chore(release): publish [skip ci]

- @ohif/extension-cornerstone@2.5.0
 - @ohif/extension-dicom-segmentation@0.1.0
 - @ohif/extension-vtk@1.3.0
 - @ohif/core@2.6.0
 - @ohif/ui@1.4.0
 - @ohif/viewer@3.8.0

.vscode/settings.json

@@ -28,5 +28,8 @@
   ],
   "prettier.disableLanguages": ["html"],
   "prettier.endOfLine": "lf",
-  "workbench.colorCustomizations": {}
+  "workbench.colorCustomizations": {},
+  "editor.codeActionsOnSave": {
+    "source.fixAll.eslint": true
+  }
 }

docs/latest/extensions/modules/panel.md

@@ -40,6 +40,10 @@ export default {
           from: 'right',
           // The target component to toggle open/close
           target: 'target-component-id',
+          // UI Hint; If the target panel is in a "disabled" state
+          isDisabled: studies => {
+            return false;
+          },
           // Overrides `defaultContext`, if specified
           context: ['ACTIVE_VIEWPORT:MAGIC'],
         },

docs/latest/extensions/modules/sop-class-handler.md

@@ -5,7 +5,7 @@ An extension can register a SOP Class Handler Module by defining a
 the other modules, as it doesn't provide a `1:1` schema for UI or provide it's
 own components. It instead defines:
 
-- `sopClassUids`: an array of string SOP Class UIDs that the
+- `sopClassUIDs`: an array of string SOP Class UIDs that the
   `getDisplaySetFromSeries` method should be applied to.
 - `getDisplaySetFromSeries`: a method that maps series and study metadata to a
   display set
@@ -15,13 +15,13 @@ A `displaySet` has the following shape:
 ```js
 return {
   plugin: 'html',
-  modality: 'SR',
-  displaySetInstanceUid: 0,
+  Modality: 'SR',
+  displaySetInstanceUID: 0,
   wadoRoot: study.getData().wadoRoot,
   wadoUri: instance.getData().wadouri,
-  sopInstanceUid: instance.getSOPInstanceUID(),
-  seriesInstanceUid: series.getSeriesInstanceUID(),
-  studyInstanceUid: study.getStudyInstanceUID(),
+  SOPInstanceUID: instance.getSOPInstanceUID(),
+  SeriesInstanceUID: series.getSeriesInstanceUID(),
+  StudyInstanceUID: study.getStudyInstanceUID(),
   authorizationHeaders,
 };
 ```
@@ -50,7 +50,7 @@ export default {
 getSopClassHandlerModule({ servicesManager, commandsManager }) {
   return {
     id: 'OHIFDicomHtmlSopClassHandler',
-    sopClassUids: Object.values(SOP_CLASS_UIDS),
+    sopClassUIDs: Object.values(SOP_CLASS_UIDS),
 
     /**
      * @param {object} series -
@@ -63,12 +63,12 @@ getSopClassHandlerModule({ servicesManager, commandsManager }) {
 
       return {
         plugin: 'html',
-        displaySetInstanceUid: 0,
+        displaySetInstanceUID: 0,
         wadoRoot: study.getData().wadoRoot,
         wadoUri: instance.getData().wadouri,
-        sopInstanceUid: instance.getSOPInstanceUID(),
-        seriesInstanceUid: series.getSeriesInstanceUID(),
-        studyInstanceUid: study.getStudyInstanceUID(),
+        SOPInstanceUID: instance.getSOPInstanceUID(),
+        SeriesInstanceUID: series.getSeriesInstanceUID(),
+        StudyInstanceUID: study.getStudyInstanceUID(),
         authorizationHeaders,
       };
     },

docs/v1/lesion-tracker/audit-trail.md

@@ -1,6 +1,7 @@
 # Lesion Tracker - Audit Trail
 
 1. To view Audit Trails, select **View Audit Log** on the Configuration menu.
-2. To filter audit logs for a column or multiple columns, type or select in the related column or columns.
+2. To filter audit logs for a column or multiple columns, type or select in the
+   related column or columns.
 
 ![Audit Trails](../assets/img/LesionTracker/LT_Audit_Trails.png)

docs/v1/lesion-tracker/study-and-timepoint-management.md

@@ -2,50 +2,74 @@
 
 ![Study List](../assets/img/LesionTracker/LT_StudyList.png)
 
-1. Study List allows to sort each column. To sort studies, click the desired column header.
-2. Study List is filterable for each column and you can filter by more than one column by typing in the column field. To filter a column, type the text in the desired column header field and press Enter.
-3. Pagination is provided for the Study List at the bottom of the page. You can change the number of rows per page or the current page.
+1. Study List allows to sort each column. To sort studies, click the desired
+   column header.
+2. Study List is filterable for each column and you can filter by more than one
+   column by typing in the column field. To filter a column, type the text in
+   the desired column header field and press Enter.
+3. Pagination is provided for the Study List at the bottom of the page. You can
+   change the number of rows per page or the current page.
 
 ## Study List Context Menu
 
-When you right-click on the study row, Study Context Menu will pop up. Study Context Menu includes operations at the study level.
+When you right-click on the study row, Study Context Menu will pop up. Study
+Context Menu includes operations at the study level.
 
 There are a couple of ways to view a study:
 
-* Simply double-click on the study row.
-* Select **View** option on the Study Context Menu, then you will be redirected to Viewer page.
+- Simply double-click on the study row.
+- Select **View** option on the Study Context Menu, then you will be redirected
+  to Viewer page.
 
 ![View Study](../assets/img/LesionTracker/LT_View_Study.png)
 
 ### Timepoint Association
 
-1. To link a study with a timepoint, right-click on the study row and select **Associate** option on the Study Context Menu. You will see Study Association dialog.
-2. To link multiple studies at the same time, hold Shift key and select studies you would like to associate, then right-click and select Associate on the Study Context Menu
+1. To link a study with a timepoint, right-click on the study row and select
+   **Associate** option on the Study Context Menu. You will see Study
+   Association dialog.
+2. To link multiple studies at the same time, hold Shift key and select studies
+   you would like to associate, then right-click and select Associate on the
+   Study Context Menu
 
 ![Select Associate](../assets/img/LesionTracker/LT_Select_Associate.png)
 
-The Study Association dialog allows you to select and unselect Timepoint Type for the selected study or studies. Also, it will include all studies within 14 days of your selected studies, in case you forgot to select a study. After you identify timepoints for the selected study or studies, click **Save** to save the association.
+The Study Association dialog allows you to select and unselect Timepoint Type
+for the selected study or studies. Also, it will include all studies within 14
+days of your selected studies, in case you forgot to select a study. After you
+identify timepoints for the selected study or studies, click **Save** to save
+the association.
 
 ![Association Dialog](../assets/img/LesionTracker/LT_Association_Dialog.png)
 
 ### Remove Timepoint Association
-To unlink a timepoint association with a study, right-click on the study row and select **Remove Association** option on the Study Context Menu. Remove Association will be disabled if the study is already dissociated.
+
+To unlink a timepoint association with a study, right-click on the study row and
+select **Remove Association** option on the Study Context Menu. Remove
+Association will be disabled if the study is already dissociated.
 
 ![Remove Associate](../assets/img/LesionTracker/LT_Remove_Associate.png)
 
 ### View Series Details
-To view details of related series, right-click on the study row and select **View Series Details** option on the Study Context Menu, then Series Details dialog will pop up. Series Details dialog gives a summary of the selected study.
+
+To view details of related series, right-click on the study row and select
+**View Series Details** option on the Study Context Menu, then Series Details
+dialog will pop up. Series Details dialog gives a summary of the selected study.
 
 ![View Series Details](../assets/img/LesionTracker/LT_View_Series_Details.png)
 
 ### Anonymize (Under Development)
+
 ...
 
 ### Send (Under Development)
+
 ...
 
 ### Export (Under Development)
+
 ...
 
 ### Delete (Under Development)
+
 ...

extensions/_example/src/index.js

@@ -21,7 +21,6 @@ export default {
   /**
    * MODULE GETTERS
    */
-
   getViewportModule() {
     return '... react component ...';
   },
@@ -64,7 +63,7 @@ const commandsModule = {
  */
 const sopClassHandlerModule = {
   id: 'OHIFDicomHtmlSopClassHandler',
-  sopClassUids: Object.values({
+  sopClassUIDs: Object.values({
     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',
@@ -78,12 +77,12 @@ const sopClassHandlerModule = {
 
     return {
       plugin: 'html',
-      displaySetInstanceUid: 0, //utils.guid(),
+      displaySetInstanceUID: 0, //utils.guid(),
       wadoRoot: study.getData().wadoRoot,
       wadoUri: instance.getData().wadouri,
-      sopInstanceUid: instance.getSOPInstanceUID(),
-      seriesInstanceUid: series.getSeriesInstanceUID(),
-      studyInstanceUid: study.getStudyInstanceUID(),
+      SOPInstanceUID: instance.getSOPInstanceUID(),
+      SeriesInstanceUID: series.getSeriesInstanceUID(),
+      StudyInstanceUID: study.getStudyInstanceUID(),
       authorizationHeaders,
     };
   },
@@ -98,6 +97,9 @@ const panelModule = {
       icon: 'th-list',
       label: 'Segments',
       target: 'segment-panel',
+      isDisabled: studies => {
+        return false;
+      },
     },
   ],
   components: [

extensions/cornerstone/CHANGELOG.md

@@ -3,6 +3,47 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+# [2.5.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.4.3...@ohif/extension-cornerstone@2.5.0) (2020-03-13)
+
+
+### Features
+
+* Segmentations Settings UI - Phase 1 [#1391](https://github.com/OHIF/Viewers/issues/1391) ([#1392](https://github.com/OHIF/Viewers/issues/1392)) ([e8842cf](https://github.com/OHIF/Viewers/commit/e8842cf8aebde98db7fc123e4867c8288552331f)), closes [#1423](https://github.com/OHIF/Viewers/issues/1423)
+
+
+
+
+
+## [2.4.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.4.2...@ohif/extension-cornerstone@2.4.3) (2020-03-09)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.4.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.4.1...@ohif/extension-cornerstone@2.4.2) (2020-03-09)
+
+
+### Bug Fixes
+
+* Remove Eraser and ROI Window ([6c950a9](https://github.com/OHIF/Viewers/commit/6c950a9669f7fbf3c46e48679fa26ee514824156))
+
+
+
+
+
+## [2.4.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.4.0...@ohif/extension-cornerstone@2.4.1) (2020-03-03)
+
+
+### Bug Fixes
+
+* bump react-cornerstone-viewport version to address critical issue ([#1473](https://github.com/OHIF/Viewers/issues/1473)) ([ee80e02](https://github.com/OHIF/Viewers/commit/ee80e026610442e94caf5e4e3e4d193220cd0ece))
+
+
+
+
+
 # [2.4.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.3.1...@ohif/extension-cornerstone@2.4.0) (2020-02-20)
 
 

extensions/cornerstone/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone",
-  "version": "2.4.0",
+  "version": "2.5.0",
   "description": "OHIF extension for Cornerstone",
   "author": "OHIF",
   "license": "MIT",
@@ -34,9 +34,9 @@
     "@ohif/ui": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-math": "^0.1.8",
-    "cornerstone-tools": "^4.12.0",
+    "cornerstone-tools": "4.12.5",
     "cornerstone-wado-image-loader": "^3.0.0",
-    "dcmjs": "^0.8.2",
+    "dcmjs": "^0.10.1",
     "dicom-parser": "^1.8.3",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",
@@ -51,7 +51,6 @@
     "classnames": "^2.2.6",
     "lodash.merge": "^4.6.2",
     "lodash.throttle": "^4.1.1",
-    "query-string": "^6.8.3",
-    "react-cornerstone-viewport": "2.x.x"
+    "react-cornerstone-viewport": "^2.3.6"
   }
 }

extensions/cornerstone/src/OHIFCornerstoneViewport.js

@@ -4,28 +4,9 @@ import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
 import OHIF from '@ohif/core';
 import PropTypes from 'prop-types';
 import cornerstone from 'cornerstone-core';
-import handleSegmentationStorage from './handleSegmentationStorage.js';
 
 const { StackManager } = OHIF.utils;
 
-// Metadata configuration
-const metadataProvider = new OHIF.cornerstone.MetadataProvider();
-
-cornerstone.metaData.addProvider(
-  metadataProvider.provider.bind(metadataProvider)
-);
-
-StackManager.setMetadataProvider(metadataProvider);
-
-const SOP_CLASSES = {
-  SEGMENTATION_STORAGE: '1.2.840.10008.5.1.4.1.1.66.4',
-};
-
-const specialCaseHandlers = {};
-specialCaseHandlers[
-  SOP_CLASSES.SEGMENTATION_STORAGE
-] = handleSegmentationStorage;
-
 class OHIFCornerstoneViewport extends Component {
   state = {
     viewportData: null,
@@ -58,34 +39,34 @@ class OHIFCornerstoneViewport extends Component {
    * Obtain the CornerstoneTools Stack for the specified display set.
    *
    * @param {Object[]} studies
-   * @param {String} studyInstanceUid
-   * @param {String} displaySetInstanceUid
-   * @param {String} [sopInstanceUid]
+   * @param {String} StudyInstanceUID
+   * @param {String} displaySetInstanceUID
+   * @param {String} [SOPInstanceUID]
    * @param {Number} [frameIndex=1]
    * @return {Object} CornerstoneTools Stack
    */
   static getCornerstoneStack(
     studies,
-    studyInstanceUid,
-    displaySetInstanceUid,
-    sopInstanceUid,
+    StudyInstanceUID,
+    displaySetInstanceUID,
+    SOPInstanceUID,
     frameIndex = 0
   ) {
     if (!studies || !studies.length) {
       throw new Error('Studies not provided.');
     }
 
-    if (!studyInstanceUid) {
+    if (!StudyInstanceUID) {
       throw new Error('StudyInstanceUID not provided.');
     }
 
-    if (!displaySetInstanceUid) {
+    if (!displaySetInstanceUID) {
       throw new Error('StudyInstanceUID not provided.');
     }
 
     // Create shortcut to displaySet
     const study = studies.find(
-      study => study.studyInstanceUid === studyInstanceUid
+      study => study.StudyInstanceUID === StudyInstanceUID
     );
 
     if (!study) {
@@ -93,7 +74,7 @@ class OHIFCornerstoneViewport extends Component {
     }
 
     const displaySet = study.displaySets.find(set => {
-      return set.displaySetInstanceUid === displaySetInstanceUid;
+      return set.displaySetInstanceUID === displaySetInstanceUID;
     });
 
     if (!displaySet) {
@@ -107,17 +88,14 @@ class OHIFCornerstoneViewport extends Component {
     const stack = Object.assign({}, storedStack);
     stack.currentImageIdIndex = frameIndex;
 
-    if (sopInstanceUid) {
+    if (SOPInstanceUID) {
       const index = stack.imageIds.findIndex(imageId => {
-        const sopCommonModule = cornerstone.metaData.get(
-          'sopCommonModule',
+        const imageIdSOPInstanceUID = cornerstone.metaData.get(
+          'SOPInstanceUID',
           imageId
         );
-        if (!sopCommonModule) {
-          return;
-        }
 
-        return sopCommonModule.sopInstanceUID === sopInstanceUid;
+        return imageIdSOPInstanceUID === SOPInstanceUID;
       });
 
       if (index > -1) {
@@ -134,44 +112,26 @@ class OHIFCornerstoneViewport extends Component {
 
   getViewportData = async (
     studies,
-    studyInstanceUid,
-    displaySetInstanceUid,
-    sopClassUid,
-    sopInstanceUid,
+    StudyInstanceUID,
+    displaySetInstanceUID,
+    SOPInstanceUID,
     frameIndex
   ) => {
     let viewportData;
 
-    switch (sopClassUid) {
-      case SOP_CLASSES.SEGMENTATION_STORAGE:
-        const specialCaseHandler =
-          specialCaseHandlers[SOP_CLASSES.SEGMENTATION_STORAGE];
+    const stack = OHIFCornerstoneViewport.getCornerstoneStack(
+      studies,
+      StudyInstanceUID,
+      displaySetInstanceUID,
+      SOPInstanceUID,
+      frameIndex
+    );
 
-        viewportData = await specialCaseHandler(
-          studies,
-          studyInstanceUid,
-          displaySetInstanceUid,
-          sopInstanceUid,
-          frameIndex
-        );
-        break;
-      default:
-        const stack = OHIFCornerstoneViewport.getCornerstoneStack(
-          studies,
-          studyInstanceUid,
-          displaySetInstanceUid,
-          sopInstanceUid,
-          frameIndex
-        );
-
-        viewportData = {
-          studyInstanceUid,
-          displaySetInstanceUid,
-          stack,
-        };
-
-        break;
-    }
+    viewportData = {
+      StudyInstanceUID,
+      displaySetInstanceUID,
+      stack,
+    };
 
     return viewportData;
   };
@@ -179,31 +139,28 @@ class OHIFCornerstoneViewport extends Component {
   setStateFromProps() {
     const { studies, displaySet } = this.props.viewportData;
     const {
-      studyInstanceUid,
-      displaySetInstanceUid,
-      sopClassUids,
-      sopInstanceUid,
+      StudyInstanceUID,
+      displaySetInstanceUID,
+      sopClassUIDs,
+      SOPInstanceUID,
       frameIndex,
     } = displaySet;
 
-    if (!studyInstanceUid || !displaySetInstanceUid) {
+    if (!StudyInstanceUID || !displaySetInstanceUID) {
       return;
     }
 
-    if (sopClassUids && sopClassUids.length > 1) {
+    if (sopClassUIDs && sopClassUIDs.length > 1) {
       console.warn(
-        'More than one SOPClassUid in the same series is not yet supported.'
+        'More than one SOPClassUID in the same series is not yet supported.'
       );
     }
 
-    const sopClassUid = sopClassUids && sopClassUids[0];
-
     this.getViewportData(
       studies,
-      studyInstanceUid,
-      displaySetInstanceUid,
-      sopClassUid,
-      sopInstanceUid,
+      StudyInstanceUID,
+      displaySetInstanceUID,
+      SOPInstanceUID,
       frameIndex
     ).then(viewportData => {
       this.setState({
@@ -217,13 +174,13 @@ class OHIFCornerstoneViewport extends Component {
   }
 
   componentDidUpdate(prevProps) {
-    const { studies, displaySet } = this.props.viewportData;
+    const { displaySet } = this.props.viewportData;
     const prevDisplaySet = prevProps.viewportData.displaySet;
 
     if (
-      displaySet.displaySetInstanceUid !==
-        prevDisplaySet.displaySetInstanceUid ||
-      displaySet.sopInstanceUid !== prevDisplaySet.sopInstanceUid ||
+      displaySet.displaySetInstanceUID !==
+        prevDisplaySet.displaySetInstanceUID ||
+      displaySet.SOPInstanceUID !== prevDisplaySet.SOPInstanceUID ||
       displaySet.frameIndex !== prevDisplaySet.frameIndex
     ) {
       this.setStateFromProps();

extensions/cornerstone/src/commandsModule.js

@@ -247,6 +247,7 @@ const commandsModule = ({ servicesManager }) => {
 
       if (enabledElement) {
         let viewport = cornerstone.getViewport(enabledElement);
+
         viewport.voi = {
           windowWidth: Number(window),
           windowCenter: Number(level),

extensions/cornerstone/src/handleSegmentationStorage.js

@@ -1,128 +0,0 @@
-import * as dcmjs from 'dcmjs';
-
-import OHIF from '@ohif/core';
-import cornerstone from 'cornerstone-core';
-import cornerstoneTools from 'cornerstone-tools';
-
-const { StackManager, DicomLoaderService } = OHIF.utils;
-
-function getDisplaySet(studies, studyInstanceUid, displaySetInstanceUid) {
-  const study = studies.find(
-    study => study.studyInstanceUid === studyInstanceUid
-  );
-
-  const displaySet = study.displaySets.find(set => {
-    return set.displaySetInstanceUid === displaySetInstanceUid;
-  });
-
-  return displaySet;
-}
-
-function getDisplaySetsBySeries(studies, studyInstanceUid, seriesInstanceUid) {
-  const study = studies.find(
-    study => study.studyInstanceUid === studyInstanceUid
-  );
-
-  return study.displaySets.filter(set => {
-    return set.seriesInstanceUid === seriesInstanceUid;
-  });
-}
-
-function parseSeg(arrayBuffer, imageIds) {
-  return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
-    imageIds,
-    arrayBuffer,
-    cornerstone.metaData
-  );
-}
-
-function addSegMetadataToCornerstoneToolState(
-  segMetadata,
-  toolState,
-  displaySetInstanceUid
-) {
-  cornerstoneTools.globalImageIdSpecificToolStateManager.restoreToolState(
-    toolState
-  );
-
-  const brushModule = cornerstoneTools.store.modules.brush;
-
-  for (let i = 0; i < segMetadata.length; i++) {
-    brushModule.setters.metadata(displaySetInstanceUid, i, segMetadata[i]);
-  }
-}
-
-async function handleSegmentationStorage(
-  studies,
-  studyInstanceUid,
-  displaySetInstanceUid
-) {
-  const study = studies.find(
-    study => study.studyInstanceUid === studyInstanceUid
-  );
-  const displaySet = getDisplaySet(
-    studies,
-    studyInstanceUid,
-    displaySetInstanceUid
-  );
-
-  const arrayBuffer = await DicomLoaderService.findDicomDataPromise(
-    displaySet,
-    studies
-  );
-  const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
-  const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
-    dicomData.dict
-  );
-
-  dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
-
-  const seriesInstanceUid = dataset.ReferencedSeriesSequence.SeriesInstanceUID;
-  const displaySets = getDisplaySetsBySeries(
-    studies,
-    studyInstanceUid,
-    seriesInstanceUid
-  );
-
-  if (displaySets.length > 1) {
-    console.warn(
-      'More than one display set with the same seriesInstanceUid. This is not supported yet...'
-    );
-  }
-
-  const referenceDisplaySet = displaySets[0];
-  const imageIds = referenceDisplaySet.images.map(image => image.getImageId());
-  const results = parseSeg(arrayBuffer, imageIds);
-
-  if (!results) {
-    throw new Error('Fractional segmentations are not supported');
-  }
-
-  const { labelmapBuffer, segMetadata, segmentsOnFrame } = results;
-  const { setters } = cornerstoneTools.getModule('segmentation');
-
-  setters.labelmap3DByFirstImageId(
-    imageIds[0],
-    labelmapBuffer,
-    0, // TODO -> Can define a color LUT based on colors in the SEG later.
-    segMetadata,
-    imageIds.length,
-    segmentsOnFrame
-  );
-
-  const cachedStack = StackManager.findOrCreateStack(
-    study,
-    referenceDisplaySet
-  );
-  const stack = Object.assign({}, cachedStack);
-
-  stack.currentImageIdIndex = 0;
-
-  return {
-    studyInstanceUid,
-    displaySetInstanceUid,
-    stack,
-  };
-}
-
-export default handleSegmentationStorage;

extensions/cornerstone/src/init.js

@@ -3,29 +3,9 @@ import { SimpleDialog } from '@ohif/ui';
 import cornerstone from 'cornerstone-core';
 import csTools from 'cornerstone-tools';
 import merge from 'lodash.merge';
-import queryString from 'query-string';
 import initCornerstoneTools from './initCornerstoneTools.js';
 import measurementServiceMappingsFactory from './utils/measurementServiceMappings/measurementServiceMappingsFactory';
 
-function fallbackMetaDataProvider(type, imageId) {
-  if (!imageId.includes('wado?requestType=WADO')) {
-    return;
-  }
-
-  // If you call for an WADO-URI imageId and get no
-  // metadata, try reformatting to WADO-RS imageId
-  const qs = queryString.parse(imageId);
-  const wadoRoot = window.store.getState().servers.servers[0].wadoRoot;
-  const wadoRsImageId = `wadors:${wadoRoot}/studies/${qs.studyUID}/series/${
-    qs.seriesUID
-    }/instances/${qs.objectUID}/frames/${qs.frame || 1}`;
-
-  return cornerstone.metaData.get(type, wadoRsImageId);
-}
-
-// Add this fallback provider with a low priority so it is handled last
-cornerstone.metaData.addProvider(fallbackMetaDataProvider, -1);
-
 /**
  *
  * @param {Object} servicesManager
@@ -58,16 +38,13 @@ export default function init({ servicesManager, configuration }) {
   };
 
   const { csToolsConfig } = configuration;
-  const { StackManager } = OHIF.utils;
-  const metadataProvider = new OHIF.cornerstone.MetadataProvider();
+  const metadataProvider = OHIF.cornerstone.metadataProvider;
 
-  // ~~ Set our MetadataProvider
   cornerstone.metaData.addProvider(
-    metadataProvider.provider.bind(metadataProvider)
+    metadataProvider.get.bind(metadataProvider),
+    9999
   );
 
-  StackManager.setMetadataProvider(metadataProvider);
-
   // ~~
   const defaultCsToolsConfig = csToolsConfig || {
     globalToolSyncEnabled: true,
@@ -81,7 +58,6 @@ export default function init({ servicesManager, configuration }) {
     touch: [csTools.PanMultiTouchTool, csTools.ZoomTouchPinchTool],
     annotations: [
       csTools.ArrowAnnotateTool,
-      csTools.EraserTool,
       csTools.BidirectionalTool,
       csTools.LengthTool,
       csTools.AngleTool,
@@ -90,7 +66,6 @@ export default function init({ servicesManager, configuration }) {
       csTools.DragProbeTool,
       csTools.RectangleRoiTool,
     ],
-    segmentation: [csTools.BrushTool],
     other: [
       csTools.PanTool,
       csTools.ZoomTool,
@@ -189,7 +164,9 @@ export default function init({ servicesManager, configuration }) {
 
 const _initMeasurementService = measurementService => {
   /* Initialization */
-  const { toAnnotation, toMeasurement } = measurementServiceMappingsFactory(measurementService);
+  const { toAnnotation, toMeasurement } = measurementServiceMappingsFactory(
+    measurementService
+  );
   const csToolsVer4MeasurementSource = measurementService.createSource(
     'CornerstoneTools',
     '4'
@@ -214,7 +191,9 @@ const _initMeasurementService = measurementService => {
 };
 
 const _connectToolsToMeasurementService = measurementService => {
-  const csToolsVer4MeasurementSource = _initMeasurementService(measurementService);
+  const csToolsVer4MeasurementSource = _initMeasurementService(
+    measurementService
+  );
   const {
     id: sourceId,
     addOrUpdate,
@@ -242,7 +221,8 @@ const _connectToolsToMeasurementService = measurementService => {
             );
             console.log('Mapped annotation:', annotation);
           }
-        });
+        }
+      );
 
       measurementService.subscribe(
         MEASUREMENT_UPDATED,

extensions/cornerstone/src/toolbarModule.js

@@ -215,15 +215,6 @@ const definitions = [
         commandName: 'setToolActive',
         commandOptions: { toolName: 'Bidirectional' },
       },
-      {
-        id: 'Eraser',
-        label: 'Eraser',
-        icon: 'eraser',
-        //
-        type: TOOLBAR_BUTTON_TYPES.SET_TOOL_ACTIVE,
-        commandName: 'setToolActive',
-        commandOptions: { toolName: 'Eraser' },
-      },
       {
         id: 'Download',
         label: 'Download',
@@ -245,7 +236,7 @@ const definitions = [
     type: TOOLBAR_BUTTON_TYPES.COMMAND,
     commandName: 'setCornerstoneLayout',
     context: 'ACTIVE_VIEWPORT::VTK',
-  }
+  },
 ];
 
 export default {

extensions/cornerstone/src/utils/measurementServiceMappings/measurementServiceMappingsFactory.js

@@ -1,6 +1,11 @@
 import cornerstone from 'cornerstone-core';
 
-const SUPPORTED_TOOLS = ['Length', 'EllipticalRoi', 'RectangleRoi', 'ArrowAnnotate'];
+const SUPPORTED_TOOLS = [
+  'Length',
+  'EllipticalRoi',
+  'RectangleRoi',
+  'ArrowAnnotate',
+];
 
 const measurementServiceMappingsFactory = measurementService => {
   /**
@@ -17,17 +22,17 @@ const measurementServiceMappingsFactory = measurementService => {
       description,
       points,
       unit,
-      sopInstanceUID,
-      frameOfReferenceUID,
+      SOPInstanceUID,
+      FrameOfReferenceUID,
       referenceSeriesUID,
     } = measurement;
 
     return {
       toolName: definition,
       measurementData: {
-        sopInstanceUid: sopInstanceUID,
-        frameOfReferenceUid: frameOfReferenceUID,
-        seriesInstanceUid: referenceSeriesUID,
+        sopInstanceUid: SOPInstanceUID,
+        frameOfReferenceUID: FrameOfReferenceUID,
+        SeriesInstanceUID: referenceSeriesUID,
         unit,
         text: label,
         description,
@@ -57,9 +62,9 @@ const measurementServiceMappingsFactory = measurementService => {
     }
 
     const {
-      sopInstanceUid,
-      frameOfReferenceUid,
-      seriesInstanceUid,
+      SOPInstanceUID,
+      FrameOfReferenceUID,
+      SeriesInstanceUID,
     } = _getAttributes(element);
 
     const points = [];
@@ -67,13 +72,16 @@ const measurementServiceMappingsFactory = measurementService => {
 
     return {
       id: measurementData._measurementServiceId,
-      sopInstanceUID: sopInstanceUid,
-      frameOfReferenceUID: frameOfReferenceUid,
-      referenceSeriesUID: seriesInstanceUid,
+      SOPInstanceUID: SOPInstanceUID,
+      FrameOfReferenceUID,
+      referenceSeriesUID: SeriesInstanceUID,
       label: measurementData.text,
       description: measurementData.description,
       unit: measurementData.unit,
-      area: measurementData.cachedStats && measurementData.cachedStats.area, /* TODO: Add concept names instead (descriptor) */
+      area:
+        measurementData.cachedStats &&
+        measurementData.cachedStats
+          .area /* TODO: Add concept names instead (descriptor) */,
       type: _getValueTypeFromToolType(tool),
       points: _getPointsFromHandles(measurementData.handles),
     };
@@ -82,13 +90,13 @@ const measurementServiceMappingsFactory = measurementService => {
   const _getAttributes = element => {
     const enabledElement = cornerstone.getEnabledElement(element);
     const imageId = enabledElement.image.imageId;
-    const sopInstance = cornerstone.metaData.get('instance', imageId);
-    const sopInstanceUid = sopInstance.sopInstanceUid;
-    const frameOfReferenceUid = sopInstance.frameOfReferenceUID;
-    const series = cornerstone.metaData.get('series', imageId);
-    const seriesInstanceUid = series.seriesInstanceUid;
+    const instance = cornerstone.metaData.get('instance', imageId);
 
-    return { sopInstanceUid, frameOfReferenceUid, seriesInstanceUid };
+    return {
+      SOPInstanceUID: instance.SOPInstanceUID,
+      FrameOfReferenceUID: instance.FrameOfReferenceUID,
+      SeriesInstanceUID: instance.SeriesInstanceUID,
+    };
   };
 
   const _getValueTypeFromToolType = toolType => {

extensions/cornerstone/src/utils/measurementServiceMappings/measurementServiceMappingsFactory.test.js

@@ -8,9 +8,9 @@ jest.mock('cornerstone-core', () => ({
   metaData: {
     ...jest.requireActual('cornerstone-core').metaData,
     get: () => ({
-      sopInstanceUid: "123",
-      frameOfReferenceUID: "123",
-      seriesInstanceUid: "123",
+      SOPInstanceUID: '123',
+      FrameOfReferenceUID: '123',
+      SeriesInstanceUID: '123',
     }),
   },
 }));
@@ -42,8 +42,8 @@ describe('measurementServiceMappings.js', () => {
       measurementData: {
         _measurementServiceId: 1,
         sopInstanceUid: '123',
-        frameOfReferenceUid: '123',
-        seriesInstanceUid: '123',
+        frameOfReferenceUID: '123',
+        SeriesInstanceUID: '123',
         handles,
         text: 'Test',
         description: 'Test',
@@ -52,8 +52,8 @@ describe('measurementServiceMappings.js', () => {
     };
     measurement = {
       id: 1,
-      sopInstanceUID: '123',
-      frameOfReferenceUID: '123',
+      SOPInstanceUID: '123',
+      FrameOfReferenceUID: '123',
       referenceSeriesUID: '123',
       label: 'Test',
       description: 'Test',
@@ -66,7 +66,10 @@ describe('measurementServiceMappings.js', () => {
 
   describe('toAnnotation()', () => {
     it('map measurement service format to annotation', async () => {
-      const mappedMeasurement = await mappings.toAnnotation(measurement, definition);
+      const mappedMeasurement = await mappings.toAnnotation(
+        measurement,
+        definition
+      );
       expect(mappedMeasurement).toEqual(csToolsAnnotation);
     });
   });

extensions/dicom-html/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.
 
