vtkImageData,
-            labelmapColorLUT,
+              labelmapColorLUT,
-          });
+            });
-        }, 200);
+          }, 200);
+        }
+      );
+    } catch (error) {
+      const errorTitle = 'Failed to load 2D MPR';
+      console.error(errorTitle, error);
+      const {
+        UINotificationService,
+        LoggerService,
+      } = this.props.servicesManager.services;
+      if (this.props.viewportIndex === 0) {
+        const message = error.message.includes('buffer')
+          ? 'Dataset is too big to display in MPR'
+          : error.message;
+        LoggerService.error({ error, message });
+        UINotificationService.show({
+          title: errorTitle,
+          message,
+          type: 'error',
+          autoClose: false,
+          action: {
+            label: 'Exit 2D MPR',
+            onClick: ({ close }) => {
+              // context: 'ACTIVE_VIEWPORT::VTK',
+              close();
+              this.props.commandsManager.runCommand('setCornerstoneLayout');
+            },
+          },
+        });
       }
-    );
+      this.setState({ isLoaded: true });
+    }
   }
 
   componentDidMount() {
@@ -387,11 +431,15 @@ class OHIFVTKViewport extends Component {
     };
 
     const onPixelDataInsertedErrorCallback = error => {
-      const { UINotificationService } = this.props.servicesManager.services;
+      const {
+        UINotificationService,
+        LoggerService,
+      } = this.props.servicesManager.services;
 
       if (!this.hasError) {
         if (this.props.viewportIndex === 0) {
           // Only show the notification from one viewport 1 in MPR2D.
+          LoggerService.error({ error, message: error.message });
           UINotificationService.show({
             title: 'MPR Load Error',
             message: error.message,

extensions/vtk/src/asyncComponent.js

@@ -1,37 +0,0 @@
-/**
- * We use this component to leverage "Code Splitting"
- *
- * Link: https://serverless-stack.com/chapters/code-splitting-in-create-react-app.html
- */
-
-import React, { Component } from 'react';
-
-export default function asyncComponent(importComponent) {
-  class AsyncComponent extends Component {
-    constructor(props) {
-      super(props);
-
-      this.state = {
-        component: null,
-      };
-    }
-
-    async componentDidMount() {
-      // Add dynamically loaded component to state
-      const { default: component } = await importComponent();
-
-      this.setState({
-        component: component,
-      });
-    }
-
-    render() {
-      const C = this.state.component;
-
-      // Render the loaded component, or null
-      return C ? <C {...this.props} /> : null;
-    }
-  }
-
-  return AsyncComponent;
-}

extensions/vtk/src/commandsModule.js

@@ -14,9 +14,12 @@ import OHIFVTKViewport from './OHIFVTKViewport';
 
 const { BlendMode } = Constants;
 
-const commandsModule = ({ commandsManager, UINotificationService }) => {
+const commandsModule = ({ commandsManager, servicesManager }) => {
+  const { UINotificationService, LoggerService } = servicesManager.services;
+
   // TODO: Put this somewhere else
   let apis = {};
+  let defaultVOI;
 
   async function _getActiveViewportVTKApi(viewports) {
     const {
@@ -119,9 +122,11 @@ const commandsModule = ({ commandsManager, UINotificationService }) => {
       return apis[index];
     },
     resetMPRView() {
-      apis.forEach(api => {
+      // Reset orientation
-        api.resetOrientation();
+      apis.forEach(api => api.resetOrientation());
-      });
+
+      // Reset VOI
+      if (defaultVOI) setVOI(defaultVOI);
 
       // Reset the crosshairs
       apis[0].svgWidgets.rotatableCrosshairsWidget.resetCrosshairs(apis, 0);
@@ -387,6 +392,7 @@ const commandsModule = ({ commandsManager, UINotificationService }) => {
 
       // Get current VOI if cornerstone viewport.
       const cornerstoneVOI = getVOIFromCornerstoneViewport();
+      defaultVOI = cornerstoneVOI;
 
       const viewportProps = [
         {
@@ -469,10 +475,12 @@ const commandsModule = ({ commandsManager, UINotificationService }) => {
         const volumeLength = dimensions[0] * dimensions[1] * dimensions[2];
 
         if (volumeLength > maxBufferLengthFloat32) {
+          const message =
+            'This volume is too large to fit in WebGL 1 textures and will display incorrectly. Please use a different browser to view this data';
+          LoggerService.error({ message });
           UINotificationService.show({
             title: 'Browser does not support WebGL 2',
-            message:
+            message,
-              'This volume is too large to fit in WebGL 1 textures and will display incorrectly. Please use a different browser to view this data',
             type: 'error',
             autoClose: false,
           });

extensions/vtk/src/index.js

@@ -1,5 +1,6 @@
 import React from 'react';
-import asyncComponent from './asyncComponent.js';
+import { asyncComponent, retryImport } from '@ohif/ui';
+
 import commandsModule from './commandsModule.js';
 import toolbarModule from './toolbarModule.js';
 import withCommandsManager from './withCommandsManager.js';
@@ -8,7 +9,9 @@ import { version } from '../package.json';
 // import loadLocales from './loadLocales';
 
 const OHIFVTKViewport = asyncComponent(() =>
-  import(/* webpackChunkName: "OHIFVTKViewport" */ './OHIFVTKViewport.js')
+  retryImport(() =>
+    import(/* webpackChunkName: "OHIFVTKViewport" */ './OHIFVTKViewport.js')
+  )
 );
 
 const vtkExtension = {
@@ -20,7 +23,11 @@ const vtkExtension = {
 
   getViewportModule({ commandsManager, servicesManager }) {
     const ExtendedVTKViewport = props => (
-      <OHIFVTKViewport {...props} servicesManager={servicesManager} />
+      <OHIFVTKViewport
+        {...props}
+        servicesManager={servicesManager}
+        commandsManager={commandsManager}
+      />
     );
     return withCommandsManager(ExtendedVTKViewport, commandsManager);
   },
@@ -28,8 +35,7 @@ const vtkExtension = {
     return toolbarModule;
   },
   getCommandsModule({ commandsManager, servicesManager }) {
-    const { UINotificationService } = servicesManager.services;
+    return commandsModule({ commandsManager, servicesManager });
-    return commandsModule({ commandsManager, UINotificationService });
   },
 };
 

extensions/vtk/src/locales/de/Buttons.json

@@ -0,0 +1,3 @@
+{
+  "Rotate": "Drehen"
+}

extensions/vtk/src/locales/de/index.js

@@ -0,0 +1,7 @@
+import Buttons from './Buttons.json';
+
+export default {
+  de: {
+    Buttons,
+  },
+};

extensions/vtk/src/locales/index.js

@@ -1,7 +1,9 @@
 import en from './en';
 import es from './es';
+import de from './de';
 
 export default {
   ...en,
-  ...es
+  ...es,
+  ...de,
 };

package.json

@@ -28,6 +28,7 @@
     "test:unit": "jest --collectCoverage",
     "test:unit:ci": "lerna run test:unit:ci --parallel --stream",
     "test:e2e": "lerna run test:e2e --stream",
+    "test:e2e:script-tag": "lerna run test:e2e:script-tag --stream",
     "test:e2e:ci": "lerna run test:e2e:ci --stream",
     "test:e2e:dist": "lerna run test:e2e:dist --stream",
     "test:e2e:serve": "lerna run test:e2e:serve --stream",

