chore(release): publish [skip ci]

- @ohif/extension-debugging@0.3.2
 - @ohif/viewer@4.12.19

.circleci/config.yml

@@ -25,11 +25,9 @@ executors:
     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:14.15.0
+    - image: cimg/node:14.18
       environment:
         TERM: xterm # Enable colors in term
         QUICK_BUILD: true
@@ -349,7 +347,8 @@ workflows:
           store_artifacts: true
           working_directory: platform/viewer
           build:
-            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            git submodule update --init &&
+            npx cross-env QUICK_BUILD=true APP_CONFIG=config/e2e.js
             yarn run build
           start: yarn run test:e2e:serve
           spec: 'cypress/integration/common/**/*,cypress/integration/pwa/**/*'
@@ -377,7 +376,8 @@ workflows:
           store_artifacts: true
           working_directory: platform/viewer
           build:
-            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            git submodule update --init &&
+            npx cross-env QUICK_BUILD=true APP_CONFIG=config/e2e.js
             yarn run build:package
           start: yarn run test:e2e:serve
           spec: 'cypress/integration/common/**/*,cypress/integration/script-tag/**/*'
@@ -410,7 +410,8 @@ workflows:
           store_artifacts: false
           working_directory: platform/viewer
           build:
-            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            git submodule update --init &&
+            npx cross-env QUICK_BUILD=true APP_CONFIG=config/e2e.js
             yarn run build
           # start server --> verify running --> percy + chrome + cypress
           command: yarn run test:e2e:dist
@@ -489,7 +490,8 @@ workflows:
           store_artifacts: false
           working_directory: platform/viewer
           build:
-            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            git submodule update --init &&
+            npx cross-env QUICK_BUILD=true APP_CONFIG=config/e2e.js
             yarn run build
           # start server --> verify running --> percy + chrome + cypress
           command: yarn run test:e2e:dist

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "testdata"]
+	path = testdata
+	url = https://github.com/OHIF/viewer-testdata-dicomweb.git

.node-version

@@ -0,0 +1 @@
+14.18.0

.webpack/webpack.base.js

@@ -28,7 +28,7 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => {
 
   const config = {
     mode: isProdBuild ? 'production' : 'development',
-    devtool: isProdBuild ? 'source-map' : 'cheap-module-eval-source-map',
+    devtool: isProdBuild ? 'source-map' : 'eval-cheap-module-source-map',
     entry: {
       app: `${SRC_DIR}/index.js`,
     },

docs/latest/deployment/recipes/nginx--image-archive.md

@@ -8,7 +8,9 @@ OHIF Viewer and its medical imaging data. This post covers one of many potential
 setups that accomplish that. Please note, noticably absent is user account
 control.
 
-Do not use this recipe to host sensitive medical data on the open web. Depending
+> **Do not use this recipe to host sensitive medical data on the open web!** 
+
+Depending
 on your company's policies, this may be an appropriate setup on an internal
 network when protected with a server's basic authentication. For a more robust
 setup, check out our [user account control recipe](./user-account-control.md)
@@ -23,13 +25,13 @@ Our two biggest hurdles when hosting our image archive and web client are:
 
 ### Handling Web Requests
 
-We mittigate our first issue by allowing [Nginx][nginx] to handle incoming web
+We mitigate our first issue by allowing [Nginx][nginx] to handle incoming web
 requests. Nginx is open source software for web serving, reverse proxying,
 caching, and more. It's designed for maximum performance and stability --
 allowing us to more reliably serve content than Orthanc's built-in server can.
 
 More specifically, we accomplish this by using a
-[`reverse proxy`](https://en.wikipedia.org/wiki/Reverse_proxy) to retrieve
+[`reverse proxy`](https://en.wikipedia.org/wiki/Reverse_proxy) to retrieve 
 resources from our image archive (Orthanc), and when accessing its web admin.
 
 > A reverse proxy is a type of proxy server that retrieves resources on behalf
@@ -38,7 +40,7 @@ resources from our image archive (Orthanc), and when accessing its web admin.
 
 ### CORS Issues
 
-Cross-Origin Resource Sharing (CORS) is a mechanism that uses HTTP headers to
+[Cross-Origin Resource Sharing][understanding-cors] (CORS) is a mechanism that uses HTTP headers to
 tell a browser which web applications have permission to access selected
 resources from a server at a different origin (domain, protocol, port). IE. By
 default, a Web App located at `http://my-website.com` can't access resources
@@ -51,9 +53,6 @@ We can solve this one of two ways:
 
 **This solution uses the first approach.**
 
-You can read more about CORS in this Medium article: [Understanding
-CORS][understanding-cors]
-
 ### Diagram
 
 This setup allows us to create a setup similar to the one pictured below:
@@ -73,6 +72,8 @@ This setup allows us to create a setup similar to the one pictured below:
 - Docker
   - [Docker for Mac](https://docs.docker.com/docker-for-mac/)
   - [Docker for Windows](https://docs.docker.com/docker-for-windows/)
+- Node 16.x with optional Python and Visual Studio Build Tools ([webpack 4 has an issue](https://github.com/webpack/webpack/issues/14532) with Node 17.x)
+  - [Node.js](https://nodejs.org/en/download/)
 
 _Not sure if you have `docker` installed already? Try running `docker --version`
 in command prompt or terminal_
@@ -81,7 +82,7 @@ in command prompt or terminal_
 
 _Spin Things Up_
 
-- Navigate to `<project-root>/docker/OpenResty-Orthanc` in your shell
+- Navigate to `./platform/viewer/.recipes/OpenResty-Orthanc` in your shell
 - Run `docker-compose up`
 
 _Upload Your First Study_
@@ -94,16 +95,16 @@ _Upload Your First Study_
 
 ### Troubleshooting
 
-_Exit code 137_
+#### Exit code 137
 
 This means Docker ran out of memory. Open Docker Desktop, go to the `advanced`
 tab, and increase the amount of Memory available.
 
-_Cannot create container for service X_
+#### Cannot create container for service X
 
 Use this one with caution: `docker system prune`
 
-_X is already running_
+#### X is already running
 
 Stop running all containers:
 
@@ -120,15 +121,12 @@ likely want to update:
 #### OHIF Viewer
 
 The OHIF Viewer's configuration is imported from a static `.js` file. The
-configuration we use is set to a specific file when we build the viewer, and
+configuration we use is set to [a specific file][config-ohif] when we build the viewer, and
 determined by the env variable: `APP_CONFIG`. You can see where we set its value
 in the `dockerfile` for this solution:
 
 `ENV APP_CONFIG=config/docker_openresty-orthanc.js`
 
-You can find the configuration we're using here:
-`/public/config/docker_openresty-orthanc.js`
-
 To rebuild the `webapp` image created by our `dockerfile` after updating the
 Viewer's configuration, you can run:
 
@@ -137,7 +135,7 @@ Viewer's configuration, you can run:
 
 #### Other
 
-All other files are found in: `/docker/OpenResty-Orthanc/`
+All other files in this directory include
 
 | Service           | Configuration                     | Docs                                        |
 | ----------------- | --------------------------------- | ------------------------------------------- |
@@ -236,6 +234,8 @@ members put together:
 [orthanc-docs]: http://book.orthanc-server.com/users/configuration.html#configuration
 [lua-resty-openidc-docs]: https://github.com/zmartzone/lua-resty-openidc
 <!-- SRC -->
+
+[config-ohif]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/public/config/docker_openresty-orthanc.js
 [dockerfile]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc/dockerfile
 [config-nginx]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc/config/nginx.conf
 [config-orthanc]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc/config/orthanc.json

extensions/cornerstone/CHANGELOG.md

@@ -3,6 +3,38 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.12.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.6...@ohif/extension-cornerstone@2.12.7) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.5...@ohif/extension-cornerstone@2.12.6) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.4...@ohif/extension-cornerstone@2.12.5) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.3...@ohif/extension-cornerstone@2.12.4) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
 ## [2.12.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.2...@ohif/extension-cornerstone@2.12.3) (2021-12-02)
 
 **Note:** Version bump only for package @ohif/extension-cornerstone

extensions/cornerstone/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone",
-  "version": "2.12.3",
+  "version": "2.12.7",
   "description": "OHIF extension for Cornerstone",
   "author": "OHIF",
   "license": "MIT",
@@ -36,7 +36,7 @@
     "cornerstone-math": "^0.1.9",
     "cornerstone-tools": "^6.0.6",
     "cornerstone-wado-image-loader": "^4.1.0",
-    "dcmjs": "0.19.1",
+    "dcmjs": "0.19.4",
     "dicom-parser": "^1.8.11",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",

extensions/cornerstone/src/ConnectedCornerstoneViewport.js

@@ -3,6 +3,7 @@ import OHIF from '@ohif/core';
 import { connect } from 'react-redux';
 import throttle from 'lodash.throttle';
 import { setEnabledElement } from './state';
+import initSRTools from './tools/initSRTools';
 
 const { setViewportActive, setViewportSpecificData } = OHIF.redux.actions;
 const {
@@ -92,6 +93,7 @@ const mapDispatchToProps = (dispatch, ownProps) => {
           plugin: 'cornerstone',
         })
       );
+      initSRTools(enabledElement);
     },
 
     onMeasurementsChanged: (event, action) => {

extensions/cornerstone/src/OHIFCornerstoneViewport.js

@@ -5,6 +5,7 @@ import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
 import OHIF from '@ohif/core';
 import PropTypes from 'prop-types';
 import cornerstone from 'cornerstone-core';
+import checkForSRAnnotations from './tools/checkForSRAnnotations';
 
 const { StackManager } = OHIF.utils;
 
@@ -187,6 +188,8 @@ class OHIFCornerstoneViewport extends Component {
       displaySet.SOPInstanceUID !== prevDisplaySet.SOPInstanceUID ||
       displaySet.frameIndex !== prevDisplaySet.frameIndex
     ) {
+      const { viewportIndex } = this.props;
+      checkForSRAnnotations({ displaySet, viewportIndex });
       this.setStateFromProps();
     }
   }

extensions/cornerstone/src/init.js

@@ -5,6 +5,8 @@ import csTools from 'cornerstone-tools';
 import merge from 'lodash.merge';
 import initCornerstoneTools from './initCornerstoneTools.js';
 import measurementServiceMappingsFactory from './utils/measurementServiceMappings/measurementServiceMappingsFactory';
+import dicomSRModule from './tools/modules/dicomSRModule';
+import srModuleId from './tools/id';
 
 /**
  *
@@ -15,6 +17,8 @@ import measurementServiceMappingsFactory from './utils/measurementServiceMapping
 export default function init({ servicesManager, configuration }) {
   const { UIDialogService, MeasurementService } = servicesManager.services;
 
+  csTools.register('module', srModuleId, dicomSRModule);
+
   const callInputDialog = (data, event, callback) => {
     if (UIDialogService) {
       let dialogId = UIDialogService.create({

extensions/cornerstone/src/tools/DICOMSRDisplayTool.js

@@ -0,0 +1,414 @@
+import csTools, {
+  importInternal,
+  getToolState,
+  toolColors,
+} from 'cornerstone-tools';
+
+import cornerstone from 'cornerstone-core';
+
+/** Internal imports */
+import TOOL_NAMES from './constants/toolNames';
+import SCOORD_TYPES from './constants/scoordTypes';
+import id from './id';
+
+/** Cornerstone 3rd party dev kit imports */
+const draw = importInternal('drawing/draw');
+const drawJoinedLines = importInternal('drawing/drawJoinedLines');
+const drawCircle = importInternal('drawing/drawCircle');
+const drawEllipse = importInternal('drawing/drawEllipse');
+const drawHandles = importInternal('drawing/drawHandles');
+const drawArrow = importInternal('drawing/drawArrow');
+const getNewContext = importInternal('drawing/getNewContext');
+const BaseTool = importInternal('base/BaseTool');
+const drawLinkedTextBox = importInternal('drawing/drawLinkedTextBox');
+
+/**
+ * @class DICOMSRDisplayTool - Renders DICOMSR data in a read only manner (i.e. as an overlay).
+ *
+ * This is a generic render tool.
+ *
+ * A single tool that, given some schema, can render
+ * POINT, MULTIPOINT, POLYLINE, CIRCLE, and ELLIPSE
+ * value types for a given imageId.
+ *
+ *
+ * @extends cornerstoneTools.BaseTool
+ */
+export default class DICOMSRDisplayTool extends BaseTool {
+  constructor(props = {}) {
+    const defaultProps = {
+      mixins: ['enabledOrDisabledBinaryTool'],
+      name: TOOL_NAMES.DICOM_SR_DISPLAY_TOOL,
+    };
+
+    const initialProps = Object.assign(defaultProps, props);
+
+    super(initialProps);
+
+    this._module = csTools.getModule(id);
+  }
+
+  renderToolData(evt) {
+    const eventData = evt.detail;
+    const { element } = eventData;
+    const module = this._module;
+
+    const toolState = getToolState(element, this.name);
+
+    if (!toolState) {
+      return;
+    }
+
+    const trackingUniqueIdentifiersForElement = module.getters.trackingUniqueIdentifiersForElement(
+      element
+    );
+
+    const {
+      activeIndex,
+      trackingUniqueIdentifiers,
+    } = trackingUniqueIdentifiersForElement;
+
+    const activeTrackingUniqueIdentifier =
+      trackingUniqueIdentifiers[activeIndex];
+
+    // Filter toolData to only render the data for the active SR.
+    const filteredToolData = toolState.data.filter(td =>
+      trackingUniqueIdentifiers.includes(td.TrackingUniqueIdentifier)
+    );
+
+    let shouldRepositionTextBoxes = false;
+
+    for (let i = 0; i < filteredToolData.length; i++) {
+      const data = filteredToolData[i];
+      const { renderableData, labels } = data;
+
+      const color =
+        data.TrackingUniqueIdentifier === activeTrackingUniqueIdentifier
+          ? toolColors.getActiveColor()
+          : toolColors.getToolColor();
+      const lineWidth = 2;
+      const options = {
+        color,
+        lineWidth,
+        handleRadius: 6,
+      };
+
+      Object.keys(renderableData).forEach(GraphicType => {
+        const renderableDataForGraphicType = renderableData[GraphicType];
+
+        switch (GraphicType) {
+          case SCOORD_TYPES.POINT:
+            this.renderPoint(renderableDataForGraphicType, eventData, options);
+            break;
+          case SCOORD_TYPES.MULTIPOINT:
+            this.renderMultipoint(
+              renderableDataForGraphicType,
+              eventData,
+              options
+            );
+            break;
+          case SCOORD_TYPES.POLYGON:
+          case SCOORD_TYPES.POLYLINE:
+            this.renderPolyLine(
+              renderableDataForGraphicType,
+              eventData,
+              options
+            );
+            break;
+          case SCOORD_TYPES.CIRCLE:
+            this.renderCircle(renderableDataForGraphicType, eventData, options);
+            break;
+          case SCOORD_TYPES.ELLIPSE:
+            this.renderEllipse(
+              renderableDataForGraphicType,
+              eventData,
+              options
+            );
+            break;
+        }
+      });
+
+      const { element } = eventData;
+      const context = getNewContext(eventData.canvasContext.canvas);
+
+      if (!data.handles || !data.handles.textBox) {
+        const textBox = {
+          active: false,
+          hasMoved: true,
+          movesIndependently: false,
+          drawnIndependently: true,
+          allowedOutsideImage: true,
+          hasBoundingBox: true,
+        };
+
+        const anchorPoints = _getTextBoxAnchorPointsForRenderableData(
+          renderableData,
+          eventData
+        );
+        textBox.anchorPoints = anchorPoints;
+
+        const bottomRight = {
+          x: Math.max(...anchorPoints.map(point => point.x)),
+          y: Math.max(...anchorPoints.map(point => point.y)),
+        };
+
+        textBox.x = bottomRight.x;
+        textBox.y = bottomRight.y;
+
+        data.handles = {};
+        data.handles.textBox = textBox;
+
+        shouldRepositionTextBoxes = true;
+      }
+
+      const text = _getTextBoxLinesFromLabels(labels);
+
+      function textBoxAnchorPoints() {
+        return data.handles.textBox.anchorPoints;
+      }
+
+      draw(context, context => {
+        drawLinkedTextBox(
+          context,
+          element,
+          data.handles.textBox,
+          text,
+          data.handles,
+          textBoxAnchorPoints,
+          color,
+          lineWidth,
+          0,
+          true
+        );
+      });
+    }
+
+    // TOOD -> text boxes may overlap with other annotations at the moment.
+    // To be fixed after we get requirements.
+    // if (shouldRepositionTextBoxes) {
+    //   this.repositionTextBox(filteredToolData, eventData);
+    // }
+  }
+
+  // repositionTextBox(toolData, eventData) {
+  //   const toolBoundingBoxes = [];
+
+  //   for (let i = 0; i < toolData.length; i++) {
+  //     const toolDataI = toolData[i];
+
+  //     const { textBox } = toolDataI.handles;
+  //     const { anchorPoints } = textBox;
+
+  //     const boundingBox = _getBoundingBoxFromAnchorPoints(anchorPoints);
+  //     // Get the textbox bounding locations.
+  //     // Get the tool extents.
+  //   }
+  // }
+
+  renderPolyLine(renderableData, eventData, options) {
+    const { element } = eventData;
+    const context = getNewContext(eventData.canvasContext.canvas);
+    renderableData.forEach(points => {
+      draw(context, context => {
+        drawJoinedLines(context, element, points[0], points, options);
+      });
+    });
+  }
+
+  renderMultipoint(renderableData, eventData, options) {
+    const context = getNewContext(eventData.canvasContext.canvas);
+
+    renderableData.forEach(points => {
+      draw(context, context => {
+        drawHandles(context, eventData, points, options);
+      });
+    });
+  }
+
+  renderPoint(renderableData, eventData, options) {
+    // Render single point as an arrow.
+    const { element, image } = eventData;
+    const { rows, columns } = image;
+    const context = getNewContext(eventData.canvasContext.canvas);
+
+    const { color, lineWidth } = options;
+
+    // Find a suitable length for the image size.
+
+    const xOffset = columns / 10;
+    const yOffset = rows / 10;
+
+    renderableData.forEach(points => {
+      const point = points[0]; // The SCOORD type is POINT so the array length is 1.
+      draw(context, context => {
+        // Draw the arrow
+        const handleStartCanvas = cornerstone.pixelToCanvas(element, point);
+        const handleEndCanvas = cornerstone.pixelToCanvas(element, {
+          x: point.x + xOffset,
+          y: point.y + yOffset,
+        });
+
+        drawArrow(
+          context,
+          handleEndCanvas,
+          handleStartCanvas,
+          color,
+          lineWidth,
+          false
+        );
+      });
+    });
+  }
+
+  renderCircle(renderableData, eventData, options) {
+    const { element } = eventData;
+
+    const context = getNewContext(eventData.canvasContext.canvas);
+
+    renderableData.forEach(circle => {
+      const { center, radius } = circle;
+
+      drawCircle(context, element, center, radius, options);
+    });
+  }
+
+  renderEllipse(renderableData, eventData, options) {
+    const { element } = eventData;
+
+    const context = getNewContext(eventData.canvasContext.canvas);
+
+    renderableData.forEach(ellipse => {
+      const { corner1, corner2 } = ellipse;
+
+      drawEllipse(
+        context,
+        element,
+        corner1,
+        corner2,
+        options,
+        'pixel',
+        0 // TODO -> Work our the initial rotation and add it here so we render appropriately rotated ellipses.
+      );
+    });
+  }
+}
+
+function _getTextBoxLinesFromLabels(labels) {
+  // TODO -> max 3 for now (label + shortAxis + longAxis), need a generic solution for this!
+
+  const labelLength = Math.min(labels.length, 3);
+  const lines = [];
+
+  for (let i = 0; i < labelLength; i++) {
+    const labelEntry = labels[i];
+    lines.push(`${_labelToShorthand(labelEntry.label)}${labelEntry.value}`);
+  }
+
+  return lines;
+}
+
+const SHORT_HAND_MAP = {
+  'Short Axis': 'W ',
+  'Long Axis': 'L ',
+  AREA: 'Area ',
+  Length: '',
+  CORNERSTONEFREETEXT: '',
+};
+
+function _labelToShorthand(label) {
+  const shortHand = SHORT_HAND_MAP[label];
+
+  if (shortHand !== undefined) {
+    return shortHand;
+  }
+
+  return label;
+}
+
+function _getTextBoxAnchorPointsForRenderableData(renderableData, eventData) {
+  let anchorPoints = [];
+
+  Object.keys(renderableData).forEach(GraphicType => {
+    const renderableDataForGraphicType = renderableData[GraphicType];
+
+    switch (GraphicType) {
+      case SCOORD_TYPES.POINT:
+        renderableDataForGraphicType.forEach(points => {
+          anchorPoints = [...anchorPoints, ...points];
+
+          // Add other arrow point based on image size.
+          const { image } = eventData;
+          const { rows, columns } = image;
+
+          const xOffset = columns / 10;
+          const yOffset = rows / 10;
+          const point = points[0];
+
+          anchorPoints.push({ x: point.x + xOffset, y: point.y + yOffset });
+        });
+
+        break;
+      case SCOORD_TYPES.MULTIPOINT:
+      case SCOORD_TYPES.POLYLINE:
+      case SCOORD_TYPES.POLYGON:
+        renderableDataForGraphicType.forEach(points => {
+          anchorPoints = [...anchorPoints, ...points];
+        });
+        break;
+      case SCOORD_TYPES.CIRCLE:
+        renderableDataForGraphicType.forEach(circle => {
+          const { center, radius } = circle;
+
+          anchorPoints.push({ x: center.x + radius, y: center.y });
+          anchorPoints.push({ x: center.x - radius, y: center.y });
+          anchorPoints.push({ x: center.x, y: center.y + radius });
+          anchorPoints.push({ x: center.x, y: center.y - radius });
+        });
+
+        break;
+      case SCOORD_TYPES.ELLIPSE:
+        renderableDataForGraphicType.forEach(ellipse => {
+          const { corner1, corner2 } = ellipse;
+
+          const halfWidth = Math.abs(corner1.x - corner2.x) / 2;
+          const halfHeight = Math.abs(corner1.y - corner2.y) / 2;
+
+          const center = {
+            x: (corner1.x + corner2.x) / 2,
+            y: (corner1.y + corner2.y) / 2,
+          };
+
+          anchorPoints.push({ x: center.x + halfWidth, y: center.y });
+          anchorPoints.push({ x: center.x - halfWidth, y: center.y });
+          anchorPoints.push({ x: center.x, y: center.y + halfHeight });
+          anchorPoints.push({ x: center.x, y: center.y - halfHeight });
+        });
+        break;
+    }
+  });
+
+  return anchorPoints;
+}
+
+function _getBoundingBoxFromAnchorPoints(anchorPoints) {
+  let minX = Infinity;
+  let maxX = -Infinity;
+  let minY = Infinity;
+  let maxY = -Infinity;
+
+  anchorPoints.forEach(point => {
+    const { x, y } = point;
+
+    if (x > maxX) {
+      maxX = x;
+    } else if (x < minX) {
+      minX = x;
+    }
+
+    if (y > maxX) {
+      maxY = y;
+    } else if (y < minY) {
+      minY = y;
+    }
+  });
+}