+## [1.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.1.0...@ohif/extension-dicom-html@1.1.1) (2020-03-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
 # [1.1.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.0.2...@ohif/extension-dicom-html@1.1.0) (2019-12-11)
 
 

extensions/dicom-html/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-html",
-  "version": "1.1.0",
+  "version": "1.1.1",
   "description": "OHIF extension for rendering structured reports to HTML",
   "author": "OHIF",
   "license": "MIT",
@@ -29,7 +29,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "^0.8.2",
+    "dcmjs": "^0.10.1",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-html/src/OHIFDicomHtmlSopClassHandler.js

@@ -11,26 +11,26 @@ const SOP_CLASS_UIDS = {
   X_RAY_RADIATION_DOSE_SR: '1.2.840.10008.5.1.4.1.1.88.67',
 };
 
-const sopClassUids = Object.values(SOP_CLASS_UIDS);
+const sopClassUIDs = Object.values(SOP_CLASS_UIDS);
 
 // TODO: Handle the case where there is more than one SOP Class Handler for the
 // same SOP Class
 const OHIFDicomHtmlSopClassHandler = {
   id: 'OHIFDicomHtmlSopClassHandler',
   type: MODULE_TYPES.SOP_CLASS_HANDLER,
-  sopClassUids,
+  sopClassUIDs,
   getDisplaySetFromSeries(series, study, dicomWebClient, authorizationHeaders) {
     const instance = series.getFirstInstance();
 
     return {
       plugin: 'html',
-      modality: 'SR',
-      displaySetInstanceUid: utils.guid(),
+      Modality: 'SR',
+      displaySetInstanceUID: utils.guid(),
       wadoRoot: study.getData().wadoRoot,
       wadoUri: instance.getData().wadouri,
-      sopInstanceUid: instance.getSOPInstanceUID(),
-      seriesInstanceUid: series.getSeriesInstanceUID(),
-      studyInstanceUid: study.getStudyInstanceUID(),
+      SOPInstanceUID: instance.getSOPInstanceUID(),
+      SeriesInstanceUID: series.getSeriesInstanceUID(),
+      StudyInstanceUID: study.getStudyInstanceUID(),
       authorizationHeaders,
     };
   },

extensions/dicom-microscopy/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.
 
+## [0.50.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.6...@ohif/extension-dicom-microscopy@0.50.7) (2020-03-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
 ## [0.50.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.5...@ohif/extension-dicom-microscopy@0.50.6) (2019-09-26)
 
 

extensions/dicom-microscopy/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-microscopy",
-  "version": "0.50.6",
+  "version": "0.50.7",
   "description": "OHIF extension for Dicom Microscopy",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js

@@ -8,7 +8,7 @@ const SOP_CLASS_UIDS = {
 
 const DicomMicroscopySopClassHandler = {
   id: 'DicomMicroscopySopClassHandlerPlugin',
-  sopClassUids: [SOP_CLASS_UIDS.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE],
+  sopClassUIDs: [SOP_CLASS_UIDS.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE],
   getDisplaySetFromSeries(series, study, dicomWebClient) {
     const instance = series.getFirstInstance();
 
@@ -16,12 +16,12 @@ const DicomMicroscopySopClassHandler = {
 
     return {
       plugin: 'microscopy',
-      modality: 'SM',
-      displaySetInstanceUid: utils.guid(),
+      Modality: 'SM',
+      displaySetInstanceUID: utils.guid(),
       dicomWebClient,
-      sopInstanceUid: instance.getSOPInstanceUID(),
-      seriesInstanceUid: series.getSeriesInstanceUID(),
-      studyInstanceUid: study.getStudyInstanceUID(),
+      SOPInstanceUID: instance.getSOPInstanceUID(),
+      SeriesInstanceUID: series.getSeriesInstanceUID(),
+      StudyInstanceUID: study.getStudyInstanceUID(),
     };
   },
 };

extensions/dicom-microscopy/src/DicomMicroscopyViewport.js

@@ -25,8 +25,8 @@ class DicomMicroscopyViewport extends Component {
     const dicomWebClient = displaySet.dicomWebClient;
 
     const searchInstanceOptions = {
-      studyInstanceUID: displaySet.studyInstanceUid,
-      seriesInstanceUID: displaySet.seriesInstanceUid,
+      studyInstanceUID: displaySet.StudyInstanceUID,
+      seriesInstanceUID: displaySet.SeriesInstanceUID,
     };
 
     dicomWebClient
@@ -34,18 +34,18 @@ class DicomMicroscopyViewport extends Component {
       .then(instances => {
         const promises = [];
         for (let i = 0; i < instances.length; i++) {
-          const sopInstanceUID = instances[i]['00080018']['Value'][0];
+          const sopInstanceUid = instances[i]['00080018']['Value'][0];
           const retrieveInstanceOptions = {
-            studyInstanceUID: displaySet.studyInstanceUid,
-            seriesInstanceUID: displaySet.seriesInstanceUid,
-            sopInstanceUID,
+            studyInstanceUID: displaySet.StudyInstanceUID,
+            seriesInstanceUID: displaySet.SeriesInstanceUID,
+            sopInstanceUid,
           };
 
           const promise = dicomWebClient
             .retrieveInstanceMetadata(retrieveInstanceOptions)
             .then(metadata => {
-              const imageType = metadata[0]['00080008']['Value'];
-              if (imageType[2] === 'VOLUME') {
+              const ImageType = metadata[0]['00080008']['Value'];
+              if (ImageType[2] === 'VOLUME') {
                 return metadata[0];
               }
             });
@@ -56,13 +56,15 @@ class DicomMicroscopyViewport extends Component {
       .then(async metadata => {
         metadata = metadata.filter(m => m);
 
-        const { api } = await import(/* webpackChunkName: "dicom-microscopy-viewer" */ 'dicom-microscopy-viewer');
+        const { api } = await import(
+          /* webpackChunkName: "dicom-microscopy-viewer" */ 'dicom-microscopy-viewer'
+        );
         const microscopyViewer = api.VLWholeSlideMicroscopyImageViewer;
 
         this.viewer = new microscopyViewer({
           client: dicomWebClient,
           metadata,
-          retrieveRendered: false
+          retrieveRendered: false,
         });
 
         this.viewer.render({ container });

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.
 
+## [1.0.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.1...@ohif/extension-dicom-pdf@1.0.2) (2020-03-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
 ## [1.0.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.0...@ohif/extension-dicom-pdf@1.0.1) (2019-12-16)
 
 

extensions/dicom-pdf/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-pdf",
-  "version": "1.0.1",
+  "version": "1.0.2",
   "description": "OHIF extension for Dicom PDF",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-pdf/src/DicomPDFViewport.js

@@ -101,9 +101,9 @@ class DicomPDFViewport extends Component {
     let pdfByteArray = byteArray;
 
     if (dataSet) {
-      const sopClassUid = dataSet.string('x00080016');
+      const SOPClassUID = dataSet.string('x00080016');
 
-      if (sopClassUid !== SOP_CLASS_UIDS.ENCAPSULATED_PDF) {
+      if (SOPClassUID !== SOP_CLASS_UIDS.ENCAPSULATED_PDF) {
         throw new Error('This is not a DICOM-encapsulated PDF');
       }
 

extensions/dicom-pdf/src/OHIFDicomPDFSopClassHandler.js

@@ -8,19 +8,19 @@ const SOP_CLASS_UIDS = {
 const OHIFDicomPDFSopClassHandler = {
   id: 'OHIFDicomPDFSopClassHandlerPlugin',
   type: MODULE_TYPES.SOP_CLASS_HANDLER,
-  sopClassUids: [SOP_CLASS_UIDS.ENCAPSULATED_PDF],
+  sopClassUIDs: [SOP_CLASS_UIDS.ENCAPSULATED_PDF],
   getDisplaySetFromSeries(series, study, dicomWebClient, authorizationHeaders) {
     const instance = series.getFirstInstance();
 
     return {
       plugin: 'pdf',
-      modality: 'DOC',
-      displaySetInstanceUid: utils.guid(),
+      Modality: 'DOC',
+      displaySetInstanceUID: utils.guid(),
       wadoRoot: study.getData().wadoRoot,
       wadoUri: instance.getData().wadouri,
-      sopInstanceUid: instance.getSOPInstanceUID(),
-      seriesInstanceUid: series.getSeriesInstanceUID(),
-      studyInstanceUid: study.getStudyInstanceUID(),
+      SOPInstanceUID: instance.getSOPInstanceUID(),
+      SeriesInstanceUID: series.getSeriesInstanceUID(),
+      StudyInstanceUID: study.getStudyInstanceUID(),
       authorizationHeaders: authorizationHeaders,
     };
   },

extensions/dicom-pdf/src/OHIFDicomPDFViewport.js

@@ -33,6 +33,7 @@ class OHIFDicomPDFViewport extends Component {
 
   componentDidMount() {
     const { displaySet, studies } = this.props.viewportData;
+
     DicomLoaderService.findDicomDataPromise(displaySet, studies).then(
       data => this.setState({ byteArray: new Uint8Array(data) }),
       error => {

extensions/dicom-segmentation/.webpack/webpack.dev.js

@@ -0,0 +1,8 @@
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+};

extensions/dicom-segmentation/.webpack/webpack.prod.js

@@ -0,0 +1,33 @@
+const webpack = require('webpack');
+const merge = require('webpack-merge');
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const pkg = require('./../package.json');
+
+const ROOT_DIR = path.join(__dirname, './..');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+
+  return merge(commonConfig, {
+    devtool: 'source-map',
+    optimization: {
+      minimize: true,
+      sideEffects: true,
+    },
+    output: {
+      path: ROOT_DIR,
+      library: 'OHIFExtDicomSeg',
+      libraryTarget: 'umd',
+      libraryExport: 'default',
+      filename: pkg.main,
+    },
+    plugins: [
+      new webpack.optimize.LimitChunkCountPlugin({
+        maxChunks: 1,
+      }),
+    ],
+  });
+};

extensions/dicom-segmentation/CHANGELOG.md

@@ -0,0 +1,11 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+# 0.1.0 (2020-03-13)
+
+
+### Features
+
+* Segmentations Settings UI - Phase 1 [#1391](https://github.com/OHIF/Viewers/issues/1391) ([#1392](https://github.com/OHIF/Viewers/issues/1392)) ([e8842cf](https://github.com/OHIF/Viewers/commit/e8842cf8aebde98db7fc123e4867c8288552331f)), closes [#1423](https://github.com/OHIF/Viewers/issues/1423)

extensions/dicom-segmentation/LICENSE

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

extensions/dicom-segmentation/README.md

@@ -0,0 +1,65 @@
+# @ohif/dicom-segmentation
+
+![npm (scoped)](https://img.shields.io/npm/v/@ohif/dicom-segmentation.svg?style=flat-square)
+
+This extension adds support to view and navigate the segments available in the DICOM SEG,
+allowing control over visibility of a given segment and providing metadata about the segment(s).
+
+<!-- TODO: Simple image or GIF? -->
+
+#### Index
+
+Extension Id: `com.ohif.dicom-segmentation`
+
+## Tool Configuration
+
+Tools can be configured through extension configuration using the tools key:
+
+```js
+  ...
+  cornerstoneExtensionConfig: {
+    tools: {
+      ArrowAnnotate: {
+        configuration: {
+          getTextCallback: (callback, eventDetails) => callback(prompt('Enter your custom annotation')),
+        },
+      },
+    },
+  },
+  ...
+```
+
+## Annotate Tools Configuration
+
+*We currently support one property for annotation tools.*
+
+### Hide handles
+This extension configuration allows you to toggle on/off handle rendering for all annotate tools:
+
+```js
+  ...
+  cornerstoneExtensionConfig: {
+    hideHandles: true,
+  },
+  ...
+
+## Resources
+
+### Repositories
+
+- [cornerstonejs/react-cornerstone-viewport][react-viewport]
+- [cornerstonejs/cornerstoneTools][cornerstone-tools]
+- [cornerstonejs/cornerstone][cornerstone]
+
+<!--
+  Links
+  -->
+
+<!-- prettier-ignore-start -->
+[docs-commands]: https://www.com
+[docs-hotkeys]: https://www.com
+[docs-userprefs]: htt
+[react-viewport]: https://github.com/cornerstonejs/react-cornerstone-viewport
+[cornerstone-tools]: https://github.com/cornerstonejs/cornerstoneTools
+[cornerstone]: https://github.com/cornerstonejs/cornerstone
+<!-- prettier-ignore-end -->

extensions/dicom-segmentation/package.json

@@ -0,0 +1,43 @@
+{
+  "name": "@ohif/extension-dicom-segmentation",
+  "version": "0.1.0",
+  "description": "OHIF extension for viewing segmentations in the 2D MPR view",
+  "author": "OHIF",
+  "license": "MIT",
+  "repository": "OHIF/Viewers",
+  "main": "dist/index.umd.js",
+  "module": "src/index.js",
+  "engines": {
+    "node": ">=10",
+    "npm": ">=6",
+    "yarn": ">=1.16.0"
+  },
+  "files": [
+    "dist",
+    "README.md"
+  ],
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
+    "dev:dicom-html": "yarn run dev",
+    "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
+    "build:package": "yarn run build",
+    "prepublishOnly": "yarn run build",
+    "start": "yarn run dev"
+  },
+  "peerDependencies": {
+    "@ohif/core": "^0.50.0",
+    "cornerstone-core": "^2.2.8",
+    "cornerstone-tools": "4.12.5",
+    "dcmjs": "^0.6.1",
+    "prop-types": "^15.6.2",
+    "react": "^16.8.6",
+    "react-dom": "^16.8.6"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.5.5",
+    "react-select": "^3.0.8"
+  }
+}

extensions/dicom-segmentation/src/OHIFDicomSegSopClassHandler.js

@@ -0,0 +1,71 @@
+import { MODULE_TYPES, utils } from '@ohif/core';
+import loadSegmentation from './loadSegmentation';
+
+// TODO: Should probably use dcmjs for this
+const SOP_CLASS_UIDS = {
+  DICOM_SEG: '1.2.840.10008.5.1.4.1.1.66.4',
+};
+
+const sopClassUIDs = Object.values(SOP_CLASS_UIDS);
+
+// TODO: Handle the case where there is more than one SOP Class Handler for the
+// same SOP Class.
+const OHIFDicomSegSopClassHandler = {
+  id: 'OHIFDicomSegSopClassHandler',
+  type: MODULE_TYPES.SOP_CLASS_HANDLER,
+  sopClassUIDs,
+  getDisplaySetFromSeries: function(
+    series,
+    study,
+    dicomWebClient,
+    authorizationHeaders
+  ) {
+    const instance = series.getFirstInstance();
+    const metadata = instance.getData().metadata;
+
+    const {
+      SeriesDate,
+      SeriesTime,
+      SeriesDescription,
+      FrameOfReferenceUID,
+      SOPInstanceUID,
+      SeriesInstanceUID,
+      StudyInstanceUID,
+    } = metadata;
+
+    const segDisplaySet = {
+      Modality: 'SEG',
+      displaySetInstanceUID: utils.guid(),
+      wadoRoot: study.getData().wadoRoot,
+      wadoUri: instance.getData().wadouri,
+      SOPInstanceUID,
+      SeriesInstanceUID,
+      StudyInstanceUID,
+      FrameOfReferenceUID,
+      authorizationHeaders,
+      metadata,
+      isDerived: true,
+      referencedDisplaySetUID: null, // Assigned when loaded.
+      labelmapIndex: null, // Assigned when loaded.
+      isLoaded: false,
+      SeriesDate,
+      SeriesTime,
+      SeriesDescription,
+    };
+
+    segDisplaySet.load = function(referencedDisplaySet, studies) {
+      return loadSegmentation(
+        segDisplaySet,
+        referencedDisplaySet,
+        studies
+      ).catch(error => {
+        segDisplaySet.isLoaded = false;
+        throw new Error(error);
+      });
+    };
+
+    return segDisplaySet;
+  },
+};
+
+export default OHIFDicomSegSopClassHandler;

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

@@ -0,0 +1,41 @@
+.dcmseg-brush-color-selector .selector-buttons button {
+  color: #333;
+  background-color: #fff;
+  padding: 4px 12px;
+  line-height: 1.4;
+  text-align: center;
+  white-space: nowrap;
+  vertical-align: middle;
+  cursor: pointer;
+  user-select: none;
+  border: 1px solid #ccc;
+  border-radius: 4px;
+  transition: all 0.15s ease;
+}
+
+.dcmseg-brush-color-selector .selector-buttons button:hover,
+.dcmseg-brush-color-selector .selector-buttons button:active,
+.dcmseg-brush-color-selector .selector-buttons button.active {
+  background-color: var(--active-color);
+  border-color: var(--ui-border-color-active);
+  color: #fff;
+}
+
+.dcmseg-brush-color-selector .selector-buttons {
+  margin-left: 10px;
+  display: flex;
+  flex-direction: row;
+  align-items: center;
+}
+
+.dcmseg-brush-color-selector .selector-buttons button:last-of-type {
+  margin-left: 5px;
+}
+
+.dcmseg-brush-color-selector .selector-active-segment {
+  border-radius: 100%;
+  width: 32px;
+  height: 32px;
+  text-align: center;
+  line-height: 32px;
+}

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

@@ -0,0 +1,32 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+
+import './BrushColorSelector.css';
+
+const BrushColorSelector = ({ defaultColor, index, onNext, onPrev }) => (
+  <div className="dcmseg-brush-color-selector">
+    <div
+      className="selector-active-segment"
+      style={{ backgroundColor: defaultColor }}
+    >
+      {index}
+    </div>
+    <div className="selector-buttons">
+      <button onClick={onPrev}>
+        Previous
+      </button>
+      <button onClick={onNext}>
+        Next
+      </button>
+    </div>
+  </div>
+);
+
+BrushColorSelector.propTypes = {
+  defaultColor: PropTypes.string.isRequired,
+  index: PropTypes.oneOfType([PropTypes.number, PropTypes.string]).isRequired,
+  onNext: PropTypes.func.isRequired,
+  onPrev: PropTypes.func.isRequired,
+};
+
+export default BrushColorSelector;

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

@@ -0,0 +1,4 @@
+.dcmseg-brush-radius label {
+  display: block;
+  margin-bottom: 8px;
+}

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

@@ -0,0 +1,36 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import { Range } from '@ohif/ui';
+
+import './BrushRadius.css';
+
+const BrushRadius = ({ value, onChange, min, max, step }) => (
+  <div className="dcmseg-brush-radius">
+    <label htmlFor="dcmseg-brush-radius">Brush Radius</label>
+    <Range
+      value={value}
+      min={min}
+      max={max}
+      step={step}
+      onChange={onChange}
+      id="dcmseg-brush-radius"
+    />
+  </div>
+);
+
+BrushRadius.propTypes = {
+  value: PropTypes.number.isRequired,
+  onChange: PropTypes.number,
+  min: PropTypes.number,
+  max: PropTypes.number,
+  step: PropTypes.number,
+};
+
+BrushRadius.defaultProps = {
+  onChange: () => { },
+  min: 1,
+  max: 50,
+  step: 1,
+};
+
+export default BrushRadius;

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

@@ -0,0 +1,64 @@
+.dcmseg-segment-item .segment-color-section {
+  display: flex;
+  justify-content: center;
+  align-items: center;
+  flex-direction: column;
+}
+
+.dcmseg-segment-item .segment-color {
+  margin-top: 8px;
+  border-radius: 100%;
+  width: 20px;
+  height: 20px;
+}
+
+.dcmseg-segment-item .segment-label {
+  overflow: hidden;
+  max-width: calc(100% - 50px);
+  text-overflow: ellipsis;
+  overflow-wrap: normal;
+  white-space: nowrap;
+}
+
+.dcmseg-segment-item .segment-info {
+  display: inline-block;
+  margin-top: 9px;
+  padding-left: 9px;
+  width: 90px;
+  border-left: 1px solid var(--text-secondary-color);
+  color: var(--text-primary-color);
+  width: 100%;
+}
+
+.dcmseg-segment-item.selected .segment-actions {
+  height: 35px;
+  visibility: visible;
+}
+
+.dcmseg-segment-item .segment-actions {
+  margin-left: -1px;
+  background-color: var(--ui-gray-darker);
+  height: 0;
+  overflow: hidden;
+  transition: all 0.3s ease;
+  visibility: hidden;
+  padding-left: 14px;
+}
+
+.dcmseg-segment-item .segment-actions .btnAction {
+  background-color: transparent;
+  border: none;
+  color: var(--default-color);
+  cursor: pointer;
+  line-height: 35px;
+  height: 35px;
+  transition: all 0.3s ease;
+}
+
+.dcmseg-segment-item .segment-actions .btnAction:hover, .dcmseg-segment-item .segment-actions .btnAction:active {
+  color: var(--text-primary-color);
+}
+
+.dcmseg-segment-item .segment-actions .btnAction i {
+  margin-right: 4px;
+}

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

@@ -0,0 +1,76 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import { TableListItem, Icon } from '@ohif/ui';
+
+import './SegmentItem.css';
+
+const ColoredCircle = ({ color }) => {
+  return (
+    <div
+      className="segment-color"
+      style={{ backgroundColor: `rgba(${color.join(',')})` }}
+    ></div>
+  );
+};
+
+ColoredCircle.propTypes = {
+  color: PropTypes.array.isRequired,
+};
+
+const SegmentItem = ({ index, label, onClick, itemClass, color }) => (
+  <div className="dcmseg-segment-item">
+    <TableListItem
+      key={index}
+      itemKey={index}
+      itemIndex={index}
+      itemClass={itemClass}
+      itemMeta={<ColoredCircle color={color} />}
+      itemMetaClass="segment-color-section"
+      onItemClick={onClick}
+    >
+      <div>
+        <div className="segment-label" style={{ marginBottom: 4 }}>
+          {label}
+        </div>
+        {false && <div className="segment-info">{'...'}</div>}
+        {false && (
+          <div className="segment-actions">
+            <button
+              className="btnAction"
+              onClick={() => console.log('Relabelling...')}
+            >
+              <span style={{ marginRight: '4px' }}>
+                <Icon name="edit" width="14px" height="14px" />
+              </span>
+              Relabel
+              </button>
+            <button
+              className="btnAction"
+              onClick={() => console.log('Editing description...')}
+            >
+              <span style={{ marginRight: '4px' }}>
+                <Icon name="edit" width="14px" height="14px" />
+              </span>
+              Description
+              </button>
+          </div>
+        )}
+      </div>
+    </TableListItem>
+  </div>
+);
+
+SegmentItem.propTypes = {
+  index: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
+  label: PropTypes.string.isRequired,
+  onClick: PropTypes.func,
+  itemClass: PropTypes.string,
+  color: PropTypes.array.isRequired,
+};
+
+SegmentItem.defaultProps = {
+  itemClass: '',
+  onClick: () => { }
+};
+
+export default SegmentItem;

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

@@ -0,0 +1,25 @@
+.dcmseg-segmentation-item {
+  display: flex;
+  justify-content: start;
+  margin: 0;
+}
+
+.dcmseg-segmentation-item .segmentation-meta {
+  display: flex;
+  flex-direction: column;
+  flex-grow: 1;
+  overflow: hidden;
+}
+
+.dcmseg-segmentation-item .segmentation-meta-title {
+  text-overflow: ellipsis;
+  overflow: hidden;
+  white-space: nowrap;
+  color: white;
+  max-width: calc(100% - 30px);
+}
+
+.dcmseg-segmentation-item .segmentation-meta-description {
+  font-size: 12px;
+  color: var(--text-secondary-color);
+}

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

@@ -0,0 +1,27 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+
+import './SegmentationItem.css';
+
+const SegmentationItem = ({ onClick, title, description }) => {
+  return (
+    <li className="dcmseg-segmentation-item" onClick={onClick}>
+      <div className="segmentation-meta">
+        <div className="segmentation-meta-title">{title}</div>
+        <div className="segmentation-meta-description">{description}</div>
+      </div>
+    </li>
+  );
+};
+
+SegmentationItem.propTypes = {
+  onClick: PropTypes.func.isRequired,
+  title: PropTypes.string.isRequired,
+  description: PropTypes.string.isRequired,
+};
+
+SegmentationItem.defaultProps = {
+  description: ''
+};
+
+export default SegmentationItem;

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

@@ -0,0 +1,61 @@
+.dcmseg-segmentation-panel {
+  color: white;
+  min-height: 200px;
+  background-color: var(--primary-background-color);
+  height: 100%;
+  width: 100%;
+  display: flex;
+  flex-direction: column;
+}
+
+.dcmseg-segmentation-panel h3 {
+  padding-left: 20px;
+  margin-top: 0;
+}
+
+.dcmseg-segmentation-panel .segmentations {
+  padding: 0 20px 20px 20px;
+}
+
+.dcmseg-segmentation-panel .cog-icon {
+  margin: 20px 20px 0 0;
+  align-self: flex-end;
+  color: var(--default-color);
+  cursor: pointer;
+}
+
+.dcmseg-segmentation-panel .cog-icon:hover {
+  color: var(--hover-color);
+}
+
+.dcmseg-segmentation-panel .segmentation-icon {
+  margin-right: 8px;
+  margin-top: 12px;
+  min-width: 14px;
+}
+
+.dcmseg-segmentation-panel .selector-form {
+  display: flex;
+  flex-direction: column;
+  justify-content: space-between;
+  align-items: center;
+  padding: 20px;
+  height: 150px;
+}
+
+.dcmseg-segmentation-panel .selector-form>div {
+  width: 100%;
+}
+
+.dcmseg-segmentation-panel .selector-form>div:first-of-type {
+  display: flex;
+  flex-direction: row;
+  justify-content: center;
+}
+
+.dcmseg-segmentation-panel .tableList .tableListHeader .numberOfItems {
+  float: unset;
+  max-width: unset;
+  flex: unset;
+  margin-right: 16px;
+}