platform/core/CHANGELOG.md

@@ -3,6 +3,184 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.13.11](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.10...@ohif/core@2.13.11) (2021-05-17)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.13.10](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.9...@ohif/core@2.13.10) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.13.9](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.8...@ohif/core@2.13.9) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.13.8](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.7...@ohif/core@2.13.8) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.13.7](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.6...@ohif/core@2.13.7) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.13.6](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.5...@ohif/core@2.13.6) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.13.5](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.4...@ohif/core@2.13.5) (2021-04-16)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.13.4](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.3...@ohif/core@2.13.4) (2021-04-15)
+
+
+### Bug Fixes
+
+* **wl:** fix metadata provider window level issues after dicomweb update (string vs number) ([8681036](https://github.com/OHIF/Viewers/commit/8681036b2133cfc325658691a256a86b5e36705f))
+
+
+
+
+
+## [2.13.3](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.2...@ohif/core@2.13.3) (2021-03-26)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.13.2](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.1...@ohif/core@2.13.2) (2021-03-25)
+
+
+### Bug Fixes
+
+* IDC-2288: Update toolbar tabs after derived displayset loaded ([#2307](https://github.com/OHIF/Viewers/issues/2307)) ([6e723eb](https://github.com/OHIF/Viewers/commit/6e723ebced58852007ca553792c740976cfc4201))
+
+
+
+
+
+## [2.13.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.0...@ohif/core@2.13.1) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+# [2.13.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.12.5...@ohif/core@2.13.0) (2021-03-04)
+
+
+### Features
+
+* **log:** add new log service ([14d6454](https://github.com/OHIF/Viewers/commit/14d6454eafaa2ccb50e133c2945c9558052ea27e))
+
+
+
+
+
+## [2.12.5](https://github.com/OHIF/Viewers/compare/@ohif/core@2.12.4...@ohif/core@2.12.5) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.12.4](https://github.com/OHIF/Viewers/compare/@ohif/core@2.12.3...@ohif/core@2.12.4) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.12.3](https://github.com/OHIF/Viewers/compare/@ohif/core@2.12.2...@ohif/core@2.12.3) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.12.2](https://github.com/OHIF/Viewers/compare/@ohif/core@2.12.1...@ohif/core@2.12.2) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.12.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.12.0...@ohif/core@2.12.1) (2021-01-21)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+# [2.12.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.11.1...@ohif/core@2.12.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
+## [2.11.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.11.0...@ohif/core@2.11.1) (2020-12-03)
+
+
+### Bug Fixes
+
+* fallback to original dataset VR for XS ([f57725a](https://github.com/OHIF/Viewers/commit/f57725ac8bfd59ea46ab334a1823882afadefba1))
+
+
+
+
+
+# [2.11.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.10.7...@ohif/core@2.11.0) (2020-12-03)
+
+
+### Features
+
+* add show scroll option to modal ([be494a7](https://github.com/OHIF/Viewers/commit/be494a7376d15777dbe598289c4ecdb9f48a6a48))
+
+
+
+
+
 ## [2.10.7](https://github.com/OHIF/Viewers/compare/@ohif/core@2.10.6...@ohif/core@2.10.7) (2020-10-07)
 
 **Note:** Version bump only for package @ohif/core

platform/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/core",
-  "version": "2.10.7",
+  "version": "2.13.11",
   "description": "Generic business logic for web-based medical imaging applications",
   "author": "OHIF Core Team",
   "license": "MIT",
@@ -39,7 +39,7 @@
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "ajv": "^6.10.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.18.5",
     "dicomweb-client": "^0.6.0",
     "immer": "6.0.2",
     "isomorphic-base64": "^1.0.2",

platform/core/src/DICOMSR/parseDicomStructuredReport.js

@@ -77,7 +77,6 @@ const parseDicomStructuredReport = (part10SRArrayBuffer, displaySets) => {
 
 /**
  * Function to create imagePath with all imageData related
- *
  * @param {string} StudyInstanceUID
  * @param {string} SeriesInstanceUID
  * @param {string} SOPInstanceUID

platform/core/src/classes/HotkeysManager.js

@@ -63,10 +63,15 @@ export class HotkeysManager {
 
       definitions.forEach(definition => this.registerHotkeys(definition));
     } catch (error) {
-      const { UINotificationService } = this._servicesManager.services;
+      const {
+        UINotificationService,
+        LoggerService,
+      } = this._servicesManager.services;
+      const message = 'Erro while setting hotkeys';
+      LoggerService.error({ error, message });
       UINotificationService.show({
         title: 'Hotkeys Manager',
-        message: 'Erro while setting hotkeys',
+        message,
         type: 'error',
       });
     }

platform/core/src/classes/MetadataProvider.js

@@ -4,6 +4,7 @@ import dicomParser from 'dicom-parser';
 import getPixelSpacingInformation from '../utils/metadataProvider/getPixelSpacingInformation';
 import fetchPaletteColorLookupTableData from '../utils/metadataProvider/fetchPaletteColorLookupTableData';
 import fetchOverlayData from '../utils/metadataProvider/fetchOverlayData';
+import validNumber from '../utils/metadataProvider/validNumber';
 
 class MetadataProvider {
   constructor() {
@@ -20,6 +21,7 @@ class MetadataProvider {
       writable: false,
       value: new Map(),
     });
+    this.datasets = {};
   }
 
   async addInstance(dicomJSONDatasetOrP10ArrayBuffer, options = {}) {
@@ -52,6 +54,7 @@ class MetadataProvider {
       SOPInstanceUID,
     } = naturalizedDataset;
 
+    this._getAndCacheStudyDataset(StudyInstanceUID, dicomJSONDataset);
     const study = this._getAndCacheStudy(StudyInstanceUID);
     const series = this._getAndCacheSeriesFromStudy(study, SeriesInstanceUID);
     const instance = this._getAndCacheInstanceFromStudy(series, SOPInstanceUID);
@@ -71,6 +74,16 @@ class MetadataProvider {
     this.imageIdToUIDs.set(imageId, uids);
   }
 
+  _getAndCacheStudyDataset(StudyInstanceUID, dataset) {
+    if (!this.datasets[StudyInstanceUID]) {
+      this.datasets[StudyInstanceUID] = dataset;
+    }
+  }
+
+  getStudyDataset(StudyInstanceUID) {
+    return this.datasets[StudyInstanceUID];
+  }
+
   _getAndCacheStudy(StudyInstanceUID) {
     const studies = this.studies;
 
@@ -83,6 +96,7 @@ class MetadataProvider {
 
     return study;
   }
+
   _getAndCacheSeriesFromStudy(study, SeriesInstanceUID) {
     let series = study.series.get(SeriesInstanceUID);
 
@@ -271,7 +285,7 @@ class MetadataProvider {
 
         break;
       case WADO_IMAGE_LOADER_TAGS.VOI_LUT_MODULE:
-        const { WindowCenter, WindowWidth } = instance;
+        let { WindowCenter, WindowWidth } = instance;
 
         const windowCenter = Array.isArray(WindowCenter)
           ? WindowCenter
@@ -281,15 +295,17 @@ class MetadataProvider {
           : [WindowWidth];
 
         metadata = {
-          windowCenter,
+          windowCenter: validNumber(windowCenter),
-          windowWidth,
+          windowWidth: validNumber(windowWidth),
         };
 
         break;
       case WADO_IMAGE_LOADER_TAGS.MODALITY_LUT_MODULE:
+        const rescaleSlope = validNumber(instance.RescaleSlope);
+        const rescaleIntercept = validNumber(instance.RescaleIntercept);
         metadata = {
-          rescaleIntercept: instance.RescaleIntercept,
+          rescaleIntercept,
-          rescaleSlope: instance.RescaleSlope,
+          rescaleSlope,
           rescaleType: instance.RescaleType,
         };
         break;

platform/core/src/classes/metadata/StudyMetadata.js

@@ -9,11 +9,11 @@ import { SeriesMetadata } from './SeriesMetadata';
 import { api } from 'dicomweb-client';
 // - createStacks
 import { isImage } from '../../utils/isImage';
-import isDisplaySetReconstructable from '../../utils/isDisplaySetReconstructable';
+import { isDisplaySetReconstructable, isSpacingUniform } from '../../utils/isDisplaySetReconstructable';
 import errorHandler from '../../errorHandler';
 import isLowPriorityModality from '../../utils/isLowPriorityModality';
 