extensions/cornerstone/src/tools/checkForSRAnnotations.js

@@ -0,0 +1,57 @@
+import csTools from 'cornerstone-tools';
+import cs from 'cornerstone-core';
+import OHIF from '@ohif/core';
+
+import { getEnabledElement } from '../state';
+import id from './id';
+
+const { studyMetadataManager } = OHIF.utils;
+
+const checkForSRAnnotations = ({ viewportIndex, displaySet }) => {
+  const srModule = csTools.getModule(id);
+
+  const element = getEnabledElement(viewportIndex);
+  if (!element) {
+    return;
+  }
+
+  const { StudyInstanceUID } = displaySet;
+  const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+  if (!studyMetadata) {
+    return;
+  }
+
+  const srDisplaySets = studyMetadata
+    .getDisplaySets()
+    .filter(ds => ds.Modality === 'SR');
+  if (srDisplaySets.length === 0) {
+    return;
+  }
+
+  const { measurements: _measurements } = srDisplaySets[0];
+  if (!_measurements || _measurements.length < 1) {
+    return;
+  }
+
+  const measurements = _measurements.filter(m => m.loaded === true);
+  const measurement = measurements[0];
+  if (!measurement) {
+    return;
+  }
+
+  srModule.setters.trackingUniqueIdentifiersForElement(
+    element,
+    measurements.map(measurement => measurement.TrackingUniqueIdentifier),
+    measurement
+  );
+
+  const { TrackingUniqueIdentifier } = measurement;
+  srModule.setters.activeTrackingUniqueIdentifierForElement(
+    element,
+    TrackingUniqueIdentifier
+  );
+
+  cs.updateImage(element);
+};
+
+export default checkForSRAnnotations;

extensions/cornerstone/src/tools/constants/scoordTypes.js

@@ -0,0 +1,8 @@
+export default {
+  POINT: 'POINT',
+  MULTIPOINT: 'MULTIPOINT',
+  POLYLINE: 'POLYLINE',
+  CIRCLE: 'CIRCLE',
+  ELLIPSE: 'ELLIPSE',
+  POLYGON: 'POLYGON',
+};

extensions/cornerstone/src/tools/constants/toolNames.js

@@ -0,0 +1,5 @@
+const TOOL_NAMES = {
+  DICOM_SR_DISPLAY_TOOL: 'DICOMSRDisplayTool',
+};
+
+export default TOOL_NAMES;

extensions/cornerstone/src/tools/id.js

@@ -0,0 +1,7 @@
+const id = 'org.ohif.dicom-sr';
+
+export default id;
+
+const SOPClassHandlerName = 'dicom-sr';
+const SOPClassHandlerId = `${id}.sopClassHandlerModule.${SOPClassHandlerName}`;
+export { SOPClassHandlerName, SOPClassHandlerId };

extensions/cornerstone/src/tools/initSRTools.js

@@ -0,0 +1,108 @@
+import cornerstoneTools from 'cornerstone-tools';
+import DICOMSRDisplayTool from './DICOMSRDisplayTool';
+import TOOL_NAMES from './constants/toolNames';
+import getToolAlias from './utils/getToolAlias';
+
+/**
+ * Initialize SR cornerstone tools.
+ *
+ * @param {*} targetElement
+ */
+const initSRTools = targetElement => {
+  const primaryToolId = 'Wwwc';
+  const toolAlias = getToolAlias(primaryToolId); // These are 1:1 for built-in only
+
+  // ~~ MAGIC
+  cornerstoneTools.addToolForElement(targetElement, DICOMSRDisplayTool);
+  cornerstoneTools.setToolEnabledForElement(
+    targetElement,
+    TOOL_NAMES.DICOM_SR_DISPLAY_TOOL
+  );
+
+  // ~~ Variants
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.LengthTool,
+    {
+      name: 'SRLength',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.ArrowAnnotateTool,
+    {
+      name: 'SRArrowAnnotate',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.BidirectionalTool,
+    {
+      name: 'SRBidirectional',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.EllipticalRoiTool,
+    {
+      name: 'SREllipticalRoi',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.RectangleRoiTool,
+    {
+      name: 'SRRectangleRoi',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.FreehandRoiTool,
+    {
+      name: 'SRFreehandRoi',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+
+  // ~~ Business as usual
+  cornerstoneTools.setToolActiveForElement(targetElement, 'PanMultiTouch', {
+    pointers: 2,
+  });
+  cornerstoneTools.setToolActiveForElement(targetElement, 'ZoomTouchPinch', {});
+
+  // TODO: Add always dashed tool alternative aliases
+  // TODO: or same name... alternative config?
+  cornerstoneTools.setToolActiveForElement(targetElement, toolAlias, {
+    mouseButtonMask: 1,
+  });
+  cornerstoneTools.setToolActiveForElement(targetElement, 'Pan', {
+    mouseButtonMask: 4,
+  });
+  cornerstoneTools.setToolActiveForElement(targetElement, 'Zoom', {
+    mouseButtonMask: 2,
+  });
+  cornerstoneTools.setToolActiveForElement(
+    targetElement,
+    'StackScrollMouseWheel',
+    {}
+  );
+};
+
+export default initSRTools;

extensions/cornerstone/src/tools/modules/dicomSRModule.js

@@ -0,0 +1,61 @@
+import cornerstone from 'cornerstone-core';
+
+const state = {
+  TrackingUniqueIdentifier: null,
+  trackingIdentifiersByEnabledElementUUID: {},
+};
+
+function setTrackingUniqueIdentifiersForElement(
+  element,
+  trackingUniqueIdentifiers,
+  activeIndex = 0
+) {
+  const enabledElement = cornerstone.getEnabledElement(element);
+  const { uuid } = enabledElement;
+
+  state.trackingIdentifiersByEnabledElementUUID[uuid] = {
+    trackingUniqueIdentifiers,
+    activeIndex,
+  };
+}
+
+function setActiveTrackingUniqueIdentifierForElement(
+  element,
+  TrackingUniqueIdentifier
+) {
+  const enabledElement = cornerstone.getEnabledElement(element);
+  const { uuid } = enabledElement;
+
+  const trackingIdentifiersForElement =
+    state.trackingIdentifiersByEnabledElementUUID[uuid];
+
+  if (trackingIdentifiersForElement) {
+    const activeIndex = trackingIdentifiersForElement.trackingUniqueIdentifiers.findIndex(
+      tuid => tuid === TrackingUniqueIdentifier
+    );
+
+    trackingIdentifiersForElement.activeIndex = activeIndex;
+  }
+}
+
+function getTrackingUniqueIdentifiersForElement(element) {
+  const enabledElement = cornerstone.getEnabledElement(element);
+  const { uuid } = enabledElement;
+
+  if (state.trackingIdentifiersByEnabledElementUUID[uuid]) {
+    return state.trackingIdentifiersByEnabledElementUUID[uuid];
+  }
+
+  return { trackingUniqueIdentifiers: [] };
+}
+
+export default {
+  state,
+  getters: {
+    trackingUniqueIdentifiersForElement: getTrackingUniqueIdentifiersForElement,
+  },
+  setters: {
+    trackingUniqueIdentifiersForElement: setTrackingUniqueIdentifiersForElement,
+    activeTrackingUniqueIdentifierForElement: setActiveTrackingUniqueIdentifierForElement,
+  },
+};

extensions/cornerstone/src/tools/utils/getToolAlias.js

@@ -0,0 +1,32 @@
+/**
+ * Get cornerstone tool alias.
+ *
+ * @param {string} toolName
+ * @returns tool alias
+ */
+export default function getToolAlias(toolName) {
+  let toolAlias = toolName;
+
+  switch (toolName) {
+    case 'Length':
+      toolAlias = 'SRLength';
+      break;
+    case 'Bidirectional':
+      toolAlias = 'SRBidirectional';
+      break;
+    case 'ArrowAnnotate':
+      toolAlias = 'SRArrowAnnotate';
+      break;
+    case 'EllipticalRoi':
+      toolAlias = 'SREllipticalRoi';
+      break;
+    case 'FreehandRoi':
+      toolAlias = 'SRFreehandRoi';
+      break;
+    case 'RectangleRoi':
+      toolAlias = 'SRRectangleRoi';
+      break;
+  }
+
+  return toolAlias;
+}

extensions/debugging/CHANGELOG.md

@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.3.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.3.1...@ohif/extension-debugging@0.3.2) (2022-03-10)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
 ## [0.3.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.3.0...@ohif/extension-debugging@0.3.1) (2021-12-02)
 
 **Note:** Version bump only for package @ohif/extension-debugging

extensions/debugging/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-debugging",
-  "version": "0.3.1",
+  "version": "0.3.2",
   "description": "OHIF extension for debugging.",
   "author": "OHIF",
   "license": "MIT",

extensions/debugging/src/DebugReportModal.css

@@ -24,3 +24,21 @@
   overflow: scroll;
   max-height: 300px;
 }
+
+.debug-overflowText {
+  margin: 0 auto;
+  max-width: 300px;
+  overflow-wrap: break-word;
+  word-wrap: break-word;
+  hyphens: auto;
+}
+
+.debug-overflowText-border {
+  margin: 0 auto;
+  max-width: 300px;
+  border: solid 2px #ccc;
+  padding: 12px;
+  overflow-wrap: break-word;
+  word-wrap: break-word;
+  hyphens: auto;
+}

extensions/debugging/src/DebugReportModal.js

@@ -2,6 +2,8 @@ import React from 'react';
 import { detect } from 'detect-browser';
 import './DebugReportModal.css';
 import { ToolbarButton } from '@ohif/ui';
+import { utils } from '@ohif/core';
+const { studyMetadataManager } = utils;
 
 const DubugReportModal = ({
   viewports,
@@ -70,7 +72,7 @@ const DubugReportModal = ({
     body += '== Viewport Layout ==\n';
     body += `Rows\t${numRows}\n`;
     body += `Columns\t${numColumns}\n\n`;
-    body += '== Viewports ==\n';
+    body += '== SeriesInstanceUIDs ==\n';
 
     Object.keys(viewportSpecificData).forEach(viewportIndex => {
       const vsd = viewportSpecificData[viewportIndex];
@@ -83,6 +85,40 @@ const DubugReportModal = ({
       body += `[${row},${column}]\t${vsd.SeriesInstanceUID}\n`;
     });
 
+    body += '== ReferencedSEGSeriesInstanceUIDs ==\n';
+
+    Object.keys(viewportSpecificData).forEach(viewportIndex => {
+      const displaySet = viewportSpecificData[viewportIndex];
+      const [
+        referencedDisplaySetsRef,
+        referencedDisplaySetsCount,
+      ] = _getReferencedSeriesInstanceUIDsString(displaySet, 'SEG');
+
+      const [row, column] = _viewportIndexToViewportPosition(
+        viewportIndex,
+        numColumns
+      );
+
+      body += `[${row},${column}]\t${referencedDisplaySetsRef}\n`;
+    });
+
+    body += '== ReferencedRTSTRUCTSeriesInstanceUIDs ==\n';
+
+    Object.keys(viewportSpecificData).forEach(viewportIndex => {
+      const displaySet = viewportSpecificData[viewportIndex];
+      const [
+        referencedDisplaySetsRef,
+        referencedDisplaySetsCount,
+      ] = _getReferencedSeriesInstanceUIDsString(displaySet, 'RTSTRUCT');
+
+      const [row, column] = _viewportIndexToViewportPosition(
+        viewportIndex,
+        numColumns
+      );
+
+      body += `[${row},${column}]\t${referencedDisplaySetsRef}\n`;
+    });
+
     return body;
   };
 
@@ -171,7 +207,7 @@ const getCurrentStudyUrl = () => {
       </tr>
       <tr>
         <td>URL</td>
-        <td>{window.location.href}</td>
+        <td className="debug-overflowText">{window.location.href}</td>
       </tr>
     </React.Fragment>
   );
@@ -222,6 +258,14 @@ const getLayout = viewports => {
         <th>SeriesInstanceUIDs</th>
       </tr>
       {getSeriesInstanceUIDsPerRow(viewports)}
+      <tr>
+        <th>ReferencedSEGSeriesInstanceUIDs</th>
+      </tr>
+      {getReferencedSEGSeriesInstanceUIDsPerRow(viewports)}
+      <tr>
+        <th>ReferencedRTSTRUCTSeriesInstanceUIDs</th>
+      </tr>
+      {getReferencedRTSTRUCTSeriesInstanceUIDsPerRow(viewports)}
     </React.Fragment>
   );
 };
@@ -256,6 +300,129 @@ const getBrowserInfo = () => {
   );
 };
 