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

@@ -0,0 +1,475 @@
+import React, { useState, useEffect } from 'react';
+import PropTypes from 'prop-types';
+import cornerstoneTools from 'cornerstone-tools';
+import cornerstone from 'cornerstone-core';
+import moment from 'moment';
+import { utils, log } from '@ohif/core';
+import { ScrollableArea, TableList, Icon } from '@ohif/ui';
+
+import {
+  BrushColorSelector,
+  BrushRadius,
+  SegmentationItem,
+  SegmentItem,
+  SegmentationSelect,
+} from '../index';
+
+import './SegmentationPanel.css';
+import SegmentationSettings from '../SegmentationSettings/SegmentationSettings';
+
+const { studyMetadataManager } = utils;
+
+const refreshViewport = () => {
+  cornerstone.getEnabledElements().forEach(enabledElement => {
+    cornerstone.updateImage(enabledElement.element);
+  });
+};
+
+/**
+ * SegmentationPanel component
+ *
+ * @param {Object} props
+ * @param {Array} props.studies
+ * @param {Array} props.viewports - viewportSpecificData
+ * @param {number} props.activeIndex - activeViewportIndex
+ * @returns component
+ */
+const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
+  /*
+   * TODO: wrap get/set interactions with the cornerstoneTools
+   * store with context to make these kind of things less blurry.
+   */
+  const segmentationModule = cornerstoneTools.getModule('segmentation');
+  const { configuration } = segmentationModule;
+  const DEFAULT_BRUSH_RADIUS = configuration.radius || 10;
+
+  const [brushRadius, setBrushRadius] = useState(DEFAULT_BRUSH_RADIUS);
+
+  /* TODO: We shouldn't hardcode this color, in the future the SEG may set the colorLUT to whatever it wants. */
+  const [brushColor, setBrushColor] = useState('rgba(221, 85, 85, 1)');
+  const [selectedSegment, setSelectedSegment] = useState();
+  const [showSegSettings, setShowSegSettings] = useState(false);
+  const [selectedSegmentation, setSelectedSegmentation] = useState();
+
+  const viewport = viewports[activeIndex];
+
+  const {
+    StudyInstanceUID,
+    SeriesInstanceUID,
+    displaySetInstanceUID,
+  } = viewport;
+
+  const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+  const firstImageId = studyMetadata.getFirstImageId(displaySetInstanceUID);
+
+  /* CornerstoneTools */
+  const [brushStackState, setBrushStackState] = useState(
+    segmentationModule.state.series[firstImageId]
+  );
+
+  useEffect(() => {
+    setShowSegSettings(showSegSettings && !isOpen);
+  }, [isOpen]);
+
+  useEffect(() => {
+    setBrushStackState(segmentationModule.state.series[firstImageId]);
+  }, [studies, viewports, activeIndex, firstImageId]);
+
+  useEffect(() => {
+    if (brushStackState) {
+      setSelectedSegmentation(brushStackState.activeLabelmapIndex);
+    }
+
+    const labelmapModifiedHandler = event => {
+      log.warn('labelmap modified', event);
+      setBrushStackState(segmentationModule.state.series[firstImageId]);
+    };
+
+    /*
+     * These are specific to each element;
+     * Need to iterate cornerstone-tools tracked enabled elements?
+     * Then only care about the one tied to active viewport?
+     */
+    cornerstoneTools.store.state.enabledElements.forEach(enabledElement =>
+      enabledElement.addEventListener(
+        'cornerstonetoolslabelmapmodified',
+        labelmapModifiedHandler
+      )
+    );
+
+    return () => {
+      cornerstoneTools.store.state.enabledElements.forEach(enabledElement =>
+        enabledElement.removeEventListener(
+          'cornerstonetoolslabelmapmodified',
+          labelmapModifiedHandler
+        )
+      );
+    };
+  });
+
+  if (!brushStackState) {
+    return null;
+  }
+
+  const labelmap3D =
+    brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
+
+  /*
+   * 2. UseEffect to update state? or to a least trigger a re-render
+   * 4. Toggle visibility of labelmap?
+   * 5. Toggle visibility of seg?
+   *
+   * If the port is cornerstone, just need to call a re-render.
+   * If the port is vtkjs, its a bit more tricky as we now need to create a new
+   */
+
+  const getLabelmapList = () => {
+    /* Get list of SEG labelmaps specific to active viewport (reference series) */
+    const referencedSegDisplaysets = _getReferencedSegDisplaysets(
+      StudyInstanceUID,
+      SeriesInstanceUID
+    );
+
+    return referencedSegDisplaysets.map((displaySet, index) => {
+      const { labelmapIndex, SeriesDate, SeriesTime } = displaySet;
+
+      /* Map to display representation */
+      const dateStr = `${SeriesDate}:${SeriesTime}`.split('.')[0];
+      const date = moment(dateStr, 'YYYYMMDD:HHmmss');
+      const isActiveLabelmap =
+        labelmapIndex === brushStackState.activeLabelmapIndex;
+      const displayDate = date.format('ddd, MMM Do YYYY');
+      const displayTime = date.format('h:mm:ss a');
+      const displayDescription = displaySet.SeriesDescription;
+
+      return {
+        value: labelmapIndex,
+        title: displayDescription,
+        description: displayDate,
+        onClick: async () => {
+          const activatedLabelmapIndex = await _setActiveLabelmap(
+            viewport,
+            studies,
+            displaySet,
+            firstImageId,
+            brushStackState.activeLabelmapIndex
+          );
+          setSelectedSegmentation(activatedLabelmapIndex);
+        },
+      };
+    });
+  };
+
+  const labelmapList = getLabelmapList();
+
+  const segmentList = [];
+
+  if (labelmap3D) {
+    /*
+     * Newly created segments have no `meta`
+     * So we instead build a list of all segment indexes in use
+     * Then find any associated metadata
+     */
+    const uniqueSegmentIndexes = labelmap3D.labelmaps2D
+      .reduce((acc, labelmap2D) => {
+        if (labelmap2D) {
+          const segmentIndexes = labelmap2D.segmentsOnLabelmap;
+
+          for (let i = 0; i < segmentIndexes.length; i++) {
+            if (!acc.includes(segmentIndexes[i]) && segmentIndexes[i] !== 0) {
+              acc.push(segmentIndexes[i]);
+            }
+          }
+        }
+
+        return acc;
+      }, [])
+      .sort((a, b) => a - b);
+
+    const colorLutTable =
+      segmentationModule.state.colorLutTables[labelmap3D.colorLUTIndex];
+    const hasLabelmapMeta = labelmap3D.metadata && labelmap3D.metadata.data;
+
+    for (let i = 0; i < uniqueSegmentIndexes.length; i++) {
+      const segmentIndex = uniqueSegmentIndexes[i];
+
+      const color = colorLutTable[segmentIndex];
+      let segmentLabel = '(unlabeled)';
+      let segmentNumber = segmentIndex;
+
+      /* Meta */
+      if (hasLabelmapMeta) {
+        const segmentMeta = labelmap3D.metadata.data[segmentIndex];
+
+        if (segmentMeta) {
+          segmentNumber = segmentMeta.SegmentNumber;
+          segmentLabel = segmentMeta.SegmentLabel;
+        }
+      }
+
+      const sameSegment = selectedSegment === segmentNumber;
+      const setCurrentSelectedSegment = () => {
+        _setActiveSegment(
+          firstImageId,
+          segmentNumber,
+          labelmap3D.activeSegmentIndex
+        );
+        setSelectedSegment(sameSegment ? null : segmentNumber);
+      };
+
+      segmentList.push(
+        <SegmentItem
+          key={segmentNumber}
+          itemClass={`segment-item ${sameSegment && 'selected'}`}
+          onClick={setCurrentSelectedSegment}
+          label={segmentLabel}
+          index={segmentNumber}
+          color={color}
+        />
+      );
+    }
+
+    /*
+     * Let's iterate over segmentIndexes ^ above
+     * If meta has a match, use it to show info
+     * If now, add "no-meta" class
+     * Show default name
+     */
+  }
+
+  const updateBrushSize = evt => {
+    const updatedRadius = Number(evt.target.value);
+
+    if (updatedRadius !== brushRadius) {
+      setBrushRadius(updatedRadius);
+      segmentationModule.setters.radius(updatedRadius);
+    }
+  };
+
+  const decrementSegment = event => {
+    event.preventDefault();
+    if (labelmap3D.activeSegmentIndex > 1) {
+      labelmap3D.activeSegmentIndex--;
+    }
+    setSelectedSegment(labelmap3D.activeSegmentIndex);
+    updateActiveSegmentColor();
+  };
+
+  const incrementSegment = event => {
+    event.preventDefault();
+    labelmap3D.activeSegmentIndex++;
+    setSelectedSegment(labelmap3D.activeSegmentIndex);
+    updateActiveSegmentColor();
+  };
+
+  const updateActiveSegmentColor = () => {
+    const color = getActiveSegmentColor();
+    setBrushColor(color);
+  };
+
+  const getActiveSegmentColor = () => {
+    if (!brushStackState) {
+      return 'rgba(255, 255, 255, 1)';
+    }
+
+    const colorLutTable =
+      segmentationModule.state.colorLutTables[labelmap3D.colorLUTIndex];
+    const color = colorLutTable[labelmap3D.activeSegmentIndex];
+
+    return `rgba(${color.join(',')})`;
+  };
+
+  const updateConfiguration = newConfiguration => {
+    /* Supported configuration */
+    configuration.renderFill = newConfiguration.renderFill;
+    configuration.renderOutline = newConfiguration.renderOutline;
+    configuration.shouldRenderInactiveLabelmaps =
+      newConfiguration.shouldRenderInactiveLabelmaps;
+    configuration.fillAlpha = newConfiguration.fillAlpha;
+    configuration.outlineAlpha = newConfiguration.outlineAlpha;
+    configuration.outlineWidth = newConfiguration.outlineWidth;
+    configuration.fillAlphaInactive = newConfiguration.fillAlphaInactive;
+    configuration.outlineAlphaInactive = newConfiguration.outlineAlphaInactive;
+    refreshViewport();
+  };
+
+  if (showSegSettings) {
+    return (
+      <SegmentationSettings
+        configuration={configuration}
+        onBack={() => setShowSegSettings(false)}
+        onChange={updateConfiguration}
+      />
+    );
+  } else {
+    return (
+      <div className="dcmseg-segmentation-panel">
+        <Icon
+          className="cog-icon"
+          name="cog"
+          width="25px"
+          height="25px"
+          onClick={() => setShowSegSettings(true)}
+        />
+        {false && (
+          <form className="selector-form">
+            <BrushColorSelector
+              defaultColor={brushColor}
+              index={labelmap3D.activeSegmentIndex}
+              onNext={incrementSegment}
+              onPrev={decrementSegment}
+            />
+            <BrushRadius
+              value={brushRadius}
+              onChange={updateBrushSize}
+              min={configuration.minRadius}
+              max={configuration.maxRadius}
+            />
+          </form>
+        )}
+        <h3>Segmentations</h3>
+        <div className="segmentations">
+          <SegmentationSelect
+            value={
+              labelmapList.find(i => i.value === selectedSegmentation) || null
+            }
+            formatOptionLabel={SegmentationItem}
+            options={labelmapList}
+          />
+        </div>
+        <ScrollableArea>
+          <TableList
+            customHeader={<SegmentsHeader count={segmentList.length} />}
+          >
+            {segmentList}
+          </TableList>
+        </ScrollableArea>
+      </div>
+    );
+  }
+};
+
+SegmentationPanel.propTypes = {
+  /*
+   * An object, with int index keys?
+   * Maps to: state.viewports.viewportSpecificData, in `viewer`
+   * Passed in MODULE_TYPES.PANEL when specifying component in viewer
+   */
+  viewports: PropTypes.shape({
+    displaySetInstanceUID: PropTypes.string,
+    frameRate: PropTypes.any,
+    InstanceNumber: PropTypes.number,
+    isMultiFrame: PropTypes.bool,
+    isReconstructable: PropTypes.bool,
+    Modality: PropTypes.string,
+    plugin: PropTypes.string,
+    SeriesDate: PropTypes.string,
+    SeriesDescription: PropTypes.string,
+    SeriesInstanceUID: PropTypes.string,
+    SeriesNumber: PropTypes.any,
+    SeriesTime: PropTypes.string,
+    sopClassUIDs: PropTypes.arrayOf(PropTypes.string),
+    StudyInstanceUID: PropTypes.string,
+  }),
+  activeIndex: PropTypes.number.isRequired,
+  studies: PropTypes.array.isRequired,
+};
+SegmentationPanel.defaultProps = {};
+
+/**
+ * Returns SEG Displaysets that reference the target series, sorted by dateTime
+ *
+ * @param {string} StudyInstanceUID
+ * @param {string} SeriesInstanceUID
+ * @returns Array
+ */
+const _getReferencedSegDisplaysets = (StudyInstanceUID, SeriesInstanceUID) => {
+  /* Referenced DisplaySets */
+  const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+  const referencedDisplaysets = studyMetadata.getDerivedDatasets({
+    referencedSeriesInstanceUID: SeriesInstanceUID,
+    Modality: 'SEG',
+  });
+
+  /* Sort */
+  referencedDisplaysets.sort((a, b) => {
+    const aNumber = Number(`${a.SeriesDate}${a.SeriesTime}`);
+    const bNumber = Number(`${b.SeriesDate}${b.SeriesTime}`);
+    return aNumber - bNumber;
+  });
+
+  return referencedDisplaysets;
+};
+
+/**
+ *
+ *
+ * @param {*} viewportSpecificData
+ * @param {*} studies
+ * @param {*} displaySet
+ * @param {*} firstImageId
+ * @param {*} activeLabelmapIndex
+ * @returns
+ */
+const _setActiveLabelmap = async (
+  viewportSpecificData,
+  studies,
+  displaySet,
+  firstImageId,
+  activeLabelmapIndex
+) => {
+  if (displaySet.labelmapIndex === activeLabelmapIndex) {
+    log.warn(`${activeLabelmapIndex} is already the active labelmap`);
+    return;
+  }
+
+  if (!displaySet.isLoaded) {
+    // What props does this expect `viewportSpecificData` to have?
+    // TODO: Should this return the `labelmapIndex`?
+    await displaySet.load(viewportSpecificData, studies);
+  }
+
+  const { state } = cornerstoneTools.getModule('segmentation');
+  const brushStackState = state.series[firstImageId];
+
+  brushStackState.activeLabelmapIndex = displaySet.labelmapIndex;
+
+  refreshViewport();
+
+  return displaySet.labelmapIndex;
+};
+
+/**
+ *
+ * @param {*} firstImageId
+ * @param {*} activeSegmentIndex
+ * @returns
+ */
+const _setActiveSegment = (firstImageId, segmentIndex, activeSegmentIndex) => {
+  if (segmentIndex === activeSegmentIndex) {
+    log.info(`${activeSegmentIndex} is already the active segment`);
+    return;
+  }
+
+  const { state } = cornerstoneTools.getModule('segmentation');
+  const brushStackState = state.series[firstImageId];
+
+  const labelmap3D =
+    brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
+  labelmap3D.activeSegmentIndex = segmentIndex;
+
+  refreshViewport();
+
+  return segmentIndex;
+};
+
+const SegmentsHeader = ({ count }) => {
+  return (
+    <React.Fragment>
+      <div className="tableListHeaderTitle">Segments</div>
+      <div className="numberOfItems">{count}</div>
+    </React.Fragment>
+  );
+};
+
+export default SegmentationPanel;

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

@@ -0,0 +1,55 @@
+import React from 'react';
+import Select from 'react-select';
+
+const SegmentationSelect = ({ value, formatOptionLabel, options }) => (
+  <Select
+    value={value}
+    formatOptionLabel={formatOptionLabel}
+    styles={segmentationSelectStyles}
+    options={options}
+  />
+);
+
+const computedstyle = getComputedStyle(document.body);
+const uiGrayDarker = computedstyle.getPropertyValue('--ui-gray-darker');
+const activeColor = computedstyle.getPropertyValue('--active-color');
+const defaultColor = computedstyle.getPropertyValue('--default-color');
+const uiGrayDark = computedstyle.getPropertyValue('--ui-gray-dark');
+
+const segmentationSelectStyles = {
+  control: (base, state) => ({
+    ...base,
+    cursor: 'pointer',
+    background: uiGrayDarker,
+    borderRadius: state.isFocused ? '5px 5px 5px 5px' : 5,
+    borderColor: state.isFocused ? activeColor : defaultColor,
+    boxShadow: state.isFocused ? null : null,
+    minHeight: '50px',
+    '&:hover': {
+      borderColor: activeColor,
+    },
+  }),
+  menu: base => ({
+    ...base,
+    borderRadius: 5,
+    background: uiGrayDarker,
+  }),
+  option: (base, state) => ({
+    ...base,
+    cursor: 'pointer',
+    '&:first-of-type': {
+      borderTopLeftRadius: 5,
+      borderTopRightRadius: 5,
+    },
+    '&:last-of-type': {
+      borderBottomLeftRadius: 5,
+      borderBottomRightRadius: 5,
+    },
+    background: state.isSelected ? uiGrayDark : uiGrayDarker,
+    '&:hover': {
+      background: uiGrayDark,
+    },
+  }),
+};
+
+export default SegmentationSelect;

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

@@ -0,0 +1,95 @@
+.dcmseg-segmentation-settings {
+  display: flex;
+  flex-direction: column;
+  padding: 20px;
+}
+
+.dcmseg-segmentation-settings .range label {
+  display: block;
+  margin-bottom: 8px;
+}
+
+.dcmseg-segmentation-settings .settings-title {
+  display: flex;
+  flex-direction: row;
+  align-items: center;
+  justify-content: space-between;
+  padding-bottom: 20px;
+}
+
+.dcmseg-segmentation-settings .settings-title h3 {
+  color: var(--text-primary-color);
+  margin: 0;
+  padding: 0;
+}
+
+.dcmseg-segmentation-settings .settings-group {
+  display: flex;
+  flex-direction: column;
+  color: var(--text-primary-color);
+  font-size: 12px;
+}
+
+.dcmseg-segmentation-settings .settings-group .range {
+  display: flex;
+  padding: 20px 15px;
+}
+
+.dcmseg-segmentation-settings .settings-group .range:not(:last-of-type) {
+  padding-bottom: 0;
+}
+
+.dcmseg-segmentation-settings .settings-group .range label {
+  margin: 0;
+  display: unset;
+  min-width: 40px;
+  max-width: 40px;
+}
+
+.dcmseg-segmentation-settings .settings-group .range input {
+  width: 100%;
+  padding: 0 20px 0 20px;
+}
+
+.dcmseg-segmentation-settings .custom-check label {
+  font-weight: bold;
+  display: flex;
+  flex-direction: row;
+  align-items: center;
+  justify-content: space-between;
+  border-bottom: 2px solid black;
+  padding: 10px 15px;
+}
+
+.dcmseg-segmentation-settings .custom-check input {
+  width: 15px;
+  height: 15px;
+}
+
+.dcmseg-segmentation-settings .settings-group {
+  background-color: var(--ui-gray-dark);
+  border-radius: 5px;
+}
+
+.dcmseg-segmentation-settings .return-button {
+  color: #333;
+  background-color: #fff;
+  padding: 4px 12px;
+  line-height: 1.4;
+  text-align: center;
+  white-space: nowrap;
+  vertical-align: middle;
+  cursor: pointer;
+  user-select: none;
+  border: 1px solid #ccc;
+  border-radius: 4px;
+  transition: all 0.15s ease;
+}
+
+.dcmseg-segmentation-settings .return-button:hover,
+.dcmseg-segmentation-settings .return-button:active,
+.dcmseg-segmentation-settings .return-button.active {
+  background-color: var(--active-color);
+  border-color: var(--ui-border-color-active);
+  color: #fff;
+}

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

@@ -0,0 +1,178 @@
+import React, { useState, useEffect } from 'react';
+import PropTypes from 'prop-types';
+import { Range } from '@ohif/ui';
+
+import './SegmentationSettings.css';
+
+const SegmentationSettings = ({ configuration, onBack, onChange }) => {
+  const [state, setState] = useState({
+    renderFill: configuration.renderFill,
+    renderOutline: configuration.renderOutline,
+    shouldRenderInactiveLabelmaps: configuration.shouldRenderInactiveLabelmaps,
+    fillAlpha: configuration.fillAlpha,
+    outlineAlpha: configuration.outlineAlpha,
+    outlineWidth: configuration.outlineWidth,
+    fillAlphaInactive: configuration.fillAlphaInactive,
+    outlineAlphaInactive: configuration.outlineAlphaInactive
+  });
+
+  useEffect(() => {
+    onChange(state);
+  }, [state]);
+
+  const check = field => {
+    setState(state => ({ ...state, [field]: !state[field] }));
+  };
+
+  const save = (field, value) => {
+    setState(state => ({ ...state, [field]: value }));
+  };
+
+  const toFloat = value => parseFloat(value / 100).toFixed(2);
+
+  return (
+    <div className="dcmseg-segmentation-settings">
+      <div className="settings-title">
+        <h3>Segmentations Settings</h3>
+        <button className="return-button" onClick={onBack}>
+          Back
+        </button>
+      </div>
+      <div
+        className="settings-group"
+        style={{ marginBottom: state.renderFill ? 15 : 0 }}
+      >
+        <CustomCheck
+          label="Segment Fill"
+          checked={state.renderFill}
+          onChange={() => check('renderFill')}
+        />
+        {state.renderFill && (
+          <CustomRange
+            label="Opacity"
+            step={1}
+            min={0}
+            max={100}
+            value={state.fillAlpha * 100}
+            onChange={event => save('fillAlpha', toFloat(event.target.value))}
+            showPercentage
+          />
+        )}
+      </div>
+      <div
+        className="settings-group"
+        style={{ marginBottom: state.renderOutline ? 15 : 0 }}
+      >
+        <CustomCheck
+          label="Segment Outline"
+          checked={state.renderOutline}
+          onChange={() => check('renderOutline')}
+        />
+        {state.renderOutline && (
+          <>
+            <CustomRange
+              value={state.outlineAlpha * 100}
+              label="Opacity"
+              showPercentage
+              step={1}
+              min={0}
+              max={100}
+              onChange={event => save('outlineAlpha', toFloat(event.target.value))}
+            />
+            <CustomRange
+              value={state.outlineWidth}
+              label="Width"
+              showValue
+              step={1}
+              min={0}
+              max={5}
+              onChange={event => save('outlineWidth', parseInt(event.target.value))}
+            />
+          </>
+        )}
+      </div>
+      {(state.renderFill || state.renderOutline) && (
+        <div
+          className="settings-group"
+          style={{ marginBottom: state.shouldRenderInactiveLabelmaps ? 15 : 0 }}
+        >
+          <CustomCheck
+            label="Render inactive segmentations"
+            checked={state.shouldRenderInactiveLabelmaps}
+            onChange={() => check('shouldRenderInactiveLabelmaps')}
+          />
+          {state.shouldRenderInactiveLabelmaps && (
+            <>
+              {state.renderFill && (
+                <CustomRange
+                  label="Fill Opacity"
+                  showPercentage
+                  step={1}
+                  min={0}
+                  max={100}
+                  value={state.fillAlphaInactive * 100}
+                  onChange={event => save('fillAlphaInactive', toFloat(event.target.value))}
+                />
+              )}
+              {state.renderOutline && (
+                <CustomRange
+                  label="Outline Opacity"
+                  showPercentage
+                  step={1}
+                  min={0}
+                  max={100}
+                  value={state.outlineAlphaInactive * 100}
+                  onChange={event => save('outlineAlphaInactive', toFloat(event.target.value))}
+                />
+              )}
+            </>
+          )}
+        </div>
+      )}
+    </div>
+  );
+};
+
+const CustomCheck = ({ label, checked, onChange }) => {
+  return (
+    <div className="custom-check">
+      <label>
+        <span>{label}</span>
+        <input type="checkbox" checked={checked} onChange={onChange} />
+      </label>
+    </div>
+  );
+};
+
+const CustomRange = props => {
+  const { label, onChange } = props;
+  return (
+    <div className="range">
+      <label htmlFor="range">{label}</label>
+      <Range
+        {...props}
+        onChange={event => {
+          event.persist();
+          onChange(event);
+        }}
+      />
+    </div>
+  );
+};
+
+SegmentationSettings.propTypes = {
+  configuration: PropTypes.shape({
+    renderFill: PropTypes.bool.isRequired,
+    renderOutline: PropTypes.bool.isRequired,
+    shouldRenderInactiveLabelmaps: PropTypes.bool.isRequired,
+    fillAlpha: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired, /* TODO: why fillAlpha is string? */
+    outlineAlpha: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired, /* TODO: why fillAlpha is string? */
+    outlineWidth: PropTypes.number.isRequired,
+    fillAlphaInactive: PropTypes.number.isRequired,
+    outlineAlphaInactive: PropTypes.number.isRequired,
+  }).isRequired,
+  onBack: PropTypes.func.isRequired,
+  onChange: PropTypes.func.isRequired,
+};
+
+export default SegmentationSettings;

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

@@ -0,0 +1,7 @@
+export { default as BrushColorSelector } from './BrushColorSelector/BrushColorSelector';
+export { default as BrushRadius } from './BrushRadius/BrushRadius';
+export { default as SegmentationItem } from './SegmentationItem/SegmentationItem';
+export { default as SegmentationSettings } from './SegmentationSettings/SegmentationSettings';
+export { default as SegmentationPanel } from './SegmentationPanel/SegmentationPanel';
+export { default as SegmentItem } from './SegmentItem/SegmentItem';
+export { default as SegmentationSelect } from './SegmentationSelect';

extensions/dicom-segmentation/src/index.js

@@ -0,0 +1,30 @@
+import init from './init.js';
+import toolbarModule from './toolbarModule.js';
+import panelModule from './panelModule.js';
+import sopClassHandlerModule from './OHIFDicomSegSopClassHandler.js';
+
+export default {
+  /**
+   * Only required property. Should be a unique value across all extensions.
+   */
+  id: 'com.ohif.dicom-segmentation',
+
+  /**
+   *
+   *
+   * @param {object} [configuration={}]
+   * @param {object|array} [configuration.csToolsConfig] - Passed directly to `initCornerstoneTools`
+   */
+  preRegistration({ servicesManager, configuration = {} }) {
+    init({ servicesManager, configuration });
+  },
+  getToolbarModule({ servicesManager }) {
+    return toolbarModule;
+  },
+  getPanelModule({ servicesManager }) {
+    return panelModule;
+  },
+  getSopClassHandlerModule({ servicesManager }) {
+    return sopClassHandlerModule;
+  },
+};

extensions/dicom-segmentation/src/init.js

@@ -0,0 +1,20 @@
+import csTools from 'cornerstone-tools';
+
+/**
+ *
+ * @param {object} configuration
+ * @param {Object|Array} configuration.csToolsConfig
+ */
+export default function init({ servicesManager, configuration = {} }) {
+  const { BrushTool, SphericalBrushTool, CorrectionScissorsTool } = csTools;
+  const tools = [BrushTool, SphericalBrushTool, CorrectionScissorsTool];
+
+  tools.forEach(tool => csTools.addTool(tool));
+
+  csTools.addTool(BrushTool, {
+    name: 'BrushEraser',
+    configuration: {
+      alwaysEraseOnClick: true,
+    },
+  });
+}

extensions/dicom-segmentation/src/loadSegmentation.js

@@ -0,0 +1,115 @@
+import OHIF from '@ohif/core';
+import * as dcmjs from 'dcmjs';
+import cornerstone from 'cornerstone-core';
+import cornerstoneTools from 'cornerstone-tools';
+
+const { DicomLoaderService } = OHIF.utils;
+
+export default async function loadSegmentation(
+  segDisplaySet,
+  referencedDisplaySet,
+  studies
+) {
+  const { StudyInstanceUID } = referencedDisplaySet;
+
+  // Set here is loading is asynchronous.
+  // If this function throws its set back to false.
+  segDisplaySet.isLoaded = true;
+
+  const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
+    segDisplaySet,
+    studies
+  );
+
+  const dicomData = dcmjs.data.DicomMessage.readFile(segArrayBuffer);
+  const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
+    dicomData.dict
+  );
+
+  dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
+
+  const imageIds = _getImageIdsForDisplaySet(
+    studies,
+    StudyInstanceUID,
+    referencedDisplaySet.SeriesInstanceUID
+  );
+
+  const results = _parseSeg(segArrayBuffer, imageIds);
+
+  if (!results) {
+    throw new Error('Fractional segmentations are not yet supported');
+  }
+
+  const { labelmapBuffer, segMetadata, segmentsOnFrame } = results;
+  const { setters } = cornerstoneTools.getModule('segmentation');
+
+  // TODO: Could define a color LUT based on colors in the SEG.
+  const labelmapIndex = _getNextLabelmapIndex(imageIds[0]);
+
+  setters.labelmap3DByFirstImageId(
+    imageIds[0],
+    labelmapBuffer,
+    labelmapIndex,
+    segMetadata,
+    imageIds.length,
+    segmentsOnFrame
+  );
+
+  segDisplaySet.labelmapIndex = labelmapIndex;
+}
+
+function _getNextLabelmapIndex(firstImageId) {
+  const { state } = cornerstoneTools.getModule('segmentation');
+  const brushStackState = state.series[firstImageId];
+
+  let labelmapIndex = 0;
+
+  if (brushStackState) {
+    const { labelmaps3D } = brushStackState;
+    labelmapIndex = labelmaps3D.length;
+
+    for (let i = 0; i < labelmaps3D.length; i++) {
+      if (!labelmaps3D[i]) {
+        labelmapIndex = i;
+        break;
+      }
+    }
+  }
+
+  return labelmapIndex;
+}
+
+function _parseSeg(arrayBuffer, imageIds) {
+  return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
+    imageIds,
+    arrayBuffer,
+    cornerstone.metaData
+  );
+}
+
+function _getImageIdsForDisplaySet(
+  studies,
+  StudyInstanceUID,
+  SeriesInstanceUID
+) {
+  const study = studies.find(
+    study => study.StudyInstanceUID === StudyInstanceUID
+  );
+
+  const displaySets = study.displaySets.filter(displaySet => {
+    return displaySet.SeriesInstanceUID === SeriesInstanceUID;
+  });
+
+  if (displaySets.length > 1) {
+    console.warn(
+      'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
+    );
+    // TODO -> We could make check the instance list and see if any match?
+    // Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
+    // ^ Will that even happen?
+  }
+
+  const referencedDisplaySet = displaySets[0];
+
+  return referencedDisplaySet.images.map(image => image.getImageId());
+}

extensions/dicom-segmentation/src/panelModule.js

@@ -0,0 +1,39 @@
+import SegmentationPanel from './components/SegmentationPanel/SegmentationPanel.js';
+
+export default {
+  menuOptions: [
+    {
+      icon: 'list',
+      label: 'Segmentations',
+      target: 'segmentation-panel',
+      isDisabled: studies => {
+        if (!studies) {
+          return true;
+        }
+
+        for (let i = 0; i < studies.length; i++) {
+          const study = studies[i];
+
+          if (study && study.series) {
+            for (let j = 0; j < study.series.length; j++) {
+              const series = study.series[j];
+
+              if (series.Modality === 'SEG') {
+                return false;
+              }
+            }
+          }
+        }
+
+        return true;
+      },
+    },
+  ],
+  components: [
+    {
+      id: 'segmentation-panel',
+      component: SegmentationPanel,
+    },
+  ],
+  defaultContext: ['VIEWER'],
+};

extensions/dicom-segmentation/src/toolbarModule.js

@@ -0,0 +1,60 @@
+/* TODO: Creation tools (future release).
+
+const TOOLBAR_BUTTON_TYPES = {
+  COMMAND: 'command',
+  SET_TOOL_ACTIVE: 'setToolActive',
+  BUILT_IN: 'builtIn',
+};
+
+*/
+
+const definitions = []; /* TODO: Creation tools (future release). [
+  {
+    id: 'SegDropdown',
+    label: 'Segmentation',
+    icon: 'ellipse-circle',
+    buttons: [
+      {
+        id: 'Brush',
+        label: 'Brush',
+        icon: 'brush',
+        //
+        type: TOOLBAR_BUTTON_TYPES.SET_TOOL_ACTIVE,
+        commandName: 'setToolActive',
+        commandOptions: { toolName: 'Brush' },
+      },
+      {
+        id: 'SphericalBrush',
+        label: 'Spherical',
+        icon: 'sphere',
+        //
+        type: TOOLBAR_BUTTON_TYPES.SET_TOOL_ACTIVE,
+        commandName: 'setToolActive',
+        commandOptions: { toolName: 'SphericalBrush' },
+      },
+      {
+        id: 'CorrectionScissors',
+        label: 'Correction Scissors',
+        icon: 'scissors',
+        //
+        type: TOOLBAR_BUTTON_TYPES.SET_TOOL_ACTIVE,
+        commandName: 'setToolActive',
+        commandOptions: { toolName: 'CorrectionScissors' },
+      },
+      {
+        id: 'BrushEraser',
+        label: 'Eraser',
+        icon: 'trash',
+        //
+        type: TOOLBAR_BUTTON_TYPES.SET_TOOL_ACTIVE,
+        commandName: 'setToolActive',
+        commandOptions: { toolName: 'BrushEraser' },
+      },
+    ],
+  },
+]; */
+
+export default {
+  definitions,
+  defaultContext: 'ACTIVE_VIEWPORT::CORNERSTONE',
+};

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.
 