-export class StudyMetadata extends Metadata {
+class StudyMetadata extends Metadata {
   constructor(data, uid) {
     super(data, uid);
     // Initialize Private Properties
@@ -226,6 +226,56 @@ export class StudyMetadata extends Metadata {
     displaySets.map(displaySet => this._derivedDisplaySets.push(displaySet));
   }
 
+
+  /**
+   * Returns the source display set of the derivated display set.
+   * @param {object} derivatedDisplaySet
+   * @param {array[StudyMetadata]} studies
+   * @return {object} source display set.
+   */
+  static getReferencedDisplaySet(derivatedDisplaySet, studies) {
+    let allDisplaySets = [];
+
+    studies.forEach(study => {
+      allDisplaySets = allDisplaySets.concat(study.displaySets);
+    });
+
+    const otherDisplaySets = allDisplaySets.filter(
+      ds => ds.displaySetInstanceUID !== derivatedDisplaySet.displaySetInstanceUID
+    );
+
+    const { metadata } = derivatedDisplaySet;
+
+    let referencedSeriesInstanceUIDs = _findReferencedSeriesInstanceUIDsFromSourceImageSequence
+    (metadata, otherDisplaySets);
+
+    let noReferencedSeriesAvailable = !referencedSeriesInstanceUIDs ||
+      referencedSeriesInstanceUIDs.length === 0;
+    if (noReferencedSeriesAvailable) {
+      referencedSeriesInstanceUIDs =
+        _findReferencedSeriesInstanceUIDsFromReferencedSeriesSequence
+          (metadata);
+    }
+
+    noReferencedSeriesAvailable = !referencedSeriesInstanceUIDs ||
+      referencedSeriesInstanceUIDs.length === 0;
+    if (noReferencedSeriesAvailable) {
+      referencedSeriesInstanceUIDs =
+      _findReferencedSeriesInstanceUIDsFromReferencedImageSequence
+          (metadata, otherDisplaySets);
+    }
+
+    const referencedSeriesAvailable = referencedSeriesInstanceUIDs &&
+      referencedSeriesInstanceUIDs.length !== 0;
+    if (referencedSeriesAvailable) {
+      const referencedDisplaySet = otherDisplaySets.find(ds =>
+        referencedSeriesInstanceUIDs.includes(ds.SeriesInstanceUID)
+      );
+      ;
+      return referencedDisplaySet;
+    }
+  };
+
   /**
    * Returns a list of derived datasets in the study, filtered by the given filter.
    * @param {object} filter An object containing search filters
@@ -252,20 +302,7 @@ export class StudyMetadata extends Metadata {
     if (referencedSeriesInstanceUID) {
       filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
         displaySet => {
-          if (!displaySet.metadata.ReferencedSeriesSequence) {
+          return StudyMetadata.getReferencedDisplaySet(displaySet, [this]).SeriesInstanceUID === referencedSeriesInstanceUID;
-            return false;
-          }
-
-          const ReferencedSeriesSequence = Array.isArray(
-            displaySet.metadata.ReferencedSeriesSequence
-          )
-            ? displaySet.metadata.ReferencedSeriesSequence
-            : [displaySet.metadata.ReferencedSeriesSequence];
-
-          return ReferencedSeriesSequence.some(
-            ReferencedSeries =>
-              ReferencedSeries.SeriesInstanceUID === referencedSeriesInstanceUID
-          );
         }
       );
     }
@@ -273,7 +310,7 @@ export class StudyMetadata extends Metadata {
     if (referencedFrameOfReferenceUID) {
       filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
         displaySet =>
-          displaySet.ReferencedFrameOfReferenceUID ===
+          displaySet.FrameOfReferenceUID ===
           referencedFrameOfReferenceUID
       );
     }
@@ -767,6 +804,16 @@ const isMultiFrame = instance => {
   return instance.getTagValue('NumberOfFrames') > 1;
 };
 
+/**
+ * Creates a display set for a series.
+ * Checks if a series is reconstructable to a 3D volume.
+ * If reconstructable, the frames are sorted.
+ *
+ * @param {SeriesMetadata} series The series metadata object from which the display sets will be created
+ * @param {Object[]} instances An array of `OHIFInstanceMetadata` objects.
+ *
+ * @returns {Object} imageSet.
+ */
 const makeDisplaySet = (series, instances) => {
   const instance = instances[0];
   const imageSet = new ImageSet(instances);
@@ -786,7 +833,7 @@ const makeDisplaySet = (series, instances) => {
     isMultiFrame: isMultiFrame(instance),
   });
 
-  // Sort the images in this series if needed
+  // Sort the images in this series by instanceNumber
   const shallSort = true; //!OHIF.utils.ObjectPath.get(Meteor, 'settings.public.ui.sortSeriesByIncomingOrder');
   if (shallSort) {
     imageSet.sortBy((a, b) => {
@@ -804,18 +851,32 @@ const makeDisplaySet = (series, instances) => {
     imageSet.getImage(0).getTagValue('InstanceNumber')
   );
 
-  const isReconstructable = isDisplaySetReconstructable(instances);
+  const displayReconstructableInfo = isDisplaySetReconstructable(instances);
-
+  imageSet.isReconstructable = displayReconstructableInfo.value;
-  imageSet.isReconstructable = isReconstructable.value;
 
+  let displaySpacingInfo = undefined;
   if (shallSort && imageSet.isReconstructable) {
+    // sort images by image position
     imageSet.sortByImagePositionPatient();
+
+    // check if the spacing is uniform and update isReconstructable
+    const datasetIs4D = displayReconstructableInfo.reconstructionIssues.find
+      (issue => issue === ReconstructionIssues.DATASET_4D);
+    displaySpacingInfo = isSpacingUniform(imageSet.images, datasetIs4D);
+    imageSet.isReconstructable = displaySpacingInfo.isUniform;
+
+    if (displaySpacingInfo.missingFrames) {
+      // TODO -> This is currently unused, but may be used for reconstructing
+      // Volumes with gaps later on.
+      imageSet.missingFrames = displaySpacingInfo.missingFrames;
+    }
   }
 