+/**
+ * Returns DisplaySets that reference the target series, sorted by dateTime
+ *
+ * @param {string} StudyInstanceUID
+ * @param {string} SeriesInstanceUID
+ * @returns Array
+ */
+const _getReferencedDisplaysets = (
+  StudyInstanceUID,
+  SeriesInstanceUID,
+  Modality
+) => {
+  /* Referenced DisplaySets */
+  const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+  const referencedDisplaysets = studyMetadata.getDerivedDatasets({
+    referencedSeriesInstanceUID: SeriesInstanceUID,
+    Modality,
+  });
+
+  /* Sort */
+  referencedDisplaysets.sort((a, b) => {
+    const aNumber = Number(`${a.SeriesDate}${a.SeriesTime}`);
+    const bNumber = Number(`${b.SeriesDate}${b.SeriesTime}`);
+    return bNumber - aNumber;
+  });
+
+  return referencedDisplaysets;
+};
+
+const _getReferencedSeriesInstanceUIDsString = (displaySet, Modality) => {
+  const referencedDisplaySets = _getReferencedDisplaysets(
+    displaySet.StudyInstanceUID,
+    displaySet.SeriesInstanceUID,
+    Modality
+  );
+
+  let referencedDisplaySetsRef = 'None';
+  const referencedDisplaySetsCount = referencedDisplaySets.length;
+  if (referencedDisplaySetsCount !== 0) {
+    referencedDisplaySetsRef = '';
+    for (let i = 0; i < referencedDisplaySetsCount - 1; i++) {
+      referencedDisplaySetsRef +=
+        referencedDisplaySets[i].SeriesInstanceUID + ', ';
+    }
+    referencedDisplaySetsRef +=
+      referencedDisplaySets[referencedDisplaySetsCount - 1].SeriesInstanceUID;
+  }
+
+  return [referencedDisplaySetsRef, referencedDisplaySetsCount];
+};
+
+const getReferencedSEGSeriesInstanceUIDsPerRow = viewports => {
+  const { viewportSpecificData, numColumns } = viewports;
+
+  // NOTE viewportSpecificData is actually an object with numerical keys.
+  return Object.keys(viewportSpecificData).map(viewportIndex => {
+    const displaySet = viewportSpecificData[viewportIndex];
+    const [
+      referencedDisplaySetsRef,
+      referencedDisplaySetsCount,
+    ] = _getReferencedSeriesInstanceUIDsString(displaySet, 'SEG');
+
+    const [row, column] = _viewportIndexToViewportPosition(
+      viewportIndex,
+      numColumns
+    );
+
+    if (referencedDisplaySetsCount > 1) {
+      return (
+        <tr>
+          <td>{`[${row},${column}]`}</td>
+          <td className="debug-overflowText-border">
+            {referencedDisplaySetsRef}
+          </td>
+        </tr>
+      );
+    } else {
+      return (
+        <tr>
+          <td>{`[${row},${column}]`}</td>
+          <td className="debug-overflowText">{referencedDisplaySetsRef}</td>
+        </tr>
+      );
+    }
+  });
+};
+
+const getReferencedRTSTRUCTSeriesInstanceUIDsPerRow = viewports => {
+  const { viewportSpecificData, numColumns } = viewports;
+
+  // NOTE viewportSpecificData is actually an object with numerical keys.
+  return Object.keys(viewportSpecificData).map(viewportIndex => {
+    const displaySet = viewportSpecificData[viewportIndex];
+    const [
+      referencedDisplaySetsRef,
+      referencedDisplaySetsCount,
+    ] = _getReferencedSeriesInstanceUIDsString(displaySet, 'RTSTRUCT');
+
+    const [row, column] = _viewportIndexToViewportPosition(
+      viewportIndex,
+      numColumns
+    );
+
+    if (referencedDisplaySetsCount > 1) {
+      return (
+        <tr>
+          <td>{`[${row},${column}]`}</td>
+          <td className="debug-overflowText-border">
+            {referencedDisplaySetsRef}
+          </td>
+        </tr>
+      );
+    } else {
+      return (
+        <tr>
+          <td>{`[${row},${column}]`}</td>
+          <td className="debug-overflowText">{referencedDisplaySetsRef}</td>
+        </tr>
+      );
+    }
+  });
+};
+
 const getSeriesInstanceUIDsPerRow = viewports => {
   const { viewportSpecificData, numColumns } = viewports;
 

extensions/dicom-html/CHANGELOG.md

@@ -3,6 +3,38 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.3.18](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.17...@ohif/extension-dicom-html@1.3.18) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.17](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.16...@ohif/extension-dicom-html@1.3.17) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.16](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.15...@ohif/extension-dicom-html@1.3.16) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.14...@ohif/extension-dicom-html@1.3.15) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
 ## [1.3.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.13...@ohif/extension-dicom-html@1.3.14) (2021-12-02)
 
 **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": "1.3.14",
+  "version": "1.3.18",
   "description": "OHIF extension for rendering structured reports to HTML",
   "author": "OHIF",
   "license": "MIT",
@@ -29,7 +29,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "0.19.1",
+    "dcmjs": "0.19.4",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-html/src/OHIFDicomHtmlSopClassHandler.js

@@ -5,11 +5,12 @@ const SOP_CLASS_UIDS = {
   BASIC_TEXT_SR: '1.2.840.10008.5.1.4.1.1.88.11',
   ENHANCED_SR: '1.2.840.10008.5.1.4.1.1.88.22',
   COMPREHENSIVE_SR: '1.2.840.10008.5.1.4.1.1.88.33',
+  COMPREHENSIVE_3D_SR: '1.2.840.10008.5.1.4.1.1.88.34',
   PROCEDURE_LOG_STORAGE: '1.2.840.10008.5.1.4.1.1.88.40',
   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',
+  ACQUISITION_CONTEXT_SR_STORAGE: '1.2.840.10008.5.1.4.1.1.88.71'
 };
 
 const sopClassUIDs = Object.values(SOP_CLASS_UIDS);
@@ -46,6 +47,8 @@ const OHIFDicomHtmlSopClassHandler = {
       SeriesTime,
       SeriesNumber,
       authorizationHeaders,
+      sopClassUids: sopClassUIDs,
+      images: series._instances,
     };
   },
 };

extensions/dicom-pdf/CHANGELOG.md

@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.1.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.1.1...@ohif/extension-dicom-pdf@1.1.2) (2022-01-29)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
 ## [1.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.1.0...@ohif/extension-dicom-pdf@1.1.1) (2021-12-02)
 
 **Note:** Version bump only for package @ohif/extension-dicom-pdf

extensions/dicom-pdf/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-pdf",
-  "version": "1.1.1",
+  "version": "1.1.2",
   "description": "OHIF extension for Dicom PDF",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-pdf/src/DicomPDFViewport.js

@@ -33,6 +33,7 @@ class DicomPDFViewport extends Component {
 
   static propTypes = {
     byteArray: TypedArrayProp.uint8,
+    rawPdf: PropTypes.bool,
     useNative: PropTypes.bool,
     viewportData: PropTypes.object,
     activeViewportIndex: PropTypes.number,
@@ -45,7 +46,8 @@ class DicomPDFViewport extends Component {
   };
 
   async componentDidMount() {
-    const dataSet = this.parseByteArray(this.props.byteArray);
+    const { rawPdf } = this.props
+    const dataSet = !rawPdf && this.parseByteArray(this.props.byteArray);
     const fileURL = this.getPDFFileUrl(dataSet, this.props.byteArray);
 
     this.setState(state => ({ ...state, fileURL }));

extensions/dicom-pdf/src/OHIFDicomPDFViewport.js

@@ -3,6 +3,7 @@ import PropTypes from 'prop-types';
 import OHIF from '@ohif/core';
 import OHIFComponentPlugin from './OHIFComponentPlugin.js';
 import DicomPDFViewport from './DicomPDFViewport';
+import { str2ab } from '@ohif/core';
 
 const { DicomLoaderService } = OHIF.utils;
 
@@ -18,6 +19,7 @@ class OHIFDicomPDFViewport extends Component {
 
   state = {
     byteArray: null,
+    rawPdf: false,
     error: null,
   };
 
@@ -34,6 +36,15 @@ class OHIFDicomPDFViewport extends Component {
   componentDidMount() {
     const { displaySet, studies } = this.props.viewportData;
 
+    if (displaySet.metadata && displaySet.metadata.EncapsulatedDocument) {
+      const { InlineBinary, BulkDataURI } = displaySet.metadata.EncapsulatedDocument;
+      if (InlineBinary) {
+        const inlineBinaryData = atob(InlineBinary);
+        const byteArray = str2ab(inlineBinaryData);
+        this.setState({ byteArray, rawPdf: true });
+        return;
+      }
+    }
     DicomLoaderService.findDicomDataPromise(displaySet, studies).then(
       data => this.setState({ byteArray: new Uint8Array(data) }),
       error => {
@@ -49,15 +60,16 @@ class OHIFDicomPDFViewport extends Component {
       viewportIndex,
       activeViewportIndex,
     } = this.props;
-    const { byteArray, error } = this.state;
+    const { byteArray, error, rawPdf } = this.state;
     const { id, init, destroy } = OHIFDicomPDFViewport;
     const pluginProps = { id, init, destroy };
 
     return (
       <OHIFComponentPlugin {...pluginProps}>
-        {byteArray && (
+        {(byteArray) && (
           <DicomPDFViewport
             byteArray={byteArray}
+            rawPdf={rawPdf}
             setViewportActive={setViewportActive}
             viewportIndex={viewportIndex}
             activeViewportIndex={activeViewportIndex}

extensions/dicom-rt/CHANGELOG.md

@@ -3,6 +3,38 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.7.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.7...@ohif/extension-dicom-rt@0.7.8) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.6...@ohif/extension-dicom-rt@0.7.7) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.5...@ohif/extension-dicom-rt@0.7.6) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.4...@ohif/extension-dicom-rt@0.7.5) (2022-01-19)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
 ## [0.7.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.3...@ohif/extension-dicom-rt@0.7.4) (2021-12-02)
 
 **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": "0.7.4",
+  "version": "0.7.8",
   "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": "^2.6.1",
     "cornerstone-tools": "^6.0.6",
-    "dcmjs": "0.19.1",
+    "dcmjs": "0.19.4",
     "gl-matrix": "^3.3.0",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",

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

@@ -81,13 +81,10 @@ const RTPanel = ({
   useEffect(() => {
     updateStructureSets();
 
-    document.addEventListener('extensiondicomrtrtloaded', updateStructureSets);
+    document.addEventListener('rt-panel-tab-updated', updateStructureSets);
 
     return () => {
-      document.removeEventListener(
-        'extensiondicomrtrtloaded',
-        updateStructureSets
-      );
+      document.removeEventListener('rt-panel-tab-updated', updateStructureSets);
     };
   }, []);
 

extensions/dicom-segmentation/CHANGELOG.md

@@ -3,6 +3,30 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.7.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.7...@ohif/extension-dicom-segmentation@0.7.8) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.6...@ohif/extension-dicom-segmentation@0.7.7) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.5...@ohif/extension-dicom-segmentation@0.7.6) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
 ## [0.7.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.4...@ohif/extension-dicom-segmentation@0.7.5) (2021-12-02)
 
 **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": "0.7.5",
+  "version": "0.7.8",
   "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": "^2.6.1",
     "cornerstone-tools": "^6.0.6",
-    "dcmjs": "0.19.1",
+    "dcmjs": "0.19.4",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-segmentation/src/getOHIFDicomSegSopClassHandler.js

@@ -150,10 +150,16 @@ export default function getSopClassHandlerModule({ servicesManager }) {
 }
 
 function _parseSeg(arrayBuffer, imageIds) {
+  const skipOverlapping = false;
+  const tolerance = 1e-2;
+  const cornerstoneToolsVersion = 4;
   return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
     imageIds,
     arrayBuffer,
-    cornerstone.metaData
+    cornerstone.metaData,
+    skipOverlapping,
+    tolerance,
+    cornerstoneToolsVersion
   );
 }
 

extensions/dicom-tag-browser/CHANGELOG.md

@@ -3,6 +3,30 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.2.19](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.18...@ohif/extension-dicom-tag-browser@0.2.19) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.18](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.17...@ohif/extension-dicom-tag-browser@0.2.18) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.17](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.16...@ohif/extension-dicom-tag-browser@0.2.17) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
 ## [0.2.16](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.15...@ohif/extension-dicom-tag-browser@0.2.16) (2021-12-10)
 
 **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": "0.2.16",
+  "version": "0.2.19",
   "description": "OHIF extension for checking DICOM headers.",
   "author": "OHIF",
   "license": "MIT",
@@ -28,7 +28,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^2.6.0",
-    "dcmjs": "0.19.1",
+    "dcmjs": "0.19.4",
     "react": "^16.8.6"
   },
   "dependencies": {

extensions/vtk/CHANGELOG.md

@@ -3,6 +3,54 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.12.16](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.15...@ohif/extension-vtk@1.12.16) (2022-02-15)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.14...@ohif/extension-vtk@1.12.15) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.13...@ohif/extension-vtk@1.12.14) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.12...@ohif/extension-vtk@1.12.13) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.11...@ohif/extension-vtk@1.12.12) (2022-01-29)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.10...@ohif/extension-vtk@1.12.11) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
 ## [1.12.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.9...@ohif/extension-vtk@1.12.10) (2022-01-13)
 
 **Note:** Version bump only for package @ohif/extension-vtk

extensions/vtk/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-vtk",
-  "version": "1.12.10",
+  "version": "1.12.16",
   "description": "OHIF extension for VTK.js",
   "author": "OHIF",
   "license": "MIT",
@@ -35,7 +35,7 @@
     "cornerstone-core": "^2.6.1",
     "cornerstone-tools": "^6.0.6",
     "cornerstone-wado-image-loader": "^4.1.0",
-    "dcmjs": "0.19.1",
+    "dcmjs": "0.19.4",
     "dicom-parser": "^1.8.11",
     "i18next": "^17.0.3",
     "i18next-browser-languagedetector": "^3.0.1",
@@ -53,8 +53,8 @@
     "react-vtkjs-viewport": "^0.14.4"
   },
   "devDependencies": {
-    "@ohif/core": "^2.16.6",
-    "@ohif/ui": "^1.10.5",
+    "@ohif/core": "^2.16.12",
+    "@ohif/ui": "^1.10.6",
     "cornerstone-tools": "^6.0.6",
     "cornerstone-wado-image-loader": "^4.1.0",
     "dicom-parser": "^1.8.11",

lerna-debug.log

@@ -0,0 +1,23 @@
+0 silly argv {
+0 silly argv   _: [ 'run' ],
+0 silly argv   stream: true,
+0 silly argv   lernaVersion: '3.18.3',
+0 silly argv   '$0': 'node_modules/.bin/lerna',
+0 silly argv   script: 'dev:viewer'
+0 silly argv }
+1 notice cli v3.18.3
+2 verbose rootPath /home/davide/Development/OIHF/Viewers
+3 info versioning independent
+4 info Executing command in 1 package: "yarn run dev:viewer"
+5 silly npmRunScript.stream [ 'dev:viewer', [], '@ohif/viewer' ]
+6 silly getExecOpts /home/davide/Development/OIHF/Viewers/platform/viewer undefined
+7 error MaxBufferError: stderr maxBuffer exceeded
+7 error     at PassThrough.<anonymous> (/home/davide/Development/OIHF/Viewers/node_modules/get-stream/index.js:41:19)
+7 error     at PassThrough.emit (events.js:412:35)
+7 error     at addChunk (internal/streams/readable.js:290:12)
+7 error     at readableAddChunk (internal/streams/readable.js:261:11)
+7 error     at PassThrough.Readable.push (internal/streams/readable.js:204:10)
+7 error     at PassThrough.Transform.push (internal/streams/transform.js:166:32)
+7 error     at PassThrough.afterTransform (internal/streams/transform.js:101:10)
+7 error     at PassThrough._transform (internal/streams/passthrough.js:46:3)
+7 error     at PassThrough.Transform._read (internal/streams/transform.js:205:10)

package.json

@@ -56,6 +56,7 @@
     "@babel/preset-env": "^7.5.0",
     "@babel/preset-react": "^7.0.0",
     "@percy/cypress": "^2.2.0",
+    "@webpack-cli/serve": "^1.6.1",
     "babel-eslint": "9.x",
     "babel-loader": "^8.0.6",
     "babel-plugin-inline-react-svg": "1.1.0",
@@ -104,8 +105,8 @@
     "stylus-loader": "^3.0.2",
     "terser-webpack-plugin": "^2.1.0",
     "webpack": "^4.35.2",
-    "webpack-cli": "^3.3.5",
-    "webpack-dev-server": "^3.7.2",
+    "webpack-cli": "^4.9.2",
+    "webpack-dev-server": "^4.7.3",
     "webpack-hot-middleware": "^2.25.0",
     "webpack-merge": "^4.2.1",
     "workbox-webpack-plugin": "^5.0.0-beta.1",
@@ -123,6 +124,7 @@
     ]
   },
   "resolutions": {
+    "**/node-gyp": "8.4.1",
     "**/@babel/runtime": "7.5.5"
   }
 }

platform/core/CHANGELOG.md

@@ -3,6 +3,54 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.16.12](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.11...@ohif/core@2.16.12) (2022-02-15)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.11](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.10...@ohif/core@2.16.11) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.10](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.9...@ohif/core@2.16.10) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.9](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.8...@ohif/core@2.16.9) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.8](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.7...@ohif/core@2.16.8) (2022-01-29)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.7](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.6...@ohif/core@2.16.7) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
 ## [2.16.6](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.5...@ohif/core@2.16.6) (2022-01-13)
 
 **Note:** Version bump only for package @ohif/core

platform/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/core",
-  "version": "2.16.6",
+  "version": "2.16.12",
   "description": "Generic business logic for web-based medical imaging applications",
   "author": "OHIF Core Team",
   "license": "MIT",
@@ -39,12 +39,13 @@
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "ajv": "^6.10.0",
-    "dcmjs": "0.19.1",
+    "dcmjs": "0.19.4",
     "dicomweb-client": "^0.8.3",
-    "immer": "6.0.2",
+    "immer": "9.0.12",
     "isomorphic-base64": "^1.0.2",
     "lodash.clonedeep": "^4.5.0",
     "lodash.merge": "^4.6.1",
+    "mathjs": "^10.1.0",
     "mousetrap": "^1.6.3",
     "retry": "^0.12.0",
     "validate.js": "^0.12.0"

platform/core/src/DICOMSR/SCOORD3D/constants/scoordTypes.js

@@ -0,0 +1,8 @@
+export default {
+  POINT: 'POINT',
+  MULTIPOINT: 'MULTIPOINT',
+  POLYLINE: 'POLYLINE',
+  CIRCLE: 'CIRCLE',
+  ELLIPSE: 'ELLIPSE',
+  POLYGON: 'POLYGON',
+};

platform/core/src/DICOMSR/SCOORD3D/constants/toolNames.js

@@ -0,0 +1,5 @@
+const TOOL_NAMES = {
+  DICOM_SR_DISPLAY_TOOL: 'DICOMSRDisplayTool',
+};
+
+export default TOOL_NAMES;

platform/core/src/DICOMSR/SCOORD3D/enums.js

@@ -0,0 +1,29 @@
+export const CodeNameCodeSequenceValues = {
+  ImagingMeasurementReport: '126000',
+  ImageLibrary: '111028',
+  ImagingMeasurements: '126010',
+  MeasurementGroup: '125007',
+  ImageLibraryGroup: '126200',
+  TrackingUniqueIdentifier: '112040',
+  TrackingIdentifier: '112039',
+  Finding: '121071',
+  FindingSite: 'G-C0E3', // SRT
+  CornerstoneFreeText: 'CORNERSTONEFREETEXT', // CST4
+  Score: '246262008',
+};
+
+export const RELATIONSHIP_TYPE = {
+  INFERRED_FROM: 'INFERRED FROM',
+  SELECTED_FROM: 'SELECTED FROM',
+};
+
+export const CodingSchemeDesignators = {
+  SRT: 'SRT',
+  cornerstoneTools4: 'CST4',
+};
+
+export default {
+  CodeNameCodeSequenceValues,
+  RELATIONSHIP_TYPE,
+  CodingSchemeDesignators,
+};