+# [1.3.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.2.24...@ohif/extension-vtk@1.3.0) (2020-03-13)
+
+
+### Features
+
+* Segmentations Settings UI - Phase 1 [#1391](https://github.com/OHIF/Viewers/issues/1391) ([#1392](https://github.com/OHIF/Viewers/issues/1392)) ([e8842cf](https://github.com/OHIF/Viewers/commit/e8842cf8aebde98db7fc123e4867c8288552331f)), closes [#1423](https://github.com/OHIF/Viewers/issues/1423)
+
+
+
+
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [1.2.24](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.2.23...@ohif/extension-vtk@1.2.24) (2020-03-09)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.2.23](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.2.22...@ohif/extension-vtk@1.2.23) (2020-03-09)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.2.22](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.2.21...@ohif/extension-vtk@1.2.22) (2020-03-06)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.2.21](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.2.20...@ohif/extension-vtk@1.2.21) (2020-02-29)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
 ## [1.2.20](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.2.19...@ohif/extension-vtk@1.2.20) (2020-02-21)
 
 **Note:** Version bump only for package @ohif/extension-vtk
@@ -396,621 +444,368 @@ See [Conventional Commits](https://conventionalcommits.org) for commit guideline
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.53.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.53.4...@ohif/extension-vtk@0.53.5) (2019-11-13)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.53.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.53.3...@ohif/extension-vtk@0.53.4) (2019-11-12)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.53.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.53.2...@ohif/extension-vtk@0.53.3) (2019-11-11)
 
-
 ### Bug Fixes
 
-* mpr2d vtkjs viewport does not render if range is set to `NaN` values ([#1157](https://github.com/OHIF/Viewers/issues/1157)) ([84a0972](https://github.com/OHIF/Viewers/commit/84a097212babc0f98198b9ced1def9743973a5a8))
-
-
-
-
+- mpr2d vtkjs viewport does not render if range is set to `NaN` values
+  ([#1157](https://github.com/OHIF/Viewers/issues/1157))
+  ([84a0972](https://github.com/OHIF/Viewers/commit/84a097212babc0f98198b9ced1def9743973a5a8))
 
 ## [0.53.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.53.1...@ohif/extension-vtk@0.53.2) (2019-11-08)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.53.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.53.0...@ohif/extension-vtk@0.53.1) (2019-11-08)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 # [0.53.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.32...@ohif/extension-vtk@0.53.0) (2019-11-06)
 
-
 ### Features
 
-* modal provider ([#1151](https://github.com/OHIF/Viewers/issues/1151)) ([75d88bc](https://github.com/OHIF/Viewers/commit/75d88bc454710d2dcdbc7d68c4d9df041159c840)), closes [#1086](https://github.com/OHIF/Viewers/issues/1086) [#1116](https://github.com/OHIF/Viewers/issues/1116) [#1116](https://github.com/OHIF/Viewers/issues/1116) [#1146](https://github.com/OHIF/Viewers/issues/1146) [#1142](https://github.com/OHIF/Viewers/issues/1142) [#1143](https://github.com/OHIF/Viewers/issues/1143) [#1110](https://github.com/OHIF/Viewers/issues/1110) [#1086](https://github.com/OHIF/Viewers/issues/1086) [#1116](https://github.com/OHIF/Viewers/issues/1116) [#1119](https://github.com/OHIF/Viewers/issues/1119)
-
-
-
-
+- modal provider ([#1151](https://github.com/OHIF/Viewers/issues/1151))
+  ([75d88bc](https://github.com/OHIF/Viewers/commit/75d88bc454710d2dcdbc7d68c4d9df041159c840)),
+  closes [#1086](https://github.com/OHIF/Viewers/issues/1086)
+  [#1116](https://github.com/OHIF/Viewers/issues/1116)
+  [#1116](https://github.com/OHIF/Viewers/issues/1116)
+  [#1146](https://github.com/OHIF/Viewers/issues/1146)
+  [#1142](https://github.com/OHIF/Viewers/issues/1142)
+  [#1143](https://github.com/OHIF/Viewers/issues/1143)
+  [#1110](https://github.com/OHIF/Viewers/issues/1110)
+  [#1086](https://github.com/OHIF/Viewers/issues/1086)
+  [#1116](https://github.com/OHIF/Viewers/issues/1116)
+  [#1119](https://github.com/OHIF/Viewers/issues/1119)
 
 ## [0.52.32](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.31...@ohif/extension-vtk@0.52.32) (2019-11-05)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.31](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.30...@ohif/extension-vtk@0.52.31) (2019-11-05)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
 ## [0.52.30](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.29...@ohif/extension-vtk@0.52.30) (2019-11-04)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.29](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.28...@ohif/extension-vtk@0.52.29) (2019-11-04)
 
-
 ### Bug Fixes
 
-* 🐛 Upgrade react-vtkjs-viewport to fix volume orientation ([#1143](https://github.com/OHIF/Viewers/issues/1143)) ([1d86b1a](https://github.com/OHIF/Viewers/commit/1d86b1a102fc422053cff103de8c12ca6f437354))
-
-
-
-
+- 🐛 Upgrade react-vtkjs-viewport to fix volume orientation
+  ([#1143](https://github.com/OHIF/Viewers/issues/1143))
+  ([1d86b1a](https://github.com/OHIF/Viewers/commit/1d86b1a102fc422053cff103de8c12ca6f437354))
 
 ## [0.52.28](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.27...@ohif/extension-vtk@0.52.28) (2019-11-04)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.27](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.26...@ohif/extension-vtk@0.52.27) (2019-10-31)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.26](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.25...@ohif/extension-vtk@0.52.26) (2019-10-30)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.25](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.24...@ohif/extension-vtk@0.52.25) (2019-10-29)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.24](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.23...@ohif/extension-vtk@0.52.24) (2019-10-29)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.23](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.22...@ohif/extension-vtk@0.52.23) (2019-10-28)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.22](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.21...@ohif/extension-vtk@0.52.22) (2019-10-28)
 
-
 ### Bug Fixes
 
-* MIP styling ([#1109](https://github.com/OHIF/Viewers/issues/1109)) ([0d21cc6](https://github.com/OHIF/Viewers/commit/0d21cc6ad0c47706b9e62e05fe2a0f1d86339760))
-
-
-
-
+- MIP styling ([#1109](https://github.com/OHIF/Viewers/issues/1109))
+  ([0d21cc6](https://github.com/OHIF/Viewers/commit/0d21cc6ad0c47706b9e62e05fe2a0f1d86339760))
 
 ## [0.52.21](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.20...@ohif/extension-vtk@0.52.21) (2019-10-26)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.20](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.19...@ohif/extension-vtk@0.52.20) (2019-10-26)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.19](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.18...@ohif/extension-vtk@0.52.19) (2019-10-25)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.18](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.17...@ohif/extension-vtk@0.52.18) (2019-10-25)
 
-
 ### Bug Fixes
 
-* 🐛 Orthographic MPR fix ([#1092](https://github.com/OHIF/Viewers/issues/1092)) ([460e375](https://github.com/OHIF/Viewers/commit/460e375f0aa75d35f7a46b4d48e6cc706019956d))
-
-
-
-
+- 🐛 Orthographic MPR fix ([#1092](https://github.com/OHIF/Viewers/issues/1092))
+  ([460e375](https://github.com/OHIF/Viewers/commit/460e375f0aa75d35f7a46b4d48e6cc706019956d))
 
 ## [0.52.17](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.16...@ohif/extension-vtk@0.52.17) (2019-10-25)
 
-
 ### Bug Fixes
 
-* 🐛 Fix crosshairs location when using MIP ([#1080](https://github.com/OHIF/Viewers/issues/1080)) ([b451ce4](https://github.com/OHIF/Viewers/commit/b451ce440796f13b0891739d2130e8ee71993d3d))
-
-
-
-
+- 🐛 Fix crosshairs location when using MIP
+  ([#1080](https://github.com/OHIF/Viewers/issues/1080))
+  ([b451ce4](https://github.com/OHIF/Viewers/commit/b451ce440796f13b0891739d2130e8ee71993d3d))
 
 ## [0.52.16](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.15...@ohif/extension-vtk@0.52.16) (2019-10-23)
 
-
 ### Bug Fixes
 
-* 🐛 Switch to orhtographic view for 2D MPR ([#1074](https://github.com/OHIF/Viewers/issues/1074)) ([13d337a](https://github.com/OHIF/Viewers/commit/13d337aaabb8dadf6366c6262c5e47e7781edd08))
-
-
-
-
+- 🐛 Switch to orhtographic view for 2D MPR
+  ([#1074](https://github.com/OHIF/Viewers/issues/1074))
+  ([13d337a](https://github.com/OHIF/Viewers/commit/13d337aaabb8dadf6366c6262c5e47e7781edd08))
 
 ## [0.52.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.14...@ohif/extension-vtk@0.52.15) (2019-10-23)
 
-
 ### Performance Improvements
 
-* ⚡️ Throttle UI refresh of synced WL value in vtk port ([#1070](https://github.com/OHIF/Viewers/issues/1070)) ([9d08e81](https://github.com/OHIF/Viewers/commit/9d08e81aa5def63a5e34f464aae099f7c29f0ac5))
-
-
-
-
+- ⚡️ Throttle UI refresh of synced WL value in vtk port
+  ([#1070](https://github.com/OHIF/Viewers/issues/1070))
+  ([9d08e81](https://github.com/OHIF/Viewers/commit/9d08e81aa5def63a5e34f464aae099f7c29f0ac5))
 
 ## [0.52.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.13...@ohif/extension-vtk@0.52.14) (2019-10-22)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.12...@ohif/extension-vtk@0.52.13) (2019-10-18)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.11...@ohif/extension-vtk@0.52.12) (2019-10-18)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.10...@ohif/extension-vtk@0.52.11) (2019-10-15)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.9...@ohif/extension-vtk@0.52.10) (2019-10-15)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.8...@ohif/extension-vtk@0.52.9) (2019-10-14)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.7...@ohif/extension-vtk@0.52.8) (2019-10-14)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.6...@ohif/extension-vtk@0.52.7) (2019-10-11)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.5...@ohif/extension-vtk@0.52.6) (2019-10-11)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.4...@ohif/extension-vtk@0.52.5) (2019-10-10)
 
-
 ### Performance Improvements
 
-* ⚡️ Update react-vtkjs-viewport for performance improvement ([6ee5094](https://github.com/OHIF/Viewers/commit/6ee5094))
-
-
-
-
+- ⚡️ Update react-vtkjs-viewport for performance improvement
+  ([6ee5094](https://github.com/OHIF/Viewers/commit/6ee5094))
 
 ## [0.52.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.3...@ohif/extension-vtk@0.52.4) (2019-10-10)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.2...@ohif/extension-vtk@0.52.3) (2019-10-09)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.52.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.1...@ohif/extension-vtk@0.52.2) (2019-10-09)
 
-
 ### Performance Improvements
 
-* 🎸 Update vtk viewport for faster image reconstruction ([#1016](https://github.com/OHIF/Viewers/issues/1016)) ([8513ad9](https://github.com/OHIF/Viewers/commit/8513ad9))
-
-
-
-
+- 🎸 Update vtk viewport for faster image reconstruction
+  ([#1016](https://github.com/OHIF/Viewers/issues/1016))
+  ([8513ad9](https://github.com/OHIF/Viewers/commit/8513ad9))
 
 ## [0.52.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.52.0...@ohif/extension-vtk@0.52.1) (2019-10-04)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 # [0.52.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.51.3...@ohif/extension-vtk@0.52.0) (2019-10-03)
 
-
 ### Features
 
-* 🎸 Synced Window Leveling ([559b637](https://github.com/OHIF/Viewers/commit/559b637)), closes [#558](https://github.com/OHIF/Viewers/issues/558)
-
-
-
-
+- 🎸 Synced Window Leveling
+  ([559b637](https://github.com/OHIF/Viewers/commit/559b637)), closes
+  [#558](https://github.com/OHIF/Viewers/issues/558)
 
 ## [0.51.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.51.2...@ohif/extension-vtk@0.51.3) (2019-10-03)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
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 ## [0.51.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.51.1...@ohif/extension-vtk@0.51.2) (2019-10-02)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.51.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.51.0...@ohif/extension-vtk@0.51.1) (2019-10-01)
 
-
 ### Bug Fixes
 
-* **rotate:** Use new MPR rotate in react-vtkjs-viewport 0.1.2 ([#964](https://github.com/OHIF/Viewers/issues/964)) ([8503cbc](https://github.com/OHIF/Viewers/commit/8503cbc))
-
-
-
-
+- **rotate:** Use new MPR rotate in react-vtkjs-viewport 0.1.2
+  ([#964](https://github.com/OHIF/Viewers/issues/964))
+  ([8503cbc](https://github.com/OHIF/Viewers/commit/8503cbc))
 
 # [0.51.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.23...@ohif/extension-vtk@0.51.0) (2019-10-01)
 
-
 ### Features
 
-* 🎸 MPR UI improvements. Added MinIP, AvgIP, slab thickness slider and mode toggle ([#947](https://github.com/OHIF/Viewers/issues/947)) ([c79c0c3](https://github.com/OHIF/Viewers/commit/c79c0c3))
-
-
-
-
+- 🎸 MPR UI improvements. Added MinIP, AvgIP, slab thickness slider and mode
+  toggle ([#947](https://github.com/OHIF/Viewers/issues/947))
+  ([c79c0c3](https://github.com/OHIF/Viewers/commit/c79c0c3))
 
 ## [0.50.23](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.22...@ohif/extension-vtk@0.50.23) (2019-10-01)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
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 ## [0.50.22](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.21...@ohif/extension-vtk@0.50.22) (2019-09-27)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
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 ## [0.50.21](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.20...@ohif/extension-vtk@0.50.21) (2019-09-27)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
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 ## [0.50.20](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.19...@ohif/extension-vtk@0.50.20) (2019-09-26)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
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 ## [0.50.19](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.18...@ohif/extension-vtk@0.50.19) (2019-09-26)
 
-
 ### Bug Fixes
 
-* Add some code splitting for PWA build ([#937](https://github.com/OHIF/Viewers/issues/937)) ([8938035](https://github.com/OHIF/Viewers/commit/8938035))
-
-
-
-
+- Add some code splitting for PWA build
+  ([#937](https://github.com/OHIF/Viewers/issues/937))
+  ([8938035](https://github.com/OHIF/Viewers/commit/8938035))
 
 ## [0.50.18](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.17...@ohif/extension-vtk@0.50.18) (2019-09-23)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
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 ## [0.50.17](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.16...@ohif/extension-vtk@0.50.17) (2019-09-19)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
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 ## [0.50.16](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.15...@ohif/extension-vtk@0.50.16) (2019-09-19)
 
-
 ### Bug Fixes
 
-* Set transfer function range to data range when loading volumes in VTK ([#930](https://github.com/OHIF/Viewers/issues/930)) ([2341b32](https://github.com/OHIF/Viewers/commit/2341b32))
-
-
-
-
+- Set transfer function range to data range when loading volumes in VTK
+  ([#930](https://github.com/OHIF/Viewers/issues/930))
+  ([2341b32](https://github.com/OHIF/Viewers/commit/2341b32))
 
 ## [0.50.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.14...@ohif/extension-vtk@0.50.15) (2019-09-19)
 
-
 ### Bug Fixes
 
-* Bump VTK viewport dependency ([#929](https://github.com/OHIF/Viewers/issues/929)) ([66a0aad](https://github.com/OHIF/Viewers/commit/66a0aad))
-* Stop adding empty labelmap to VTK Viewports for now. Wait until paint tools are implemented ([#926](https://github.com/OHIF/Viewers/issues/926)) ([7f642a0](https://github.com/OHIF/Viewers/commit/7f642a0))
-
-
-
-
+- Bump VTK viewport dependency
+  ([#929](https://github.com/OHIF/Viewers/issues/929))
+  ([66a0aad](https://github.com/OHIF/Viewers/commit/66a0aad))
+- Stop adding empty labelmap to VTK Viewports for now. Wait until paint tools
+  are implemented ([#926](https://github.com/OHIF/Viewers/issues/926))
+  ([7f642a0](https://github.com/OHIF/Viewers/commit/7f642a0))
 
 ## [0.50.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.13...@ohif/extension-vtk@0.50.14) (2019-09-17)
 
-
 ### Bug Fixes
 
-* bump cornerstone-tools version in peerDeps ([4afc88c](https://github.com/OHIF/Viewers/commit/4afc88c))
-
-
-
-
+- bump cornerstone-tools version in peerDeps
+  ([4afc88c](https://github.com/OHIF/Viewers/commit/4afc88c))
 
 ## [0.50.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.12...@ohif/extension-vtk@0.50.13) (2019-09-12)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.50.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.11...@ohif/extension-vtk@0.50.12) (2019-09-12)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.50.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.10...@ohif/extension-vtk@0.50.11) (2019-09-10)
 
-
 ### Bug Fixes
 
-* simplify runtime-extension usage ([ac5dbda](https://github.com/OHIF/Viewers/commit/ac5dbda))
-
-
-
-
+- simplify runtime-extension usage
+  ([ac5dbda](https://github.com/OHIF/Viewers/commit/ac5dbda))
 
 ## [0.50.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.9...@ohif/extension-vtk@0.50.10) (2019-09-10)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.50.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.8...@ohif/extension-vtk@0.50.9) (2019-09-10)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.50.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.7...@ohif/extension-vtk@0.50.8) (2019-09-09)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.50.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.6...@ohif/extension-vtk@0.50.7) (2019-09-06)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.50.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.5...@ohif/extension-vtk@0.50.6) (2019-09-04)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.50.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.4...@ohif/extension-vtk@0.50.5) (2019-09-04)
 
-
 ### Bug Fixes
 
-* measurementsAPI issue caused by production build ([#842](https://github.com/OHIF/Viewers/issues/842)) ([49d3439](https://github.com/OHIF/Viewers/commit/49d3439))
-
-
-
-
+- measurementsAPI issue caused by production build
+  ([#842](https://github.com/OHIF/Viewers/issues/842))
+  ([49d3439](https://github.com/OHIF/Viewers/commit/49d3439))
 
 ## [0.50.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.3...@ohif/extension-vtk@0.50.4) (2019-08-26)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.50.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.2...@ohif/extension-vtk@0.50.3) (2019-08-22)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.50.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.1...@ohif/extension-vtk@0.50.2) (2019-08-15)
 
-
 ### Bug Fixes
 
-* Update vtk and viewport dependencies ([98c40bc](https://github.com/OHIF/Viewers/commit/98c40bc))
-
-
-
-
+- Update vtk and viewport dependencies
+  ([98c40bc](https://github.com/OHIF/Viewers/commit/98c40bc))
 
 ## [0.50.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.0-alpha.10...@ohif/extension-vtk@0.50.1) (2019-08-14)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 # [0.50.0-alpha.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.1.4-alpha.9...@ohif/extension-vtk@0.50.0-alpha.10) (2019-08-14)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## [0.1.4-alpha.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.1.4-alpha.8...@ohif/extension-vtk@0.1.4-alpha.9) (2019-08-14)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 ## 0.1.4-alpha.8 (2019-08-14)
 
 **Note:** Version bump only for package @ohif/extension-vtk
 
-
-
-
-
 # Change Log
 
 All notable changes to this project will be documented in this file. See

extensions/vtk/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-vtk",
-  "version": "1.2.20",
+  "version": "1.3.0",
   "description": "OHIF extension for VTK.js",
   "author": "OHIF",
   "license": "MIT",
@@ -33,8 +33,9 @@
     "@ohif/i18n": "^0.50.0",
     "@ohif/ui": "^0.50.0",
     "cornerstone-core": "^2.2.8",
+    "cornerstone-tools": "4.12.5",
     "cornerstone-wado-image-loader": "^3.0.0",
-    "dcmjs": "^0.8.2",
+    "dcmjs": "^0.10.1",
     "dicom-parser": "^1.8.3",
     "i18next": "^17.0.3",
     "i18next-browser-languagedetector": "^3.0.1",
@@ -52,9 +53,9 @@
     "react-vtkjs-viewport": "^0.8.3"
   },
   "devDependencies": {
-    "@ohif/core": "^2.5.1",
-    "@ohif/ui": "^1.3.0",
-    "cornerstone-tools": "^4.12.0",
+    "@ohif/core": "^2.6.0",
+    "@ohif/ui": "^1.4.0",
+    "cornerstone-tools": "4.12.5",
     "cornerstone-wado-image-loader": "^3.0.0",
     "dicom-parser": "^1.8.3",
     "gh-pages": "^2.0.1",

extensions/vtk/src/OHIFVTKViewport.js

@@ -1,46 +1,34 @@
 import React, { Component } from 'react';
 import { getImageData, loadImageData } from 'react-vtkjs-viewport';
-
 import ConnectedVTKViewport from './ConnectedVTKViewport';
 import LoadingIndicator from './LoadingIndicator.js';
 import OHIF from '@ohif/core';
 import PropTypes from 'prop-types';
 import cornerstone from 'cornerstone-core';
-import handleSegmentationStorage from './handleSegmentationStorage.js';
+import cornerstoneTools from 'cornerstone-tools';
 import vtkDataArray from 'vtk.js/Sources/Common/Core/DataArray';
 import vtkImageData from 'vtk.js/Sources/Common/DataModel/ImageData';
 import vtkVolume from 'vtk.js/Sources/Rendering/Core/Volume';
 import vtkVolumeMapper from 'vtk.js/Sources/Rendering/Core/VolumeMapper';
 
+const segmentationModule = cornerstoneTools.getModule('segmentation');
+
 const { StackManager } = OHIF.utils;
 
-// Metadata configuration
-const metadataProvider = new OHIF.cornerstone.MetadataProvider();
-
-cornerstone.metaData.addProvider(
-  metadataProvider.provider.bind(metadataProvider)
-);
-
-StackManager.setMetadataProvider(metadataProvider);
-
-const SOP_CLASSES = {
-  SEGMENTATION_STORAGE: '1.2.840.10008.5.1.4.1.1.66.4',
-};
-
-const specialCaseHandlers = {};
-specialCaseHandlers[
-  SOP_CLASSES.SEGMENTATION_STORAGE
-] = handleSegmentationStorage;
-
 // TODO: Figure out where we plan to put this long term
 const volumeCache = {};
+const labelmapCache = {};
 
 /**
  * Create a labelmap image with the same dimensions as our background volume.
  *
  * @param backgroundImageData vtkImageData
  */
+/* TODO: Not currently used until we have drawing tools in vtkjs.
 function createLabelMapImageData(backgroundImageData) {
+  // TODO => Need to do something like this if we start drawing a new segmentation
+  // On a vtkjs viewport.
+
   const labelMapData = vtkImageData.newInstance(
     backgroundImageData.get('spacing', 'origin', 'direction')
   );
@@ -55,7 +43,7 @@ function createLabelMapImageData(backgroundImageData) {
   labelMapData.getPointData().setScalars(dataArray);
 
   return labelMapData;
-}
+} */
 
 class OHIFVTKViewport extends Component {
   state = {
@@ -68,10 +56,10 @@ class OHIFVTKViewport extends Component {
     viewportData: PropTypes.shape({
       studies: PropTypes.array,
       displaySet: PropTypes.shape({
-        studyInstanceUid: PropTypes.string,
-        displaySetInstanceUid: PropTypes.string,
-        sopClassUids: PropTypes.arrayOf(PropTypes.string),
-        sopInstanceUid: PropTypes.string,
+        StudyInstanceUID: PropTypes.string,
+        displaySetInstanceUID: PropTypes.string,
+        sopClassUIDs: PropTypes.arrayOf(PropTypes.string),
+        SOPInstanceUID: PropTypes.string,
         frameIndex: PropTypes.number,
       }),
     }),
@@ -97,18 +85,18 @@ class OHIFVTKViewport extends Component {
 
   static getCornerstoneStack(
     studies,
-    studyInstanceUid,
-    displaySetInstanceUid,
-    sopInstanceUid,
+    StudyInstanceUID,
+    displaySetInstanceUID,
+    SOPInstanceUID,
     frameIndex
   ) {
     // Create shortcut to displaySet
     const study = studies.find(
-      study => study.studyInstanceUid === studyInstanceUid
+      study => study.StudyInstanceUID === StudyInstanceUID
     );
 
     const displaySet = study.displaySets.find(set => {
-      return set.displaySetInstanceUid === displaySetInstanceUid;
+      return set.displaySetInstanceUID === displaySetInstanceUID;
     });
 
     // Get stack from Stack Manager
@@ -119,17 +107,14 @@ class OHIFVTKViewport extends Component {
 
     if (frameIndex !== undefined) {
       stack.currentImageIdIndex = frameIndex;
-    } else if (sopInstanceUid) {
+    } else if (SOPInstanceUID) {
       const index = stack.imageIds.findIndex(imageId => {
-        const sopCommonModule = cornerstone.metaData.get(
-          'sopCommonModule',
+        const imageIdSOPInstanceUID = cornerstone.metaData.get(
+          'SOPInstanceUID',
           imageId
         );
-        if (!sopCommonModule) {
-          return;
-        }
 
-        return sopCommonModule.sopInstanceUID === sopInstanceUid;
+        return imageIdSOPInstanceUID === SOPInstanceUID;
       });
 
       if (index > -1) {
@@ -144,48 +129,73 @@ class OHIFVTKViewport extends Component {
 
   getViewportData = (
     studies,
-    studyInstanceUid,
-    displaySetInstanceUid,
-    sopClassUid,
-    sopInstanceUid,
+    StudyInstanceUID,
+    displaySetInstanceUID,
+    SOPClassUID,
+    SOPInstanceUID,
     frameIndex
   ) => {
     const stack = OHIFVTKViewport.getCornerstoneStack(
       studies,
-      studyInstanceUid,
-      displaySetInstanceUid,
-      sopClassUid,
-      sopInstanceUid,
+      StudyInstanceUID,
+      displaySetInstanceUID,
+      SOPClassUID,
+      SOPInstanceUID,
       frameIndex
     );
 
-    let imageDataObject;
+    const imageDataObject = getImageData(stack.imageIds, displaySetInstanceUID);
     let labelmapDataObject;
+    let labelmapColorLUT;
 
-    switch (sopClassUid) {
-      case SOP_CLASSES.SEGMENTATION_STORAGE:
-        throw new Error('Not yet implemented');
-      /*
-        const data = handleSegmentationStorage(
-          stack.imageIds,
-          displaySetInstanceUid
+    const firstImageId = stack.imageIds[0];
+    const { state } = segmentationModule;
+    const brushStackState = state.series[firstImageId];
+
+    if (brushStackState) {
+      const { activeLabelmapIndex } = brushStackState;
+      const labelmap3D = brushStackState.labelmaps3D[activeLabelmapIndex];
+
+      const vtkLabelmapID = `${firstImageId}_${activeLabelmapIndex}`;
+
+      if (labelmapCache[vtkLabelmapID]) {
+        labelmapDataObject = labelmapCache[vtkLabelmapID];
+      } else {
+        // TODO -> We need an imageId based getter in cornerstoneTools
+        const labelmapBuffer = labelmap3D.buffer;
+
+        // Create VTK Image Data with buffer as input
+        labelmapDataObject = vtkImageData.newInstance();
+
+        const dataArray = vtkDataArray.newInstance({
+          numberOfComponents: 1, // labelmap with single component
+          values: new Uint16Array(labelmapBuffer),
+        });
+
+        labelmapDataObject.getPointData().setScalars(dataArray);
+        labelmapDataObject.setDimensions(...imageDataObject.dimensions);
+        labelmapDataObject.setSpacing(
+          ...imageDataObject.vtkImageData.getSpacing()
+        );
+        labelmapDataObject.setOrigin(
+          ...imageDataObject.vtkImageData.getOrigin()
+        );
+        labelmapDataObject.setDirection(
+          ...imageDataObject.vtkImageData.getDirection()
         );
 
-        imageDataObject = data.referenceDataObject;
-        labelmapDataObject = data.labelmapDataObject;
+        // Cache the labelmap volume.
+        labelmapCache[vtkLabelmapID] = labelmapDataObject;
+      }
 
-        return loadImageData(imageDataObject).then(() => {
-          return {
-            data: imageDataObject.vtkImageData,
-            labelmap: labelmapDataObject,
-          };
-        });
-        */
-      default:
-        imageDataObject = getImageData(stack.imageIds, displaySetInstanceUid);
-
-        return imageDataObject;
+      labelmapColorLUT = state.colorLutTables[labelmap3D.colorLUTIndex];
     }
+
+    return {
+      imageDataObject,
+      labelmapDataObject,
+      labelmapColorLUT,
+    };
   };
 
   /**
@@ -194,25 +204,31 @@ class OHIFVTKViewport extends Component {
    * @param {object} imageDataObject
    * @param {object} imageDataObject.vtkImageData
    * @param {object} imageDataObject.imageMetaData0
-   * @param {number} [imageDataObject.imageMetaData0.windowWidth] - The volume's initial windowWidth
-   * @param {number} [imageDataObject.imageMetaData0.windowCenter] - The volume's initial windowCenter
-   * @param {string} imageDataObject.imageMetaData0.modality - CT, MR, PT, etc
-   * @param {string} displaySetInstanceUid
+   * @param {number} [imageDataObject.imageMetaData0.WindowWidth] - The volume's initial WindowWidth
+   * @param {number} [imageDataObject.imageMetaData0.WindowCenter] - The volume's initial WindowCenter
+   * @param {string} imageDataObject.imageMetaData0.Modality - CT, MR, PT, etc
+   * @param {string} displaySetInstanceUID
    * @returns vtkVolumeActor
    * @memberof OHIFVTKViewport
    */
-  getOrCreateVolume(imageDataObject, displaySetInstanceUid) {
-    if (volumeCache[displaySetInstanceUid]) {
-      return volumeCache[displaySetInstanceUid];
+  getOrCreateVolume(imageDataObject, displaySetInstanceUID) {
+    if (volumeCache[displaySetInstanceUID]) {
+      return volumeCache[displaySetInstanceUID];
     }
 
     const { vtkImageData, imageMetaData0 } = imageDataObject;
-    const { windowWidth, windowCenter, modality } = imageMetaData0;
+    // TODO -> Should update react-vtkjs-viewport and react-cornerstone-viewports
+    // internals to use naturalized DICOM JSON names.
+    const {
+      windowWidth: WindowWidth,
+      windowCenter: WindowCenter,
+      modality: Modality,
+    } = imageMetaData0;
 
     const { lower, upper } = _getRangeFromWindowLevels(
-      windowWidth,
-      windowCenter,
-      modality
+      WindowWidth,
+      WindowCenter,
+      Modality
     );
     const volumeActor = vtkVolume.newInstance();
     const volumeMapper = vtkVolumeMapper.newInstance();
@@ -236,7 +252,7 @@ class OHIFVTKViewport extends Component {
     // TODO: maybe we should auto adjust samples to 1000.
     volumeMapper.setMaximumSamplesPerRay(4000);
 
-    volumeCache[displaySetInstanceUid] = volumeActor;
+    volumeCache[displaySetInstanceUID] = volumeActor;
 
     return volumeActor;
   }
@@ -244,53 +260,61 @@ class OHIFVTKViewport extends Component {
   setStateFromProps() {
     const { studies, displaySet } = this.props.viewportData;
     const {
-      studyInstanceUid,
-      displaySetInstanceUid,
-      sopClassUids,
-      sopInstanceUid,
+      StudyInstanceUID,
+      displaySetInstanceUID,
+      sopClassUIDs,
+      SOPInstanceUID,
       frameIndex,
     } = displaySet;
 
-    if (sopClassUids.length > 1) {
+    if (sopClassUIDs.length > 1) {
       console.warn(
-        'More than one SOPClassUid in the same series is not yet supported.'
+        'More than one SOPClassUID in the same series is not yet supported.'
       );
     }
 