-  if (isReconstructable.missingFrames) {
+  if (!imageSet.displayReconstructableInfo) {
-    // TODO -> This is currently unused, but may be used for reconstructing
+    // It is not reconstrabale Save type of warning
-    // Volumes with gaps later on.
+    imageSet.reconstructionIssues = displaySpacingInfo ?
-    imageSet.missingFrames = isReconstructable.missingFrames;
+      displayReconstructableInfo.reconstructionIssues.concat(displaySpacingInfo.reconstructionIssues) :
+        displayReconstructableInfo.reconstructionIssues;
   }
 
   return imageSet;
@@ -892,3 +953,147 @@ function _getDisplaySetFromSopClassModule(
   }
   return displaySet;
 }
+
+/**
+  * Returns the referenced series instance UIDs by searching the information in the
+  * ReferencedSeriesSequence.
+  * @param {object} derivatedDisplaySet.metadata
+  * @return {array[string]} referenced series instance UIDs.
+  */
+function _findReferencedSeriesInstanceUIDsFromReferencedSeriesSequence (
+  metadata,
+) {
+  if (!metadata.ReferencedSeriesSequence) {
+    return;
+  }
+
+  let referencedSeriesInstanceUIDs;
+  const ReferencedSeriesSequence = _toArray(
+    metadata.ReferencedSeriesSequence
+  );
+
+  referencedSeriesInstanceUIDs = ReferencedSeriesSequence.map(
+    ReferencedSeries => ReferencedSeries.SeriesInstanceUID
+  );
+
+  return referencedSeriesInstanceUIDs;
+};
+
+/**
+  * Returns the referenced series instance UIDs by searching the information in the
+  * ReferencedImageSequence.
+  * @param {object} derivatedDisplaySet.metadata
+  * @param {array[object]} displaysets
+  * @return {array[string]} referenced series instance UIDs.
+  */
+function _findReferencedSeriesInstanceUIDsFromReferencedImageSequence (
+  metadata,
+  displaySets
+) {
+  if (!metadata.ReferencedImageSequence) {
+    return;
+  }
+
+  let referencedSeriesInstanceUIDs;
+  const referencedImageArray = _toArray(metadata.ReferencedImageSequence);
+  for (let i = 0; i < referencedImageArray.length; i++) {
+    const { ReferencedSOPInstanceUID } = referencedImageArray[i];
+    if (!ReferencedSOPInstanceUID) {
+      continue;
+    }
+
+    referencedSeriesInstanceUIDs = _findReferencedSeriesInstanceUIDsFromSOPInstanceUID(
+      displaySets,
+      ReferencedSOPInstanceUID
+    );
+
+    if (referencedSeriesInstanceUIDs && referencedSeriesInstanceUIDs.length !== 0) {
+      break;
+    }
+  }
+
+  return referencedSeriesInstanceUIDs;
+};
+
+/**
+  * Returns the referenced series instance UIDs by searching the information in the
+  * SourceImageSequence.
+  * @param {object} derivatedDisplaySet.metadata
+  * @param {array[object]} displaysets
+  * @return {array[string]} referenced series instance UIDs.
+  */
+function _findReferencedSeriesInstanceUIDsFromSourceImageSequence (
+  metadata,
+  displaySets
+) {
+  let SourceImageSequence;
+
+  if (metadata.SourceImageSequence) {
+    SourceImageSequence = metadata.SourceImageSequence;
+  } else {
+    const { PerFrameFunctionalGroupsSequence } = metadata;
+    const firstFunctionalGroups = _toArray(
+      PerFrameFunctionalGroupsSequence
+    )[0];
+    if (firstFunctionalGroups) {
+      const { DerivationImageSequence } = firstFunctionalGroups;
+      SourceImageSequence = DerivationImageSequence;
+    }
+  }
+
+  if (!SourceImageSequence) {
+    return;
+  }
+
+  const sourceImageArray = _toArray(SourceImageSequence);
+
+  let referencedSeriesInstanceUIDs;
+  for (let i = 0; i < sourceImageArray.length; i++) {
+    const { ReferencedSOPInstanceUID } = sourceImageArray[i];
+    referencedSeriesInstanceUIDs = _findReferencedSeriesInstanceUIDsFromSOPInstanceUID(
+      displaySets,
+      ReferencedSOPInstanceUID
+    );
+    if (referencedSeriesInstanceUIDs && referencedSeriesInstanceUIDs.length !== 0) {
+      break;
+    }
+  }
+
+  return referencedSeriesInstanceUIDs;
+};
+
+/**
+  * Returns the referenced series instance UIDs by searching the information in the
+  * SOPInstanceUID of the displaySets.
+  * @param {array[object]} displaysets
+  * @param {string} SOPInstanceUID
+  * @return {array[string]} referenced series instance UIDs.
+  */
+function _findReferencedSeriesInstanceUIDsFromSOPInstanceUID (
+  displaySets,
+  SOPInstanceUID
+) {
+  const imageSets = displaySets.filter(ds => ds instanceof ImageSet);
+
+  for (let i = 0; i < imageSets.length; i++) {
+    const { images } = imageSets[i];
+    if (!images) {
+      continue;
+    }
+    for (let j = 0; j < images.length; j++) {
+      const image = images[j];
+      if (!image) {
+        continue;
+      }
+      if (image.SOPInstanceUID === SOPInstanceUID) {
+        return [image.getData().metadata.SeriesInstanceUID];
+      }
+    }
+  }
+};
+
+function _toArray(arrayOrObject) {
+  return Array.isArray(arrayOrObject) ? arrayOrObject : [arrayOrObject];
+}
+
+export {StudyMetadata};

platform/core/src/enums.js

@@ -0,0 +1,11 @@
+const ReconstructionIssues = {
+  DATASET_4D: 'datasetis4D',
+  VARYING_IMAGESDIMENSIONS: 'imagesdimensionsvarying',
+  VARYING_IMAGESCOMPONENTS: 'imagescomponentsvarying',
+  VARYING_IMAGESORIENTATION: 'imagesorientationvarying',
+  MISSING_FRAMES: 'missingframes',
+  IRREGULAR_SPACING: 'irregularspacing',
+  MULTIFFRAMES: 'multiframe',
+};
+
+export {ReconstructionIssues};

platform/core/src/index.js

@@ -26,6 +26,7 @@ import {
   UIModalService,
   UIDialogService,
   MeasurementService,
+  LoggerService,
 } from './services';
 
 const OHIF = {
@@ -60,6 +61,7 @@ const OHIF = {
   UIModalService,
   UIDialogService,
   MeasurementService,
+  LoggerService,
 };
 
 export {
@@ -93,6 +95,7 @@ export {
   UIModalService,
   UIDialogService,
   MeasurementService,
+  LoggerService,
 };
 
 export { OHIF };

platform/core/src/index.test.js

@@ -14,6 +14,7 @@ describe('Top level exports', () => {
       'UIModalService',
       'UIDialogService',
       'MeasurementService',
+      'LoggerService',
       //
       'utils',
       'hotkeys',

platform/core/src/services/LoggerService/index.js

@@ -0,0 +1,67 @@
+const name = 'LoggerService';
+
+const publicAPI = {
+  name,
+  info: _info,
+  error: _error,
+  setServiceImplementation,
+};
+
+const serviceImplementation = {
+  _info: () => console.warn('info() NOT IMPLEMENTED'),
+  _error: () => console.warn('error() NOT IMPLEMENTED'),
+};
+
+/**
+ * Logs an info
+ *
+ * @param {object} props { message, displayOnConsole }
+ */
+function _info({ message, displayOnConsole }) {
+  return serviceImplementation._info({
+    message,
+    displayOnConsole,
+  });
+}
+
+/**
+ * Logs an error
+ *
+ * @param {object} props { error, stack, message, displayOnConsole }
+ * @returns void
+ */
+function _error({ error, stack, message, displayOnConsole }) {
+  return serviceImplementation._error({
+    error,
+    stack,
+    message,
+    displayOnConsole,
+  });
+}
+
+/**
+ *
+ *
+ * @param {*} {
+ *   info: infoImplementation,
+ *   error: errorImplementation,
+ * }
+ */
+function setServiceImplementation({
+  info: infoImplementation,
+  error: errorImplementation,
+}) {
+  if (infoImplementation) {
+    serviceImplementation._info = infoImplementation;
+  }
+  if (errorImplementation) {
+    serviceImplementation._error = errorImplementation;
+  }
+}
+
+export default {
+  name,
+  create: ({ configuration = {} }) => {
+    return publicAPI;
+  },
+};