platform/core/src/DICOMSR/SCOORD3D/parseSCOORD3D.js

@@ -0,0 +1,155 @@
+import { ImageSet } from '../../classes';
+import getMeasurements from './utils/getMeasurements';
+import getReferencedImagesList from './utils/getReferencedImagesList';
+import isRehydratable from './utils/isRehydratable';
+import addMeasurement from './utils/addMeasurement';
+
+const parseSCOORD3D = ({ servicesManager, displaySets }) => {
+  const { MeasurementService } = servicesManager.services;
+
+  const srDisplaySets = displaySets.filter(ds => ds.Modality === 'SR');
+
+  srDisplaySets.forEach(srDisplaySet => {
+    const firstInstance = srDisplaySet.metadata;
+    if (!firstInstance) {
+      return;
+    }
+
+    const { ContentSequence } = firstInstance;
+
+    srDisplaySet.referencedImages = getReferencedImagesList(ContentSequence);
+    srDisplaySet.measurements = getMeasurements(ContentSequence, srDisplaySet);
+    const mappings = MeasurementService.getSourceMappings(
+      'CornerstoneTools',
+      '4'
+    );
+
+    srDisplaySet.isHydrated = false;
+    srDisplaySet.isRehydratable = isRehydratable(srDisplaySet, mappings);
+    srDisplaySet.isLoaded = true;
+
+    const imageDisplaySets = displaySets.filter(
+      ds =>
+        ds.Modality !== 'SR' &&
+        ds.Modality !== 'SEG' &&
+        ds.Modality !== 'RTSTRUCT' &&
+        ds.Modality !== 'RTDOSE'
+    );
+    imageDisplaySets.forEach(imageDisplaySet => {
+      // Check currently added displaySets and add measurements if the sources exist.
+      checkIfCanAddMeasurementsToDisplaySet(srDisplaySet, imageDisplaySet);
+    });
+  });
+};
+
+const checkIfCanAddMeasurementsToDisplaySet = (
+  srDisplaySet,
+  imageDisplaySet
+) => {
+  let measurements = srDisplaySet.measurements;
+
+  /**
+   * Look for image sets.
+   * This also filters out _this_ displaySet, as it is not an image set.
+   */
+  if (!(imageDisplaySet instanceof ImageSet)) {
+    return;
+  }
+
+  const { sopClassUIDs, images } = imageDisplaySet;
+
+  /**
+   * Filter measurements that references the correct sop class.
+   */
+  measurements = measurements.filter(measurement => {
+    return measurement.coords.some(coord => {
+      if (coord.ReferencedSOPSequence === undefined) {
+        /** we miss the referenced information. We can compare the annotation SCOORD3D coordinates with
+         * the ImagePatientPosition of the frames. However (WARNING!!!),
+         * if more than a source series is present, this logic can find the wrong frame
+         * (i.e. two source series, with the same frameOfReferenceUID,
+         * that have each a frame with the same ImagePositionPatient of the annotation 3D coordinates)
+         */
+        for (let i = 0; i < images.length; ++i) {
+          const imageMetadata = images[i].getData().metadata;
+          if (
+            imageMetadata.FrameOfReferenceUID !==
+            coord.ReferencedFrameOfReferenceSequence
+          ) {
+            continue;
+          }
+
+          let sliceNormal = [0, 0, 0];
+          const orientation = imageMetadata.ImageOrientationPatient;
+          sliceNormal[0] =
+            orientation[1] * orientation[5] - orientation[2] * orientation[4];
+          sliceNormal[1] =
+            orientation[2] * orientation[3] - orientation[0] * orientation[5];
+          sliceNormal[2] =
+            orientation[0] * orientation[4] - orientation[1] * orientation[3];
+
+          let distanceAlongNormal = 0;
+          for (let j = 0; j < 3; ++j) {
+            distanceAlongNormal +=
+              sliceNormal[j] * imageMetadata.ImagePositionPatient[j];
+          }
+
+          // assuming 1 mm tolerance
+          if (Math.abs(distanceAlongNormal - coord.GraphicData[2]) > 1) {
+            continue;
+          }
+
+          coord.ReferencedSOPSequence = {
+            ReferencedSOPClassUID: imageMetadata.SOPClassUID,
+            ReferencedSOPInstanceUID: imageMetadata.SOPInstanceUID,
+          };
+
+          break;
+        }
+
+        if (coord.ReferencedSOPSequence === undefined) {
+          return false;
+        }
+      }
+
+      return sopClassUIDs.includes(
+        coord.ReferencedSOPSequence.ReferencedSOPClassUID
+      );
+    });
+  });
+
+  /**
+   * New display set doesn't have measurements that references the correct sop class.
+   */
+  if (measurements.length === 0) {
+    return;
+  }
+
+  const imageIds = images.map(i => i.getImageId());
+  const SOPInstanceUIDs = images.map(i => i.SOPInstanceUID);
+  measurements.forEach(measurement => {
+    const { coords } = measurement;
+
+    coords.forEach(coord => {
+      if (coord.ReferencedSOPSequence !== undefined) {
+        const imageIndex = SOPInstanceUIDs.findIndex(
+          SOPInstanceUID =>
+            SOPInstanceUID ===
+            coord.ReferencedSOPSequence.ReferencedSOPInstanceUID
+        );
+        if (imageIndex > -1) {
+          const imageId = imageIds[imageIndex];
+          const imageMetadata = images[imageIndex].getData().metadata;
+          addMeasurement(
+            measurement,
+            imageId,
+            imageMetadata,
+            imageDisplaySet.displaySetInstanceUID
+          );
+        }
+      }
+    });
+  });
+};
+
+export default parseSCOORD3D;

platform/core/src/DICOMSR/SCOORD3D/utils/addMeasurement.js

@@ -0,0 +1,102 @@
+import csTools from 'cornerstone-tools';
+import OHIF from '../../../';
+
+/** Internal imports */
+import TOOL_NAMES from '../constants/toolNames';
+import getRenderableData from './getRenderableData';
+
+const globalImageIdSpecificToolStateManager =
+  csTools.globalImageIdSpecificToolStateManager;
+
+/**
+ * Add a measurement to a display set.
+ *
+ * @param {*} measurement
+ * @param {*} imageId
+ * @param {*} displaySetInstanceUID
+ */
+export default function addMeasurement(
+  measurement,
+  imageId,
+  imageMetadata,
+  displaySetInstanceUID
+) {
+  // TODO -> Render rotated ellipse .
+  const toolName = TOOL_NAMES.DICOM_SR_DISPLAY_TOOL;
+
+  const measurementData = {
+    TrackingUniqueIdentifier: measurement.TrackingUniqueIdentifier,
+    renderableData: {},
+    labels: measurement.labels,
+  };
+
+  measurement.coords.forEach(coord => {
+    const { GraphicType, GraphicData, ValueType } = coord;
+
+    if (measurementData.renderableData[GraphicType] === undefined) {
+      measurementData.renderableData[GraphicType] = [];
+    }
+    measurementData.renderableData[GraphicType].push(
+      getRenderableData(GraphicType, GraphicData, ValueType, imageMetadata)
+    );
+  });
+
+  const toolState = globalImageIdSpecificToolStateManager.saveToolState();
+
+  if (toolState[imageId] === undefined) {
+    toolState[imageId] = {};
+  }
+
+  const imageIdToolState = toolState[imageId];
+
+  // If we don't have tool state for this type of tool, add an empty object
+  if (imageIdToolState[toolName] === undefined) {
+    imageIdToolState[toolName] = {
+      data: [],
+    };
+  }
+
+  const toolData = imageIdToolState[toolName];
+
+  measurementData.description = `Read-only annotation`;
+  measurementData.isReadOnly = true;
+  toolData.data.push(measurementData);
+
+  addToMeasurementApi({ measurementData, toolName, imageId });
+
+  measurement.loaded = true;
+  measurement.imageId = imageId;
+  measurement.displaySetInstanceUID = displaySetInstanceUID;
+
+  // Remove the unneeded coord now its processed, but keep the SOPInstanceUID.
+  // NOTE: We assume that each SCOORD in the MeasurementGroup maps onto one frame,
+  // It'd be super werid if it didn't anyway as a SCOORD.
+  measurement.ReferencedSOPInstanceUID =
+    measurement.coords[0].ReferencedSOPSequence.ReferencedSOPInstanceUID;
+
+  return measurement;
+}
+
+const addToMeasurementApi = ({ measurementData, toolName, imageId }) => {
+  const measurementApi = OHIF.measurements.MeasurementApi.Instance;
+
+  const toolType = toolName;
+  const collection = measurementApi.tools[toolType];
+  if (!collection) return;
+  if (!measurementData || measurementData.cancelled) return;
+
+  const imageAttributes = OHIF.measurements.getImageAttributes(null, imageId);
+  const measurement = Object.assign({}, measurementData, imageAttributes, {
+    lesionNamingNumber: measurementData.lesionNamingNumber,
+    userId: OHIF.user.getUserId(),
+    toolType,
+  });
+
+  const addedMeasurement = measurementApi.addMeasurement(toolType, measurement);
+  Object.assign(measurementData, addedMeasurement);
+
+  const measurementLabel = OHIF.measurements.getLabel(measurementData);
+  if (measurementLabel) {
+    measurementData.labels = [measurementLabel];
+  }
+};

platform/core/src/DICOMSR/SCOORD3D/utils/getCoordsFromSCOORDOrSCOORD3D.js

@@ -0,0 +1,31 @@
+const getCoordsFromSCOORDOrSCOORD3D = (graphicItem, displaySet) => {
+  const { ValueType, RelationshipType, GraphicType, GraphicData } = graphicItem;
+
+  // if (RelationshipType !== RELATIONSHIP_TYPE.INFERRED_FROM) {
+  //   console.warn(
+  //     `Relationshiptype === ${RelationshipType}. Cannot deal with NON TID-1400 SCOORD group with RelationshipType !== "INFERRED FROM."`
+  //   );
+  //   return;
+  // }
+
+  const coords = { ValueType, GraphicType, GraphicData };
+
+  // ContentSequence has length of 1 as RelationshipType === 'INFERRED FROM'
+  if (ValueType === 'SCOORD') {
+    const { ReferencedSOPSequence } = graphicItem.ContentSequence;
+    coords.ReferencedSOPSequence = ReferencedSOPSequence;
+  } else if (ValueType === 'SCOORD3D') {
+    if (graphicItem.ReferencedFrameOfReferenceUID) {
+      coords.ReferencedFrameOfReferenceSequence = graphicItem.ReferencedFrameOfReferenceUID;
+    } else if (graphicItem.ContentSequence) {
+      const {
+        ReferencedFrameOfReferenceSequence,
+      } = graphicItem.ContentSequence;
+      coords.ReferencedFrameOfReferenceSequence = ReferencedFrameOfReferenceSequence;
+    }
+  }
+
+  return coords;
+};
+
+export default getCoordsFromSCOORDOrSCOORD3D;

platform/core/src/DICOMSR/SCOORD3D/utils/getLabelFromMeasuredValueSequence.js

@@ -0,0 +1,19 @@
+const getLabelFromMeasuredValueSequence = (
+  ConceptNameCodeSequence,
+  MeasuredValueSequence
+) => {
+  const { CodeMeaning } = ConceptNameCodeSequence;
+  const { NumericValue, MeasurementUnitsCodeSequence } = MeasuredValueSequence;
+  const { CodeValue } = MeasurementUnitsCodeSequence;
+
+  const formatedNumericValue = NumericValue
+    ? Number(NumericValue).toFixed(1)
+    : '';
+
+  return {
+    label: CodeMeaning,
+    value: `${formatedNumericValue} ${CodeValue}`,
+  }; // E.g. Long Axis: 31.0 mm
+};
+
+export default getLabelFromMeasuredValueSequence;

platform/core/src/DICOMSR/SCOORD3D/utils/getMeasurements.js

@@ -0,0 +1,47 @@
+import { CodeNameCodeSequenceValues } from '../enums';
+import getSequenceAsArray from './getSequenceAsArray';
+import getMergedContentSequencesByTrackingUniqueIdentifiers from './getMergedContentSequencesByTrackingUniqueIdentifiers';
+import processMeasurement from './processMeasurement';
+
+const getMeasurements = (
+  ImagingMeasurementReportContentSequence,
+  displaySet
+) => {
+  const ImagingMeasurements = ImagingMeasurementReportContentSequence.find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.ImagingMeasurements
+  );
+
+  const MeasurementGroups = getSequenceAsArray(
+    ImagingMeasurements.ContentSequence
+  ).filter(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.MeasurementGroup
+  );
+
+  const mergedContentSequencesByTrackingUniqueIdentifiers = getMergedContentSequencesByTrackingUniqueIdentifiers(
+    MeasurementGroups
+  );
+
+  let measurements = [];
+
+  Object.keys(mergedContentSequencesByTrackingUniqueIdentifiers).forEach(
+    trackingUniqueIdentifier => {
+      const mergedContentSequence =
+        mergedContentSequencesByTrackingUniqueIdentifiers[
+          trackingUniqueIdentifier
+        ];
+
+      const measurement = processMeasurement(mergedContentSequence, displaySet);
+      if (measurement) {
+        measurements.push(measurement);
+      }
+    }
+  );
+
+  return measurements;
+};
+
+export default getMeasurements;

platform/core/src/DICOMSR/SCOORD3D/utils/getMergedContentSequencesByTrackingUniqueIdentifiers.js

@@ -0,0 +1,54 @@
+import getSequenceAsArray from './getSequenceAsArray';
+import { CodeNameCodeSequenceValues } from '../enums';
+
+const getMergedContentSequencesByTrackingUniqueIdentifiers = MeasurementGroups => {
+  const mergedContentSequencesByTrackingUniqueIdentifiers = {};
+
+  MeasurementGroups.forEach(MeasurementGroup => {
+    const ContentSequence = getSequenceAsArray(
+      MeasurementGroup.ContentSequence
+    );
+
+    const TrackingUniqueIdentifierItem = ContentSequence.find(
+      item =>
+        item.ConceptNameCodeSequence.CodeValue ===
+        CodeNameCodeSequenceValues.TrackingUniqueIdentifier
+    );
+
+    if (!TrackingUniqueIdentifierItem) {
+      console.warn(
+        'No Tracking Unique Identifier, skipping ambiguous measurement.'
+      );
+    }
+
+    const trackingUniqueIdentifier = TrackingUniqueIdentifierItem.UID;
+
+    if (
+      mergedContentSequencesByTrackingUniqueIdentifiers[
+        trackingUniqueIdentifier
+      ] === undefined
+    ) {
+      // Add the full ContentSequence
+      mergedContentSequencesByTrackingUniqueIdentifiers[
+        trackingUniqueIdentifier
+      ] = [...ContentSequence];
+    } else {
+      // Add the ContentSequence minus the tracking identifier, as we have this
+      // Information in the merged ContentSequence anyway.
+      ContentSequence.forEach(item => {
+        if (
+          item.ConceptNameCodeSequence.CodeValue !==
+          CodeNameCodeSequenceValues.TrackingUniqueIdentifier
+        ) {
+          mergedContentSequencesByTrackingUniqueIdentifiers[
+            trackingUniqueIdentifier
+          ].push(item);
+        }
+      });
+    }
+  });
+
+  return mergedContentSequencesByTrackingUniqueIdentifiers;
+};
+
+export default getMergedContentSequencesByTrackingUniqueIdentifiers;

platform/core/src/DICOMSR/SCOORD3D/utils/getReferencedImagesList.js

@@ -0,0 +1,43 @@
+import getSequenceAsArray from './getSequenceAsArray';
+import { CodeNameCodeSequenceValues } from '../enums';
+
+const getReferencedImagesList = ImagingMeasurementReportContentSequence => {
+  const referencedImages = [];
+
+  const ImageLibrary = ImagingMeasurementReportContentSequence.find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.ImageLibrary
+  );
+
+  if (!ImageLibrary.ContentSequence) {
+    return referencedImages;
+  }
+
+  const ImageLibraryGroup = getSequenceAsArray(
+    ImageLibrary.ContentSequence
+  ).find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.ImageLibraryGroup
+  );
+
+  getSequenceAsArray(ImageLibraryGroup.ContentSequence).forEach(item => {
+    const { ReferencedSOPSequence } = item;
+    if (ReferencedSOPSequence) {
+      const {
+        ReferencedSOPClassUID,
+        ReferencedSOPInstanceUID,
+      } = ReferencedSOPSequence;
+
+      referencedImages.push({
+        ReferencedSOPClassUID,
+        ReferencedSOPInstanceUID,
+      });
+    }
+  });
+
+  return referencedImages;
+};
+
+export default getReferencedImagesList;