-    const sopClassUid = sopClassUids[0];
-    const imageDataObject = this.getViewportData(
+    const study = studies.find(
+      study => study.StudyInstanceUID === StudyInstanceUID
+    );
+
+    const dataDetails = {
+      studyDate: study.studyDate,
+      studyTime: study.studyTime,
+      studyDescription: study.studyDescription,
+      patientName: study.patientName,
+      patientId: study.patientId,
+      seriesNumber: String(displaySet.seriesNumber),
+      seriesDescription: displaySet.seriesDescription,
+    };
+
+    const {
+      imageDataObject,
+      labelmapDataObject,
+      labelmapColorLUT,
+    } = this.getViewportData(
       studies,
-      studyInstanceUid,
-      displaySetInstanceUid,
-      sopClassUid,
-      sopInstanceUid,
+      StudyInstanceUID,
+      displaySetInstanceUID,
+      SOPInstanceUID,
       frameIndex
     );
 
     this.imageDataObject = imageDataObject;
 
-    // TODO: Temporarily disabling this since it is not yet
-    // being used and hurts performance significantly.
-    /*if (!labelmap) {
+    /* TODO: Not currently used until we have drawing tools in vtkjs.
+    if (!labelmap) {
       labelmap = createLabelMapImageData(data);
-    }*/
+    } */
 
     const volumeActor = this.getOrCreateVolume(
       imageDataObject,
-      displaySetInstanceUid
+      displaySetInstanceUID
     );
 
-    this.setState({
-      paintFilterBackgroundImageData: imageDataObject.vtkImageData,
-      paintFilterLabelMapImageData: null, // TODO
-      percentComplete: 0,
-    });
-
     this.setState(
       {
-        paintFilterBackgroundImageData: imageDataObject.vtkImageData,
-        paintFilterLabelMapImageData: null, // TODO
         percentComplete: 0,
+        dataDetails,
       },
       () => {
         this.loadProgressively(imageDataObject);
@@ -302,6 +326,9 @@ class OHIFVTKViewport extends Component {
         setTimeout(() => {
           this.setState({
             volumes: [volumeActor],
+            paintFilterLabelMapImageData: labelmapDataObject,
+            paintFilterBackgroundImageData: imageDataObject.vtkImageData,
+            labelmapColorLUT,
           });
         }, 200);
       }
@@ -313,13 +340,13 @@ class OHIFVTKViewport extends Component {
   }
 
   componentDidUpdate(prevProps) {
-    const { studies, displaySet } = this.props.viewportData;
+    const { displaySet } = this.props.viewportData;
     const prevDisplaySet = prevProps.viewportData.displaySet;
 
     if (
-      displaySet.displaySetInstanceUid !==
-        prevDisplaySet.displaySetInstanceUid ||
-      displaySet.sopInstanceUid !== prevDisplaySet.sopInstanceUid ||
+      displaySet.displaySetInstanceUID !==
+        prevDisplaySet.displaySetInstanceUID ||
+      displaySet.SOPInstanceUID !== prevDisplaySet.SOPInstanceUID ||
       displaySet.frameIndex !== prevDisplaySet.frameIndex
     ) {
       this.setStateFromProps();
@@ -331,7 +358,7 @@ class OHIFVTKViewport extends Component {
 
     const { isLoading, insertPixelDataPromises } = imageDataObject;
 
-    const numberOfFrames = insertPixelDataPromises.length;
+    const NumberOfFrames = insertPixelDataPromises.length;
 
     if (!isLoading) {
       this.setState({ isLoaded: true });
@@ -341,7 +368,7 @@ class OHIFVTKViewport extends Component {
     insertPixelDataPromises.forEach(promise => {
       promise.then(numberProcessed => {
         const percentComplete = Math.floor(
-          (numberProcessed * 100) / numberOfFrames
+          (numberProcessed * 100) / NumberOfFrames
         );
 
         if (percentComplete !== this.state.percentComplete) {
@@ -353,12 +380,15 @@ class OHIFVTKViewport extends Component {
     });
 
     Promise.all(insertPixelDataPromises).then(() => {
-      this.setState({ isLoaded: true });
+      this.setState({
+        isLoaded: true,
+      });
     });
   }
 
   render() {
     let childrenWithProps = null;
+    const { configuration } = segmentationModule;
 
     // TODO: Does it make more sense to use Context?
     if (this.props.children && this.props.children.length) {
@@ -375,6 +405,10 @@ class OHIFVTKViewport extends Component {
 
     const style = { width: '100%', height: '100%', position: 'relative' };
 
+    const visible = configuration.renderFill || configuration.renderOutline;
+    const opacity = configuration.fillAlpha;
+    const outlineThickness = configuration.outlineThickness;
+
     return (
       <>
         <div style={style}>
@@ -391,6 +425,14 @@ class OHIFVTKViewport extends Component {
                 this.state.paintFilterBackgroundImageData
               }
               viewportIndex={this.props.viewportIndex}
+              dataDetails={this.state.dataDetails}
+              labelmapRenderingOptions={{
+                colorLUT: this.state.labelmapColorLUT,
+                globalOpacity: opacity,
+                visible,
+                outlineThickness,
+                renderOutline: true,
+              }}
               onScroll={this.props.onScroll}
             />
           )}
@@ -409,21 +451,21 @@ class OHIFVTKViewport extends Component {
  * @private
  * @param {number} [width] - the width of our window
  * @param {number} [center] - the center of our window
- * @param {string} [modality] - 'PT', 'CT', etc.
+ * @param {string} [Modality] - 'PT', 'CT', etc.
  * @returns { lower, upper } - range
  */
-function _getRangeFromWindowLevels(width, center, modality = undefined) {
+function _getRangeFromWindowLevels(width, center, Modality = undefined) {
+  // For PET just set the range to 0-5 SUV
+  if (Modality === 'PT') {
+    return { lower: 0, upper: 5 };
+  }
+
   const levelsAreNotNumbers = isNaN(center) || isNaN(width);
 
   if (levelsAreNotNumbers) {
     return { lower: 0, upper: 512 };
   }
 
-  // For PET just set the range to 0-5 SUV
-  if (modality === 'PT') {
-    return { lower: 0, upper: 5 };
-  }
-
   return {
     lower: center - width / 2.0,
     upper: center + width / 2.0,

extensions/vtk/src/VTKViewport.js

@@ -19,8 +19,8 @@ const VTKViewport = props => {
   useEffect(() => {
     const handleScrollEvent = evt => {
       const vtkViewportApiReference = props.onScroll(props.viewportIndex) || {};
-      const viewportUid = vtkViewportApiReference.uid;
-      const viewportWasScrolled = viewportUid === evt.detail.uid;
+      const viewportUID = vtkViewportApiReference.uid;
+      const viewportWasScrolled = viewportUID === evt.detail.uid;
 
       if (viewportWasScrolled) {
         setViewportActiveHandler();

extensions/vtk/src/commandsModule.js

@@ -70,12 +70,9 @@ const commandsModule = ({ commandsManager }) => {
     if (cornerstoneElement) {
       const imageId = cornerstoneElement.image.imageId;
 
-      const { modality } = cornerstone.metaData.get(
-        'generalSeriesModule',
-        imageId
-      );
+      const Modality = cornerstone.metaData.get('Modality', imageId);
 
-      if (modality !== 'PT') {
+      if (Modality !== 'PT') {
         const { windowWidth, windowCenter } = cornerstoneElement.viewport.voi;
 
         return {

extensions/vtk/src/handleSegmentationStorage.js

@@ -1,150 +0,0 @@
-import * as dcmjs from "dcmjs";
-
-import OHIF from "@ohif/core";
-import { api } from "dicomweb-client";
-
-const { StackManager } = OHIF.utils;
-
-function getDisplaySet(studies, studyInstanceUid, displaySetInstanceUid) {
-  const study = studies.find(
-    study => study.studyInstanceUid === studyInstanceUid
-  );
-
-  const displaySet = study.displaySets.find(set => {
-    return set.displaySetInstanceUid === displaySetInstanceUid;
-  });
-
-  return displaySet;
-}
-
-function getDisplaySetsBySeries(studies, studyInstanceUid, seriesInstanceUid) {
-  const study = studies.find(
-    study => study.studyInstanceUid === studyInstanceUid
-  );
-
-  return study.displaySets.filter(set => {
-    return set.seriesInstanceUid === seriesInstanceUid;
-  });
-}
-
-function getCornerstoneStack(studies, studyInstanceUid, displaySetInstanceUid) {
-  const study = studies.find(
-    study => study.studyInstanceUid === studyInstanceUid
-  );
-
-  // Create shortcut to displaySet
-  const displaySet = getDisplaySet(
-    studies,
-    studyInstanceUid,
-    displaySetInstanceUid
-  );
-
-  // Get stack from Stack Manager
-  const stack = StackManager.findOrCreateStack(study, displaySet);
-
-  // Clone the stack here so we don't mutate it later
-  const stackClone = Object.assign({}, stack);
-  stackClone.currentImageIdIndex = 0;
-
-  return stackClone;
-}
-
-function retrieveDicomData(
-  studyInstanceUID,
-  seriesInstanceUID,
-  sopInstanceUID,
-  wadoRoot
-) {
-  const config = {
-    url: wadoRoot,
-    headers: DICOMWeb.getAuthorizationHeader()
-  };
-
-  const dicomWeb = new api.DICOMwebClient(config);
-  const options = {
-    studyInstanceUID,
-    seriesInstanceUID,
-    sopInstanceUID
-  };
-
-  return dicomWeb.retrieveInstance(options);
-}
-
-async function handleSegmentationStorage(
-  studies,
-  studyInstanceUid,
-  displaySetInstanceUid
-) {
-  const study = studies.find(
-    study => study.studyInstanceUid === studyInstanceUid
-  );
-  const displaySet = getDisplaySet(
-    studies,
-    studyInstanceUid,
-    displaySetInstanceUid
-  );
-
-  // TODO: This is terrible but we need to use WADO-RS or we can't retrieve the SEG
-  // from google cloud
-  const wadoRoot = displaySet.images[0].getData().wadoRoot;
-
-  const StudyInstanceUID = displaySet.images[0].getStudyInstanceUID();
-  const SeriesInstanceUID = displaySet.images[0].getSeriesInstanceUID();
-  const SOPInstanceUID = displaySet.images[0].getSOPInstanceUID();
-
-  const arrayBuffer = await retrieveDicomData(
-    StudyInstanceUID,
-    SeriesInstanceUID,
-    SOPInstanceUID,
-    wadoRoot
-  );
-
-  const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
-  const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
-    dicomData.dict
-  );
-
-  const segments = dcmjs.adapters.VTKjs.Segmentation.generateSegments(dataset);
-
-  dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
-
-  const seriesInstanceUid = dataset.ReferencedSeriesSequence.SeriesInstanceUID;
-  const displaySets = getDisplaySetsBySeries(
-    studies,
-    studyInstanceUid,
-    seriesInstanceUid
-  );
-
-  if (displaySets.length > 1) {
-    console.warn(
-      "More than one display set with the same seriesInstanceUid. This is not supported yet..."
-    );
-  }
-
-  const referenceDisplaySet = displaySets[0];
-  const imageIds = referenceDisplaySet.images.map(image => image.getImageId());
-
-  if (!results) {
-    throw new Error("Fractional segmentations are not supported");
-  }
-
-  const cachedStack = StackManager.findOrCreateStack(
-    study,
-    referenceDisplaySet
-  );
-  const stack = Object.assign({}, cachedStack);
-  stack.currentImageIdIndex = 0;
-
-  return {
-    referenceDataObject,
-    labelmapDataObject
-  };
-
-  return {
-    studyInstanceUid,
-    displaySetInstanceUid,
-    stack
-  };
-}
-
-export default handleSegmentationStorage;

extensions/vtk/src/toolbarComponents/VTKMPRToolbarButton.js

@@ -13,21 +13,21 @@ const _isDisplaySetReconstructable = (viewportSpecificData = {}, activeViewportI
     return false;
   };
 
-  const { displaySetInstanceUid, studyInstanceUid } = viewportSpecificData[
+  const { displaySetInstanceUID, StudyInstanceUID } = viewportSpecificData[
     activeViewportIndex
   ];
 
   const studies = studyMetadataManager.all();
 
   const study = studies.find(
-    study => study.studyInstanceUID === studyInstanceUid
+    study => study.studyInstanceUID === StudyInstanceUID
   );
 
   if (!study) {
     return false;
   }
 
-  const displaySet = study._displaySets.find(set => set.displaySetInstanceUid === displaySetInstanceUid);
+  const displaySet = study._displaySets.find(set => set.displaySetInstanceUID === displaySetInstanceUID);
 
   if (!displaySet) {
     return false;

platform/core/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.
 
+# [2.6.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.5.3...@ohif/core@2.6.0) (2020-03-13)
+
+
+### Features
+
+* Segmentations Settings UI - Phase 1 [#1391](https://github.com/OHIF/Viewers/issues/1391) ([#1392](https://github.com/OHIF/Viewers/issues/1392)) ([e8842cf](https://github.com/OHIF/Viewers/commit/e8842cf8aebde98db7fc123e4867c8288552331f)), closes [#1423](https://github.com/OHIF/Viewers/issues/1423)
+
+
+
+
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [2.5.3](https://github.com/OHIF/Viewers/compare/@ohif/core@2.5.2...@ohif/core@2.5.3) (2020-03-09)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.5.2](https://github.com/OHIF/Viewers/compare/@ohif/core@2.5.1...@ohif/core@2.5.2) (2020-03-06)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
 ## [2.5.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.5.0...@ohif/core@2.5.1) (2020-02-21)
 
 
@@ -288,339 +320,239 @@ See [Conventional Commits](https://conventionalcommits.org) for commit guideline
 
 # [1.9.0](https://github.com/OHIF/Viewers/compare/@ohif/core@1.8.0...@ohif/core@1.9.0) (2019-11-13)
 
-
 ### Features
 
-* expose UiNotifications service ([#1172](https://github.com/OHIF/Viewers/issues/1172)) ([5c04e34](https://github.com/OHIF/Viewers/commit/5c04e34c8fb2394ab7acd9eb4f2ab12afeb2f255))
-
-
-
-
+- expose UiNotifications service
+  ([#1172](https://github.com/OHIF/Viewers/issues/1172))
+  ([5c04e34](https://github.com/OHIF/Viewers/commit/5c04e34c8fb2394ab7acd9eb4f2ab12afeb2f255))
 
 # [1.8.0](https://github.com/OHIF/Viewers/compare/@ohif/core@1.7.1...@ohif/core@1.8.0) (2019-11-12)
 
-
 ### Features
 
-* 🎸 Update hotkeys and user preferences modal ([#1135](https://github.com/OHIF/Viewers/issues/1135)) ([e62f5f8](https://github.com/OHIF/Viewers/commit/e62f5f8dd28ab363f23671cd21cee115abb870ff)), closes [#923](https://github.com/OHIF/Viewers/issues/923)
-
-
-
-
+- 🎸 Update hotkeys and user preferences modal
+  ([#1135](https://github.com/OHIF/Viewers/issues/1135))
+  ([e62f5f8](https://github.com/OHIF/Viewers/commit/e62f5f8dd28ab363f23671cd21cee115abb870ff)),
+  closes [#923](https://github.com/OHIF/Viewers/issues/923)
 
 ## [1.7.1](https://github.com/OHIF/Viewers/compare/@ohif/core@1.7.0...@ohif/core@1.7.1) (2019-11-08)
 
-
 ### Bug Fixes
 
-* Add a fallback metadata provider which pulls metadata from WADO-… ([#1158](https://github.com/OHIF/Viewers/issues/1158)) ([31b1adf](https://github.com/OHIF/Viewers/commit/31b1adfa5993d6c8e3e9c8b03fa9856f2621b037))
-
-
-
-
+- Add a fallback metadata provider which pulls metadata from WADO-…
+  ([#1158](https://github.com/OHIF/Viewers/issues/1158))
+  ([31b1adf](https://github.com/OHIF/Viewers/commit/31b1adfa5993d6c8e3e9c8b03fa9856f2621b037))
 
 # [1.7.0](https://github.com/OHIF/Viewers/compare/@ohif/core@1.6.2...@ohif/core@1.7.0) (2019-11-05)
 
-
 ### Features
 
-* 🎸 Filter by url query param for seriesInstnaceUID ([#1117](https://github.com/OHIF/Viewers/issues/1117)) ([e208f2e](https://github.com/OHIF/Viewers/commit/e208f2e6a9c49b16dadead0a917f657cf023929a)), closes [#1118](https://github.com/OHIF/Viewers/issues/1118)
-
-
-
-
+- 🎸 Filter by url query param for seriesInstnaceUID
+  ([#1117](https://github.com/OHIF/Viewers/issues/1117))
+  ([e208f2e](https://github.com/OHIF/Viewers/commit/e208f2e6a9c49b16dadead0a917f657cf023929a)),
+  closes [#1118](https://github.com/OHIF/Viewers/issues/1118)
 
 ## [1.6.2](https://github.com/OHIF/Viewers/compare/@ohif/core@1.6.1...@ohif/core@1.6.2) (2019-11-05)
 
-
 ### Bug Fixes
 
-* [#1075](https://github.com/OHIF/Viewers/issues/1075) Returning to the Study List before all series have finishe… ([#1090](https://github.com/OHIF/Viewers/issues/1090)) ([ecaf578](https://github.com/OHIF/Viewers/commit/ecaf578f92dc40294cec7ff9b272fb432dec4125))
-
-
-
-
+- [#1075](https://github.com/OHIF/Viewers/issues/1075) Returning to the Study
+  List before all series have finishe…
+  ([#1090](https://github.com/OHIF/Viewers/issues/1090))
+  ([ecaf578](https://github.com/OHIF/Viewers/commit/ecaf578f92dc40294cec7ff9b272fb432dec4125))
 
 ## [1.6.1](https://github.com/OHIF/Viewers/compare/@ohif/core@1.6.0...@ohif/core@1.6.1) (2019-10-31)
 
-
 ### Bug Fixes
 
-* application crash if patientName is an object ([#1138](https://github.com/OHIF/Viewers/issues/1138)) ([64cf3b3](https://github.com/OHIF/Viewers/commit/64cf3b324da2383a927af1df2d46db2fca5318aa))
-
-
-
-
+- application crash if patientName is an object
+  ([#1138](https://github.com/OHIF/Viewers/issues/1138))
+  ([64cf3b3](https://github.com/OHIF/Viewers/commit/64cf3b324da2383a927af1df2d46db2fca5318aa))
 
 # [1.6.0](https://github.com/OHIF/Viewers/compare/@ohif/core@1.5.2...@ohif/core@1.6.0) (2019-10-26)
 
-
 ### Features
 
-* Snapshot Download Tool ([#840](https://github.com/OHIF/Viewers/issues/840)) ([450e098](https://github.com/OHIF/Viewers/commit/450e0981a5ba054fcfcb85eeaeb18371af9088f8))
-
-
-
-
+- Snapshot Download Tool ([#840](https://github.com/OHIF/Viewers/issues/840))
+  ([450e098](https://github.com/OHIF/Viewers/commit/450e0981a5ba054fcfcb85eeaeb18371af9088f8))
 
 ## [1.5.2](https://github.com/OHIF/Viewers/compare/@ohif/core@1.5.1...@ohif/core@1.5.2) (2019-10-25)
 
-
 ### Bug Fixes
 
-* set SR in ActiveViewport by clicking thumb ([#1091](https://github.com/OHIF/Viewers/issues/1091)) ([986b7ae](https://github.com/OHIF/Viewers/commit/986b7ae2bf4f7d27f326e62f93285ce20eaf0a79))
-
-
-
-
+- set SR in ActiveViewport by clicking thumb
+  ([#1091](https://github.com/OHIF/Viewers/issues/1091))
+  ([986b7ae](https://github.com/OHIF/Viewers/commit/986b7ae2bf4f7d27f326e62f93285ce20eaf0a79))
 
 ## [1.5.1](https://github.com/OHIF/Viewers/compare/@ohif/core@1.5.0...@ohif/core@1.5.1) (2019-10-25)
 
-
 ### Bug Fixes
 
-* 🐛 Orthographic MPR fix ([#1092](https://github.com/OHIF/Viewers/issues/1092)) ([460e375](https://github.com/OHIF/Viewers/commit/460e375f0aa75d35f7a46b4d48e6cc706019956d))
-
-
-
-
+- 🐛 Orthographic MPR fix ([#1092](https://github.com/OHIF/Viewers/issues/1092))
+  ([460e375](https://github.com/OHIF/Viewers/commit/460e375f0aa75d35f7a46b4d48e6cc706019956d))
 
 # [1.5.0](https://github.com/OHIF/Viewers/compare/@ohif/core@1.4.0...@ohif/core@1.5.0) (2019-10-25)
 
-
 ### Features
 
-* 🎸 Allow routes to load Google Cloud DICOM Stores in the Study List ([#1069](https://github.com/OHIF/Viewers/issues/1069)) ([21b586b](https://github.com/OHIF/Viewers/commit/21b586b08f3dde6613859712a9e0577dece564db))
-
-
-
-
+- 🎸 Allow routes to load Google Cloud DICOM Stores in the Study List
+  ([#1069](https://github.com/OHIF/Viewers/issues/1069))
+  ([21b586b](https://github.com/OHIF/Viewers/commit/21b586b08f3dde6613859712a9e0577dece564db))
 
 # [1.4.0](https://github.com/OHIF/Viewers/compare/@ohif/core@1.3.2...@ohif/core@1.4.0) (2019-10-15)
 
-
 ### Features
 
-* 🎸 Only allow reconstruction of datasets that make sense ([#1010](https://github.com/OHIF/Viewers/issues/1010)) ([2d75e01](https://github.com/OHIF/Viewers/commit/2d75e01)), closes [#561](https://github.com/OHIF/Viewers/issues/561)
-
-
-
-
+- 🎸 Only allow reconstruction of datasets that make sense
+  ([#1010](https://github.com/OHIF/Viewers/issues/1010))
+  ([2d75e01](https://github.com/OHIF/Viewers/commit/2d75e01)), closes
+  [#561](https://github.com/OHIF/Viewers/issues/561)
 
 ## [1.3.2](https://github.com/OHIF/Viewers/compare/@ohif/core@1.3.1...@ohif/core@1.3.2) (2019-10-14)
 
-
 ### Bug Fixes
 
-* Return display sets in StudyMetadata._createDisplaySetsForSeries ([#1042](https://github.com/OHIF/Viewers/issues/1042)) ([fc01532](https://github.com/OHIF/Viewers/commit/fc01532))
-
-
-
-
+- Return display sets in StudyMetadata.\_createDisplaySetsForSeries
+  ([#1042](https://github.com/OHIF/Viewers/issues/1042))
+  ([fc01532](https://github.com/OHIF/Viewers/commit/fc01532))
 
 ## [1.3.1](https://github.com/OHIF/Viewers/compare/@ohif/core@1.3.0...@ohif/core@1.3.1) (2019-10-11)
 
 **Note:** Version bump only for package @ohif/core
 
-
-
-
-
 # [1.3.0](https://github.com/OHIF/Viewers/compare/@ohif/core@1.2.0...@ohif/core@1.3.0) (2019-10-11)
 
-
 ### Features
 
-* 🎸 Improve usability of Google Cloud adapter, including direct routes to studies ([#989](https://github.com/OHIF/Viewers/issues/989)) ([2bc361c](https://github.com/OHIF/Viewers/commit/2bc361c))
-
-
-
-
+- 🎸 Improve usability of Google Cloud adapter, including direct routes to
+  studies ([#989](https://github.com/OHIF/Viewers/issues/989))
+  ([2bc361c](https://github.com/OHIF/Viewers/commit/2bc361c))
 
 # [1.2.0](https://github.com/OHIF/Viewers/compare/@ohif/core@1.1.0...@ohif/core@1.2.0) (2019-10-09)
 
-
 ### Bug Fixes
 
-* OHIF-1002 Study lazy load should be true by default ([#1004](https://github.com/OHIF/Viewers/issues/1004)) ([66d8bc6](https://github.com/OHIF/Viewers/commit/66d8bc6))
-
+- OHIF-1002 Study lazy load should be true by default
+  ([#1004](https://github.com/OHIF/Viewers/issues/1004))
+  ([66d8bc6](https://github.com/OHIF/Viewers/commit/66d8bc6))
 
 ### Features
 
-* Allow a server requestOptions.auth to be a function that returns the Authorization header. ([#928](https://github.com/OHIF/Viewers/issues/928)) ([0064a4b](https://github.com/OHIF/Viewers/commit/0064a4b))
-
-
-
-
+- Allow a server requestOptions.auth to be a function that returns the
+  Authorization header. ([#928](https://github.com/OHIF/Viewers/issues/928))
+  ([0064a4b](https://github.com/OHIF/Viewers/commit/0064a4b))
 
 # [1.1.0](https://github.com/OHIF/Viewers/compare/@ohif/core@1.0.2...@ohif/core@1.1.0) (2019-10-03)
 
-
 ### Features
 
-* Use QIDO + WADO to load series metadata individually rather than the entire study metadata at once ([#953](https://github.com/OHIF/Viewers/issues/953)) ([9e10c2b](https://github.com/OHIF/Viewers/commit/9e10c2b))
-
-
-
-
+- Use QIDO + WADO to load series metadata individually rather than the entire
+  study metadata at once ([#953](https://github.com/OHIF/Viewers/issues/953))
+  ([9e10c2b](https://github.com/OHIF/Viewers/commit/9e10c2b))
 
 ## [1.0.2](https://github.com/OHIF/Viewers/compare/@ohif/core@1.0.1...@ohif/core@1.0.2) (2019-10-02)
 
-
 ### Bug Fixes
 
-* Temporarily sort SEG files to the end of the display set list as a workaround for several metadata issues ([#987](https://github.com/OHIF/Viewers/issues/987)) ([b3b4c10](https://github.com/OHIF/Viewers/commit/b3b4c10))
-
-
-
-
+- Temporarily sort SEG files to the end of the display set list as a workaround
+  for several metadata issues
+  ([#987](https://github.com/OHIF/Viewers/issues/987))
+  ([b3b4c10](https://github.com/OHIF/Viewers/commit/b3b4c10))
 
 ## [1.0.1](https://github.com/OHIF/Viewers/compare/@ohif/core@1.0.0...@ohif/core@1.0.1) (2019-09-27)
 
-
 ### Bug Fixes
 
-* Check for Value in 00081155 sequence (Few patient protocol images doesn't have this value) and removed a duplicate declaration ([#921](https://github.com/OHIF/Viewers/issues/921)) ([d0ec9cf](https://github.com/OHIF/Viewers/commit/d0ec9cf))
-
-
-
-
+- Check for Value in 00081155 sequence (Few patient protocol images doesn't have
+  this value) and removed a duplicate declaration
+  ([#921](https://github.com/OHIF/Viewers/issues/921))
+  ([d0ec9cf](https://github.com/OHIF/Viewers/commit/d0ec9cf))
 
 # [1.0.0](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.10...@ohif/core@1.0.0) (2019-09-27)
 
-
 ### Bug Fixes
 
-* 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support in local file and WADO-RS-only use cases ([#862](https://github.com/OHIF/Viewers/issues/862)) ([e7e1a8a](https://github.com/OHIF/Viewers/commit/e7e1a8a)), closes [#838](https://github.com/OHIF/Viewers/issues/838)
-
+- 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support
+  in local file and WADO-RS-only use cases
+  ([#862](https://github.com/OHIF/Viewers/issues/862))
+  ([e7e1a8a](https://github.com/OHIF/Viewers/commit/e7e1a8a)), closes
+  [#838](https://github.com/OHIF/Viewers/issues/838)
 
 ### BREAKING CHANGES
 
-* DICOM Seg
-
-
-
-
+- DICOM Seg
 
 ## [0.50.10](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.9...@ohif/core@0.50.10) (2019-09-23)
 
-
 ### Bug Fixes
 
-* Avoid using variable name "module" ([#942](https://github.com/OHIF/Viewers/issues/942)) ([72427fe](https://github.com/OHIF/Viewers/commit/72427fe)), closes [#940](https://github.com/OHIF/Viewers/issues/940)
-
-
-
-
+- Avoid using variable name "module"
+  ([#942](https://github.com/OHIF/Viewers/issues/942))
+  ([72427fe](https://github.com/OHIF/Viewers/commit/72427fe)), closes
+  [#940](https://github.com/OHIF/Viewers/issues/940)
 
 ## [0.50.9](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.8...@ohif/core@0.50.9) (2019-09-17)
 
-
 ### Bug Fixes
 
-* bump cornerstone-tools version in peerDeps ([4afc88c](https://github.com/OHIF/Viewers/commit/4afc88c))
-
-
-
-
+- bump cornerstone-tools version in peerDeps
+  ([4afc88c](https://github.com/OHIF/Viewers/commit/4afc88c))
 
 ## [0.50.8](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.7...@ohif/core@0.50.8) (2019-09-10)
 
 **Note:** Version bump only for package @ohif/core
 
-
-
-
-
 ## [0.50.7](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.6...@ohif/core@0.50.7) (2019-09-10)
 
-
 ### Bug Fixes
 
-* remove requestOptions when key is not needed ([32bc47d](https://github.com/OHIF/Viewers/commit/32bc47d))
-
-
-
-
+- remove requestOptions when key is not needed
+  ([32bc47d](https://github.com/OHIF/Viewers/commit/32bc47d))
 
 ## [0.50.6](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.5...@ohif/core@0.50.6) (2019-09-09)
 
 **Note:** Version bump only for package @ohif/core
 
-
-
-
-
 ## [0.50.5](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.4...@ohif/core@0.50.5) (2019-09-04)
 
 **Note:** Version bump only for package @ohif/core
 
-
-
-
-
 ## [0.50.4](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.3...@ohif/core@0.50.4) (2019-09-04)
 
-
 ### Bug Fixes
 
-* measurementsAPI issue caused by production build ([#842](https://github.com/OHIF/Viewers/issues/842)) ([49d3439](https://github.com/OHIF/Viewers/commit/49d3439))
-
-
-
-
+- measurementsAPI issue caused by production build
+  ([#842](https://github.com/OHIF/Viewers/issues/842))
+  ([49d3439](https://github.com/OHIF/Viewers/commit/49d3439))
 
 ## [0.50.3](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.2...@ohif/core@0.50.3) (2019-08-26)
 
-
 ### Bug Fixes
 
-* **Studies:** Qidosupportsincludefield should be true by default ([#801](https://github.com/OHIF/Viewers/issues/801)) ([a88d865](https://github.com/OHIF/Viewers/commit/a88d865))
-
-
-
-
+- **Studies:** Qidosupportsincludefield should be true by default
+  ([#801](https://github.com/OHIF/Viewers/issues/801))
+  ([a88d865](https://github.com/OHIF/Viewers/commit/a88d865))
 
 ## [0.50.2](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.1...@ohif/core@0.50.2) (2019-08-22)
 
 **Note:** Version bump only for package @ohif/core
 
-
-
-
-
 ## [0.50.1](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.0-alpha.10...@ohif/core@0.50.1) (2019-08-14)
 