platform/core/src/services/UIModalService/index.js

@@ -9,6 +9,8 @@
  * @property {boolean} [closeButton=true] Should the modal body render the close button.
  * @property {string} [title=null] Should the modal render the title independently of the body content.
  * @property {string} [customClassName=null] The custom class to style the modal.
+ * @property {boolean} [showScrollbar=false] Show or hide scrollbar.
+ * @property {boolean} [noScroll=false] Disable or not the scrollbar.
  */
 
 const name = 'UIModalService';
@@ -28,7 +30,7 @@ const serviceImplementation = {
 /**
  * Show a new UI modal;
  *
- * @param {ModalProps} props { content, contentProps, shouldCloseOnEsc, isOpen, onClose, closeButton, title, customClassName }
+ * @param {ModalProps} props { content, contentProps, shouldCloseOnEsc, isOpen, onClose, closeButton, title, customClassName, showScrollbar, noScroll }
  */
 function _show({
   content = null,
@@ -40,6 +42,8 @@ function _show({
   title = null,
   fullscreen = false,
   customClassName = null,
+  showScrollbar = false,
+  noScroll = false,
 }) {
   return serviceImplementation._show({
     content,
@@ -51,6 +55,8 @@ function _show({
     title,
     fullscreen,
     customClassName,
+    showScrollbar,
+    noScroll,
   });
 }
 

platform/core/src/services/UINotificationService/index.js

@@ -8,6 +8,7 @@
  * @property {string} [position="bottomRight"] -"topLeft" | "topCenter | "topRight" | "bottomLeft" | "bottomCenter" | "bottomRight"
  * @property {string} [type="info"] - "info" | "error" | "warning" | "success"
  * @property {boolean} [autoClose=true]
+ * @property {object} [action=null]
  */
 
 const name = 'UINotificationService';
@@ -34,7 +35,7 @@ const serviceImplementation = {
  * Create and show a new UI notification; returns the
  * ID of the created notification.
  *
- * @param {Notification} notification { title, message, duration, position, type, autoClose}
+ * @param {Notification} notification { title, message, duration, position, type, autoClose, action}
  * @returns {number} id
  */
 function _show({
@@ -44,6 +45,7 @@ function _show({
   position = 'bottomRight',
   type = 'info',
   autoClose = true,
+  action = null,
 }) {
   return serviceImplementation._show({
     title,
@@ -52,6 +54,7 @@ function _show({
     position,
     type,
     autoClose,
+    action,
   });
 }
 

platform/core/src/services/index.js

@@ -3,6 +3,7 @@ import UINotificationService from './UINotificationService';
 import UIModalService from './UIModalService';
 import UIDialogService from './UIDialogService';
 import MeasurementService from './MeasurementService';
+import LoggerService from './LoggerService';
 
 export {
   UINotificationService,
@@ -10,4 +11,5 @@ export {
   UIDialogService,
   ServicesManager,
   MeasurementService,
+  LoggerService,
 };

platform/core/src/utils/Queue.test.js

@@ -21,12 +21,12 @@ describe('Queue', () => {
     const mockedTimeout = jest.fn(timeout);
     const timer = queue.bind(mockedTimeout);
     const start = Date.now();
-    timer(120).then(now => {
+    timer(1200).then(now => {
       const elapsed = now - start;
-      expect(elapsed >= 120 && elapsed < 240).toBe(true);
+      expect(elapsed >= 1200 && elapsed < 2400).toBe(true);
     });
-    const end = await timer(120);
+    const end = await timer(1200);
-    expect(end - start > 240).toBe(true);
+    expect(end - start > 2400).toBe(true);
     expect(mockedTimeout).toBeCalledTimes(2);
   });
   it('should prevent task execution when queue limit is reached', async () => {
@@ -34,15 +34,15 @@ describe('Queue', () => {
     const mockedTimeout = jest.fn(timeout);
     const timer = queue.bind(mockedTimeout);
     const start = Date.now();
-    const promise = timer(120).then(time => time - start);
+    const promise = timer(1200).then(time => time - start);
     try {
-      await timer(120);
+      await timer(1200);
     } catch (e) {
-      expect(Date.now() - start < 120).toBe(true);
+      expect(Date.now() - start < 1200).toBe(true);
       expect(e.message).toBe('Queue limit reached');
     }
     const elapsed = await promise;
-    expect(elapsed >= 120 && elapsed < 240).toBe(true);
+    expect(elapsed >= 1200 && elapsed < 2400).toBe(true);
     expect(mockedTimeout).toBeCalledTimes(1);
   });
   it('should safely bind tasks to the queue', async () => {
@@ -51,16 +51,16 @@ describe('Queue', () => {
     const mockedTimeout = jest.fn(timeout);
     const timer = queue.bindSafe(mockedTimeout, mockedErrorHandler);
     const start = Date.now();
-    const promise = timer(120).then(time => time - start);
+    const promise = timer(1200).then(time => time - start);
-    await timer(120);
+    await timer(1200);
-    expect(Date.now() - start < 120).toBe(true);
+    expect(Date.now() - start < 1200).toBe(true);
     expect(mockedErrorHandler).toBeCalledTimes(1);
     expect(mockedErrorHandler).nthCalledWith(
       1,
       expect.objectContaining({ message: 'Queue limit reached' })
     );
     const elapsed = await promise;
-    expect(elapsed >= 120 && elapsed < 240).toBe(true);
+    expect(elapsed >= 1200 && elapsed < 2400).toBe(true);
     expect(mockedTimeout).toBeCalledTimes(1);
   });
 });

platform/core/src/utils/isDisplaySetReconstructable.js

@@ -1,9 +1,14 @@
+import { ReconstructionIssues } from './../enums.js';
+
+
 /**
  * Checks if a series is reconstructable to a 3D volume.
  *
- * @param {Object[]} instances An array of `OHIFInstanceMetadata` objects.
+ * @param {Object[]} An array of `OHIFInstanceMetadata` objects.
+ *
+ * @returns {Object} value, reconstructionIssues.
  */
-export default function isDisplaySetReconstructable(instances) {
+function isDisplaySetReconstructable(instances) {
   if (!instances.length) {
     return { value: false };
   }
@@ -23,31 +28,45 @@ export default function isDisplaySetReconstructable(instances) {
   }
 
   if (isMultiframe) {
-    return processMultiframe(instances[0]);
+    return processMultiframe();
   } else {
     return processSingleframe(instances);
   }
 }
 
-function processMultiframe(instance) {
+/**
-  //TODO: deal with multriframe checks! return false for now as can't reconstruct.
+ * Process reconstructable multiframes checks
-  return { value: false };
+ * TODO: deal with multriframe checks! return false for now as can't reconstruct.
+ * *
+ * @returns {Object} value and reconstructionIssues.
+ */
+function processMultiframe() {
+  const reconstructionIssues = [ReconstructionIssues.MULTIFRAMES];
+  return { value: false, reconstructionIssues };
 }
 