platform/core/src/DICOMSR/SCOORD3D/utils/getRenderableData.js

@@ -0,0 +1,192 @@
+import csMath from 'cornerstone-math';
+import SCOORD_TYPES from '../constants/scoordTypes';
+import { inv } from 'mathjs';
+
+const getRenderableData = (
+  GraphicType,
+  GraphicData,
+  ValueType,
+  imageMetadata
+) => {
+  let renderableData;
+
+  const orientation = imageMetadata.ImageOrientationPatient;
+  const position = imageMetadata.ImagePositionPatient;
+  const pixelSpacing = imageMetadata.PixelSpacing;
+  const sliceSpacing = imageMetadata.SliceThickness
+    ? imageMetadata.SliceThickness
+    : 1;
+  //  https://nipy.org/nibabel/dicom/dicom_orientation.html
+  const M = [
+    [
+      orientation[0] * pixelSpacing[0],
+      orientation[3] * pixelSpacing[1],
+      sliceSpacing,
+      position[0],
+    ],
+    [
+      orientation[1] * pixelSpacing[0],
+      orientation[4] * pixelSpacing[1],
+      sliceSpacing,
+      position[1],
+    ],
+    [
+      orientation[2] * pixelSpacing[0],
+      orientation[5] * pixelSpacing[1],
+      sliceSpacing,
+      position[2],
+    ],
+    [0, 0, 0, 1],
+  ];
+
+  // we need to go from 3D to pixel (cornerstone2D works in pixel coordinates),
+  // we take the inverse.
+  const M1 = inv(M);
+
+  const worldToIJK = (point, M1) => {
+    const worldPoint = {
+      x:
+        M1[0][0] * point.x + M1[0][1] * point.y + M1[0][2] * point.z + M1[0][3],
+      y:
+        M1[1][0] * point.x + M1[1][1] * point.y + M1[1][2] * point.z + M1[1][3],
+      z:
+        M1[2][0] * point.x + M1[2][1] * point.y + M1[2][2] * point.z + M1[2][3],
+    };
+    return worldPoint;
+  };
+
+  // https://dicom.innolitics.com/ciods/procedure-log/sr-document-content/00700023
+  switch (GraphicType) {
+    case SCOORD_TYPES.POINT:
+      renderableData = [];
+
+      if (ValueType === 'SCOORD3D') {
+        for (let i = 0; i < GraphicData.length; i += 3) {
+          const point = {
+            x: GraphicData[i],
+            y: GraphicData[i + 1],
+            z: GraphicData[i + 2],
+          };
+
+          renderableData.push(worldToIJK(point, M1));
+        }
+      } else {
+        for (let i = 0; i < GraphicData.length; i += 2) {
+          renderableData.push({ x: GraphicData[i], y: GraphicData[i + 1] });
+        }
+      }
+
+      break;
+    case SCOORD_TYPES.MULTIPOINT:
+      renderableData = [];
+
+      if (ValueType === 'SCOORD3D') {
+        for (let i = 0; i < GraphicData.length; i += 3) {
+          const point = {
+            x: GraphicData[i],
+            y: GraphicData[i + 1],
+            z: GraphicData[i + 2],
+          };
+
+          renderableData.push(worldToIJK(point, M1));
+        }
+      } else {
+        for (let i = 0; i < GraphicData.length; i += 2) {
+          renderableData.push({ x: GraphicData[i], y: GraphicData[i + 1] });
+        }
+      }
+
+      break;
+    case SCOORD_TYPES.POLYLINE:
+      renderableData = [];
+
+      if (ValueType === 'SCOORD3D') {
+        for (let i = 0; i < GraphicData.length; i += 3) {
+          const point = {
+            x: GraphicData[i],
+            y: GraphicData[i + 1],
+            z: GraphicData[i + 2],
+          };
+
+          renderableData.push(worldToIJK(point, M1));
+        }
+      } else {
+        for (let i = 0; i < GraphicData.length; i += 2) {
+          renderableData.push({ x: GraphicData[i], y: GraphicData[i + 1] });
+        }
+      }
+
+      break;
+    case SCOORD_TYPES.POLYGON:
+      // this is only scoord3d
+      renderableData = [];
+      for (let i = 0; i < GraphicData.length; i += 3) {
+        const point = {
+          x: GraphicData[i],
+          y: GraphicData[i + 1],
+          z: GraphicData[i + 2],
+        };
+
+        renderableData.push(worldToIJK(point, M1));
+      }
+      break;
+    case SCOORD_TYPES.CIRCLE: {
+      // this is only scoord
+      const center = { x: GraphicData[0], y: GraphicData[1] };
+      const onPerimeter = { x: GraphicData[2], y: GraphicData[3] };
+
+      const radius = csMath.point.distance(center, onPerimeter);
+
+      renderableData = {
+        center,
+        radius,
+      };
+      break;
+    }
+    case SCOORD_TYPES.ELLIPSE: {
+      console.warn('ROTATED ELLIPSE NOT YET SUPPORTED!');
+      // To Do: scoord3d ellips, need data for testing
+      const majorAxis = [
+        { x: GraphicData[0], y: GraphicData[1] },
+        { x: GraphicData[2], y: GraphicData[3] },
+      ];
+      const minorAxis = [
+        { x: GraphicData[4], y: GraphicData[5] },
+        { x: GraphicData[6], y: GraphicData[7] },
+      ];
+
+      // Calculate two opposite corners of box defined by two axes.
+
+      const minorAxisLength = csMath.point.distance(minorAxis[0], minorAxis[1]);
+
+      const minorAxisDirection = {
+        x: (minorAxis[1].x - minorAxis[0].x) / minorAxisLength,
+        y: (minorAxis[1].y - minorAxis[0].y) / minorAxisLength,
+      };
+
+      const halfMinorAxisLength = minorAxisLength / 2;
+
+      // First end point of major axis + half minor axis vector
+      const corner1 = {
+        x: majorAxis[0].x + minorAxisDirection.x * halfMinorAxisLength,
+        y: majorAxis[0].y + minorAxisDirection.y * halfMinorAxisLength,
+      };
+
+      // Second end point of major axis - half of minor axis vector
+      const corner2 = {
+        x: majorAxis[1].x - minorAxisDirection.x * halfMinorAxisLength,
+        y: majorAxis[1].y - minorAxisDirection.y * halfMinorAxisLength,
+      };
+
+      renderableData = {
+        corner1,
+        corner2,
+      };
+      break;
+    }
+  }
+
+  return renderableData;
+};
+
+export default getRenderableData;

platform/core/src/DICOMSR/SCOORD3D/utils/getSequenceAsArray.js

@@ -0,0 +1,4 @@
+const getSequenceAsArray = sequence =>
+  Array.isArray(sequence) ? sequence : [sequence];
+
+export default getSequenceAsArray;

platform/core/src/DICOMSR/SCOORD3D/utils/isRehydratable.js

@@ -0,0 +1,48 @@
+import { adapters } from 'dcmjs';
+
+const cornerstoneAdapters = adapters.Cornerstone;
+
+/**
+ * Checks if the given `displaySet`can be rehydrated into the `MeasurementService`.
+ *
+ * @param {object} displaySet The SR `displaySet` to check.
+ * @param {object[]} mappings The CornerstoneTools 4 mappings to the `MeasurementService`.
+ * @returns {boolean} True if the SR can be rehydrated into the `MeasurementService`.
+ */
+export default function isRehydratable(displaySet, mappings) {
+  if (!mappings || !mappings.length) {
+    return false;
+  }
+
+  const mappingDefinitions = mappings.map(m => m.definition);
+  const { measurements } = displaySet;
+
+  const adapterKeys = Object.keys(cornerstoneAdapters).filter(
+    adapterKey =>
+      typeof cornerstoneAdapters[adapterKey]
+        .isValidCornerstoneTrackingIdentifier === 'function'
+  );
+
+  const adapters = [];
+
+  adapterKeys.forEach(key => {
+    if (mappingDefinitions.includes(key)) {
+      // Must have both a dcmjs adapter and a MeasurementService
+      // Definition in order to be a candidate for import.
+      adapters.push(cornerstoneAdapters[key]);
+    }
+  });
+
+  for (let i = 0; i < measurements.length; i++) {
+    const TrackingIdentifier = measurements[i].TrackingIdentifier;
+    const hydratable = adapters.some(adapter =>
+      adapter.isValidCornerstoneTrackingIdentifier(TrackingIdentifier)
+    );
+
+    if (hydratable) {
+      return true;
+    }
+  }
+
+  return false;
+}

platform/core/src/DICOMSR/SCOORD3D/utils/processMeasurement.js

@@ -0,0 +1,16 @@
+import processTID1410Measurement from './processTID1410Measurement';
+import processNonGeometricallyDefinedMeasurement from './processNonGeometricallyDefinedMeasurement';
+
+const processMeasurement = (mergedContentSequence, displaySet) => {
+  if (
+    mergedContentSequence.some(
+      group => group.ValueType === 'SCOORD' || group.ValueType === 'SCOORD3D'
+    )
+  ) {
+    return processTID1410Measurement(mergedContentSequence, displaySet);
+  }
+
+  return processNonGeometricallyDefinedMeasurement(mergedContentSequence);
+};
+
+export default processMeasurement;

platform/core/src/DICOMSR/SCOORD3D/utils/processNonGeometricallyDefinedMeasurement.js

@@ -0,0 +1,117 @@
+import getLabelFromMeasuredValueSequence from './getLabelFromMeasuredValueSequence';
+import getCoordsFromSCOORDOrSCOORD3D from './getCoordsFromSCOORDOrSCOORD3D';
+import { CodeNameCodeSequenceValues, CodingSchemeDesignators } from '../enums';
+
+const CORNERSTONE_FREETEXT_CODE_VALUE = 'CORNERSTONEFREETEXT';
+
+const processNonGeometricallyDefinedMeasurement = mergedContentSequence => {
+  const NUMContentItems = mergedContentSequence.filter(
+    group => group.ValueType === 'NUM'
+  );
+
+  const UIDREFContentItem = mergedContentSequence.find(
+    group => group.ValueType === 'UIDREF'
+  );
+
+  const TrackingIdentifierContentItem = mergedContentSequence.find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.TrackingIdentifier
+  );
+
+  const Finding = mergedContentSequence.find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.Finding
+  );
+
+  const FindingSites = mergedContentSequence.filter(
+    item =>
+      item.ConceptNameCodeSequence.CodingSchemeDesignator ===
+        CodingSchemeDesignators.SRT &&
+      item.ConceptNameCodeSequence.CodeValue ===
+        CodeNameCodeSequenceValues.FindingSite
+  );
+
+  const measurement = {
+    loaded: false,
+    labels: [],
+    coords: [],
+    TrackingUniqueIdentifier: UIDREFContentItem.UID,
+    TrackingIdentifier: TrackingIdentifierContentItem.TextValue,
+  };
+
+  if (
+    Finding &&
+    Finding.ConceptCodeSequence.CodingSchemeDesignator ===
+      CodingSchemeDesignators.cornerstoneTools4 &&
+    Finding.ConceptCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.CornerstoneFreeText
+  ) {
+    measurement.labels.push({
+      label: CORNERSTONE_FREETEXT_CODE_VALUE,
+      value: Finding.ConceptCodeSequence.CodeMeaning,
+    });
+  }
+
+  // TODO -> Eventually hopefully support SNOMED or some proper code library, just free text for now.
+  if (FindingSites.length) {
+    const cornerstoneFreeTextFindingSite = FindingSites.find(
+      FindingSite =>
+        FindingSite.ConceptCodeSequence.CodingSchemeDesignator ===
+          CodingSchemeDesignators.cornerstoneTools4 &&
+        FindingSite.ConceptCodeSequence.CodeValue ===
+          CodeNameCodeSequenceValues.CornerstoneFreeText
+    );
+
+    if (cornerstoneFreeTextFindingSite) {
+      measurement.labels.push({
+        label: CORNERSTONE_FREETEXT_CODE_VALUE,
+        value: cornerstoneFreeTextFindingSite.ConceptCodeSequence.CodeMeaning,
+      });
+    }
+  }
+
+  NUMContentItems.forEach(item => {
+    const {
+      ConceptNameCodeSequence,
+      ContentSequence,
+      MeasuredValueSequence,
+    } = item;
+
+    if (!ContentSequence) {
+      console.warn(`Graphic ${ContentSequence} missing, skipping annotation.`);
+
+      return;
+    }
+
+    const { ValueType } = ContentSequence;
+
+    if (!ValueType === 'SCOORD' && !ValueType === 'SCOORD3D') {
+      console.warn(
+        `Graphic ${ValueType} not currently supported, skipping annotation.`
+      );
+
+      return;
+    }
+
+    const coords = getCoordsFromSCOORDOrSCOORD3D(ContentSequence);
+
+    if (coords) {
+      measurement.coords.push(coords);
+    }
+
+    if (MeasuredValueSequence) {
+      measurement.labels.push(
+        getLabelFromMeasuredValueSequence(
+          ConceptNameCodeSequence,
+          MeasuredValueSequence
+        )
+      );
+    }
+  });
+
+  return measurement;
+};
+
+export default processNonGeometricallyDefinedMeasurement;

platform/core/src/DICOMSR/SCOORD3D/utils/processTID1410Measurement.js

@@ -0,0 +1,88 @@
+import getLabelFromMeasuredValueSequence from './getLabelFromMeasuredValueSequence';
+import getCoordsFromSCOORDOrSCOORD3D from './getCoordsFromSCOORDOrSCOORD3D';
+import { RELATIONSHIP_TYPE, CodeNameCodeSequenceValues } from '../enums';
+
+/**
+ * TID 1410 Planar ROI Measurements and Qualitative Evaluations.
+ *
+ * @param {*} mergedContentSequence
+ * @returns
+ */
+const processTID1410Measurement = (mergedContentSequence, displaySet) => {
+  // Need to deal with TID 1410 style measurements, which will have a SCOORD or SCOORD3D at the top level,
+  // And non-geometric representations where each NUM has "INFERRED FROM" SCOORD/SCOORD3D
+
+  const graphicItem = mergedContentSequence.find(
+    group => group.ValueType === 'SCOORD' || group.ValueType === 'SCOORD3D'
+  );
+
+  if (!graphicItem) {
+    console.warn(
+      `graphic ValueType ${graphicItem.ValueType} not currently supported, skipping annotation.`
+    );
+    return;
+  }
+
+  const UIDREFContentItem = mergedContentSequence.find(
+    group => group.ValueType === 'UIDREF'
+  );
+
+  const TrackingIdentifierContentItem = mergedContentSequence.find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.TrackingIdentifier
+  );
+
+  const NUMContentItems = mergedContentSequence.filter(
+    group => group.ValueType === 'NUM'
+  );
+
+  const measurement = {
+    loaded: false,
+    labels: [],
+    coords: [getCoordsFromSCOORDOrSCOORD3D(graphicItem, displaySet)],
+    TrackingUniqueIdentifier: UIDREFContentItem.UID,
+    TrackingIdentifier: TrackingIdentifierContentItem.TextValue,
+  };
+
+  NUMContentItems.forEach(item => {
+    const {
+      ConceptNameCodeSequence,
+      ContentSequence,
+      MeasuredValueSequence,
+    } = item;
+
+    if (
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.Score
+    ) {
+      ContentSequence.forEach(item => {
+        if (
+          [
+            RELATIONSHIP_TYPE.SELECTED_FROM,
+            RELATIONSHIP_TYPE.INFERRED_FROM,
+          ].includes(item.RelationshipType)
+        ) {
+          if (item.ReferencedSOPSequence) {
+            measurement.coords.forEach(coord => {
+              coord.ReferencedSOPSequence = item.ReferencedSOPSequence;
+            });
+          }
+        }
+      });
+    }
+
+    if (MeasuredValueSequence) {
+      measurement.labels.push(
+        getLabelFromMeasuredValueSequence(
+          ConceptNameCodeSequence,
+          MeasuredValueSequence
+        )
+      );
+    }
+  });
+
+  return measurement;
+};
+
+export default processTID1410Measurement;

platform/core/src/DICOMSR/dataExchange.js

@@ -19,9 +19,10 @@ import findMostRecentStructuredReport from './utils/findMostRecentStructuredRepo
  * Function to be registered into MeasurementAPI to retrieve measurements from DICOM Structured Reports
  *
  * @param {serverType} server
+ * @param {object} external
  * @returns {Promise} Should resolve with OHIF measurementData object
  */
-const retrieveMeasurements = server => {
+const retrieveMeasurements = (server, external = {}) => {
   log.info('[DICOMSR] retrieveMeasurements');
 
   if (!server || server.type !== 'dicomWeb') {
@@ -36,7 +37,7 @@ const retrieveMeasurements = server => {
 
   if (!latestSeries) return Promise.resolve({});
 
-  return retrieveMeasurementFromSR(latestSeries, studies, serverUrl);
+  return retrieveMeasurementFromSR(latestSeries, studies, serverUrl, external);
 };
 
 /**

platform/core/src/DICOMSR/handleStructuredReport.js

@@ -17,9 +17,15 @@ const TRANSFER_SYNTAX_UID = '1.2.840.10008.1.2.1';
  * @param {Array} series - List of all series metaData loaded
  * @param {Array} studies - List of all studies metaData loaded
  * @param {string} serverUrl - Server URL to be used on request
+ * @param {object} external
  * @returns {Object} MeasurementData
  */
-const retrieveMeasurementFromSR = async (series, studies, serverUrl) => {
+const retrieveMeasurementFromSR = async (
+  series,
+  studies,
+  serverUrl,
+  external
+) => {
   const config = {
     url: serverUrl,
     headers: DICOMWeb.getAuthorizationHeader(),
@@ -40,7 +46,8 @@ const retrieveMeasurementFromSR = async (series, studies, serverUrl) => {
   const displaySets = getAllDisplaySets(studies);
   const measurementsData = parseDicomStructuredReport(
     part10SRArrayBuffer,
-    displaySets
+    displaySets,
+    external
   );
 
   return measurementsData;

platform/core/src/DICOMSR/parseDicomStructuredReport.js

@@ -1,5 +1,6 @@
 import dcmjs from 'dcmjs';
 import classes from '../classes';
+import parseSCOORD3D from './SCOORD3D/parseSCOORD3D';
 
 import findInstanceMetadataBySopInstanceUID from './utils/findInstanceMetadataBySopInstanceUid';
 
@@ -12,11 +13,19 @@ const { LogManager } = classes;
  *
  * @param {ArrayBuffer} part10SRArrayBuffer
  * @param {Array} displaySets
+ * @param {object} external
  * @returns
  */
-const parseDicomStructuredReport = (part10SRArrayBuffer, displaySets) => {
-  // Get the dicom data as an Object
+const parseDicomStructuredReport = (
+  part10SRArrayBuffer,
+  displaySets,
+  external
+) => {
+  if (external && external.servicesManager) {
+    parseSCOORD3D({ servicesManager: external.servicesManager, displaySets });
+  }
 
+  // Get the dicom data as an Object
   const dicomData = dcmjs.data.DicomMessage.readFile(part10SRArrayBuffer);
   const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
     dicomData.dict

platform/core/src/DICOMSR/utils/findMostRecentStructuredReport.js

@@ -41,6 +41,7 @@ const isStructuredReportSeries = series => {
   const supportedSopClassUIDs = [
     '1.2.840.10008.5.1.4.1.1.88.22',
     '1.2.840.10008.5.1.4.1.1.11.1',
+    '1.2.840.10008.5.1.4.1.1.88.34', // COMPREHENSIVE_3D_SR
   ];
 
   const firstInstance = series.getFirstInstance();

platform/core/src/index.js

@@ -20,6 +20,7 @@ import ui from './ui';
 import user from './user.js';
 import errorHandler from './errorHandler.js';
 import utils, { hotkeys } from './utils/';
+import str2ab from './utils/str2ab';
 
 import {
   UINotificationService,
@@ -96,6 +97,8 @@ export {
   UIDialogService,
   MeasurementService,
   LoggerService,
+
+  str2ab,
 };
 
 export { OHIF };

platform/core/src/index.test.js

@@ -26,6 +26,7 @@ describe('Top level exports', () => {
       'cornerstone',
       'default', //
       'errorHandler',
+      'str2ab',
       'string',
       'ui',
       'user',

platform/core/src/measurements/classes/MeasurementApi.js

@@ -802,6 +802,10 @@ export default class MeasurementApi {
       collection.push(addedMeasurement);
     }
 
+    if (measurement.isReadOnly) {
+      addedMeasurement.isReadOnly = measurement.isReadOnly;
+    }
+
     if (!emptyItem) {
       // Reflect the entry in the tool group collection
       groupCollection.push({

platform/core/src/measurements/lib/getImageAttributes.js

@@ -1,9 +1,11 @@
 import cornerstone from 'cornerstone-core';
 
-export default function(element) {
-  // Get the Cornerstone imageId
-  const enabledElement = cornerstone.getEnabledElement(element);
-  const imageId = enabledElement.image.imageId;
+export default function(element, imageId) {
+  if (!imageId) {
+    // Get the Cornerstone imageId
+    const enabledElement = cornerstone.getEnabledElement(element);
+    imageId = enabledElement.image.imageId;
+  }
 