 **Note:** Version bump only for package @ohif/core
 
-
-
-
-
 # [0.50.0-alpha.10](https://github.com/OHIF/Viewers/compare/@ohif/core@0.11.1-alpha.9...@ohif/core@0.50.0-alpha.10) (2019-08-14)
 
 **Note:** Version bump only for package @ohif/core
 
-
-
-
-
 ## [0.11.1-alpha.9](https://github.com/OHIF/Viewers/compare/@ohif/core@0.11.1-alpha.8...@ohif/core@0.11.1-alpha.9) (2019-08-14)
 
 **Note:** Version bump only for package @ohif/core
 
-
-
-
-
 ## 0.11.1-alpha.8 (2019-08-14)
 
 **Note:** Version bump only for package @ohif/core
 
-
-
-
-
 # Change Log
 
 All notable changes to this project will be documented in this file. See

platform/core/README.md

@@ -66,8 +66,8 @@ import { studies } from '@ohif/core';
 
 const studiesMetadata = await studies.retrieveStudiesMetadata(
   server, // Object
-  studyInstanceUids, // Array
-  seriesInstanceUids // Array (optional)
+  studyInstanceUIDs, // Array
+  seriesInstanceUIDs // Array (optional)
 );
 ```
 

platform/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/core",
-  "version": "2.5.1",
+  "version": "2.6.0",
   "description": "Generic business logic for web-based medical imaging applications",
   "author": "OHIF Core Team",
   "license": "MIT",
@@ -32,7 +32,7 @@
   },
   "peerDependencies": {
     "cornerstone-core": "^2.2.8",
-    "cornerstone-tools": "^4.12.0",
+    "cornerstone-tools": "4.12.5",
     "cornerstone-wado-image-loader": "^3.0.0",
     "dicom-parser": "^1.8.3"
   },

platform/core/src/DICOMSR/dataExchange.js

@@ -31,6 +31,7 @@ const retrieveMeasurements = server => {
 
   const serverUrl = server.wadoRoot;
   const studies = utils.studyMetadataManager.all();
+
   const latestSeries = findMostRecentStructuredReport(studies);
 
   if (!latestSeries) return Promise.resolve({});
@@ -57,17 +58,17 @@ const storeMeasurements = async (measurementData, filter, server) => {
   const serverUrl = server.wadoRoot;
   const firstMeasurementKey = Object.keys(measurementData)[0];
   const firstMeasurement = measurementData[firstMeasurementKey][0];
-  const studyInstanceUid =
-    firstMeasurement && firstMeasurement.studyInstanceUid;
+  const StudyInstanceUID =
+    firstMeasurement && firstMeasurement.StudyInstanceUID;
 
   try {
     await stowSRFromMeasurements(measurementData, serverUrl);
-    if (studyInstanceUid) {
-      studies.deleteStudyMetadataPromise(studyInstanceUid);
+    if (StudyInstanceUID) {
+      studies.deleteStudyMetadataPromise(StudyInstanceUID);
     }
 
     return {
-      message: 'Measurements were saved with success',
+      message: 'Measurements saved successfully',
     };
   } catch (error) {
     log.error(

platform/core/src/DICOMSR/parseDicomStructuredReport.js

@@ -1,6 +1,6 @@
 import * as dcmjs from 'dcmjs';
 
-import findInstanceMetadataBySopInstanceUid from './utils/findInstanceMetadataBySopInstanceUid';
+import findInstanceMetadataBySopInstanceUID from './utils/findInstanceMetadataBySopInstanceUid';
 
 /**
  * Function to parse the part10 array buffer that comes from a DICOM Structured report into measurementData
@@ -13,6 +13,7 @@ import findInstanceMetadataBySopInstanceUid from './utils/findInstanceMetadataBy
  */
 const parseDicomStructuredReport = (part10SRArrayBuffer, displaySets) => {
   // Get the dicom data as an Object
+
   const dicomData = dcmjs.data.DicomMessage.readFile(part10SRArrayBuffer);
   const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
     dicomData.dict
@@ -30,17 +31,18 @@ const parseDicomStructuredReport = (part10SRArrayBuffer, displaySets) => {
     measurementData[toolName] = [];
 
     measurements.forEach(measurement => {
-      const instanceMetadata = findInstanceMetadataBySopInstanceUid(
+      const instanceMetadata = findInstanceMetadataBySopInstanceUID(
         displaySets,
         measurement.sopInstanceUid
       );
+
       const { _study: study, _series: series } = instanceMetadata;
-      const { studyInstanceUid, patientId } = study;
-      const { seriesInstanceUid } = series;
+      const { StudyInstanceUID, PatientID } = study;
+      const { SeriesInstanceUID } = series;
       const { sopInstanceUid, frameIndex } = measurement;
       const imagePath = getImagePath(
-        studyInstanceUid,
-        seriesInstanceUid,
+        StudyInstanceUID,
+        SeriesInstanceUID,
         sopInstanceUid,
         frameIndex
       );
@@ -56,9 +58,10 @@ const parseDicomStructuredReport = (part10SRArrayBuffer, displaySets) => {
       const toolData = Object.assign({}, measurement, {
         imageId,
         imagePath,
-        seriesInstanceUid,
-        studyInstanceUid,
-        patientId,
+        SOPInstanceUID: sopInstanceUid,
+        SeriesInstanceUID,
+        StudyInstanceUID,
+        PatientID,
         measurementNumber: ++measurementNumber,
         timepointId: currentTimepointId,
         toolType: toolName,
@@ -75,19 +78,19 @@ const parseDicomStructuredReport = (part10SRArrayBuffer, displaySets) => {
 /**
  * Function to create imagePath with all imageData related
  *
- * @param {string} studyInstanceUid
- * @param {string} seriesInstanceUid
- * @param {string} sopInstanceUid
+ * @param {string} StudyInstanceUID
+ * @param {string} SeriesInstanceUID
+ * @param {string} SOPInstanceUID
  * @param {string} frameIndex
  * @returns
  */
 const getImagePath = (
-  studyInstanceUid,
-  seriesInstanceUid,
-  sopInstanceUid,
+  StudyInstanceUID,
+  SeriesInstanceUID,
+  SOPInstanceUID,
   frameIndex
 ) => {
-  return [studyInstanceUid, seriesInstanceUid, sopInstanceUid, frameIndex].join(
+  return [StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID, frameIndex].join(
     '_'
   );
 };

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

@@ -2,17 +2,18 @@
  *  Should Find the requested instance metadata into the displaySets and return
  *
  * @param {Array} displaySets - List of displaySets
- * @param {string} sopInstanceUid - sopInstanceUID to look for
+ * @param {string} SOPInstanceUID - sopInstanceUID to look for
  * @returns {Object} - instance metadata found
  */
-const findInstanceMetadataBySopInstanceUid = (displaySets, sopInstanceUid) => {
+const findInstanceMetadataBySopInstanceUID = (displaySets, SOPInstanceUID) => {
   let instanceFound;
 
   displaySets.find(displaySet => {
     if (!displaySet.images) return false;
 
     instanceFound = displaySet.images.find(
-      instanceMetadata => instanceMetadata._sopInstanceUID === sopInstanceUid
+      instanceMetadata =>
+        instanceMetadata.getSOPInstanceUID() === SOPInstanceUID
     );
 
     return !!instanceFound;
@@ -21,4 +22,4 @@ const findInstanceMetadataBySopInstanceUid = (displaySets, sopInstanceUid) => {
   return instanceFound;
 };
 
-export default findInstanceMetadataBySopInstanceUid;
+export default findInstanceMetadataBySopInstanceUID;

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

@@ -37,9 +37,9 @@ const isStructuredReportSeries = series => {
   ];
 
   const firstInstance = series.getFirstInstance();
-  const sopClassUid = firstInstance._instance.sopClassUid;
+  const SOPClassUID = firstInstance.getData().metadata.SOPClassUID;
 
-  return supportedSopClassUIDs.includes(sopClassUid);
+  return supportedSopClassUIDs.includes(SOPClassUID);
 };
 
 /**
@@ -51,9 +51,9 @@ const isStructuredReportSeries = series => {
  */
 const compareSeriesDate = (series1, series2) => {
   return (
-    series1._data.seriesDate > series2._data.seriesDate ||
-    (series1._data.seriesDate === series2._data.seriesDate &&
-      series1._data.seriesTime > series2._data.seriesTime)
+    series1._data.SeriesDate > series2._data.SeriesDate ||
+    (series1._data.SeriesDate === series2._data.SeriesDate &&
+      series1._data.SeriesTime > series2._data.SeriesTime)
   );
 };
 

platform/core/src/DICOMWeb/getModalities.js

@@ -1,23 +1,23 @@
-export default function getModalities(modality, modalitiesInStudy) {
-  if (!modality && !modalitiesInStudy) {
+export default function getModalities(Modality, ModalitiesInStudy) {
+  if (!Modality && !ModalitiesInStudy) {
     return {};
   }
 
-  const modalities = modality || {
+  const modalities = Modality || {
     vr: 'CS',
     Value: [],
   };
 
-  if (modalitiesInStudy) {
-    if (modalities.vr && modalities.vr === modalitiesInStudy.vr) {
-      for (let i = 0; i < modalitiesInStudy.Value.length; i++) {
-        const value = modalitiesInStudy.Value[i];
+  if (ModalitiesInStudy) {
+    if (modalities.vr && modalities.vr === ModalitiesInStudy.vr) {
+      for (let i = 0; i < ModalitiesInStudy.Value.length; i++) {
+        const value = ModalitiesInStudy.Value[i];
         if (modalities.Value.indexOf(value) === -1) {
           modalities.Value.push(value);
         }
       }
     } else {
-      return modalitiesInStudy;
+      return ModalitiesInStudy;
     }
   }
 

platform/core/src/DICOMWeb/getModalities.test.js

@@ -1,74 +1,74 @@
 import getModalities from './getModalities';
 
 describe('getModalities', () => {
-  test('should return an empty object when modality and modalitiesInStudy are not present', () => {
-    const modality = null;
-    const modalitiesInStudy = null;
+  test('should return an empty object when Modality and ModalitiesInStudy are not present', () => {
+    const Modality = null;
+    const ModalitiesInStudy = null;
 
-    expect(getModalities(modality, modalitiesInStudy)).toEqual({});
+    expect(getModalities(Modality, ModalitiesInStudy)).toEqual({});
   });
 
-  test('should return an empty object when modality and modalitiesInStudy are not present', () => {
-    const modality = null;
-    const modalitiesInStudy = null;
+  test('should return an empty object when Modality and ModalitiesInStudy are not present', () => {
+    const Modality = null;
+    const ModalitiesInStudy = null;
 
-    expect(getModalities(modality, modalitiesInStudy)).toEqual({});
+    expect(getModalities(Modality, ModalitiesInStudy)).toEqual({});
   });
 
-  test('should return modalities in Study when modality is not defined', () => {
-    const modality = null;
+  test('should return modalities in Study when Modality is not defined', () => {
+    const Modality = null;
 
-    const modalitiesInStudy = {
+    const ModalitiesInStudy = {
       Value: ['MOCKED_VALUE'],
       vr: 'MOCKED_VALUE',
     };
 
-    expect(getModalities(modality, modalitiesInStudy)).toEqual(
-      modalitiesInStudy
+    expect(getModalities(Modality, ModalitiesInStudy)).toEqual(
+      ModalitiesInStudy
     );
   });
 
-  test('should return only the modalitues that exists in modalitiesInStudy', () => {
-    const modality = {
+  test('should return only the modalitues that exists in ModalitiesInStudy', () => {
+    const Modality = {
       Value: ['DESIRED_VALUE'],
       vr: 'DESIRED_VR',
     };
 
-    const modalitiesInStudy = {
+    const ModalitiesInStudy = {
       Value: ['DESIRED_VALUE', 'NOT_DESIRED_VALUE'],
       vr: 'DESIRED_VR',
     };
 
-    expect(getModalities(modality, modalitiesInStudy)).toEqual(modality);
+    expect(getModalities(Modality, ModalitiesInStudy)).toEqual(Modality);
   });
 
-  test('should return the seek modality when the desired modality does not exist in modalitiesInStudy', () => {
-    const modality = {
+  test('should return the seek Modality when the desired Modality does not exist in ModalitiesInStudy', () => {
+    const Modality = {
       Value: ['DESIRED_VALUE'],
       vr: 'DESIRED_VR',
     };
 
-    const modalitiesInStudy = {
+    const ModalitiesInStudy = {
       Value: ['NOT_DESIRED_VALUE'],
       vr: 'DESIRED_VR',
     };
 
-    expect(getModalities(modality, modalitiesInStudy)).toEqual(modality);
+    expect(getModalities(Modality, ModalitiesInStudy)).toEqual(Modality);
   });
 
-  test('should return the seek modality when the desired modality does not exist in modalitiesInStudy VR', () => {
-    const modality = {
+  test('should return the seek Modality when the desired Modality does not exist in ModalitiesInStudy VR', () => {
+    const Modality = {
       Value: ['DESIRED_VALUE'],
       vr: 'DESIRED_VR',
     };
 
-    const modalitiesInStudy = {
+    const ModalitiesInStudy = {
       Value: ['NOT_DESIRED_VALUE'],
       vr: 'ANOTHER_VR',
     };
 
-    expect(getModalities(modality, modalitiesInStudy)).toEqual(
-      modalitiesInStudy
+    expect(getModalities(Modality, ModalitiesInStudy)).toEqual(
+      ModalitiesInStudy
     );
   });
 });

platform/core/src/classes/ImageSet.js

@@ -1,5 +1,6 @@
 import guid from '../utils/guid.js';
 import OHIFError from './OHIFError';
+import { Vector3 } from 'cornerstone-math';
 
 const OBJECT = 'object';
 
@@ -63,6 +64,60 @@ class ImageSet {
   sortBy(sortingCallback) {
     return this.images.sort(sortingCallback);
   }
+
+  sortByImagePositionPatient() {
+    const images = this.images;
+    const referenceImagePositionPatient = _getImagePositionPatient(images[0]);
+
+    const refIppVec = new Vector3(
+      referenceImagePositionPatient[0],
+      referenceImagePositionPatient[1],
+      referenceImagePositionPatient[2]
+    );
+
+    const ImageOrientationPatient = _getImageOrientationPatient(images[0]);
+
+    const scanAxisNormal = new Vector3(
+      ImageOrientationPatient[0],
+      ImageOrientationPatient[1],
+      ImageOrientationPatient[2]
+    ).cross(
+      new Vector3(
+        ImageOrientationPatient[3],
+        ImageOrientationPatient[4],
+        ImageOrientationPatient[5]
+      )
+    );
+
+    const distanceImagePairs = images.map(function(image) {
+      const ippVec = new Vector3(..._getImagePositionPatient(image));
+      const positionVector = refIppVec.clone().sub(ippVec);
+      const distance = positionVector.dot(scanAxisNormal);
+
+      return {
+        distance,
+        image,
+      };
+    });
+
+    distanceImagePairs.sort(function(a, b) {
+      return b.distance - a.distance;
+    });
+
+    const sortedImages = distanceImagePairs.map(a => a.image);
+
+    images.sort(function(a, b) {
+      return sortedImages.indexOf(a) - sortedImages.indexOf(b);
+    });
+  }
+}
+
+function _getImagePositionPatient(image) {
+  return image.getData().metadata.ImagePositionPatient;
+}
+
+function _getImageOrientationPatient(image) {
+  return image.getData().metadata.ImageOrientationPatient;
 }
 
 export default ImageSet;

platform/core/src/classes/MetadataProvider.js

@@ -1,412 +1,508 @@
-import { parsingUtils } from '../lib/parsingUtils';
-
-const FUNCTION = 'function';
+import * as dcmjs from 'dcmjs';
+import queryString from 'query-string';
+import dicomParser from 'dicom-parser';
+import { getFallbackTagFromInstance } from '../utils/metadataProvider/metadataProviderFallbackTags';
+import fetchPaletteColorLookupTableData from '../utils/metadataProvider/fetchPaletteColorLookupTableData';
+import fetchOverlayData from '../utils/metadataProvider/fetchOverlayData';
 
 class MetadataProvider {
   constructor() {
     // Define the main "metadataLookup" private property as an immutable property.
-    Object.defineProperty(this, 'metadataLookup', {
+    Object.defineProperty(this, 'studies', {
       configurable: false,
       enumerable: false,
       writable: false,
       value: new Map(),
     });
-
-    // Local reference to provider function bound to current instance.
-    Object.defineProperty(this, '_provider', {
+    Object.defineProperty(this, 'imageIdToUIDs', {
       configurable: false,
       enumerable: false,
-      writable: true,
-      value: null,
+      writable: false,
+      value: new Map(),
     });
   }
 
-  /**
-   * Cornerstone Metadata provider to store image meta data
-   * Data from instances, series, and studies are associated with
-   * imageIds to facilitate usage of this information by Cornerstone's Tools
-   *
-   * e.g. the imagePlane metadata object contains instance information about
-   * row/column pixel spacing, patient position, and patient orientation. It
-   * is used in CornerstoneTools to position reference lines and orientation markers.
-   *
-   * @param {String} imageId The Cornerstone ImageId
-   * @param {Object} data An object containing instance, series, and study metadata
-   */
-  addMetadata(imageId, data) {
-    const instanceMetadata = data.instance;
-    const seriesMetadata = data.series;
-    const studyMetadata = data.study;
-    const numImages = data.numImages;
-    const metadata = {};
+  async addInstance(dicomJSONDatasetOrP10ArrayBuffer, options = {}) {
+    let dicomJSONDataset;
 
-    metadata.frameNumber = data.frameNumber;
+    // If Arraybuffer, parse to DICOMJSON before naturalizing.
+    if (dicomJSONDatasetOrP10ArrayBuffer instanceof ArrayBuffer) {
+      const dicomData = DicomMessage.readFile(dicomJSONDatasetOrP10ArrayBuffer);
 
-    metadata.study = {
-      accessionNumber: studyMetadata.accessionNumber,
-      patientId: studyMetadata.patientId,
-      studyInstanceUid: studyMetadata.studyInstanceUid,
-      studyDate: studyMetadata.studyDate,
-      studyTime: studyMetadata.studyTime,
-      studyDescription: studyMetadata.studyDescription,
-      institutionName: studyMetadata.institutionName,
-      patientHistory: studyMetadata.patientHistory,
-    };
-
-    metadata.series = {
-      seriesDescription: seriesMetadata.seriesDescription,
-      seriesNumber: seriesMetadata.seriesNumber,
-      seriesDate: seriesMetadata.seriesDate,
-      seriesTime: seriesMetadata.seriesTime,
-      modality: seriesMetadata.modality,
-      seriesInstanceUid: seriesMetadata.seriesInstanceUid,
-      numImages: numImages,
-    };
-
-    metadata.instance = instanceMetadata;
-
-    metadata.patient = {
-      name: studyMetadata.patientName,
-      id: studyMetadata.patientId,
-      birthDate: studyMetadata.patientBirthDate,
-      sex: studyMetadata.patientSex,
-      age: studyMetadata.patientAge,
-    };
-
-    // If there is sufficient information, populate
-    // the imagePlane object for easier use in the Viewer
-    metadata.imagePlane = this.getImagePlane(instanceMetadata);
-
-    // Add the metadata to the imageId lookup object
-    this.metadataLookup.set(imageId, metadata);
-  }
-
-  /**
-   * Return the metadata for the given imageId
-   * @param {String} imageId The Cornerstone ImageId
-   * @returns image metadata
-   */
-  getMetadata(imageId) {
-    return this.metadataLookup.get(imageId);
-  }
-
-  /**
-   * Adds a set of metadata to the Cornerstone metadata provider given a specific
-   * imageId, type, and dataset
-   *
-   * @param imageId
-   * @param type (e.g. series, instance, tagDisplay)
-   * @param data
-   */
-  addSpecificMetadata(imageId, type, data) {
-    const metadata = {};
-    metadata[type] = data;
-
-    const oldMetadata = this.metadataLookup.get(imageId);
-    this.metadataLookup.set(imageId, Object.assign(oldMetadata, metadata));
-  }
-
-  getFromImage(image, type, tag, attrName, defaultValue) {
-    let value;
-
-    if (image.data) {
-      value = this.getFromDataSet(image.data, type, tag);
+      dicomJSONDataset = dicomData.dict;
     } else {
-      value = image.instance[attrName];
+      dicomJSONDataset = dicomJSONDatasetOrP10ArrayBuffer;
     }
 
-    return value === null ? defaultValue : value;
-  }
+    // Check if dataset is already naturalized.
 
-  getFromDataSet(dataSet, type, tag) {
-    if (!dataSet) {
-      return;
-    }
+    let naturalizedDataset;
 
-    const fn = dataSet[type];
-    if (!fn) {
-      return;
-    }
-
-    return fn.call(dataSet, tag);
-  }
-
-  getFrameIncrementPointer(image) {
-    const dataSet = image.data;
-    let frameInstancePointer = '';
-
-    if (parsingUtils.isValidDataSet(dataSet)) {
-      const frameInstancePointerNames = {
-        x00181063: 'frameTime',
-        x00181065: 'frameTimeVector',
-      };
-
-      // (0028,0009) = Frame Increment Pointer
-      const frameInstancePointerTag = parsingUtils.attributeTag(
-        dataSet,
-        'x00280009'
+    if (dicomJSONDataset['SeriesInstanceUID'] === undefined) {
+      naturalizedDataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
+        dicomJSONDataset
       );
-      frameInstancePointer = frameInstancePointerNames[frameInstancePointerTag];
     } else {
-      frameInstancePointer = image.instance.frameIncrementPointer;
+      naturalizedDataset = dicomJSONDataset;
     }
 
-    return frameInstancePointer || '';
-  }
+    const {
+      StudyInstanceUID,
+      SeriesInstanceUID,
+      SOPInstanceUID,
+    } = naturalizedDataset;
 
-  getFrameTimeVector(image) {
-    const dataSet = image.data;
+    const study = this._getAndCacheStudy(StudyInstanceUID);
+    const series = this._getAndCacheSeriesFromStudy(study, SeriesInstanceUID);
+    const instance = this._getAndCacheInstanceFromStudy(series, SOPInstanceUID);
 
-    if (parsingUtils.isValidDataSet(dataSet)) {
-      // Frame Increment Pointer points to Frame Time Vector (0018,1065) field
-      return parsingUtils.floatArray(dataSet, 'x00181065');
+    Object.assign(instance, naturalizedDataset);
+
+    if (options.server) {
+      await this._checkBulkDataAndInlineBinaries(instance, options.server);
     }
 
-    return image.instance.frameTimeVector;
+    return instance;
   }
 
-  getFrameTime(image) {
-    const dataSet = image.data;
+  addImageIdToUIDs(imageId, uids) {
+    // This method is a fallback for when you don't have WADO-URI or WADO-RS.
+    // You can add instances fetched by any method by calling addInstance, and hook an imageId to point at it here.
+    // An example would be dicom hosted at some random site.
 
-    if (parsingUtils.isValidDataSet(dataSet)) {
-      // Frame Increment Pointer points to Frame Time (0018,1063) field or is not defined (for addtional flexibility).
-      // Yet another value is possible for this field (5200,9230 for Multi-frame Functional Groups)
-      // but that case is currently not supported.
-      return dataSet.floatString('x00181063', -1);
+    this.imageIdToUIDs.set(imageId, uids);
+  }
+
+  _getAndCacheStudy(StudyInstanceUID) {
+    const studies = this.studies;
+
+    let study = studies.get(StudyInstanceUID);
+
+    if (!study) {
+      study = { series: new Map() };
+      studies.set(StudyInstanceUID, study);
     }
 
-    return image.instance.frameTime;
+    return study;
+  }
+  _getAndCacheSeriesFromStudy(study, SeriesInstanceUID) {
+    let series = study.series.get(SeriesInstanceUID);
+
+    if (!series) {
+      series = { instances: new Map() };
+      study.series.set(SeriesInstanceUID, series);
+    }
+
+    return series;
   }
 
-  /**
-   * Updates the related metadata for missing fields given a specified image
-   *
-   * @param image
-   */
-  updateMetadata(image) {
-    const imageMetadata = this.metadataLookup.get(image.imageId);
-    if (!imageMetadata) {
+  _getAndCacheInstanceFromStudy(series, SOPInstanceUID) {
+    let instance = series.instances.get(SOPInstanceUID);
+
+    if (!instance) {
+      instance = {};
+      series.instances.set(SOPInstanceUID, instance);
+    }
+
+    return instance;
+  }
+
+  async _checkBulkDataAndInlineBinaries(instance, server) {
+    await fetchOverlayData(instance, server);
+
+    if (instance.PhotometricInterpretation === 'PALETTE COLOR') {
+      await fetchPaletteColorLookupTableData(instance, server);
+    }
+  }
+
+  _getInstance(imageId) {
+    const uids = this._getUIDsFromImageID(imageId);
+
+    if (!uids) {
       return;
     }
 
-    imageMetadata.patient.age =
-      imageMetadata.patient.age ||
-      this.getFromDataSet(image.data, 'string', 'x00101010');
+    const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = uids;
 
-    imageMetadata.instance.rows = imageMetadata.instance.rows || image.rows;
-    imageMetadata.instance.columns =
-      imageMetadata.instance.columns || image.columns;
-
-    imageMetadata.instance.sopClassUid =
-      imageMetadata.instance.sopClassUid ||
-      this.getFromDataSet(image.data, 'string', 'x00080016');
-    imageMetadata.instance.sopInstanceUid =
-      imageMetadata.instance.sopInstanceUid ||
-      this.getFromDataSet(image.data, 'string', 'x00080018');
-
-    imageMetadata.instance.pixelSpacing =
-      imageMetadata.instance.pixelSpacing ||
-      this.getFromDataSet(image.data, 'string', 'x00280030');
-    imageMetadata.instance.frameOfReferenceUID =
-      imageMetadata.instance.frameOfReferenceUID ||
-      this.getFromDataSet(image.data, 'string', 'x00200052');
-    imageMetadata.instance.imageOrientationPatient =
-      imageMetadata.instance.imageOrientationPatient ||
-      this.getFromDataSet(image.data, 'string', 'x00200037');
-    imageMetadata.instance.imagePositionPatient =
-      imageMetadata.instance.imagePositionPatient ||
-      this.getFromDataSet(image.data, 'string', 'x00200032');
-
-    imageMetadata.instance.sliceThickness =
-      imageMetadata.instance.sliceThickness ||
-      this.getFromDataSet(image.data, 'string', 'x00180050');
-    imageMetadata.instance.sliceLocation =
-      imageMetadata.instance.sliceLocation ||
-      this.getFromDataSet(image.data, 'string', 'x00201041');
-    imageMetadata.instance.tablePosition =
-      imageMetadata.instance.tablePosition ||
-      this.getFromDataSet(image.data, 'string', 'x00189327');
-    imageMetadata.instance.spacingBetweenSlices =
-      imageMetadata.instance.spacingBetweenSlices ||
-      this.getFromDataSet(image.data, 'string', 'x00180088');
-
-    imageMetadata.instance.lossyImageCompression =
-      imageMetadata.instance.lossyImageCompression ||
-      this.getFromDataSet(image.data, 'string', 'x00282110');
-    imageMetadata.instance.lossyImageCompressionRatio =
-      imageMetadata.instance.lossyImageCompressionRatio ||
-      this.getFromDataSet(image.data, 'string', 'x00282112');
-
-    imageMetadata.instance.frameIncrementPointer =
-      imageMetadata.instance.frameIncrementPointer ||
-      this.getFromDataSet(image.data, 'string', 'x00280009');
-    imageMetadata.instance.frameTime =
-      imageMetadata.instance.frameTime ||
-      this.getFromDataSet(image.data, 'string', 'x00181063');
-    imageMetadata.instance.frameTimeVector =
-      imageMetadata.instance.frameTimeVector ||
-      this.getFromDataSet(image.data, 'string', 'x00181065');
-
-    if (
-      (image.data || image.instance) &&
-      !imageMetadata.instance.multiframeMetadata
-    ) {
-      imageMetadata.instance.multiframeMetadata = this.getMultiframeModuleMetadata(
-        image
-      );
-    }
-
-    imageMetadata.imagePlane =
-      imageMetadata.imagePlane || this.getImagePlane(imageMetadata.instance);
-  }
-
-  /**
-   * Constructs and returns the imagePlane given the metadata instance
-   *
-   * @param metadataInstance The metadata instance (InstanceMetadata class) containing information to construct imagePlane
-   * @returns imagePlane The constructed imagePlane to be used in viewer easily
-   */
-  getImagePlane(instance) {
-    if (
-      !instance.rows ||
-      !instance.columns ||
-      !instance.pixelSpacing ||
-      !instance.frameOfReferenceUID ||
-      !instance.imageOrientationPatient ||
-      !instance.imagePositionPatient
-    ) {
-      return;
-    }
-
-    const imageOrientation = instance.imageOrientationPatient.split('\\');
-    const imagePosition = instance.imagePositionPatient.split('\\');
-
-    let columnPixelSpacing = 1.0;
-    let rowPixelSpacing = 1.0;
-    if (instance.pixelSpacing) {
-      const split = instance.pixelSpacing.split('\\');
-      rowPixelSpacing = parseFloat(split[0]);
-      columnPixelSpacing = parseFloat(split[1]);
-    }
-
-    return {
-      frameOfReferenceUID: instance.frameOfReferenceUID,
-      rows: instance.rows,
-      columns: instance.columns,
-      rowCosines: [
-        parseFloat(imageOrientation[0]),
-        parseFloat(imageOrientation[1]),
-        parseFloat(imageOrientation[2]),
-      ],
-      columnCosines: [
-        parseFloat(imageOrientation[3]),
-        parseFloat(imageOrientation[4]),
-        parseFloat(imageOrientation[5]),
-      ],
-      imagePositionPatient: [
-        parseFloat(imagePosition[0]),
-        parseFloat(imagePosition[1]),
-        parseFloat(imagePosition[2]),
-      ],
-      rowPixelSpacing,
-      columnPixelSpacing,
-    };
-  }
-
-  /**
-   * This function extracts miltiframe information from a dicomParser.DataSet object.
-   *
-   * @param dataSet {Object} An instance of dicomParser.DataSet object where multiframe information can be found.
-   * @return {Object} An object containing multiframe image metadata (frameIncrementPointer, frameTime, frameTimeVector, etc).
-   */
-  getMultiframeModuleMetadata(image) {
-    const imageInfo = {
-      isMultiframeImage: false,
-      frameIncrementPointer: null,
-      numberOfFrames: 0,
-      frameTime: 0,
-      frameTimeVector: null,
-      averageFrameRate: 0, // backwards compatibility only... it might be useless in the future
-    };
-
-    let frameTime;
-
-    const numberOfFrames = this.getFromImage(
-      image,
-      'intString',
-      'x00280008',
-      'numberOfFrames',
-      -1
+    return this._getInstanceData(
+      StudyInstanceUID,
+      SeriesInstanceUID,
+      SOPInstanceUID
     );
+  }
 
-    if (numberOfFrames > 0) {
-      // set multi-frame image indicator
-      imageInfo.isMultiframeImage = true;
-      imageInfo.numberOfFrames = numberOfFrames;
+  get(query, imageId, options = { fallback: false }) {
+    const instance = this._getInstance(imageId);
 
-      // (0028,0009) = Frame Increment Pointer
-      const frameIncrementPointer = this.getFrameIncrementPointer(image);
+    if (query === INSTANCE) {
+      return instance;
+    }
 
-      if (frameIncrementPointer === 'frameTimeVector') {
-        // Frame Increment Pointer points to Frame Time Vector (0018,1065) field
-        const frameTimeVector = this.getFrameTimeVector(image);
+    return this.getTagFromInstance(query, instance, options);
+  }
 
-        if (frameTimeVector instanceof Array && frameTimeVector.length > 0) {
-          imageInfo.frameIncrementPointer = frameIncrementPointer;
-          imageInfo.frameTimeVector = frameTimeVector;
-          frameTime =
-            frameTimeVector.reduce((a, b) => a + b) / frameTimeVector.length;
-          imageInfo.averageFrameRate = 1000 / frameTime;
-        }
-      } else if (
-        frameIncrementPointer === 'frameTime' ||
-        frameIncrementPointer === ''
-      ) {
-        frameTime = this.getFrameTime(image);
+  getTag(query, imageId, options) {
+    return this.get(query, imageId, options);
+  }
 
-        if (frameTime > 0) {
-          imageInfo.frameIncrementPointer = frameIncrementPointer;
-          imageInfo.frameTime = frameTime;
-          imageInfo.averageFrameRate = 1000 / frameTime;
-        }
+  getInstance(imageId) {
+    return this.get(INSTANCE, imageId);
+  }
+
+  getTagFromInstance(
+    naturalizedTagOrWADOImageLoaderTag,
+    instance,