+/**
+ * Process reconstructable single frame checks
+ *
+ * @param {Object[]} An array of `OHIFInstanceMetadata` objects.
+ *
+ * @returns {Object} value and reconstructionIssues.
+ */
 function processSingleframe(instances) {
+  const n = instances.length;
   const firstImage = instances[0].getData().metadata;
   const firstImageRows = firstImage.Rows;
   const firstImageColumns = firstImage.Columns;
   const firstImageSamplesPerPixel = firstImage.SamplesPerPixel;
   const firstImageOrientationPatient = firstImage.ImageOrientationPatient;
-  const firstImagePositionPatient = firstImage.ImagePositionPatient;
 
+  const reconstructionIssues = [];
   // Can't reconstruct if we:
   // -- Have a different dimensions within a displaySet.
   // -- Have a different number of components within a displaySet.
   // -- Have different orientations within a displaySet.
-  for (let i = 1; i < instances.length; i++) {
+  for (let ii = 1; ii < n; ++ii) {
-    const instance = instances[i].getData().metadata;
+    const instance = instances[ii].getData().metadata;
     const {
       Rows,
       Columns,
@@ -55,67 +74,146 @@ function processSingleframe(instances) {
       ImageOrientationPatient,
     } = instance;
 
-    if (
+    if (Rows !== firstImageRows || Columns !== firstImageColumns) {
-      Rows !== firstImageRows ||
+      reconstructionIssues.push(ReconstructionIssues.VARYING_IMAGESDIMENSIONS);
-      Columns !== firstImageColumns ||
+    } else if (SamplesPerPixel !== firstImageSamplesPerPixel) {
-      SamplesPerPixel !== firstImageSamplesPerPixel ||
+      reconstructionIssues.push(ReconstructionIssues.VARYING_IMAGESCOMPONENTS);
-      !_isSameOrientation(ImageOrientationPatient, firstImageOrientationPatient)
+    } else if (!_isSameArray(ImageOrientationPatient, firstImageOrientationPatient)) {
-    ) {
+      reconstructionIssues.push(ReconstructionIssues.VARYING_IMAGESORIENTATION);
-      return { value: false };
+    }
+
+    if (reconstructionIssues.length !== 0) {
+      break;
     }
   }
 
+  // check if dataset is 4D
+  if (_isDataset4D(instances)) {
+    reconstructionIssues.push(ReconstructionIssues.DATASET_4D);
+  }
+
+  return { value: reconstructionIssues.length === 0 ? true : false, reconstructionIssues };
+}
+
+/**
+ *  Check is the spacing is uniform.
+ *  The input metadata array has to be ordered by image position.
+ *
+ * @param {Object[]} An array of `OHIFInstanceMetadata` objects.
+ * @param {boolean} is the dataset 4D.
+ *
+ * @returns {Object} isUniform, reconstructionIssues and missingFrames
+ */
+function isSpacingUniform(instances, datasetIs4D) {
+  const n = instances.length;
+  const firstImage = instances[0].getData().metadata;
+  const firstImagePositionPatient = firstImage.ImagePositionPatient;
+
+  const reconstructionIssues = [];
   let missingFrames = 0;
 
   // Check if frame spacing is approximately equal within a spacingTolerance.
   // If spacing is on a uniform grid but we are missing frames,
   // Allow reconstruction, but pass back the number of missing frames.
-  if (instances.length > 2) {
+  if (n > 2) {
-    const lastIpp = instances[instances.length - 1].getData().metadata
+    const lastIpp = instances[n - 1].getData().metadata
       .ImagePositionPatient;
 
     // We can't reconstruct if we are missing ImagePositionPatient values
-    if (!firstImagePositionPatient || !lastIpp) {
+    if (firstImagePositionPatient && lastIpp) {
-      return { value: false };
+      const averageSpacingBetweenFrames =
-    }
+        _getPerpendicularDistance(firstImagePositionPatient, lastIpp) /
+        (n - 1);
 
-    const averageSpacingBetweenFrames =
+      let previousImagePositionPatient = firstImagePositionPatient;
-      _getPerpendicularDistance(firstImagePositionPatient, lastIpp) /
-      (instances.length - 1);
 
-    let previousImagePositionPatient = firstImagePositionPatient;
+      for (let ii = 1; ii < n; ++ii) {
+        const instance = instances[ii].getData().metadata;
+        const { ImagePositionPatient } = instance;
 
-    for (let i = 1; i < instances.length; i++) {
+        const spacingBetweenFrames = _getPerpendicularDistance(
-      const instance = instances[i].getData().metadata;
+          ImagePositionPatient,
-      const { ImagePositionPatient } = instance;
+          previousImagePositionPatient
+        );
 
-      const spacingBetweenFrames = _getPerpendicularDistance(
+        if (datasetIs4D && spacingBetweenFrames < 1.e-3) {
-        ImagePositionPatient,
+          // the dataset is 4D, if the distance is zero, means that we are
-        previousImagePositionPatient
+          // checking the 4th dimension. Do not return, since we want still to
-      );
+          // check the 3rd dimension spacing.
-      const spacingIssue = _getSpacingIssue(
+          continue;
-        spacingBetweenFrames,
-        averageSpacingBetweenFrames
-      );
-
-      if (spacingIssue) {
-        const issue = spacingIssue.issue;
-
-        if (issue === reconstructionIssues.MISSING_FRAMES) {
-          missingFrames += spacingIssue.missingFrames;
-        } else if (issue === reconstructionIssues.IRREGULAR_SPACING) {
-          return { value: false };
         }
-      }
 
-      previousImagePositionPatient = ImagePositionPatient;
+        const spacingIssue = _getSpacingIssue(
+          spacingBetweenFrames,
+          averageSpacingBetweenFrames
+        );
+
+        if (spacingIssue) {
+          const issue = spacingIssue.issue;
+
+          if (issue === ReconstructionIssues.MISSING_FRAMES) {
+            missingFrames += spacingIssue.missingFrames;
+          } else if (issue === ReconstructionIssues.IRREGULAR_SPACING) {
+            reconstructionIssues.push(issue);
+            break;
+          }
+        }
+
+        previousImagePositionPatient = ImagePositionPatient;
+      }
     }
   }
 
-  return { value: true, missingFrames };
+  return { isUniform: reconstructionIssues.length === 0 ? true : false, missingFrames, reconstructionIssues };
 }
 
-function _isSameOrientation(iop1, iop2) {
+
+/**
+ *  Check if 4D dataset.
+ *
+ *  Assuming that slices at different time have the same position, here we just check if
+ *  there are multiple slices for the same ImagePositionPatient and disable MPR.
+ *
+ *  A better heuristic would be checking 4D tags, e.g. the presence of multiple TemporalPositionIdentifier values.
+ *  However, some studies (e.g. https://github.com/OHIF/Viewers/issues/2113) do not have such tags.
+ *
+ * @param {Object[]} instances An array of `OHIFInstanceMetadata` objects.
+ *
+ * @returns {boolean} dataset4D value.
+ */
+ function _isDataset4D(instances) {
+  const n = instances.length;
+  for (let ii = 0; ii < n; ++ii) {
+    const instanceMetadataControl = instances[ii].getData().metadata;
+    if (
+      !instanceMetadataControl ||
+      instanceMetadataControl === undefined ||
+      !instanceMetadataControl.ImagePositionPatient ||
+      instanceMetadataControl.ImagePositionPatient === undefined
+    ) {
+      continue;
+    }
+    for (let jj = ii + 1; jj < n; ++jj) {
+      const instanceMetadata = instances[jj].getData().metadata;
+      if (
+        !instanceMetadata ||
+        instanceMetadata === undefined ||
+        !instanceMetadata.ImagePositionPatient ||
+        instanceMetadata.ImagePositionPatient === undefined
+      ) {
+        continue;
+      }
+
+      if (_isSameArray(instanceMetadataControl.ImagePositionPatient, instanceMetadata.ImagePositionPatient)) {
+        return true;
+      }
+    }
+  }
+
+  return false;
+}
+
+function _isSameArray(iop1, iop2) {
   if (iop1 === undefined || !iop2 === undefined) {
     return;
   }
@@ -156,12 +254,12 @@ function _getSpacingIssue(spacing, averageSpacing) {
 
   if (errorForEachSpacing < spacingTolerance * averageSpacing) {
     return {
-      issue: reconstructionIssues.MISSING_FRAMES,
+      issue: ReconstructionIssues.MISSING_FRAMES,
       missingFrames: numberOfSpacings - 1,
     };
   }
 