   // Get StudyInstanceUID & PatientID
   const {

platform/core/src/measurements/tools/dicomSRDisplayTool.js

@@ -0,0 +1,22 @@
+export const dicomSRDisplayTool = {
+  id: 'DICOMSRDisplayTool',
+  name: 'DICOMSRDisplayTool',
+  toolGroup: 'allTools',
+  cornerstoneToolType: 'DICOMSRDisplayTool',
+  options: {
+    measurementTable: {
+      displayFunction: data => {
+        return `(SR) ${data.lesionNamingNumber ||
+          data.measurementNumber ||
+          data.text ||
+          ''}`;
+      },
+    },
+    caseProgress: {
+      include: true,
+      evaluate: true,
+    },
+  },
+};
+
+export default dicomSRDisplayTool;

platform/core/src/measurements/tools/index.js

@@ -10,6 +10,7 @@ import { angle } from './angle';
 import { targetCR } from './targetCR';
 import { targetNE } from './targetNE';
 import { targetUN } from './targetUN';
+import dicomSRDisplayTool from './dicomSRDisplayTool';
 
 export {
   arrowAnnotate,
@@ -24,4 +25,5 @@ export {
   targetCR,
   targetNE,
   targetUN,
+  dicomSRDisplayTool,
 };

platform/core/src/services/MeasurementService/MeasurementService.js

@@ -1,5 +1,7 @@
+/** Internal imports */
 import log from '../../log';
 import guid from '../../utils/guid';
+import pubSubServiceInterface from '../_shared/pubSubServiceInterface';
 
 /**
  * Measurement source schema
@@ -15,7 +17,7 @@ import guid from '../../utils/guid';
  *
  * @typedef {Object} Measurement
  * @property {number} id -
- * @property {string} sopInstanceUid -
+ * @property {string} SOPInstanceUID -
  * @property {string} FrameOfReferenceUID -
  * @property {string} referenceSeriesUID -
  * @property {string} label -
@@ -32,24 +34,37 @@ const MEASUREMENT_SCHEMA_KEYS = [
   'id',
   'SOPInstanceUID',
   'FrameOfReferenceUID',
+  'referenceStudyUID',
   'referenceSeriesUID',
   'label',
   'description',
   'type',
   'unit',
   'area', // TODO: Add concept names instead (descriptor)
+  'mean',
+  'stdDev',
+  'length',
+  'shortestDiameter',
+  'longestDiameter',
+  'text', // NOTE: There is nothing like this in SR.
   'points',
   'source',
 ];
 
 const EVENTS = {
   MEASUREMENT_UPDATED: 'event::measurement_updated',
+  INTERNAL_MEASUREMENT_UPDATED: 'event:internal_measurement_updated',
   MEASUREMENT_ADDED: 'event::measurement_added',
+  RAW_MEASUREMENT_ADDED: 'event::raw_measurement_added',
+  MEASUREMENT_REMOVED: 'event::measurement_removed',
+  MEASUREMENTS_CLEARED: 'event::measurements_cleared',
+  JUMP_TO_MEASUREMENT: 'event:jump_to_measurement',
 };
 
 const VALUE_TYPES = {
   POLYLINE: 'value_type::polyline',
   POINT: 'value_type::point',
+  BIDIRECTIONAL: 'value_type::shortAxisLongAxis', // TODO -> Discuss with Danny. => just using SCOORD values isn't enough here.
   ELLIPSE: 'value_type::ellipse',
   MULTIPOINT: 'value_type::multipoint',
   CIRCLE: 'value_type::circle',
@@ -61,6 +76,7 @@ class MeasurementService {
     this.mappings = {};
     this.measurements = {};
     this.listeners = {};
+    this._jumpToMeasurementCache = {};
     Object.defineProperty(this, 'EVENTS', {
       value: EVENTS,
       writable: false,
@@ -73,6 +89,8 @@ class MeasurementService {
       enumerable: true,
       configurable: false,
     });
+
+    Object.assign(this, pubSubServiceInterface);
   }
 
   /**
@@ -91,7 +109,7 @@ class MeasurementService {
   /**
    * Get specific measurement by its id.
    *
-   * @param {string} id If of the measurement
+   * @param {string} id Id of the measurement
    * @return {Measurement} Measurement instance
    */
   getMeasurement(id) {
@@ -114,13 +132,11 @@ class MeasurementService {
    */
   createSource(name, version) {
     if (!name) {
-      log.warn('Source name not provided. Exiting early.');
-      return;
+      throw new Error('Source name not provided.');
     }
 
     if (!version) {
-      log.warn('Source version not provided. Exiting early.');
-      return;
+      throw new Error('Source version not provided.');
     }
 
     const id = guid();
@@ -132,6 +148,9 @@ class MeasurementService {
     source.addOrUpdate = (definition, measurement) => {
       return this.addOrUpdate(source, definition, measurement);
     };
+    source.remove = id => {
+      return this.remove(id, source);
+    };
     source.getAnnotation = (definition, measurementId) => {
       return this.getAnnotation(source, definition, measurementId);
     };
@@ -142,6 +161,32 @@ class MeasurementService {
     return source;
   }
 
+  getSource(name, version) {
+    const { sources } = this;
+    const id = this._getSourceId(name, version);
+
+    return sources[id];
+  }
+
+  getSourceMappings(name, version) {
+    const { mappings } = this;
+    const id = this._getSourceId(name, version);
+
+    return mappings[id];
+  }
+
+  _getSourceId(name, version) {
+    const { sources } = this;
+
+    const sourceId = Object.keys(sources).find(sourceId => {
+      const source = sources[sourceId];
+
+      return source.name === name && source.version === version;
+    });
+
+    return sourceId;
+  }
+
   /**
    * Add a new measurement matching criteria along with mapping functions.
    *
@@ -160,28 +205,23 @@ class MeasurementService {
     toMeasurementSchema
   ) {
     if (!this._isValidSource(source)) {
-      log.warn('Invalid source. Exiting early.');
-      return;
+      throw new Error('Invalid source.');
     }
 
     if (!matchingCriteria) {
-      log.warn('Matching criteria not provided. Exiting early.');
-      return;
+      throw new Error('Matching criteria not provided.');
     }
 
     if (!definition) {
-      log.warn('Definition not provided. Exiting early.');
-      return;
+      throw new Error('Definition not provided.');
     }
 
     if (!toSourceSchema) {
-      log.warn('Source mapping function not provided. Exiting early.');
-      return;
+      throw new Error('Mapping function to source schema not provided.');
     }
 
     if (!toMeasurementSchema) {
-      log.warn('Measurement mapping function not provided. Exiting early.');
-      return;
+      throw new Error('Measurement mapping function not provided.');
     }
 
     const mapping = {
@@ -227,9 +267,9 @@ class MeasurementService {
       measurementId,
       definition
     );
+    const measurement = this.getMeasurement(measurementId);
     if (mapping) return mapping.toSourceSchema(measurement, definition);
 
-    const measurement = this.getMeasurement(measurementId);
     const matchingMapping = this._getMatchingMapping(
       source,
       definition,
@@ -243,15 +283,50 @@ class MeasurementService {
     }
   }
 
+  update(id, measurement, notYetUpdatedAtSource = false) {
+    if (this.measurements[id]) {
+      const updatedMeasurement = {
+        ...measurement,
+        modifiedTimestamp: Math.floor(Date.now() / 1000),
+      };
+
+      log.info(
+        `Updating internal measurement representation...`,
+        updatedMeasurement
+      );
+
+      this.measurements[id] = updatedMeasurement;
+
+      this.publish(
+        // Add an internal flag to say the measurement has not yet been updated at source.
+        this.EVENTS.MEASUREMENT_UPDATED,
+        {
+          source: measurement.source,
+          measurement: updatedMeasurement,
+          notYetUpdatedAtSource,
+        }
+      );
+
+      return updatedMeasurement.id;
+    }
+  }
+
   /**
-   * Adds or update persisted measurements.
-   *
-   * @param {MeasurementSource} source The measurement source instance
-   * @param {string} definition The source definition
-   * @param {Measurement} measurement The source measurement
-   * @return {string} A measurement id
+   * Add a raw measurement into a source so that it may be
+   * Converted to/from annotation in the same way. E.g. import serialized data
+   * Of the same form as the measurement source.
+   * @param {MeasurementSource} source The measurement source instance.
+   * @param {string} definition The source definition you want to add the measurement to.
+   * @param {object} data The data you wish to add to the source.
+   * @param {function} toMeasurementSchema A function to get the `data` into the same shape as the source definition.
    */
-  addOrUpdate(source, definition, sourceMeasurement) {
+  addRawMeasurement(
+    source,
+    definition,
+    data,
+    toMeasurementSchema,
+    dataSource = {}
+  ) {
     if (!this._isValidSource(source)) {
       log.warn('Invalid source. Exiting early.');
       return;
@@ -273,14 +348,8 @@ class MeasurementService {
 
     let measurement = {};
     try {
-      const sourceMappings = this.mappings[source.id];
-      const { toMeasurementSchema } = sourceMappings.find(
-        mapping => mapping.definition === definition
-      );
-
       /* Convert measurement */
-      measurement = toMeasurementSchema(sourceMeasurement);
-
+      measurement = toMeasurementSchema(data);
       /* Assign measurement source instance */
       measurement.source = source;
     } catch (error) {
@@ -298,7 +367,7 @@ class MeasurementService {
       return;
     }
 
-    let internalId = sourceMeasurement.id;
+    let internalId = data.id;
     if (!internalId) {
       internalId = guid();
       log.warn(`Measurement ID not found. Generating UID: ${internalId}`);
@@ -316,49 +385,167 @@ class MeasurementService {
         newMeasurement
       );
       this.measurements[internalId] = newMeasurement;
-      this._broadcastChange(
-        this.EVENTS.MEASUREMENT_UPDATED,
+      this.publish(this.EVENTS.MEASUREMENT_UPDATED, {
         source,
-        newMeasurement
-      );
+        measurement: newMeasurement,
+      });
     } else {
       log.info(`Measurement added.`, newMeasurement);
       this.measurements[internalId] = newMeasurement;
-      this._broadcastChange(
-        this.EVENTS.MEASUREMENT_ADDED,
+      this.publish(this.EVENTS.RAW_MEASUREMENT_ADDED, {
         source,
-        newMeasurement
-      );
+        measurement: newMeasurement,
+        data,
+        dataSource,
+      });
     }
 
     return newMeasurement.id;
   }
 
   /**
-   * Subscribe to measurement updates.
+   * Adds or update persisted measurements.
    *
-   * @param {string} eventName The name of the event
-   * @param {Function} callback Events callback
-   * @return {Object} Observable object with actions
+   * @param {MeasurementSource} source The measurement source instance
+   * @param {string} definition The source definition
+   * @param {Measurement} measurement The source measurement
+   * @return {string} A measurement id
    */
-  subscribe(eventName, callback) {
-    if (this._isValidEvent(eventName)) {
-      const listenerId = guid();
-      const subscription = { id: listenerId, callback };
-
-      console.info(`Subscribing to '${eventName}'.`);
-      if (Array.isArray(this.listeners[eventName])) {
-        this.listeners[eventName].push(subscription);
-      } else {
-        this.listeners[eventName] = [subscription];
-      }
-
-      return {
-        unsubscribe: () => this._unsubscribe(eventName, listenerId),
-      };
-    } else {
-      throw new Error(`Event ${eventName} not supported.`);
+  addOrUpdate(source, definition, sourceMeasurement) {
+    if (!this._isValidSource(source)) {
+      throw new Error('Invalid source.');
     }
+
+    if (!definition) {
+      throw new Error('No source definition provided.');
+    }
+
+    const sourceInfo = this._getSourceInfo(source);
+
+    if (!this._sourceHasMappings(source)) {
+      throw new Error(
+        `No measurement mappings found for '${sourceInfo}' source. Exiting early.`
+      );
+    }
+
+    let measurement = {};
+    try {
+      const sourceMappings = this.mappings[source.id];
+      const { toMeasurementSchema } = sourceMappings.find(
+        mapping => mapping.definition === definition
+      );
+
+      /* Convert measurement */
+      measurement = toMeasurementSchema(sourceMeasurement);
+
+      /* Assign measurement source instance */
+      measurement.source = source;
+    } catch (error) {
+      throw new Error(
+        `Failed to map '${sourceInfo}' measurement for definition ${definition}:`,
+        error.message
+      );
+    }
+
+    if (!this._isValidMeasurement(measurement)) {
+      throw new Error(
+        `Attempting to add or update a invalid measurement provided by '${sourceInfo}'. Exiting early.`
+      );
+    }
+
+    let internalId = sourceMeasurement.id;
+    if (!internalId) {
+      internalId = guid();
+      log.info(`Measurement ID not found. Generating UID: ${internalId}`);
+    }
+
+    const newMeasurement = {
+      ...measurement,
+      modifiedTimestamp: Math.floor(Date.now() / 1000),
+      id: internalId,
+    };
+
+    if (this.measurements[internalId]) {
+      log.info(
+        `Measurement already defined. Updating measurement.`,
+        newMeasurement
+      );
+      this.measurements[internalId] = newMeasurement;
+      this.publish(this.EVENTS.MEASUREMENT_UPDATED, {
+        source,
+        measurement: newMeasurement,
+        notYetUpdatedAtSource: false,
+      });
+    } else {
+      log.info('Measurement added.', newMeasurement);
+      this.measurements[internalId] = newMeasurement;
+      this.publish(this.EVENTS.MEASUREMENT_ADDED, {
+        source,
+        measurement: newMeasurement,
+      });
+    }
+
+    return newMeasurement.id;
+  }
+
+  /**
+   * Removes a measurement and broadcasts the removed event.
+   *
+   * @param {string} id The measurement id
+   * @param {MeasurementSource} source The measurement source instance
+   * @return {string} The removed measurement id
+   */
+  remove(id, source) {
+    if (!id || !this.measurements[id]) {
+      log.warn(`No id provided, or unable to find measurement by id.`);
+      return;
+    }
+
+    delete this.measurements[id];
+    this.publish(this.EVENTS.MEASUREMENT_REMOVED, {
+      source,
+      measurement: id, // This is weird :shrug:
+    });
+  }
+
+  clearMeasurements() {
+    this.measurements = {};
+    this._jumpToMeasurementCache = {};
+    this.publish(this.EVENTS.MEASUREMENTS_CLEARED);
+  }
+
+  jumpToMeasurement(viewportIndex, id) {
+    const measurement = this.measurements[id];
+
+    if (!measurement) {
+      log.warn(`No id provided, or unable to find measurement by id.`);
+      return;
+    }
+
+    this._addJumpToMeasurement(viewportIndex, id);
+
+    const eventName = this.EVENTS.JUMP_TO_MEASUREMENT;
+
+    const hasListeners = Object.keys(this.listeners).length > 0;
+    const hasCallbacks = Array.isArray(this.listeners[eventName]);
+
+    if (hasListeners && hasCallbacks) {
+      this.listeners[eventName].forEach(listener => {
+        listener.callback({ viewportIndex, measurement });
+      });
+    }
+  }
+
+  _addJumpToMeasurement(viewportIndex, id) {
+    this._jumpToMeasurementCache[viewportIndex] = id;
+  }
+
+  getJumpToMeasurement(viewportIndex) {
+    return this._jumpToMeasurementCache[viewportIndex];
+  }
+
+  removeJumpToMeasurement(viewportIndex) {
+    delete this._jumpToMeasurementCache[viewportIndex];
   }
 
   _getMappingByMeasurementSource(measurementId, definition) {
@@ -370,12 +557,20 @@ class MeasurementService {
     }
   }
 
+  /**
+   * Clear all measurements and broadcasts cleared event.
+   */
+  clear() {
+    this.measurements = {};
+    this.publish(this.EVENTS.MEASUREMENTS_CLEARED);
+  }
+
   /**
    * Get measurement mapping function if matching criteria.
    *
    * @param {MeasurementSource} source Measurement source instance
    * @param {string} definition The source definition
-   * @param {string} measurement The measurement serice measurement
+   * @param {Measurement} measurement The measurement service measurement
    * @return {Object} The mapping based on matched criteria
    */
   _getMatchingMapping(source, definition, measurement) {
@@ -387,10 +582,27 @@ class MeasurementService {
 
     /* Criteria Matching */
     return sourceMappingsByDefinition.find(({ matchingCriteria }) => {
-      return (
+      if (matchingCriteria.type !== measurement.type) {
+        return false;
+      }
+
+      if (
+        matchingCriteria.properties &&
+        matchingCriteria.properties.every(name =>
+          measurement.hasOwnProperty(name)
+        )
+      ) {
+        return true;
+      }
+
+      if (
         measurement.points &&
         measurement.points.length === matchingCriteria.points
-      );
+      ) {
+        return true;
+      }
+
+      return false;
     });
   }
 
@@ -426,47 +638,6 @@ class MeasurementService {
     );
   }
 
-  /**
-   * Broadcasts measurement changes.
-   *
-   * @param {string} measurementId The measurement id
-   * @param {MeasurementSource} source The measurement source
-   * @param {string} eventName The event name
-   * @return void
-   */
-  _broadcastChange(eventName, source, measurement) {
-    const hasListeners = Object.keys(this.listeners).length > 0;
-    const hasCallbacks = Array.isArray(this.listeners[eventName]);
-
-    if (hasListeners && hasCallbacks) {
-      this.listeners[eventName].forEach(listener => {
-        listener.callback({ source, measurement });
-      });
-    }
-  }
-
-  /**
-   * Unsubscribe to measurement updates.
-   *
-   * @param {string} eventName The name of the event
-   * @param {string} listenerId The listeners id
-   * @return void
-   */
-  _unsubscribe(eventName, listenerId) {
-    if (!this.listeners[eventName]) {
-      return;
-    }
-
-    const listeners = this.listeners[eventName];
-    if (Array.isArray(listeners)) {
-      this.listeners[eventName] = listeners.filter(
-        ({ id }) => id !== listenerId
-      );
-    } else {
-      this.listeners[eventName] = undefined;
-    }
-  }
-
   /**
    * Check if a given measurement data is valid.
    *
@@ -489,10 +660,10 @@ class MeasurementService {
    *
    * @param {string} eventName The name of the event
    * @return {boolean} Event name validation
-   */
-  _isValidEvent(eventName) {
-    return Object.values(this.EVENTS).includes(eventName);
-  }
+  //  */
+  // _isValidEvent(eventName) {
+  //   return Object.values(this.EVENTS).includes(eventName);
+  // }
 
   /**
    * Converts object of objects to array.

platform/core/src/services/MeasurementService/MeasurementService.test.js

@@ -13,7 +13,7 @@ describe('MeasurementService.js', () => {
   let source;
   let definition;
   let matchingCriteria;
-  let toAnnotation;
+  let toSourceSchema;
   let toMeasurement;
   let annotation;
 