+    options = { fallback: false }
+  ) {
+    if (!instance) {
+      return;
+    }
+
+    // If its a naturalized dcmjs tag present on the instance, return.
+    if (instance[naturalizedTagOrWADOImageLoaderTag]) {
+      return instance[naturalizedTagOrWADOImageLoaderTag];
+    }
+
+    if (options.fallback) {
+      // Perhaps the tag has fallbacks?
+      const fallbackTag = getFallbackTagFromInstance(
+        naturalizedTagOrWADOImageLoaderTag,
+        instance
+      );
+
+      if (fallbackTag) {
+        return fallbackTag;
       }
     }
 
-    return imageInfo;
+    // Maybe its a legacy CornerstoneWADOImageLoader tag then:
+    return this._getCornerstoneWADOImageLoaderTag(
+      naturalizedTagOrWADOImageLoaderTag,
+      instance
+    );
   }
 
-  /**
-   * Get a bound reference to the provider function.
-   */
-  getProvider() {
-    let provider = this._provider;
-    if (typeof this._provider !== FUNCTION) {
-      provider = this.provider.bind(this);
-      this._provider = provider;
+  _getCornerstoneWADOImageLoaderTag(wadoImageLoaderTag, instance) {
+    let metadata;
+
+    switch (wadoImageLoaderTag) {
+      case WADO_IMAGE_LOADER_TAGS.GENERAL_SERIES_MODULE:
+        const { SeriesDate, SeriesTime } = instance;
+
+        let seriesDate;
+        let seriesTime;
+
+        if (SeriesDate) {
+          seriesDate = dicomParser.parseDA(SeriesDate);
+        }
+
+        if (SeriesTime) {
+          seriesTime = dicomParser.parseTM(SeriesTime);
+        }
+
+        metadata = {
+          modality: instance.Modality,
+          seriesInstanceUID: instance.SeriesInstanceUID,
+          seriesNumber: instance.SeriesNumber,
+          studyInstanceUID: instance.StudyInstanceUID,
+          seriesDate,
+          seriesTime,
+        };
+        break;
+      case WADO_IMAGE_LOADER_TAGS.PATIENT_STUDY_MODULE:
+        metadata = {
+          patientAge: instance.PatientAge,
+          patientSize: instance.PatientSize,
+          patientWeight: instance.PatientWeight,
+        };
+        break;
+      case WADO_IMAGE_LOADER_TAGS.IMAGE_PLANE_MODULE:
+        const { ImageOrientationPatient } = instance;
+
+        // Fallback for DX images.
+        const PixelSpacing = getFallbackTagFromInstance(
+          'PixelSpacing',
+          instance
+        );
+
+        let rowPixelSpacing;
+        let columnPixelSpacing;
+
+        let rowCosines;
+        let columnCosines;
+
+        if (PixelSpacing) {
+          rowPixelSpacing = PixelSpacing[0];
+          columnPixelSpacing = PixelSpacing[1];
+        }
+
+        if (ImageOrientationPatient) {
+          rowCosines = ImageOrientationPatient.slice(0, 3);
+          columnCosines = ImageOrientationPatient.slice(3, 6);
+        }
+
+        metadata = {
+          frameOfReferenceUID: instance.FrameOfReferenceUID,
+          rows: instance.Rows,
+          columns: instance.Columns,
+          imageOrientationPatient: ImageOrientationPatient,
+          rowCosines,
+          columnCosines,
+          imagePositionPatient: instance.ImagePositionPatient,
+          sliceThickness: instance.SliceThickness,
+          sliceLocation: instance.SliceLocation,
+          pixelSpacing: PixelSpacing,
+          rowPixelSpacing,
+          columnPixelSpacing,
+        };
+        break;
+      case WADO_IMAGE_LOADER_TAGS.IMAGE_PIXEL_MODULE:
+        metadata = {
+          samplesPerPixel: instance.SamplesPerPixel,
+          photometricInterpretation: instance.PhotometricInterpretation,
+          rows: instance.Rows,
+          columns: instance.Columns,
+          bitsAllocated: instance.BitsAllocated,
+          bitsStored: instance.BitsStored,
+          highBit: instance.HighBit,
+          pixelRepresentation: instance.PixelRepresentation,
+          planarConfiguration: instance.PlanarConfiguration,
+          pixelAspectRatio: instance.PixelAspectRatio,
+          smallestPixelValue: instance.SmallestPixelValue,
+          largestPixelValue: instance.LargestPixelValue,
+          redPaletteColorLookupTableDescriptor:
+            instance.RedPaletteColorLookupTableDescriptor,
+          greenPaletteColorLookupTableDescriptor:
+            instance.GreenPaletteColorLookupTableDescriptor,
+          bluePaletteColorLookupTableDescriptor:
+            instance.BluePaletteColorLookupTableDescriptor,
+          redPaletteColorLookupTableData:
+            instance.RedPaletteColorLookupTableData,
+          greenPaletteColorLookupTableData:
+            instance.GreenPaletteColorLookupTableData,
+          bluePaletteColorLookupTableData:
+            instance.BluePaletteColorLookupTableData,
+        };
+
+        break;
+      case WADO_IMAGE_LOADER_TAGS.VOI_LUT_MODULE:
+        const { WindowCenter, WindowWidth } = instance;
+
+        const windowCenter = Array.isArray(WindowCenter)
+          ? WindowCenter
+          : [WindowCenter];
+        const windowWidth = Array.isArray(WindowWidth)
+          ? WindowWidth
+          : [WindowWidth];
+
+        metadata = {
+          windowCenter,
+          windowWidth,
+        };
+
+        break;
+      case WADO_IMAGE_LOADER_TAGS.MODALITY_LUT_MODULE:
+        metadata = {
+          rescaleIntercept: instance.RescaleIntercept,
+          rescaleSlope: instance.RescaleSlope,
+          rescaleType: instance.RescaleType,
+        };
+        break;
+      case WADO_IMAGE_LOADER_TAGS.SOP_COMMON_MODULE:
+        metadata = {
+          sopClassUID: instance.SOPClassUID,
+          sopInstanceUID: instance.SOPInstanceUID,
+        };
+        break;
+      case WADO_IMAGE_LOADER_TAGS.PET_ISOTOPE_MODULE:
+        const { RadiopharmaceuticalInformationSequence } = instance;
+
+        if (RadiopharmaceuticalInformationSequence) {
+          const RadiopharmaceuticalInformation = Array.isArray(
+            RadiopharmaceuticalInformationSequence
+          )
+            ? RadiopharmaceuticalInformationSequence[0]
+            : RadiopharmaceuticalInformationSequence;
+
+          const {
+            RadiopharmaceuticalStartTime,
+            RadionuclideTotalDose,
+            RadionuclideHalfLife,
+          } = RadiopharmaceuticalInformation;
+
+          const radiopharmaceuticalInfo = {
+            radiopharmaceuticalStartTime: dicomParser.parseTM(
+              RadiopharmaceuticalStartTime
+            ),
+            radionuclideTotalDose: RadionuclideTotalDose,
+            radionuclideHalfLife: RadionuclideHalfLife,
+          };
+          metadata = {
+            radiopharmaceuticalInfo,
+          };
+        }
+
+        break;
+      case WADO_IMAGE_LOADER_TAGS.OVERLAY_PLANE_MODULE:
+        metadata = [];
+
+        for (
+          let overlayGroup = 0x00;
+          overlayGroup <= 0x1e;
+          overlayGroup += 0x02
+        ) {
+          let groupStr = `60${overlayGroup.toString(16)}`;
+
+          if (groupStr.length === 3) {
+            groupStr = `600${overlayGroup.toString(16)}`;
+          }
+
+          const OverlayDataTag = `${groupStr}3000`;
+          const OverlayData = instance[OverlayDataTag];
+
+          if (!OverlayData) {
+            continue;
+          }
+
+          const OverlayRowsTag = `${groupStr}0010`;
+          const OverlayColumnsTag = `${groupStr}0011`;
+          const OverlayType = `${groupStr}0040`;
+          const OverlayOriginTag = `${groupStr}0050`;
+          const OverlayDescriptionTag = `${groupStr}0022`;
+          const OverlayLabelTag = `${groupStr}1500`;
+          const ROIAreaTag = `${groupStr}1301`;
+          const ROIMeanTag = `${groupStr}1302`;
+          const ROIStandardDeviationTag = `${groupStr}1303`;
+          const OverlayOrigin = instance[OverlayOriginTag];
+
+          const overlay = {
+            rows: instance[OverlayRowsTag],
+            columns: instance[OverlayColumnsTag],
+            type: instance[OverlayType],
+            x: OverlayOrigin[0],
+            y: OverlayOrigin[1],
+            pixelData: OverlayData,
+            description: instance[OverlayDescriptionTag],
+            label: instance[OverlayLabelTag],
+            roiArea: instance[ROIAreaTag],
+            roiMean: instance[ROIMeanTag],
+            roiStandardDeviation: instance[ROIStandardDeviationTag],
+          };
+
+          metadata.push(overlay);
+        }
+
+        break;
+
+      case WADO_IMAGE_LOADER_TAGS.PATIENT_MODULE:
+        const { PatientName } = instance;
+
+        let patientName;
+        if (PatientName) {
+          patientName = PatientName.Alphabetic;
+        }
+
+        metadata = {
+          patientName,
+          patientId: instance.PatientID,
+        };
+
+        break;
+
+      case WADO_IMAGE_LOADER_TAGS.GENERAL_IMAGE_MODULE:
+        metadata = {
+          instanceNumber: instance.InstanceNumber,
+          lossyImageCompression: instance.LossyImageCompression,
+          lossyImageCompressionRatio: instance.LossyImageCompressionRatio,
+          lossyImageCompressionMethod: instance.LossyImageCompressionMethod,
+        };
+
+        break;
+      case WADO_IMAGE_LOADER_TAGS.GENERAL_STUDY_MODULE:
+        metadata = {
+          studyDescription: instance.StudyDescription,
+          studyDate: instance.StudyDate,
+          studyTime: instance.StudyTime,
+          accessionNumber: instance.AccessionNumber,
+        };
+
+        break;
+      case WADO_IMAGE_LOADER_TAGS.CINE_MODULE:
+        metadata = {
+          frameTime: instance.FrameTime,
+        };
+
+        break;
     }
 
-    return provider;
+    return metadata;
   }
 
-  /**
-   * Looks up metadata for Cornerstone Tools given a specified type and imageId
-   * A type may be, e.g. 'study', or 'patient', or 'imagePlaneModule'. These types
-   * are keys in the stored metadata objects.
-   *
-   * @param type
-   * @param imageId
-   * @returns {Object} Relevant metadata of the specified type
-   */
-  provider(type, imageId) {
-    const imageMetadata = this.metadataLookup.get(imageId);
-    if (!imageMetadata) {
+  _getInstanceData(StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID) {
+    const study = this.studies.get(StudyInstanceUID);
+
+    if (!study) {
       return;
     }
 
-    if (imageMetadata.hasOwnProperty(type)) {
-      return imageMetadata[type];
+    const series = study.series.get(SeriesInstanceUID);
+
+    if (!series) {
+      return;
+    }
+
+    const instance = series.instances.get(SOPInstanceUID);
+
+    return instance;
+  }
+
+  _getUIDsFromImageID(imageId) {
+    if (imageId.includes('wadors:')) {
+      const strippedImageId = imageId.split('studies/')[1];
+      const splitImageId = strippedImageId.split('/');
+
+      return {
+        StudyInstanceUID: splitImageId[0], // Note: splitImageId[1] === 'series'
+        SeriesInstanceUID: splitImageId[2], // Note: splitImageId[3] === 'instances'
+        SOPInstanceUID: splitImageId[4],
+      };
+    }
+    if (imageId.includes('wado?requestType=WADO')) {
+      const qs = queryString.parse(imageId);
+
+      return {
+        StudyInstanceUID: qs.studyUID,
+        SeriesInstanceUID: qs.seriesUID,
+        SOPInstanceUID: qs.objectUID,
+      };
+    } else {
+      // Maybe its a non-standard imageId
+      return this.imageIdToUIDs.get(imageId);
     }
   }
 }
 
-export default MetadataProvider;
+const metadataProvider = new MetadataProvider();
+
+export default metadataProvider;
+
+const WADO_IMAGE_LOADER_TAGS = {
+  // CornerstoneWADOImageLoader specific
+  GENERAL_SERIES_MODULE: 'generalSeriesModule',
+  PATIENT_STUDY_MODULE: 'patientStudyModule',
+  IMAGE_PLANE_MODULE: 'imagePlaneModule',
+  IMAGE_PIXEL_MODULE: 'imagePixelModule',
+  VOI_LUT_MODULE: 'voiLutModule',
+  MODALITY_LUT_MODULE: 'modalityLutModule',
+  SOP_COMMON_MODULE: 'sopCommonModule',
+  PET_ISOTOPE_MODULE: 'petIsotopeModule',
+  OVERLAY_PLANE_MODULE: 'overlayPlaneModule',
+
+  // react-cornerstone-viewport specifc
+  PATIENT_MODULE: 'patientModule',
+  GENERAL_IMAGE_MODULE: 'generalImageModule',
+  GENERAL_STUDY_MODULE: 'generalStudyModule',
+  CINE_MODULE: 'cineModule',
+};
+
+const INSTANCE = 'instance';

platform/core/src/classes/OHIFStudyMetadataSource.js

@@ -1,9 +1,8 @@
-import { studyMetadataManager, updateMetaDataManager } from '../utils';
+import { studyMetadataManager } from '../utils';
 
 import OHIFError from './OHIFError';
 import { StudyMetadata } from './metadata/StudyMetadata';
 import { StudyMetadataSource } from './StudyMetadataSource.js';
-import { StudySummary } from './metadata/StudySummary';
 import { retrieveStudyMetadata } from '../studies/retrieveStudyMetadata.js';
 
 export class OHIFStudyMetadataSource extends StudyMetadataSource {
@@ -19,12 +18,12 @@ export class OHIFStudyMetadataSource extends StudyMetadataSource {
 
   /**
    * Load study info (OHIF.viewer.Studies) and study metadata (OHIF.viewer.StudyMetadataList) for a given study.
-   * @param {StudySummary|StudyMetadata} study of StudySummary or StudyMetadata object.
+   * @param {StudyMetadata} study StudyMetadata object.
    */
   loadStudy(study) {
-    if (!(study instanceof StudyMetadata) && !(study instanceof StudySummary)) {
+    if (!(study instanceof StudyMetadata)) {
       throw new OHIFError(
-        'OHIFStudyMetadataSource::loadStudy study is not an instance of StudySummary or StudyMetadata'
+        'OHIFStudyMetadataSource::loadStudy study is not an instance of StudyMetadata'
       );
     }
 
@@ -33,7 +32,7 @@ export class OHIFStudyMetadataSource extends StudyMetadataSource {
 
       if (study instanceof StudyMetadata) {
         const alreadyLoaded = OHIF.viewer.Studies.findBy({
-          studyInstanceUid: studyInstanceUID,
+          StudyInstanceUID: studyInstanceUID,
         });
 
         if (!alreadyLoaded) {
@@ -49,7 +48,7 @@ export class OHIFStudyMetadataSource extends StudyMetadataSource {
           // Create study metadata object
           const studyMetadata = new StudyMetadata(
             studyInfo,
-            studyInfo.studyInstanceUid
+            studyInfo.StudyInstanceUID
           );
 
           // Get Study display sets
@@ -72,10 +71,6 @@ export class OHIFStudyMetadataSource extends StudyMetadataSource {
     // Set some studyInfo properties
     studyInfo.selected = true;
     studyInfo.displaySets = studyMetadata.getDisplaySets();
-
-    // Updates WADO-RS metaDataManager
-    updateMetaDataManager(studyInfo);
-
     studyMetadataManager.add(studyMetadata);
   }
 }

platform/core/src/classes/OHIFStudySummary.js

@@ -1,55 +0,0 @@
-import StudySummary from './StudySummary';
-
-/**
- * Constants
- */
-
-const STRING = 'string';
-const propertyReplacementMap = {
-  modalities: 'ModalitiesInStudy',
-  patientBirthdate: 'PatientBirthDate',
-};
-
-/**
- * OHIF Viewers specialized version of StudySummary class
- */
-export class OHIFStudySummary extends StudySummary {
-  // @Override
-  addTags(tagMap) {
-    const _hasOwn = Object.prototype.hasOwnProperty;
-    const _tagMap = Object.create(null);
-    for (let property in tagMap) {
-      if (_hasOwn.call(tagMap, property)) {
-        let standardProperty = OHIFStudySummary.getStandardPropertyName(
-          property
-        );
-        if (standardProperty) {
-          _tagMap[standardProperty] = tagMap[property];
-        }
-      }
-    }
-    super.addTags(_tagMap);
-  }
-
-  /**
-   * Turns a non-standard, OHIF specific, DICOM property name into a standard one.
-   * @param {string} property A string representing a non-conforming keyword.
-   * @returns {string|undefined} Returns a standard-conforming property name.
-   */
-  static getStandardPropertyName(property) {
-    let standardProperty;
-    if (typeof property === STRING && property.charAt(0) !== '_') {
-      if (property in propertyReplacementMap) {
-        standardProperty = propertyReplacementMap[propertyReplacementMap];
-      } else {
-        standardProperty = property
-          .replace(/^sop/, 'SOP')
-          .replace(/Uid$/, 'UID')
-          .replace(/Id$/, 'ID');
-        standardProperty =
-          standardProperty.charAt(0).toUpperCase() + standardProperty.substr(1);
-      }
-    }
-    return standardProperty;
-  }
-}

platform/core/src/classes/StudyLoadingListener.js

@@ -60,8 +60,8 @@ class BaseLoadingListener {
   }
 
   _getProgressId() {
-    const displaySetInstanceUid = this.stack.displaySetInstanceUid;
-    return 'StackProgress:' + displaySetInstanceUid;
+    const displaySetInstanceUID = this.stack.displaySetInstanceUID;
+    return 'StackProgress:' + displaySetInstanceUID;
   }
 
   _clearProgress() {
@@ -362,7 +362,7 @@ class StackLoadingListener extends BaseLoadingListener {
 
   _logProgress() {
     const totalFramesCount = this.stack.imageIds.length;
-    const displaySetInstanceUid = this.stack.displaySetInstanceUid;
+    const displaySetInstanceUID = this.stack.displaySetInstanceUID;
     let progressBar = '[';
 
     for (let i = 0; i < totalFramesCount; i++) {
@@ -371,7 +371,7 @@ class StackLoadingListener extends BaseLoadingListener {
     }
 
     progressBar += ']';
-    log.info(`${displaySetInstanceUid}: ${progressBar}`);
+    log.info(`${displaySetInstanceUID}: ${progressBar}`);
   }
 }
 
@@ -388,12 +388,12 @@ class StudyLoadingListener {
       return;
     }
 
-    const displaySetInstanceUid = stack.displaySetInstanceUid;
+    const displaySetInstanceUID = stack.displaySetInstanceUID;
 
-    if (!this.listeners[displaySetInstanceUid]) {
+    if (!this.listeners[displaySetInstanceUID]) {
       const listener = this._createListener(stack, stackMetaData);
       if (listener) {
-        this.listeners[displaySetInstanceUid] = listener;
+        this.listeners[displaySetInstanceUID] = listener;
       }
     }
   }
@@ -424,12 +424,12 @@ class StudyLoadingListener {
   }
 
   clear() {
-    const displaySetInstanceUids = Object.keys(this.listeners);
-    const length = displaySetInstanceUids.length;
+    const displaySetInstanceUIDs = Object.keys(this.listeners);
+    const length = displaySetInstanceUIDs.length;
 
     for (let i = 0; i < length; i++) {
-      const displaySetInstanceUid = displaySetInstanceUids[i];
-      const displaySet = this.listeners[displaySetInstanceUid];
+      const displaySetInstanceUID = displaySetInstanceUIDs[i];
+      const displaySet = this.listeners[displaySetInstanceUID];
 
       displaySet.destroy();
     }

platform/core/src/classes/StudyMetadataSource.js

@@ -19,7 +19,7 @@ export class StudyMetadataSource {
 
   /**
    * Load study info and study metadata for a given study into the viewer.
-   * @param {StudySummary|StudyMetadata} study of StudySummary or StudyMetadata object.
+   * @param {StudyMetadata} study StudyMetadata object.
    */
   loadStudy(study) {
     /**

platform/core/src/classes/StudyPrefetcher.js

@@ -94,17 +94,23 @@ export class StudyPrefetcher {
   }
 
   getStudy(image) {
-    const studyMetadata = cornerstone.metaData.get('study', image.imageId);
+    const StudyInstanceUID = cornerstone.metaData.get(
+      'StudyInstanceUID',
+      image.imageId
+    );
     return OHIF.viewer.Studies.find(
-      study => study.studyInstanceUid === studyMetadata.studyInstanceUid
+      study => study.StudyInstanceUID === StudyInstanceUID
     );
   }
 
   getSeries(study, image) {
-    const seriesMetadata = cornerstone.metaData.get('series', image.imageId);
+    const SeriesInstanceUID = cornerstone.metaData.get(
+      'SeriesInstanceUID',
+      image.imageId
+    );
     const studyMetadata = OHIF.viewerbase.getStudyMetadata(study);
 
-    return studyMetadata.getSeriesByUID(seriesMetadata.seriesInstanceUid);
+    return studyMetadata.getSeriesByUID(SeriesInstanceUID);
   }
 
   getInstance(series, image) {
@@ -112,13 +118,13 @@ export class StudyPrefetcher {
       'instance',
       image.imageId
     );
-    return series.getInstanceByUID(instanceMetadata.sopInstanceUid);
+    return series.getInstanceByUID(instanceMetadata.SOPInstanceUID);
   }
 
   getActiveDisplaySet(displaySets, instance) {
     return displaySets.find(displaySet => {
       return displaySet.images.some(displaySetImage => {
-        return displaySetImage.sopInstanceUid === instance.sopInstanceUid;
+        return displaySetImage.SOPInstanceUID === instance.SOPInstanceUID;
       });
     });
   }

platform/core/src/classes/index.js

@@ -1,15 +1,10 @@
-import {
-  InstanceMetadata,
-  SeriesMetadata,
-  StudyMetadata,
-  StudySummary,
-} from './metadata';
+import { InstanceMetadata, SeriesMetadata, StudyMetadata } from './metadata';
 
 import CommandsManager from './CommandsManager.js';
 import { DICOMFileLoadingListener } from './StudyLoadingListener';
 import HotkeysManager from './HotkeysManager.js';
 import ImageSet from './ImageSet';
-import MetadataProvider from './MetadataProvider.js';
+import MetadataProvider from './MetadataProvider';
 import OHIFError from './OHIFError.js';
 import { OHIFStudyMetadataSource } from './OHIFStudyMetadataSource';
 import { StackLoadingListener } from './StudyLoadingListener';
@@ -31,7 +26,6 @@ export {
   StudyMetadata,
   SeriesMetadata,
   InstanceMetadata,
-  StudySummary,
   TypeSafeCollection,
   OHIFError,
   StudyMetadataSource,
@@ -50,7 +44,6 @@ const classes = {
   StudyMetadata,
   SeriesMetadata,
   InstanceMetadata,
-  StudySummary,
   TypeSafeCollection,
   OHIFError,
   StudyMetadataSource,

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

@@ -8,20 +8,12 @@ import OHIFError from '../OHIFError.js';
 
 const UNDEFINED = 'undefined';
 const STRING = 'string';
-const STUDY_INSTANCE_UID = 'x0020000d';
-const SERIES_INSTANCE_UID = 'x0020000e';
 
 export class InstanceMetadata extends Metadata {
   constructor(data, uid) {
     super(data, uid);
     // Initialize Private Properties
     Object.defineProperties(this, {
-      _sopInstanceUID: {
-        configurable: true, // configurable so that it can be redefined in sub-classes...
-        enumerable: false,
-        writable: true,
-        value: null,
-      },
       _imageId: {
         configurable: true, // configurable so that it can be redefined in sub-classes...
         enumerable: false,
@@ -43,14 +35,14 @@ export class InstanceMetadata extends Metadata {
    */
   _definePublicProperties() {
     /**
-     * Property: this.sopInstanceUID
+     * Property: this.SOPInstanceUID
      * Same as this.getSOPInstanceUID()
      * It's specially useful in contexts where a method call is not suitable like in search criteria. For example:
      * sopInstanceCollection.findBy({
-     *   sopInstanceUID: '1.2.3.4.5.6.77777.8888888.99999999999.0'
+     *   SOPInstanceUID: '1.2.3.4.5.6.77777.8888888.99999999999.0'
      * });
      */
-    Object.defineProperty(this, 'sopInstanceUID', {
+    Object.defineProperty(this, 'SOPInstanceUID', {
       configurable: false,
       enumerable: false,
       get: function() {
@@ -67,21 +59,21 @@ export class InstanceMetadata extends Metadata {
    * Returns the StudyInstanceUID of the current instance. This method is basically a shorthand the full "getTagValue" method call.
    */
   getStudyInstanceUID() {
-    return this.getTagValue(STUDY_INSTANCE_UID, null);
+    return this.getTagValue('StudyInstanceUID', null);
   }
 
   /**
    * Returns the SeriesInstanceUID of the current instance. This method is basically a shorthand the full "getTagValue" method call.
    */
   getSeriesInstanceUID() {
-    return this.getTagValue(SERIES_INSTANCE_UID, null);
+    return this.getTagValue('SeriesInstanceUID', null);
   }
 
   /**
    * Returns the SOPInstanceUID of the current instance.
    */
   getSOPInstanceUID() {
-    return this._sopInstanceUID;
+    return this.getTagValue('SOPInstanceUID', null);
   }
 
   // @TODO: Improve this... (E.g.: blob data)
@@ -127,13 +119,6 @@ export class InstanceMetadata extends Metadata {
     return typeof value === STRING ? parseInt(value) : value;
   }
 
-  /**
-   * @deprecated Please use getTagValue instead.
-   */
-  getRawValue(tagOrProperty, defaultValue) {
-    return this.getTagValue(tagOrProperty, defaultValue);
-  }
-
   /**
    * This function should be overriden by specialized classes in order to allow client libraries or viewers to take advantage of the Study Metadata API.
    */

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

@@ -1,5 +1,4 @@
 import { InstanceMetadata } from './InstanceMetadata';
-import { DICOMTagDescriptions } from '../../utils/DICOMTagDescriptions.js';
 import getImageId from '../../utils/getImageId.js';
 
 export class OHIFInstanceMetadata extends InstanceMetadata {
@@ -20,7 +19,7 @@ export class OHIFInstanceMetadata extends InstanceMetadata {
         configurable: false,
         enumerable: false,
         writable: false,
-        value: instance.sopInstanceUid,
+        value: instance.SOPInstanceUID,
       },
       _study: {
         configurable: false,
@@ -56,16 +55,16 @@ export class OHIFInstanceMetadata extends InstanceMetadata {
       return this._cache[tagOrProperty];
     }
 
-    const propertyName = OHIFInstanceMetadata.getPropertyName(tagOrProperty);
+    const instanceData = this._instance.metadata;
 
     // Search property value in the whole study metadata chain...
     let rawValue;
-    if (propertyName in this._instance) {
-      rawValue = this._instance[propertyName];
-    } else if (propertyName in this._series) {
-      rawValue = this._series[propertyName];
-    } else if (propertyName in this._study) {
-      rawValue = this._study[propertyName];
+    if (tagOrProperty in instanceData) {
+      rawValue = instanceData[tagOrProperty];
+    } else if (tagOrProperty in this._series) {
+      rawValue = this._series[tagOrProperty];
+    } else if (tagOrProperty in this._study) {
+      rawValue = this._study[tagOrProperty];
     }
 
     if (rawValue !== void 0) {
@@ -79,12 +78,10 @@ export class OHIFInstanceMetadata extends InstanceMetadata {
 
   // Override
   tagExists(tagOrProperty) {
-    const propertyName = OHIFInstanceMetadata.getPropertyName(tagOrProperty);
-
     return (
-      propertyName in this._instance ||
-      propertyName in this._series ||
-      propertyName in this._study
+      tagOrProperty in this._instance.metadata ||
+      tagOrProperty in this._series ||
+      tagOrProperty in this._study
     );
   }
 
@@ -97,28 +94,4 @@ export class OHIFInstanceMetadata extends InstanceMetadata {
 
     return this._imageId;
   }
-
-  /**
-   * Static methods
-   */
-
-  // @TODO: The current mapping of standard DICOM property names to local property names is not optimal.
-  // The inconsistency in property naming makes this function increasingly complex.
-  // A possible solution to improve this would be adapt retriveMetadata names to use DICOM standard names as in dicomTagDescriptions.js
-  static getPropertyName(tagOrProperty) {
-    let propertyName;
-    const tagInfo = DICOMTagDescriptions.find(tagOrProperty);
-
-    if (tagInfo !== void 0) {
-      // This function tries to translate standard DICOM property names into local naming convention.
-      propertyName = tagInfo.keyword
-        .replace(/^SOP/, 'sop')
-        .replace(/UID$/, 'Uid')
-        .replace(/ID$/, 'Id');
-      propertyName =
-        propertyName.charAt(0).toLowerCase() + propertyName.substr(1);
-    }
-
-    return propertyName;
-  }
 }

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

@@ -18,7 +18,7 @@ export class OHIFSeriesMetadata extends SeriesMetadata {
       configurable: false,
       enumerable: false,
       writable: false,
-      value: series.seriesInstanceUid,
+      value: series.SeriesInstanceUID,
     });
 
     // populate internal list of instances...

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

@@ -18,11 +18,11 @@ export class OHIFStudyMetadata extends StudyMetadata {
       configurable: false,
       enumerable: false,
       writable: false,
-      value: study.studyInstanceUid,
+      value: study.StudyInstanceUID,
     });
 
     // populate internal list of series
-    study.seriesList.forEach(series => {
+    study.series.forEach(series => {
       this.addSeries(new OHIFSeriesMetadata(series, study));
     });
   }

platform/core/src/classes/metadata/README.md

@@ -83,10 +83,10 @@ well (again, flexibility and extensibility are design goals). Most implemented
 methods rely on the implementation of an unimplemented method. For example, the
 method `getStringValue` from `InstanceMetadata` class, which has indeed been
 implemented and is meant to retrieve a metadata value as a string, internally
-calls the `getRawValue` method which _was NOT implemented_ and is meant to query
+calls the `getTagValue` method which _was NOT implemented_ and is meant to query
 the internal data structures for the requested metadata value and return it _as
 is_. Used in that way, an application would not benefit much from the already
-implemented methods. On the other hand, by simply overriding the `getRawValue`
+implemented methods. On the other hand, by simply overriding the `getTagValue`
 method on a specialized class to deal with the intrinsics of its internal data
 structures, this very application would now benefit from all already implemented
 methods.
@@ -99,12 +99,12 @@ The following code snippet tries to illustrate the idea:
 
 class InstanceMetadata {
     [ ... ]
-    getRawValue(tagOrProperty, defaultValue) {
+    getTagValue(tagOrProperty, defaultValue) {
         // Please implement this method in a specialized subclass...
     }
     [ ... ]
     getStringValue(tagOrProperty, index, defaultValue) {
-        let rawValue = this.getRawValue(tagOrProperty, '');
+        let rawValue = this.getTagValue(tagOrProperty, '');
         // parse the returned value into a string...
         [ ... ]
         return stringValue;
@@ -117,11 +117,11 @@ class InstanceMetadata {
 class MyFancyAppInstanceMetadata extends InstanceMetadata {
     // Overriding this method will make all methods implemented in the super class
     // that rely on it to be immediately available...
-    getRawValue(tagOrProperty, defaultValue) {
-        let rawValue;
+    getTagValue(tagOrProperty, defaultValue) {
+        let tagValue;
         // retrieve raw value from internal data structures...
         [ ... ]
-        return rawValue;
+        return tagValue;
     }
 }
 
@@ -135,9 +135,9 @@ if (sopInstaceMetadata instanceof MyFancyAppInstanceMetadata) { // true
 if (sopInstaceMetadata instanceof InstanceMetadata) { // also true
     // this code will also be executed...
 }
-// The following will also work since the internal "getRawValue" call inside
+// The following will also work since the internal "getTagValue" call inside
 // "getStringValue" method will now be satisfied... (thanks to the override)
-let patientName = sopInstaceMetadata.getStringValue('PatientName', '');
+let PatientName = sopInstaceMetadata.getStringValue('PatientName', '');
 [ ... ]
 