-  return { issue: reconstructionIssues.IRREGULAR_SPACING };
+  return { issue: ReconstructionIssues.IRREGULAR_SPACING };
 }
 
 function _getPerpendicularDistance(a, b) {
@@ -173,7 +271,5 @@ function _getPerpendicularDistance(a, b) {
 }
 
 const constructableModalities = ['MR', 'CT', 'PT', 'NM'];
-const reconstructionIssues = {
+
-  MISSING_FRAMES: 'missingframes',
+export {isDisplaySetReconstructable, isSpacingUniform};
-  IRREGULAR_SPACING: 'irregularspacing',
-};

platform/core/src/utils/loadAndCacheDerivedDisplaySets.js

@@ -45,13 +45,13 @@ import studyMetadataManager from './studyMetadataManager';
  * @param {string} referencedDisplaySet.studyInstanceUid
  * @param {Array} referencedDisplaySet.sopClassUids
  * @param {Study[]} studies Collection of studies
+ * @param {object} logger
+ * @param {object} snackbar
  * @returns void
  */
-const loadAndCacheDerivedDisplaySets = (referencedDisplaySet, studies) => {
+async function loadAndCacheDerivedDisplaySets(referencedDisplaySet, studies, logger, snackbar) {
   const { StudyInstanceUID, SeriesInstanceUID } = referencedDisplaySet;
-
   const promises = [];
-
   const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
 
   if (!studyMetadata) {
@@ -80,11 +80,10 @@ const loadAndCacheDerivedDisplaySets = (referencedDisplaySet, studies) => {
   });
 
   // For each type, see if any are loaded, if not load the most recent.
-  Object.keys(displaySetsPerModality).forEach(key => {
+  await Promise.all(Object.keys(displaySetsPerModality).map(async (key) => {
     const displaySets = displaySetsPerModality[key];
 
     const isLoaded = displaySets.some(displaySet => displaySet.isLoaded);
-
     if (isLoaded) {
       return;
     }
@@ -107,12 +106,34 @@ const loadAndCacheDerivedDisplaySets = (referencedDisplaySet, studies) => {
       }
     });
 
-    recentDisplaySet.isLoading = true;
+    try {
+      if (recentDisplaySet.hasOwnProperty('getSourceDisplaySet') &&
+        typeof recentDisplaySet.getSourceDisplaySet === 'function') {
+        await recentDisplaySet.getSourceDisplaySet(studies);
+      } else {
+        await recentDisplaySet.load(referencedDisplaySet, studies);
+      }
+    } catch (error) {
+      recentDisplaySet.isLoaded = false;
+      recentDisplaySet.loadError = true;
+      logger.error({ error, message: error.message });
+      snackbar.show({
+        title: 'Error loading derived display set:',
+        message: error.message,
+        type: 'error',
+        error,
+        autoClose: false,
+      });
+    }
+  }));
 
-    promises.push(recentDisplaySet.load(referencedDisplaySet, studies));
+  /*
-  });
+  * TODO: Improve the way we notify parts of the app
-
+  * that depends on derived display sets to be loaded.
-  return promises;
+  * (Implement pubsub for better tracking of derived display sets)
+  */
+  const event = new CustomEvent('deriveddisplaysetsloadedandcached');
+  document.dispatchEvent(event);
 };
 
 export default loadAndCacheDerivedDisplaySets;

platform/core/src/utils/metadataProvider/validNumber.js

@@ -0,0 +1,9 @@
+const validNumber = val => {
+  if (Array.isArray(val)) {
+    return val.map(v => (v !== undefined ? Number(v) : v));
+  } else {
+    return val !== undefined ? Number(val) : val;
+  }
+};
+
+export default validNumber;

platform/i18n/CHANGELOG.md

@@ -3,6 +3,23 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+# [0.53.0](https://github.com/OHIF/Viewers/compare/@ohif/i18n@0.52.8...@ohif/i18n@0.53.0) (2020-11-30)
+
+
+### Bug Fixes
+
+* Add syncTranslations script ([b161016](https://github.com/OHIF/Viewers/commit/b161016edb8808ff0d17ea637820837dca1ca3ce))
+
+
+### Features
+
+* **i18n:** Added de (German) translations ([2fff2d5](https://github.com/OHIF/Viewers/commit/2fff2d511fa1d36bdd6476da4ffa5684bf55374f))
+* **i18n:** Added Russian language localization. ([d5b8974](https://github.com/OHIF/Viewers/commit/d5b89748c92c2cf5a88f54ae491adc31a1679705))
+
+
+
+
+
 ## [0.52.8](https://github.com/OHIF/Viewers/compare/@ohif/i18n@0.52.7...@ohif/i18n@0.52.8) (2020-04-07)
 
 **Note:** Version bump only for package @ohif/i18n

platform/i18n/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/i18n",
-  "version": "0.52.8",
+  "version": "0.53.0",
   "description": "Internationalization library for The OHIF Viewer",
   "author": "OHIF",
   "license": "MIT",

platform/i18n/src/locales/ar/UserPreferencesModal.json

@@ -1,3 +0,0 @@
-{
-  "No hotkeys found": "Nenhuma tecla de atalho está configurada para este aplicativo. As teclas de atalho podem ser configuradas no arquivo app-config.js do aplicativo."
-}

platform/i18n/src/locales/ar/index.js

@@ -1,7 +0,0 @@
-import UserPreferencesModal from './UserPreferencesModal.json';
-
-export default { 
-  'ar': {
-    UserPreferencesModal,
-  }
-};

platform/i18n/src/locales/de/AboutModal.json

@@ -0,0 +1,14 @@
+{
+  "Browser": "Browser",
+  "Build Number": "Build Number",
+  "Latest Master Commits": "Letzter Master Commit",
+  "More details": "Mehr Details",
+  "Name": "Name",
+  "OHIF Viewer - About": "OHIF Viewer",
+  "OS": "OS",
+  "Report an issue": "Problem melden",
+  "Repository URL": "Repository URL",
+  "Value": "Wert",
+  "Version Information": "Versionsinformation",
+  "Visit the forum": "Das Forum besuchen"
+}