@@ -34,11 +34,20 @@ describe('MeasurementService.js', () => {
       unit: 'mm',
       area: 123,
       type: measurementService.VALUE_TYPES.POLYLINE,
-      points: [{ x: 1, y: 2 }, { x: 1, y: 2 }],
+      points: [
+        { x: 1, y: 2 },
+        { x: 1, y: 2 },
+      ],
       source: source,
     };
-    toAnnotation = () => annotation;
-    toMeasurement = () => measurement;
+    toSourceSchema = () => annotation;
+    toMeasurement = () => {
+      if (Object.keys(measurement).includes('invalidProperty')) {
+        throw new Error('Measurement does not match schema');
+      }
+
+      return measurement;
+    }
     matchingCriteria = {
       valueType: measurementService.VALUE_TYPES.POLYLINE,
       points: 2,
@@ -52,16 +61,16 @@ describe('MeasurementService.js', () => {
       measurementService.createSource('Testing', '1');
     });
 
-    it('logs warning and return early if no name provided', () => {
-      measurementService.createSource(null, '1');
-
-      expect(log.warn.mock.calls.length).toBe(1);
+    it('throws Error if no name provided', () => {
+      expect(() => {
+        measurementService.createSource(null, '1')
+      }).toThrow(new Error('Source name not provided.'));
     });
 
-    it('logs warning and return early if no version provided', () => {
-      measurementService.createSource('Testing', null);
-
-      expect(log.warn.mock.calls.length).toBe(1);
+    it('throws Error if no version provided', () => {
+      expect(() => {
+        measurementService.createSource('Testing', null)
+      }).toThrow(new Error('Source version not provided.'));
     });
   });
 
@@ -71,83 +80,84 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
     });
 
-    it('logs warning and return early if no matching criteria provided', () => {
-      measurementService.addMapping(
-        source,
-        definition,
-        null,
-        toAnnotation,
-        toMeasurement
-      );
+    it('throws Error if invalid source provided', () => {
+      expect(() => {
+        const invalidSource = {};
 
-      expect(log.warn.mock.calls.length).toBe(1);
+        measurementService.addMapping(
+          invalidSource,
+          definition,
+          matchingCriteria,
+          toSourceSchema,
+          toMeasurement
+        );
+      }).toThrow(new Error('Invalid source.'));
     });
 
-    it('logs warning and return early if invalid source provided', () => {
-      const invalidSoure = {};
-
-      measurementService.addMapping(
-        invalidSoure,
-        definition,
-        matchingCriteria,
-        toAnnotation,
-        toMeasurement
-      );
-
-      expect(log.warn.mock.calls.length).toBe(1);
+    it('throws Error if no matching criteria provided', () => {
+      expect(() => {
+        measurementService.addMapping(
+          source,
+          definition,
+          null,
+          toSourceSchema,
+          toMeasurement
+        );
+      }).toThrow(new Error('Matching criteria not provided.'));
     });
 
-    it('logs warning and return early if no source provided', () => {
-      measurementService.addMapping(
-        null /* source */,
-        definition,
-        matchingCriteria,
-        toAnnotation,
-        toMeasurement
-      );
 
-      expect(log.warn.mock.calls.length).toBe(1);
+    it('throws Error if no source provided', () => {
+      expect(() => {
+        measurementService.addMapping(
+          null /* source */,
+          definition,
+          matchingCriteria,
+          toSourceSchema,
+          toMeasurement
+        );
+      }).toThrow(new Error('Invalid source.'));
     });
 
     it('logs warning and return early if no definition provided', () => {
-      measurementService.addMapping(
-        source,
-        null /* definition */,
-        matchingCriteria,
-        toAnnotation,
-        toMeasurement
-      );
-
-      expect(log.warn.mock.calls.length).toBe(1);
+      expect(() => {
+        measurementService.addMapping(
+          source,
+          null /* definition */,
+          matchingCriteria,
+          toSourceSchema,
+          toMeasurement
+        );
+      }).toThrow(new Error('Definition not provided.'));
     });
 
-    it('logs warning and return early if no measurement mapping function provided', () => {
-      measurementService.addMapping(
-        source,
-        definition,
-        matchingCriteria,
-        null /* toAnnotation */,
-        toMeasurement
-      );
-
-      expect(log.warn.mock.calls.length).toBe(1);
+    it('throws Error if no measurement mapping function provided', () => {
+      expect(() => {
+        measurementService.addMapping(
+          source,
+          definition,
+          matchingCriteria,
+          null /* toSourceSchema */,
+          toMeasurement
+        );
+      }).toThrow(new Error('Mapping function to source schema not provided.'));
     });
 
-    it('logs warning and return early if no annotation mapping function provided', () => {
-      measurementService.addMapping(
-        source,
-        definition,
-        matchingCriteria,
-        toAnnotation,
-        null /* toMeasurement */
-      );
-
-      expect(log.warn.mock.calls.length).toBe(1);
+    it('throws Error if no annotation mapping function provided', () => {
+      expect(() => {
+        measurementService.addMapping(
+          source,
+          definition,
+          matchingCriteria,
+          toSourceSchema,
+          null /* toMeasurement */
+        );
+      }).toThrow(new Error('Measurement mapping function not provided.'));
     });
   });
 
@@ -157,7 +167,7 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
       const measurementId = source.addOrUpdate(definition, annotation);
@@ -171,7 +181,7 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         {},
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
       const measurementId = source.addOrUpdate(definition, annotation);
@@ -193,7 +203,7 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
 
@@ -212,7 +222,7 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
 
@@ -232,7 +242,7 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
 
@@ -245,9 +255,9 @@ describe('MeasurementService.js', () => {
     });
 
     it('fails to add new measurements when no mapping', () => {
-      source.addOrUpdate(definition, measurement);
-
-      expect(log.warn.mock.calls.length).toBe(1);
+      expect(() => {
+        source.addOrUpdate(definition, measurement);
+      }).toThrow()
     });
 
     it('fails to add new measurements when invalid mapping function', () => {
@@ -255,13 +265,13 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         1 /* Invalid */
       );
 
-      source.addOrUpdate(definition, measurement);
-
-      expect(log.warn.mock.calls.length).toBe(1);
+      expect(() => {
+        source.addOrUpdate(definition, measurement);
+      }).toThrow()
     });
 
     it('adds new measurement with custom id', () => {
@@ -271,7 +281,7 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
 
@@ -288,28 +298,28 @@ describe('MeasurementService.js', () => {
       expect(newMeasurement).toEqual(savedMeasurement);
     });
 
-    it('logs warning and return if adding invalid measurement', () => {
+    it('throws Error if adding invalid measurement', () => {
       measurement.invalidProperty = {};
 
       measurementService.addMapping(
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
 
-      source.addOrUpdate(definition, measurement);
-
-      expect(log.warn.mock.calls.length).toBe(2);
+      expect(() => {
+        source.addOrUpdate(definition, measurement);
+      }).toThrow()
     });
 
-    it('updates existent measurement', () => {
+    it('updates existing measurement', () => {
       measurementService.addMapping(
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
 
@@ -330,7 +340,7 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
 
@@ -354,7 +364,7 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
 
@@ -381,7 +391,7 @@ describe('MeasurementService.js', () => {
         source,
         definition,
         matchingCriteria,
-        toAnnotation,
+        toSourceSchema,
         toMeasurement
       );
 

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

@@ -0,0 +1,3 @@
+import pubSubServiceInterface from './pubSubServiceInterface';
+
+export { pubSubServiceInterface };

platform/core/src/services/_shared/pubSubServiceInterface.js

@@ -0,0 +1,88 @@
+import guid from '../../utils/guid';
+
+/**
+ * Consumer must implement:
+ * this.listeners = {}
+ * this.EVENTS = { "EVENT_KEY": "EVENT_VALUE" }
+ */
+export default {
+  subscribe,
+  publish,
+  _unsubscribe,
+  _isValidEvent,
+};
+
+/**
+ * Subscribe to updates.
+ *
+ * @param {string} eventName The name of the event
+ * @param {Function} callback Events callback
+ * @return {Object} Observable object with actions
+ */
+function subscribe(eventName, callback) {
+  if (this._isValidEvent(eventName)) {
+    const listenerId = guid();
+    const subscription = { id: listenerId, callback };
+
+    console.info(`Subscribing to '${eventName}'.`);
+    if (Array.isArray(this.listeners[eventName])) {
+      this.listeners[eventName].push(subscription);
+    } else {
+      this.listeners[eventName] = [subscription];
+    }
+
+    return {
+      unsubscribe: () => this._unsubscribe(eventName, listenerId),
+    };
+  } else {
+    throw new Error(`Event ${eventName} not supported.`);
+  }
+}
+
+/**
+ * Unsubscribe to measurement updates.
+ *
+ * @param {string} eventName The name of the event
+ * @param {string} listenerId The listeners id
+ * @return void
+ */
+function _unsubscribe(eventName, listenerId) {
+  if (!this.listeners[eventName]) {
+    return;
+  }
+
+  const listeners = this.listeners[eventName];
+  if (Array.isArray(listeners)) {
+    this.listeners[eventName] = listeners.filter(({ id }) => id !== listenerId);
+  } else {
+    this.listeners[eventName] = undefined;
+  }
+}
+
+/**
+ * Check if a given event is valid.
+ *
+ * @param {string} eventName The name of the event
+ * @return {boolean} Event name validation
+ */
+function _isValidEvent(eventName) {
+  return Object.values(this.EVENTS).includes(eventName);
+}
+
+/**
+ * Broadcasts changes.
+ *
+ * @param {string} eventName - The event name
+ * @param {func} callbackProps - Properties to pass callback
+ * @return void
+ */
+function publish(eventName, callbackProps) {
+  const hasListeners = Object.keys(this.listeners).length > 0;
+  const hasCallbacks = Array.isArray(this.listeners[eventName]);
+
+  if (hasListeners && hasCallbacks) {
+    this.listeners[eventName].forEach(listener => {
+      listener.callback(callbackProps);
+    });
+  }
+}

platform/core/src/studies/services/qido/StaticWadoClient.js

@@ -9,38 +9,27 @@ import { api } from 'dicomweb-client';
  */
 export default class StaticWadoClient extends api.DICOMwebClient {
   static filterKeys = {
-    StudyInstanceUID: '0020000D',
-    PatientName: '00100010',
-    PatientID: '00100020',
-    StudyDescription: '00081030',
-    ModalitiesInStudy: '00080061',
+    "StudyInstanceUID": "0020000D",
+    "PatientName": "00100010",
+    "00100020": "mrn",
+    "PatientID": "00100020",
+    "StudyDescription": "00081030",
+    "StudyDate": "00080020",
+    "ModalitiesInStudy": "00080061",
+    AccessionNumber: "00080050",
   };
 
   constructor(qidoConfig) {
     super(qidoConfig);
     this.staticWado = qidoConfig.staticWado;
-    this.extendMetadataWithInstances = qidoConfig.extendMetadataWithInstances;
-  }
-
-  async retrieveSeriesMetadata(options) {
-    if (!this.extendMetadataWithInstances)
-      return super.retrieveSeriesMetadata(options);
-    const results = await Promise.all([
-      super.retrieveSeriesMetadata(options),
-      this.searchForInstances(options),
-    ]);
-    const metadata = results[0];
-    const instances = results[1];
-    return metadata.map(item => {
-      const sopUID = item['00080018'].Value[0];
-      const instance = instances.find(
-        instance => instance['00080018'].Value[0] == sopUID
-      );
-      Object.assign(item, instance);
-      return item;
-    });
   }
 
+  /**
+   * Replace the search for studies remote query with a local version which
+   * retrieves a complete query list and then sub-selects from it locally.
+   * @param {*} options
+   * @returns
+   */
   async searchForStudies(options) {
     if (!this.staticWado) return super.searchForStudies(options);
 
@@ -56,6 +45,62 @@ export default class StaticWadoClient extends api.DICOMwebClient {
     return filtered;
   }
 
+  /**
+   * Compares values, matching any instance of desired to any instance of
+   * actual by recursively go through the paired set of values.  That is,
+   * this is O(m*n) where m is how many items in desired and n is the length of actual
+   * Then, at the individual item node, compares the Alphabetic name if present,
+   * and does a sub-string matching on string values, and otherwise does an
+   * exact match comparison.
+   *
+   * @param {*} desired
+   * @param {*} actual
+   * @returns true if the values match
+   */
+  compareValues(desired, actual) {
+    if (Array.isArray(desired)) {
+      return desired.find(item => this.compareValues(item, actual));
+    }
+    if (Array.isArray(actual)) {
+      return actual.find(actualItem => this.compareValues(desired, actualItem));
+    }
+    if (actual && actual.Alphabetic) {
+      actual = actual.Alphabetic;
+    }
+    if (typeof (actual) == 'string') {
+      if (actual.length === 0) return true;
+      if (desired.length === 0 || desired === '*') return true;
+      if (desired[0] === '*' && desired[desired.length - 1] === '*') {
+        console.log(`Comparing ${actual} to ${desired.substring(1, desired.length - 1)}`)
+        return actual.indexOf(desired.substring(1, desired.length - 1)) != -1;
+      } else if (desired[desired.length - 1] === '*') {
+        return actual.indexOf(desired.substring(0, desired.length - 1)) != -1;
+      } else if (desired[0] === '*') {
+        return actual.indexOf(desired.substring(1)) === actual.length - desired.length + 1;
+      }
+    }
+    return desired === actual;
+  }
+
+  /** Compares a pair of dates to see if the value is within the range */
+  compareDateRange(range, value) {
+    if (!value) return true;
+    const dash = range.indexOf('-');
+    if (dash === -1) return this.compareValues(range, value);
+    const start = range.substring(0, dash);
+    const end = range.substring(dash + 1);
+    return (!start || value >= start) &&
+      (!end || value <= end);
+  }
+
+  /**
+   * Filters the return list by the query parameters.
+   *
+   * @param {*} key
+   * @param {*} queryParams
+   * @param {*} study
+   * @returns
+   */
   filterItem(key, queryParams, study) {
     const altKey = StaticWadoClient.filterKeys[key] || key;
     if (!queryParams) return true;
@@ -63,23 +108,8 @@ export default class StaticWadoClient extends api.DICOMwebClient {
     if (!testValue) return true;
     const valueElem = study[key] || study[altKey];
     if (!valueElem) return false;
+    if (valueElem.vr == 'DA') return this.compareDateRange(testValue, valueElem.Value[0]);
     const value = valueElem.Value;
-    return this.eqItem(testValue, value);
-  }
-
-  eqItem(testValue, value) {
-    if (testValue.filter) {
-      return (
-        testValue.filter(testItem => this.eqItem(testItem, value)).length > 0
-      );
-    }
-    if (value === testValue) return true;
-    if (typeof value == 'string') {
-      return value.indexOf(testValue) != -1;
-    }
-    if (value.Alphabetic) return this.eqItem(testValue, value.Alphabetic);
-    if (value.filter)
-      return value.filter(item => this.eqItem(testValue, item)).length > 0;
-    return false;
+    return this.compareValues(testValue, value) && true;
   }
 }

platform/ui/CHANGELOG.md

@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.10.6](https://github.com/OHIF/Viewers/compare/@ohif/ui@1.10.5...@ohif/ui@1.10.6) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/ui
+
+
+
+
+
 ## [1.10.5](https://github.com/OHIF/Viewers/compare/@ohif/ui@1.10.4...@ohif/ui@1.10.5) (2021-11-30)
 
 **Note:** Version bump only for package @ohif/ui

platform/ui/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/ui",
-  "version": "1.10.5",
+  "version": "1.10.6",
   "description": "A set of React components for Medical Imaging Viewers",
   "author": "OHIF Contributors",
   "license": "MIT",

platform/ui/src/components/measurementTable/MeasurementTable.js

@@ -139,7 +139,6 @@ class MeasurementTable extends Component {
       const itemIndex = measurement.itemNumber || index + 1;
       const itemClass =
         selectedKey === key && !this.props.readOnly ? 'selected' : '';
-
       return (
         <MeasurementTableItem
           key={key}

platform/ui/src/components/measurementTable/MeasurementTableItem.js

@@ -22,11 +22,15 @@ class MeasurementTableItem extends Component {
   };
 
   render() {
-    const { warningTitle = '', hasWarnings } = this.props.measurementData;
+    const {
+      warningTitle = '',
+      hasWarnings,
+      isReadOnly,
+    } = this.props.measurementData;
 
     return (
       <React.Fragment>
-        {hasWarnings ? (
+        {hasWarnings && !isReadOnly ? (
           <OverlayTrigger
             key={this.props.itemIndex}
             placement="left"
@@ -44,8 +48,8 @@ class MeasurementTableItem extends Component {
             <div>{this.getTableListItem()}</div>
           </OverlayTrigger>
         ) : (
-            <React.Fragment>{this.getTableListItem()}</React.Fragment>
-          )}
+          <React.Fragment>{this.getTableListItem()}</React.Fragment>
+        )}
       </React.Fragment>
     );
   }
@@ -62,9 +66,11 @@ class MeasurementTableItem extends Component {
   };
 
   getTableListItem = () => {
-    const hasWarningClass = this.props.measurementData.hasWarnings
-      ? 'hasWarnings'
-      : '';
+    const hasWarningClass =
+      this.props.measurementData.hasWarnings &&
+      !this.props.measurementData.isReadOnly
+        ? 'hasWarnings'
+        : '';
 
     const actionButtons = [];
 
@@ -102,7 +108,9 @@ class MeasurementTableItem extends Component {
             })}
           </div>
           <div className="displayTexts">{this.getDataDisplayText()}</div>
-          <div className="rowActions">{actionButtons}</div>
+          {!this.props.measurementData.isReadOnly && (
+            <div className="rowActions">{actionButtons}</div>
+          )}
         </div>
       </TableListItem>
     );

platform/ui/src/components/studyBrowser/ImageThumbnail.js

@@ -59,9 +59,9 @@ function ImageThumbnail(props) {
       })
       .catch(error => {
         if (error.isCanceled) return;
-        setLoading(false);
-        setError(true);
-        throw new Error(error);
+        // setLoading(false);
+        // setError(true);
+        // throw new Error(error);
       });
   };
 

platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/docker-compose.yml

@@ -10,9 +10,9 @@ services:
   ohif_viewer:
     build:
       # Project root
-      context: ./../../
+      context: ./../../../../
       # Relative to context
-      dockerfile: ./docker/OpenResty-Orthanc-Keycloak/dockerfile
+      dockerfile: ./platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/dockerfile
     image: webapp:latest
     container_name: webapp
     volumes:
@@ -35,7 +35,7 @@ services:
   # TODO: Update to use Postgres
   # https://github.com/mrts/docker-postgresql-multiple-databases
   orthanc:
-    image: jodogne/orthanc-plugins:1.5.6
+    image: jodogne/orthanc-plugins:1.9.7
     hostname: orthanc
     container_name: orthanc
     volumes:
@@ -47,7 +47,7 @@ services:
 
   # LINK: https://hub.docker.com/r/jboss/keycloak
   keycloak:
-    image: jboss/keycloak:6.0.1
+    image: jboss/keycloak:16.1.0
     hostname: keycloak
     container_name: keycloak
     volumes:

platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/dockerfile

@@ -23,7 +23,9 @@
 
 
 # Stage 1: Build the application
-FROM node:11.2.0-slim as builder
+
+# Needs to be pinned at 16.x for now because of https://github.com/webpack/webpack/issues/14532
+FROM node:lts-slim as builder
 
 RUN mkdir /usr/src/app
 WORKDIR /usr/src/app
@@ -36,12 +38,12 @@ COPY yarn.lock /usr/src/app/yarn.lock
 
 ADD . /usr/src/app/
 RUN yarn install
-RUN yarn run build:web
+RUN yarn run build
 
 # Stage 2: Bundle the built application into a Docker container
 # which runs openresty (nginx) using Alpine Linux
 # LINK: https://hub.docker.com/r/openresty/openresty
-FROM openresty/openresty:1.15.8.1rc1-0-alpine-fat
+FROM openresty/openresty:1.19.9.1-4-alpine-fat
 
 RUN mkdir /var/log/nginx
 RUN apk add --no-cache openssl
@@ -60,6 +62,6 @@ RUN luarocks install lua-resty-openidc
 RUN luarocks install luacrypto
 
 # Copy build output to image
-COPY --from=builder /usr/src/app/build /var/www/html
+COPY --from=builder /usr/src/app/platform/viewer/dist /var/www/html
 
 ENTRYPOINT ["/usr/local/openresty/nginx/sbin/nginx", "-g", "daemon off;"]

platform/viewer/.recipes/OpenResty-Orthanc/docker-compose.yml

@@ -10,9 +10,9 @@ services:
   ohif_viewer:
     build:
       # Project root
-      context: ./../../
+      context: ./../../../../
       # Relative to context
-      dockerfile: ./docker/OpenResty-Orthanc/dockerfile
+      dockerfile: ./platform/viewer/.recipes/OpenResty-Orthanc/dockerfile
     image: webapp:latest
     container_name: webapp
     volumes:
@@ -34,7 +34,7 @@ services:
   # TODO: Update to use Postgres
   # https://github.com/mrts/docker-postgresql-multiple-databases
   orthanc:
-    image: jodogne/orthanc-plugins:1.5.6
+    image: jodogne/orthanc-plugins:1.9.7
     hostname: orthanc
     container_name: orthanc
     volumes:

platform/viewer/.recipes/OpenResty-Orthanc/dockerfile

@@ -23,7 +23,9 @@
 
 
 # Stage 1: Build the application
-FROM node:11.2.0-slim as builder
+
+# Needs to be pinned at 16.x for now because of https://github.com/webpack/webpack/issues/14532
+FROM node:lts-slim as builder
 
 RUN mkdir /usr/src/app
 WORKDIR /usr/src/app
@@ -36,12 +38,12 @@ COPY yarn.lock /usr/src/app/yarn.lock
 
 ADD . /usr/src/app/
 RUN yarn install
-RUN yarn run build:web
+RUN yarn run build
 
 # Stage 2: Bundle the built application into a Docker container
 # which runs openresty (nginx) using Alpine Linux
 # LINK: https://hub.docker.com/r/openresty/openresty
-FROM openresty/openresty:1.15.8.1rc1-0-alpine-fat
+FROM openresty/openresty:1.19.9.1-4-alpine-fat
 
 RUN mkdir /var/log/nginx
 RUN apk add --no-cache openssl
@@ -60,6 +62,6 @@ RUN luarocks install lua-resty-openidc
 RUN luarocks install luacrypto
 
 # Copy build output to image
-COPY --from=builder /usr/src/app/build /var/www/html
+COPY --from=builder /usr/src/app/platform/viewer/dist /var/www/html
 
 ENTRYPOINT ["/usr/local/openresty/nginx/sbin/nginx", "-g", "daemon off;"]

platform/viewer/.webpack/webpack.pwa.js

@@ -26,6 +26,16 @@ const PROXY_TARGET = process.env.PROXY_TARGET;
 const PROXY_DOMAIN = process.env.PROXY_DOMAIN;
 const ENTRY_TARGET = process.env.ENTRY_TARGET || `${SRC_DIR}/index.js`;
 
+
+const setHeaders = (res, path) => {
+  res.setHeader('Content-Type', 'text/plain')
+  if (path.indexOf('.gz') !== -1) {
+    res.setHeader('Content-Encoding', 'gzip')
+  } else if (path.indexOf('.br') !== -1) {
+    res.setHeader('Content-Encoding', 'br')
+  }
+}
+
 module.exports = (env, argv) => {
   const baseConfig = webpackBase(env, argv, { SRC_DIR, DIST_DIR });
   const isProdBuild = process.env.NODE_ENV === 'production';
@@ -134,11 +144,40 @@ module.exports = (env, argv) => {
       hot: true,
       open: true,
       port: 3000,
-      host: '0.0.0.0',
-      public: 'http://localhost:' + 3000,
+      client: {
+        overlay: { errors: true, warnings: false },
+      },
+      'static': [
+        {
+          directory: path.join(require('os').homedir(), 'dicomweb'),
+          staticOptions: {
+            extensions: ['gz', 'br'],
+            index: "index.json.gz",
+            redirect: true,
+            setHeaders,
+          },
+          publicPath: '/dicomweb',
+        },
+        {
+          directory: '../../testdata',
+          staticOptions: {
+            extensions: ['gz', 'br'],
+            index: "index.json.gz",
+            redirect: true,
+            setHeaders,
+          },
+          publicPath: '/testdata',
+        },
+      ],
+      //public: 'http://localhost:' + 3000,
+      //writeToDisk: true,
       historyApiFallback: {
         disableDotRule: true,
       },
+      headers: {
+        'Cross-Origin-Embedder-Policy': 'require-corp',
+        'Cross-Origin-Opener-Policy': 'same-origin',
+      },
     },
   });
 

platform/viewer/CHANGELOG.md

@@ -3,6 +3,78 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.12.19](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.18...@ohif/viewer@4.12.19) (2022-03-10)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.18](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.17...@ohif/viewer@4.12.18) (2022-02-15)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.17](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.16...@ohif/viewer@4.12.17) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.16](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.15...@ohif/viewer@4.12.16) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.15](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.14...@ohif/viewer@4.12.15) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.14](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.13...@ohif/viewer@4.12.14) (2022-01-31)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.13](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.12...@ohif/viewer@4.12.13) (2022-01-29)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.12](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.11...@ohif/viewer@4.12.12) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.11](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.10...@ohif/viewer@4.12.11) (2022-01-19)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
 ## [4.12.10](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.9...@ohif/viewer@4.12.10) (2022-01-13)
 
 **Note:** Version bump only for package @ohif/viewer

platform/viewer/cypress/support/commands.js

@@ -1,4 +1,5 @@
 import '@percy/cypress';
+import { enable } from 'cornerstone-core';
 import 'cypress-file-upload';
 import { DragSimulator } from '../helpers/DragSimulator.js';
 import {
@@ -199,6 +200,11 @@ Cypress.Commands.add('waitDicomImage', (timeout = 50000) => {
       .its('cornerstone')
       .then({ timeout }, $cornerstone => {
         return new Cypress.Promise(resolve => {
+          const onEnabled = enabledEvt => {
+            const element = enabledEvt.detail.element;
+
+            element.addEventListener('cornerstoneimagerendered', onEvent);
+          };
           const onEvent = renderedEvt => {
             const element = renderedEvt.detail.element;
 
@@ -209,15 +215,17 @@ Cypress.Commands.add('waitDicomImage', (timeout = 50000) => {
             );
             resolve();
           };
-          const onEnabled = enabledEvt => {
-            const element = enabledEvt.detail.element;
-
-            element.addEventListener('cornerstoneimagerendered', onEvent);
-          };
-          $cornerstone.events.addEventListener(
-            'cornerstoneelementenabled',
-            onEnabled
-          );
+          const enabledElements = $cornerstone.getEnabledElements();
+          if (enabledElements && enabledElements.length && !enabledElements[0].invalid) {
+            // Sometimes the page finishes rendering before this gets run,
+            // if so, just resolve immediately.
+            resolve();
+          } else {
+            $cornerstone.events.addEventListener(
+              'cornerstoneelementenabled',
+              onEnabled
+            );
+          }
         });
       });
   }

platform/viewer/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/viewer",
-  "version": "4.12.10",
+  "version": "4.12.19",
   "description": "OHIF Viewer",
   "author": "OHIF Contributors",
   "license": "MIT",
@@ -22,8 +22,8 @@
     "build:viewer:ci": "cross-env NODE_ENV=production PUBLIC_URL=/pwa/ APP_CONFIG=config/netlify.js QUICK_BUILD=true node --max_old_space_size=4096 ./../../node_modules/webpack/bin/webpack.js --config .webpack/webpack.pwa.js",
     "build:viewer:demo": "cross-env NODE_ENV=production APP_CONFIG=config/demo.js HTML_TEMPLATE=rollbar.html QUICK_BUILD=true node --max_old_space_size=4096 ./../../node_modules/webpack/bin/webpack.js --progress --config .webpack/webpack.pwa.js",
     "build:viewer:package": "yarn run build:package",
-    "dev": "cross-env NODE_ENV=development webpack-dev-server --config .webpack/webpack.pwa.js --watch",
-    "dev:orthanc": "cross-env NODE_ENV=development PROXY_TARGET=/dicom-web PROXY_DOMAIN=http://localhost:8042 APP_CONFIG=config/docker_nginx-orthanc.js webpack-dev-server --config .webpack/webpack.pwa.js --watch",
+    "dev": "cross-env NODE_ENV=development webpack-dev-server --config .webpack/webpack.pwa.js",
+    "dev:orthanc": "cross-env NODE_ENV=development PROXY_TARGET=/dicom-web PROXY_DOMAIN=http://localhost:8042 APP_CONFIG=config/docker_nginx-orthanc.js webpack-dev-server --config .webpack/webpack.pwa.js",
     "dev:viewer": "yarn run dev",
     "start": "yarn run dev",
     "test:e2e": "cypress open",
@@ -31,7 +31,7 @@
     "test:e2e:script-tag": "cypress run --config video=false --browser chrome --spec 'cypress/integration/common/**/*,cypress/integration/script-tag/**/*'",
     "test:e2e:local": "cypress run --config video=false --browser chrome --spec 'cypress/integration/common/**/*,cypress/integration/pwa/**/*'",
     "test:e2e:dist": "start-server-and-test test:e2e:serve http://localhost:3000 test:e2e:ci",
-    "test:e2e:serve": "serve -n -l 3000 -s dist",
+    "test:e2e:serve": "cross-env APP_CONFIG=config/e2e.js yarn start",
     "test:unit": "jest --watchAll",
     "test:unit:ci": "jest --ci --runInBand --collectCoverage",
     "prepublishOnly": "yarn run build:package",
@@ -47,18 +47,18 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
-    "@ohif/core": "^2.16.6",
-    "@ohif/extension-cornerstone": "^2.12.3",
-    "@ohif/extension-debugging": "^0.3.1",
-    "@ohif/extension-dicom-html": "^1.3.14",
+    "@ohif/core": "^2.16.12",
+    "@ohif/extension-cornerstone": "^2.12.7",
+    "@ohif/extension-debugging": "^0.3.2",
+    "@ohif/extension-dicom-html": "^1.3.18",
     "@ohif/extension-dicom-microscopy": "^0.52.0",
-    "@ohif/extension-dicom-pdf": "^1.1.1",
-    "@ohif/extension-dicom-rt": "^0.7.4",
-    "@ohif/extension-dicom-segmentation": "^0.7.5",
+    "@ohif/extension-dicom-pdf": "^1.1.2",
+    "@ohif/extension-dicom-rt": "^0.7.8",
+    "@ohif/extension-dicom-segmentation": "^0.7.8",
     "@ohif/extension-lesion-tracker": "^0.2.1",
-    "@ohif/extension-vtk": "^1.12.10",
+    "@ohif/extension-vtk": "^1.12.16",
     "@ohif/i18n": "^0.53.0",
-    "@ohif/ui": "^1.10.5",
+    "@ohif/ui": "^1.10.6",
     "@tanem/react-nprogress": "^1.1.25",
     "classnames": "^2.2.6",
     "core-js": "^3.2.1",
@@ -66,7 +66,7 @@
     "cornerstone-math": "^0.1.9",
     "cornerstone-tools": "^6.0.6",
     "cornerstone-wado-image-loader": "^4.1.0",
-    "dcmjs": "0.19.1",
+    "dcmjs": "0.19.4",
     "dicom-parser": "^1.8.11",
     "dicomweb-client": "^0.8.3",
     "hammerjs": "^2.0.8",
@@ -94,7 +94,7 @@
     "cypress": "^6.0.0",
     "gh-pages": "2.0.1",
     "identity-obj-proxy": "3.0.x",
-    "lodash": "4.17.15",
+    "lodash": "4.17.21",
     "lodash.clonedeep": "4.5.0"
   }
 }

platform/viewer/public/config/e2e.js

@@ -0,0 +1,116 @@
+window.config = {
+  routerBasename: '/',
+  showStudyList: true,
+  servers: {
+    dicomWeb: [
+      {
+        name: 'LocalStatic',
+        wadoUriRoot: '/testdata',
+        qidoRoot: '/testdata',
+        wadoRoot: '/testdata',
+        qidoSupportsIncludeField: false,
+        imageRendering: 'wadors',
+        enableStudyLazyLoad: true,
+        supportsFuzzyMatching: false,
+        staticWado: true,
+      },
+    ],
+  },
+  // Extensions should be able to suggest default values for these?
+  // Or we can require that these be explicitly set
+  hotkeys: [
+    // ~ Global
+    {
+      commandName: 'incrementActiveViewport',
+      label: 'Next Viewport',
+      keys: ['right'],
+    },
+    {
+      commandName: 'decrementActiveViewport',
+      label: 'Previous Viewport',
+      keys: ['left'],
+    },
+    // Supported Keys: https://craig.is/killing/mice
+    // ~ Cornerstone Extension
+    { commandName: 'rotateViewportCW', label: 'Rotate Right', keys: ['r'] },
+    { commandName: 'rotateViewportCCW', label: 'Rotate Left', keys: ['l'] },
+    { commandName: 'invertViewport', label: 'Invert', keys: ['i'] },
+    {
+      commandName: 'flipViewportVertical',
+      label: 'Flip Horizontally',
+      keys: ['h'],
+    },
+    {
+      commandName: 'flipViewportHorizontal',
+      label: 'Flip Vertically',
+      keys: ['v'],
+    },
+    { commandName: 'scaleUpViewport', label: 'Zoom In', keys: ['+'] },
+    { commandName: 'scaleDownViewport', label: 'Zoom Out', keys: ['-'] },
+    { commandName: 'fitViewportToWindow', label: 'Zoom to Fit', keys: ['='] },
+    { commandName: 'resetViewport', label: 'Reset', keys: ['space'] },
+    // clearAnnotations
+    { commandName: 'nextImage', label: 'Next Image', keys: ['down'] },
+    { commandName: 'previousImage', label: 'Previous Image', keys: ['up'] },
+    // firstImage
+    // lastImage
+    {
+      commandName: 'previousViewportDisplaySet',
+      label: 'Previous Series',
+      keys: ['pagedown'],
+    },
+    {
+      commandName: 'nextViewportDisplaySet',
+      label: 'Next Series',
+      keys: ['pageup'],
+    },
+    // ~ Cornerstone Tools
+    { commandName: 'setZoomTool', label: 'Zoom', keys: ['z'] },
+    // ~ Window level presets
+    {
+      commandName: 'windowLevelPreset1',
+      label: 'W/L Preset 1',
+      keys: ['1'],
+    },
+    {
+      commandName: 'windowLevelPreset2',
+      label: 'W/L Preset 2',
+      keys: ['2'],
+    },
+    {
+      commandName: 'windowLevelPreset3',
+      label: 'W/L Preset 3',
+      keys: ['3'],
+    },
+    {
+      commandName: 'windowLevelPreset4',
+      label: 'W/L Preset 4',
+      keys: ['4'],
+    },
+    {
+      commandName: 'windowLevelPreset5',
+      label: 'W/L Preset 5',
+      keys: ['5'],
+    },
+    {
+      commandName: 'windowLevelPreset6',
+      label: 'W/L Preset 6',
+      keys: ['6'],
+    },
+    {
+      commandName: 'windowLevelPreset7',
+      label: 'W/L Preset 7',
+      keys: ['7'],
+    },
+    {
+      commandName: 'windowLevelPreset8',
+      label: 'W/L Preset 8',
+      keys: ['8'],
+    },
+    {
+      commandName: 'windowLevelPreset9',
+      label: 'W/L Preset 9',
+      keys: ['9'],
+    },
+  ],
+};

platform/viewer/public/config/local_static.js

@@ -5,9 +5,9 @@ window.config = {
     dicomWeb: [
       {
         name: 'LocalStatic',
-        wadoUriRoot: 'http://localhost:5000/',
-        qidoRoot: 'http://localhost:5000',
-        wadoRoot: 'http://localhost:5000/',
+        wadoUriRoot: '/dicomweb',
+        qidoRoot: '/dicomweb',
+        wadoRoot: '/dicomweb',
         qidoSupportsIncludeField: false,
         imageRendering: 'wadors',
         thumbnailRendering: 'thumbnail',

platform/viewer/src/appExtensions/MeasurementsPanel/ConnectedMeasurementTable.js

@@ -136,6 +136,7 @@ function convertMeasurementsToTableData(toolCollections, timepoints) {
         measurementNumber,
         lesionNamingNumber,
         toolType,
+        isReadOnly
       } = measurementData;
       const measurementId = measurementData._id;
 
@@ -154,6 +155,7 @@ function convertMeasurementsToTableData(toolCollections, timepoints) {
         lesionNamingNumber,
         toolType,
         hasWarnings,
+        isReadOnly,
         warningTitle,
         warningList,
         isSplitLesion: false, //TODO

platform/viewer/src/connectedComponents/Viewer.js

@@ -11,7 +11,7 @@ import ConnectedStudyBrowser from './ConnectedStudyBrowser.js';
 import ConnectedViewerMain from './ConnectedViewerMain.js';
 import SidePanel from './../components/SidePanel.js';
 import ErrorBoundaryDialog from './../components/ErrorBoundaryDialog';
-import { extensionManager } from './../App.js';
+import { extensionManager, servicesManager } from './../App.js';
 import { ReconstructionIssues } from './../../../core/src/enums.js';
 
 // Contexts
@@ -70,9 +70,11 @@ class Viewer extends Component {
     const { activeServer } = this.props;
     const server = Object.assign({}, activeServer);
 
+    const external = { servicesManager };
+
     OHIF.measurements.MeasurementApi.setConfiguration({
       dataExchange: {
-        retrieve: DICOMSR.retrieveMeasurements,
+        retrieve: server => DICOMSR.retrieveMeasurements(server, external),
         store: DICOMSR.storeMeasurements,
       },
       server,

runtime.txt

@@ -0,0 +1 @@
+3.7