platform/i18n/src/locales/de/Buttons.json

@@ -0,0 +1,43 @@
+{
+  "Acquired": "Akquiriert",
+  "Angle": "Winkel",
+  "Axial": "Axial",
+  "Bidirectional": "Bidirektional",
+  "Brush": "Pinsel",
+  "CINE": "CINE",
+  "Cancel": "Abbruch",
+  "Circle": "Kreis",
+  "Clear": "Entfernen",
+  "Coronal": "Coronal",
+  "Crosshairs": "Kreuzlinien",
+  "Download": "Herunterladen",
+  "Ellipse": "Ellipse",
+  "Elliptical": "Elliptisch",
+  "Flip H": "Spiegeln H",
+  "Flip V": "Spiegeln V",
+  "Freehand": "Freihand",
+  "Invert": "Invertieren",
+  "Layout": "$t(Common:Layout)",
+  "Length": "Länge",
+  "Levels": "Levels",
+  "Magnify": "Vergrössern",
+  "Manual": "Manuell",
+  "Measurements": "Messungen",
+  "More": "$t(Common:More)",
+  "Next": "$t(Common:Next)",
+  "Pan": "Verschieben",
+  "Play": "$t(Common:Play)",
+  "Previous": "$t(Common:Previous)",
+  "Probe": "Messung",
+  "ROI Window": "ROI Fenster",
+  "Rectangle": "Rechteck",
+  "Reset": "$t(Common:Reset)",
+  "Reset to Defaults": "Standardwerte",
+  "Rotate Right": "Rechts drehen",
+  "Sagittal": "Sagittal",
+  "Save": "Speichern",
+  "Stack Scroll": "Stapel",
+  "Stop": "$t(Common:Stop)",
+  "Themes": "Themes",
+  "Zoom": "Zoom"
+}

platform/i18n/src/locales/de/CineDialog.json

@@ -0,0 +1,8 @@
+{
+  "Next image": "$t(Common:Next) $t(Common:Image)",
+  "Play / Stop": "$t(Common:Play) / $t(Common:Stop)",
+  "Previous image": "$t(Common:Previous) $t(Common:Image)",
+  "Skip to first image": "Zum ersten $t(Common:Image)",
+  "Skip to last image": "Zum letzten $t(Common:Image)",
+  "fps": "fps"
+}

platform/i18n/src/locales/de/Common.json

@@ -0,0 +1,16 @@
+{
+  "Close": "Schliessen",
+  "Image": "Bild",
+  "Layout": "Layout",
+  "Measurements": "Messungen",
+  "More": "Mehr",
+  "Next": "Nächstes",
+  "Play": "Abspielen",
+  "Previous": "Zurück",
+  "Reset": "Zurücksetzen",
+  "RowsPerPage": "Zeilen pro Seite",
+  "Series": "Serie",
+  "Show": "Zeigen",
+  "Stop": "Stopp",
+  "StudyDate": "Studien Datum"
+}

platform/i18n/src/locales/de/DatePicker.json

@@ -0,0 +1,5 @@
+{
+  "Clear dates": "Zeiträume löschen",
+  "End Date": "Bis",
+  "Start Date": "Ab"
+}

platform/i18n/src/locales/de/Header.json

@@ -0,0 +1,8 @@
+{
+  "About": "Über",
+  "Back to Viewer": "Zurück zum Viewer",
+  "INVESTIGATIONAL USE ONLY": "NICHT ZUR BEFUNDUNG FREIGEGEBEN",
+  "Options": "Optionen",
+  "Preferences": "Einstellungen",
+  "Study list": "Studienliste"
+}

platform/i18n/src/locales/de/MeasurementTable.json

@@ -0,0 +1,9 @@
+{
+  "Criteria nonconformities": "Kriterien für Nichtkonformität",
+  "Delete": "Löschen",
+  "Description": "Beschreibung",
+  "MAX": "MAX",
+  "NonTargets": "NichtZiele",
+  "Relabel": "Umbenennen",
+  "Targets": "Ziele"
+}

platform/i18n/src/locales/de/StudyList.json

@@ -0,0 +1,10 @@
+{
+  "AccessionNumber": "Accession #",
+  "Empty": "Leer",
+  "MRN": "MRN",
+  "Modality": "Modalität",
+  "PatientName": "Patientenname",
+  "StudyDate": "Studiendatum",
+  "StudyDescription": "Beschreibung",
+  "StudyList": "Studienliste"
+}

platform/i18n/src/locales/de/UserPreferencesModal.json

@@ -0,0 +1,9 @@
+{
+  "Cancel": "$t(Buttons:Cancel)",
+  "No hotkeys found": "Keine Tastaturkürzel konfiguriert. Tastaturkürzel können in der app-config.js Datei der Anwendung konfiguriert werden.",
+  "Reset to Defaults": "$t(Buttons:Reset to Defaults)",
+  "ResetDefaultMessage": "Einstellungen erfolgreich zurückgesetzt. <br /> Sie müssen <strong>Speichern</strong> um dieses abzuschliessen.",
+  "Save": "$t(Buttons:Save)",
+  "SaveMessage": "Einstellungen gesichert",
+  "User Preferences": "Benutzereinstellungen"
+}

platform/i18n/src/locales/de/ViewportDownloadForm.json

@@ -0,0 +1,14 @@
+{
+  "emptyFilenameError": "Dateiname kann nicht leer sein.",
+  "fileType": "Dateityp",
+  "filename": "Dateiname",
+  "formTitle": "Bitte geben Sie die Dimensionen, Dateiname und den gewünschten Dateityp an.",
+  "imageHeight": "Bildhöhe (px)",
+  "imagePreview": "Bild Vorschau",
+  "imageWidth": "Bildbreite (px)",
+  "keepAspectRatio": "Seitenverhältnis erbehalten",
+  "loadingPreview": "Bildvorschau laden...",
+  "minHeightError": "Die minimale Höhe beträgt 100 Pixel.",
+  "minWidthError": "Die minimale Breiete beträgt 100 Pixel.",
+  "showAnnotations": "Annotationen anzeigen"
+}

platform/i18n/src/locales/de/index.js

@@ -0,0 +1,25 @@
+import AboutModal from './AboutModal.json';
+import Buttons from './Buttons.json';
+import CineDialog from './CineDialog.json';
+import Common from './Common.json';
+import DatePicker from './DatePicker.json';
+import Header from './Header.json';
+import MeasurementTable from './MeasurementTable.json';
+import StudyList from './StudyList.json';
+import UserPreferencesModal from './UserPreferencesModal.json';
+import ViewportDownloadForm from './ViewportDownloadForm.json';
+
+export default { 
+  'de': {
+    AboutModal,
+    Buttons,
+    CineDialog,
+    Common,
+    DatePicker,
+    Header,
+    MeasurementTable,
+    StudyList,
+    UserPreferencesModal,
+    ViewportDownloadForm,
+  }
+};

platform/i18n/src/locales/es/AboutModal.json

@@ -0,0 +1 @@
+{}

platform/i18n/src/locales/es/DatePicker.json

@@ -0,0 +1 @@
+{}

platform/i18n/src/locales/es/ViewportDownloadForm.json

@@ -0,0 +1 @@
+{}

platform/i18n/src/locales/es/index.js

@@ -1,19 +1,25 @@
+import AboutModal from './AboutModal.json';
 import Buttons from './Buttons.json';
 import CineDialog from './CineDialog.json';
 import Common from './Common.json';
+import DatePicker from './DatePicker.json';
 import Header from './Header.json';
 import MeasurementTable from './MeasurementTable.json';
 import StudyList from './StudyList.json';
 import UserPreferencesModal from './UserPreferencesModal.json';
+import ViewportDownloadForm from './ViewportDownloadForm.json';
 
 export default { 
   'es': {
+    AboutModal,
     Buttons,
     CineDialog,
     Common,
+    DatePicker,
     Header,
     MeasurementTable,
     StudyList,
     UserPreferencesModal,
+    ViewportDownloadForm,
   }
 };

platform/i18n/src/locales/fr/AboutModal.json

@@ -0,0 +1 @@
+{}