 ```

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

@@ -35,6 +35,12 @@ export class StudyMetadata extends Metadata {
         writable: false,
         value: [],
       },
+      _derivedDisplaySets: {
+        configurable: false,
+        enumerable: false,
+        writable: false,
+        value: [],
+      },
       _firstSeries: {
         configurable: false,
         enumerable: false,
@@ -110,18 +116,22 @@ export class StudyMetadata extends Metadata {
       return;
     }
 
-    const sopClassUids = getSopClassUids(series);
+    const sopClassUIDs = getSopClassUIDs(series);
 
     if (sopClassHandlerModules && sopClassHandlerModules.length > 0) {
       const displaySet = _getDisplaySetFromSopClassModule(
         sopClassHandlerModules,
         series,
         study,
-        sopClassUids
+        sopClassUIDs
       );
       if (displaySet) {
         displaySet.sopClassModule = true;
-        displaySets.push(displaySet);
+
+        displaySet.isDerived
+          ? this._addDerivedDisplaySet(displaySet)
+          : displaySets.push(displaySet);
+
         return displaySets;
       }
     }
@@ -135,10 +145,10 @@ export class StudyMetadata extends Metadata {
     // series into another display set.
     const stackableInstances = [];
     series.forEachInstance(instance => {
-      // All imaging modalities must have a valid value for sopClassUid (x00080016) or rows (x00280010)
+      // All imaging modalities must have a valid value for SOPClassUID (x00080016) or Rows (x00280010)
       if (
-        !isImage(instance.getRawValue('x00080016')) &&
-        !instance.getRawValue('x00280010')
+        !isImage(instance.getTagValue('SOPClassUID')) &&
+        !instance.getTagValue('Rows')
       ) {
         return;
       }
@@ -149,23 +159,23 @@ export class StudyMetadata extends Metadata {
         displaySet = makeDisplaySet(series, [instance]);
 
         displaySet.setAttributes({
-          sopClassUids,
+          sopClassUIDs,
           isClip: true,
-          seriesInstanceUid: series.getSeriesInstanceUID(),
-          studyInstanceUid: study.getStudyInstanceUID(), // Include the study instance Uid for drag/drop purposes
-          numImageFrames: instance.getRawValue('x00280008'), // Override the default value of instances.length
-          instanceNumber: instance.getRawValue('x00200013'), // Include the instance number
-          acquisitionDatetime: instance.getRawValue('x0008002a'), // Include the acquisition datetime
+          SeriesInstanceUID: series.getSeriesInstanceUID(),
+          StudyInstanceUID: study.getStudyInstanceUID(), // Include the study instance UID for drag/drop purposes
+          numImageFrames: instance.getTagValue('NumberOfFrames'), // Override the default value of instances.length
+          InstanceNumber: instance.getTagValue('InstanceNumber'), // Include the instance number
+          AcquisitionDatetime: instance.getTagValue('AcquisitionDateTime'), // Include the acquisition datetime
         });
         displaySets.push(displaySet);
-      } else if (isSingleImageModality(instance.modality)) {
+      } else if (isSingleImageModality(instance.Modality)) {
         displaySet = makeDisplaySet(series, [instance]);
         displaySet.setAttributes({
-          sopClassUids,
-          studyInstanceUid: study.getStudyInstanceUID(), // Include the study instance Uid
-          seriesInstanceUid: series.getSeriesInstanceUID(),
-          instanceNumber: instance.getRawValue('x00200013'), // Include the instance number
-          acquisitionDatetime: instance.getRawValue('x0008002a'), // Include the acquisition datetime
+          sopClassUIDs,
+          StudyInstanceUID: study.getStudyInstanceUID(), // Include the study instance UID
+          SeriesInstanceUID: series.getSeriesInstanceUID(),
+          InstanceNumber: instance.getTagValue('InstanceNumber'), // Include the instance number
+          AcquisitionDatetime: instance.getTagValue('AcquisitionDateTime'), // Include the acquisition datetime
         });
         displaySets.push(displaySet);
       } else {
@@ -175,9 +185,9 @@ export class StudyMetadata extends Metadata {
 
     if (stackableInstances.length) {
       const displaySet = makeDisplaySet(series, stackableInstances);
-      displaySet.setAttribute('studyInstanceUid', study.getStudyInstanceUID());
+      displaySet.setAttribute('StudyInstanceUID', study.getStudyInstanceUID());
       displaySet.setAttributes({
-        sopClassUids,
+        sopClassUIDs,
       });
       displaySets.push(displaySet);
     }
@@ -186,9 +196,73 @@ export class StudyMetadata extends Metadata {
   }
 
   /**
-   * Creates a set of series to be placed in the Study Metadata
-   * The series that appear in the Study Metadata must represent
-   * imaging modalities.
+   * Adds the displaySets to the studies list of derived displaySets.
+   * @param {object} displaySet The displaySet to append to the derived displaysets list.
+   */
+  _addDerivedDisplaySet(displaySet) {
+    this._derivedDisplaySets.push(displaySet);
+    // --> Perhaps that logic should exist in the extension sop class handler and this be a dumb list.
+    // TODO -> Get x Modality by referencedSeriesInstanceUid, FoR, etc.
+  }
+
+  /**
+   * Returns a list of derived datasets in the study, filtered by the given filter.
+   * @param {object} filter An object containing search filters
+   * @param {object} filter.modality
+   * @param {object} filter.referencedSeriesInstanceUID
+   * @param {object} filter.referencedFrameOfReferenceUID
+   * @return {Array} filtered derived display sets
+   */
+  getDerivedDatasets(filter) {
+    const {
+      modality,
+      referencedSeriesInstanceUID,
+      referencedFrameOfReferenceUID,
+    } = filter;
+    let filteredDerivedDisplaySets = this._derivedDisplaySets;
+
+    if (modality) {
+      filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
+        displaySet => displaySet.Modality === Modality
+      );
+    }
+
+    if (referencedSeriesInstanceUID) {
+      filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
+        displaySet => {
+          if (!displaySet.metadata.ReferencedSeriesSequence) {
+            return false;
+          }
+
+          const ReferencedSeriesSequence = Array.isArray(
+            displaySet.metadata.ReferencedSeriesSequence
+          )
+            ? displaySet.metadata.ReferencedSeriesSequence
+            : [displaySet.metadata.ReferencedSeriesSequence];
+
+          return ReferencedSeriesSequence.some(
+            ReferencedSeries =>
+              ReferencedSeries.SeriesInstanceUID === referencedSeriesInstanceUID
+          );
+        }
+      );
+    }
+
+    if (referencedFrameOfReferenceUID) {
+      filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
+        displaySet =>
+          displaySet.ReferencedFrameOfReferenceUID ===
+          ReferencedFrameOfReferenceUID
+      );
+    }
+
+    return filteredDerivedDisplaySets;
+  }
+
+  /**
+   * Creates a set of displaySets to be placed in the Study Metadata
+   * The displaySets that appear in the Study Metadata must represent
+   * imaging modalities. A series may be split into one or more displaySets.
    *
    * Furthermore, for drag/drop functionality,
    * it is easiest if the stack objects also contain information about
@@ -416,7 +490,7 @@ export class StudyMetadata extends Metadata {
    *     needs series sorted by the same criteria used for sorting display sets.
    */
   sortSeriesByDisplaySets() {
-    // Object for mapping display sets' index by seriesInstanceUid
+    // Object for mapping display sets' index by SeriesInstanceUID
     const displaySetsMapping = {};
 
     // Loop through each display set to create the mapping
@@ -428,8 +502,8 @@ export class StudyMetadata extends Metadata {
       }
 
       // In case of multiframe studies, just get the first index occurence
-      if (displaySetsMapping[displaySet.seriesInstanceUid] === void 0) {
-        displaySetsMapping[displaySet.seriesInstanceUid] = index;
+      if (displaySetsMapping[displaySet.SeriesInstanceUID] === void 0) {
+        displaySetsMapping[displaySet.SeriesInstanceUID] = index;
       }
     });
 
@@ -482,6 +556,22 @@ export class StudyMetadata extends Metadata {
     return series;
   }
 
+  /**
+   * Get the first image id given display instance uid.
+   * @return {string} The image id.
+   */
+  getFirstImageId(displaySetInstanceUID) {
+    try {
+      const displaySet = this.findDisplaySet(
+        displaySet => displaySet.displaySetInstanceUID === displaySetInstanceUID
+      );
+      return displaySet.images[0].getImageId();
+    } catch (error) {
+      console.error('Failed to retrieve image metadata');
+      return null;
+    }
+  }
+
   /**
    * Get the first instance of the current study retaining a consistent result across multiple calls.
    * @return {InstanceMetadata} An instance of the InstanceMetadata class or null if it does not exist.
@@ -581,8 +671,7 @@ export class StudyMetadata extends Metadata {
 const dwc = api.DICOMwebClient;
 
 const isMultiFrame = instance => {
-  // NumberOfFrames (0028,0008)
-  return instance.getRawValue('x00280008') > 1;
+  return instance.getTagValue('NumberOfFrames') > 1;
 };
 
 const makeDisplaySet = (series, instances) => {
@@ -592,15 +681,15 @@ const makeDisplaySet = (series, instances) => {
 
   // set appropriate attributes to image set...
   imageSet.setAttributes({
-    displaySetInstanceUid: imageSet.uid, // create a local alias for the imageSet UID
-    seriesDate: seriesData.seriesDate,
-    seriesTime: seriesData.seriesTime,
-    seriesInstanceUid: series.getSeriesInstanceUID(),
-    seriesNumber: instance.getRawValue('x00200011'),
-    seriesDescription: instance.getRawValue('x0008103e'),
+    displaySetInstanceUID: imageSet.uid, // create a local alias for the imageSet UID
+    SeriesDate: seriesData.SeriesDate,
+    SeriesTime: seriesData.SeriesTime,
+    SeriesInstanceUID: series.getSeriesInstanceUID(),
+    SeriesNumber: instance.getTagValue('SeriesNumber'),
+    SeriesDescription: instance.getTagValue('SeriesDescription'),
     numImageFrames: instances.length,
-    frameRate: instance.getRawValue('x00181063'),
-    modality: instance.getRawValue('x00080060'),
+    frameRate: instance.getTagValue('FrameTime'),
+    Modality: instance.getTagValue('Modality'),
     isMultiFrame: isMultiFrame(instance),
   });
 
@@ -610,22 +699,26 @@ const makeDisplaySet = (series, instances) => {
     imageSet.sortBy((a, b) => {
       // Sort by InstanceNumber (0020,0013)
       return (
-        (parseInt(a.getRawValue('x00200013', 0)) || 0) -
-        (parseInt(b.getRawValue('x00200013', 0)) || 0)
+        (parseInt(a.getTagValue('InstanceNumber', 0)) || 0) -
+        (parseInt(b.getTagValue('InstanceNumber', 0)) || 0)
       );
     });
   }
 
   // Include the first image instance number (after sorted)
   imageSet.setAttribute(
-    'instanceNumber',
-    imageSet.getImage(0).getRawValue('x00200013')
+    'InstanceNumber',
+    imageSet.getImage(0).getTagValue('InstanceNumber')
   );
 
-  const isReconstructable = isDisplaySetReconstructable(series, instances);
+  const isReconstructable = isDisplaySetReconstructable(instances);
 
   imageSet.isReconstructable = isReconstructable.value;
 
+  if (shallSort && imageSet.isReconstructable) {
+    imageSet.sortByImagePositionPatient();
+  }
+
   if (isReconstructable.missingFrames) {
     // TODO -> This is currently unused, but may be used for reconstructing
     // Volumes with gaps later on.
@@ -635,57 +728,57 @@ const makeDisplaySet = (series, instances) => {
   return imageSet;
 };
 
-const isSingleImageModality = modality => {
-  return modality === 'CR' || modality === 'MG' || modality === 'DX';
+const isSingleImageModality = Modality => {
+  return Modality === 'CR' || Modality === 'MG' || Modality === 'DX';
 };
 
-function getSopClassUids(series) {
-  const uniqueSopClassUidsInSeries = new Set();
+function getSopClassUIDs(series) {
+  const uniqueSopClassUIDsInSeries = new Set();
   series.forEachInstance(instance => {
-    const instanceSopClassUid = instance.getRawValue('x00080016');
+    const instanceSopClassUID = instance.getTagValue('SOPClassUID');
 
-    uniqueSopClassUidsInSeries.add(instanceSopClassUid);
+    uniqueSopClassUIDsInSeries.add(instanceSopClassUID);
   });
-  const sopClassUids = Array.from(uniqueSopClassUidsInSeries);
+  const sopClassUIDs = Array.from(uniqueSopClassUIDsInSeries);
 
-  return sopClassUids;
+  return sopClassUIDs;
 }
 
 /**
  * @private
  * @param {SeriesMetadata} series
  * @param {StudyMetadata} study
- * @param {string[]} sopClassUids
+ * @param {string[]} sopClassUIDs
  */
 function _getDisplaySetFromSopClassModule(
   sopClassHandlerExtensions, // TODO: Update Usage
   series,
   study,
-  sopClassUids
+  sopClassUIDs
 ) {
-  // TODO: For now only use the plugins if all instances have the same sopClassUid
-  if (sopClassUids.length !== 1) {
+  // TODO: For now only use the plugins if all instances have the same SOPClassUID
+  if (sopClassUIDs.length !== 1) {
     console.warn(
-      'getDisplaySetFromSopClassPlugin: More than one SOPClassUid in the same series is not yet supported.'
+      'getDisplaySetFromSopClassPlugin: More than one SOPClassUID in the same series is not yet supported.'
     );
     return;
   }
 
-  const sopClassUid = sopClassUids[0];
+  const SOPClassUID = sopClassUIDs[0];
   const sopClassHandlerModules = sopClassHandlerExtensions.map(extension => {
     return extension.module;
   });
 
-  const handlersForSopClassUid = sopClassHandlerModules.filter(module => {
-    return module.sopClassUids.includes(sopClassUid);
+  const handlersForSopClassUID = sopClassHandlerModules.filter(module => {
+    return module.sopClassUIDs.includes(SOPClassUID);
   });
 
   // TODO: Sort by something, so we can determine which plugin to use
-  if (!handlersForSopClassUid || !handlersForSopClassUid.length) {
+  if (!handlersForSopClassUID || !handlersForSopClassUID.length) {
     return;
   }
 
-  const plugin = handlersForSopClassUid[0];
+  const plugin = handlersForSopClassUID[0];
   const headers = DICOMWeb.getAuthorizationHeader();
   const dicomWebClient = new dwc({
     url: study.getData().wadoRoot,
@@ -698,15 +791,15 @@ function _getDisplaySetFromSopClassModule(
     dicomWebClient,
     headers
   );
-  if (displaySet && !displaySet.modality) {
+  if (displaySet && !displaySet.Modality) {
     const instance = series.getFirstInstance();
-    displaySet.modality = instance.getRawValue('x00080060');
+    displaySet.Modality = instance.getTagValue('Modality');
   }
   return displaySet;
 }
 
 /**
- * Sort series primarily by modality (i.e., series with references to other
+ * Sort series primarily by Modality (i.e., series with references to other
  * series like SEG, KO or PR are grouped in the end of the list) and then by
  * series number:
  *
@@ -724,8 +817,8 @@ function _getDisplaySetFromSopClassModule(
  */
 
 function seriesSortingCriteria(a, b) {
-  const isLowPriorityA = isLowPriorityModality(a.modality);
-  const isLowPriorityB = isLowPriorityModality(b.modality);
+  const isLowPriorityA = isLowPriorityModality(a.Modality);
+  const isLowPriorityB = isLowPriorityModality(b.Modality);
   if (!isLowPriorityA && isLowPriorityB) {
     return -1;
   }
@@ -742,7 +835,7 @@ function seriesSortingCriteria(a, b) {
  */
 function sortBySeriesNumber(a, b) {
   const seriesNumberAIsGreaterOrUndefined =
-    a.seriesNumber > b.seriesNumber || (!a.seriesNumber && b.seriesNumber);
+    a.SeriesNumber > b.SeriesNumber || (!a.SeriesNumber && b.SeriesNumber);
 
   return seriesNumberAIsGreaterOrUndefined ? 1 : -1;
 }

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

@@ -1,73 +0,0 @@
-import { Metadata } from './Metadata';
-import { DICOMTagDescriptions } from '../../utils/DICOMTagDescriptions';
-
-/**
- * Constants
- */
-
-const STUDY_INSTANCE_UID = 'x0020000d';
-
-/**
- * Class Definition
- */
-
-export class StudySummary extends Metadata {
-  constructor(tagMap, attributeMap, uid) {
-    // Call the superclass constructor passing an plain object with no prototype to be used as the main "_data" attribute.
-    const _data = Object.create(null);
-    super(_data, uid);
-
-    // Initialize internal tag map if first argument is given.
-    if (tagMap !== void 0) {
-      this.addTags(tagMap);
-    }
-
-    // Initialize internal property map if second argument is given.
-    if (attributeMap !== void 0) {
-      this.setCustomAttributes(attributeMap);
-    }
-  }
-
-  getStudyInstanceUID() {
-    // This method should return null if StudyInstanceUID is not available to keep compatibility StudyMetadata API
-    return this.getTagValue(STUDY_INSTANCE_UID) || null;
-  }
-
-  /**
-   * Append tags to internal tag map.
-   * @param {Object} tagMap An object whose own properties will be used as tag values and appended to internal tag map.
-   */
-  addTags(tagMap) {
-    const _hasOwn = Object.prototype.hasOwnProperty;
-    const _data = this._data;
-    for (let tag in tagMap) {
-      if (_hasOwn.call(tagMap, tag)) {
-        const description = DICOMTagDescriptions.find(tag);
-        // When a description is available, use its tag as internal key...
-        if (description) {
-          _data[description.tag] = tagMap[tag];
-        } else {
-          _data[tag] = tagMap[tag];
-        }
-      }
-    }
-  }
-
-  tagExists(tagName) {
-    const _data = this._data;
-    const description = DICOMTagDescriptions.find(tagName);
-    if (description) {
-      return description.tag in _data;
-    }
-    return tagName in _data;
-  }
-
-  getTagValue(tagName) {
-    const _data = this._data;
-    const description = DICOMTagDescriptions.find(tagName);
-    if (description) {
-      return _data[description.tag];
-    }
-    return _data[tagName];
-  }
-}

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

@@ -1,48 +0,0 @@
-export class WadoRsMetaDataBuilder {
-  constructor() {
-    this.tags = {};
-  }
-
-  addTag(tag, value, multi) {
-    this.tags[tag] = {
-      tag,
-      value,
-      multi,
-    };
-
-    return this;
-  }
-
-  toJSON() {
-    const json = {};
-    const keys = Object.keys(this.tags);
-
-    keys.forEach(key => {
-      if (!this.tags.hasOwnProperty(key)) {
-        return;
-      }
-
-      const tag = this.tags[key];
-      const multi = !!tag.multi;
-      let value = tag.value;
-
-      if (value == null || (value.length === 1 && value[0] == null)) {
-        return;
-      }
-
-      if (typeof value === 'string' && multi) {
-        value = value.split('\\');
-      }
-
-      if (!Array.isArray(value)) {
-        value = [value];
-      }
-
-      json[key] = {
-        Value: value,
-      };
-    });
-
-    return json;
-  }
-}

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

@@ -5,13 +5,9 @@ import { OHIFSeriesMetadata } from './OHIFSeriesMetadata';
 import { OHIFStudyMetadata } from './OHIFStudyMetadata';
 import { SeriesMetadata } from './SeriesMetadata';
 import { StudyMetadata } from './StudyMetadata';
-import { StudySummary } from './StudySummary';
-import { WadoRsMetaDataBuilder } from './WadoRsMetaDataBuilder';
 
 const metadata = {
   Metadata,
-  StudySummary,
-  WadoRsMetaDataBuilder,
   StudyMetadata,
   SeriesMetadata,
   InstanceMetadata,
@@ -22,8 +18,6 @@ const metadata = {
 
 export {
   Metadata,
-  StudySummary,
-  WadoRsMetaDataBuilder,
   StudyMetadata,
   SeriesMetadata,
   InstanceMetadata,

platform/core/src/cornerstone.js

@@ -1,4 +1,4 @@
-import MetadataProvider from './classes/MetadataProvider';
+import metadataProvider from './classes/MetadataProvider';
 import {
   getBoundingBox,
   pixelToPage,
@@ -6,7 +6,7 @@ import {
 } from './lib/cornerstone.js';
 
 const cornerstone = {
-  MetadataProvider,
+  metadataProvider,
   getBoundingBox,
   pixelToPage,
   repositionTextBox,

platform/core/src/hanging-protocols/HPMatcher.js

@@ -6,24 +6,19 @@ import { CustomAttributeRetrievalCallbacks } from './customAttributes';
 /**
  * Import Constants
  */
-const { StudySummary, InstanceMetadata } = metadata;
+const { InstanceMetadata } = metadata;
 
 /**
  * Match a Metadata instance against rules using Validate.js for validation.
- * @param  {StudySummary|InstanceMetadata} metadataInstance Metadata instance object
+ * @param  {InstanceMetadata} metadataInstance Metadata instance object
  * @param  {Array} rules Array of MatchingRules instances (StudyMatchingRule|SeriesMatchingRule|ImageMatchingRule) for the match
  * @return {Object}      Matching Object with score and details (which rule passed or failed)
  */
 const match = (metadataInstance, rules) => {
   // Make sure the supplied data is valid.
-  if (
-    !(
-      metadataInstance instanceof StudySummary ||
-      metadataInstance instanceof InstanceMetadata
-    )
-  ) {
+  if (!(metadataInstance instanceof InstanceMetadata)) {
     throw new OHIFError(
-      'HPMatcher::match metadataInstance must be an instance of StudySummary or InstanceMetadata'
+      'HPMatcher::match metadataInstance must be an instance of InstanceMetadata'
     );
   }
 

platform/core/src/hanging-protocols/ProtocolEngine.js

@@ -13,7 +13,7 @@ import { ProtocolStore } from './protocolStore/classes';
 /**
  * Import Constants
  */
-const { StudyMetadata, InstanceMetadata, StudySummary } = metadata;
+const { StudyMetadata, InstanceMetadata } = metadata;
 
 // Useful constants
 const ABSTRACT_PRIOR_VALUE = 'abstractPriorValue';
@@ -298,10 +298,7 @@ export default class ProtocolEngine {
         }
 
         // Invalid data
-        if (
-          !(priorStudy instanceof StudyMetadata) &&
-          !(priorStudy instanceof StudySummary)
-        ) {
+        if (!priorStudy instanceof StudyMetadata) {
           return;
         }
 
@@ -385,11 +382,9 @@ export default class ProtocolEngine {
           // This tests to make sure there is actually image data in this instance
           // TODO: Change this when we add PDF and MPEG support
           // See https://ohiforg.atlassian.net/browse/LT-227
-          // sopClassUid = x00080016
-          // rows = x00280010
           if (
-            !isImage(instance.getTagValue('x00080016')) &&
-            !instance.getTagValue('x00280010')
+            !isImage(instance.getTagValue('SOPClassUID')) &&
+            !instance.getTagValue('Rows')
           ) {
             return;
           }
@@ -436,19 +431,19 @@ export default class ProtocolEngine {
           const currentSOPInstanceUID = instance.getSOPInstanceUID();
 
           const imageDetails = {
-            studyInstanceUid: study.getStudyInstanceUID(),
-            seriesInstanceUid: series.getSeriesInstanceUID(),
-            sopInstanceUid: currentSOPInstanceUID,
+            StudyInstanceUID: study.getStudyInstanceUID(),
+            SeriesInstanceUID: series.getSeriesInstanceUID(),
+            SOPInstanceUID: currentSOPInstanceUID,
             currentImageIdIndex: index,
             matchingScore: totalMatchScore,
             matchDetails: matchDetails,
             sortingInfo: {
               score: totalMatchScore,
               study:
-                instance.getTagValue('x00080020') +
-                instance.getTagValue('x00080030'), // StudyDate = x00080020 StudyTime = x00080030
-              series: parseInt(instance.getTagValue('x00200011')), // TODO: change for seriesDateTime SeriesNumber = x00200011
-              instance: parseInt(instance.getTagValue('x00200013')), // TODO: change for acquisitionTime InstanceNumber = x00200013
+                instance.getTagValue('StudyDate') +
+                instance.getTagValue('StudyTime'),
+              series: parseInt(instance.getTagValue('SeriesNumber')), // TODO: change for seriesDateTime
+              instance: parseInt(instance.getTagValue('InstanceNumber')), // TODO: change for acquisitionTime
             },
           };
 
@@ -461,7 +456,7 @@ export default class ProtocolEngine {
 
           // If the instance was found, set the displaySet ID
           if (displaySet) {
-            imageDetails.displaySetInstanceUid = displaySet.getUID();
+            imageDetails.displaySetInstanceUID = displaySet.getUID();
             imageDetails.imageId = instance.getImageId();
           }
 
@@ -654,25 +649,25 @@ export default class ProtocolEngine {
       }
 
       if (currentMatch && currentMatch.imageId) {
-        currentViewportData.studyInstanceUid = currentMatch.studyInstanceUid;
-        currentViewportData.seriesInstanceUid = currentMatch.seriesInstanceUid;
-        currentViewportData.sopInstanceUid = currentMatch.sopInstanceUid;
+        currentViewportData.StudyInstanceUID = currentMatch.StudyInstanceUID;
+        currentViewportData.SeriesInstanceUID = currentMatch.SeriesInstanceUID;
+        currentViewportData.SOPInstanceUID = currentMatch.SOPInstanceUID;
         currentViewportData.currentImageIdIndex =
           currentMatch.currentImageIdIndex;
-        currentViewportData.displaySetInstanceUid =
-          currentMatch.displaySetInstanceUid;
+        currentViewportData.displaySetInstanceUID =
+          currentMatch.displaySetInstanceUID;
         currentViewportData.imageId = currentMatch.imageId;
       }
 
       // @TODO Why should we throw an exception when a best match is not found? This was aborting the whole process.
-      // if (!currentViewportData.displaySetInstanceUid) {
+      // if (!currentViewportData.displaySetInstanceUID) {
       //     throw new OHIFError('ProtocolEngine::updateViewports No matching display set found?');
       // }
 
       viewportData.push(currentViewportData);
     });
 
-    this.setLayout(layoutProps.rows, layoutProps.columns);
+    this.setLayout(layoutProps.Rows, layoutProps.Columns);
 
     if (typeof this.options.setViewportSpecificData !== 'function') {
       log.error(

platform/core/src/hanging-protocols/classes/Rule.js

@@ -6,7 +6,7 @@ const EQUALS_REGEXP = /^equals$/;
 /**
  * This Class represents a Rule to be evaluated given a set of attributes
  * Rules have:
- * - An attribute (e.g. 'seriesDescription')
+ * - An attribute (e.g. 'SeriesDescription')
  * - A constraint Object, in the form required by Validate.js:
  *
  * rule.constraint = {

platform/core/src/hanging-protocols/classes/ViewportStructure.js

@@ -45,9 +45,9 @@ export default class ViewportStructure {
     // Viewport structure can be updated later when we build more complex display layouts
     switch (this.type) {
       case 'grid':
-        // For the typical grid layout, we only need to multiply rows by columns to
+        // For the typical grid layout, we only need to multiply Rows by Columns to
         // obtain the number of viewports
-        return this.properties.rows * this.properties.columns;
+        return this.properties.Rows * this.properties.Columns;
     }
   }
 }

platform/core/src/hanging-protocols/protocolStore/defaultProtocol.js

@@ -9,8 +9,8 @@ function getDefaultProtocol() {
   protocol.locked = true;
 
   const oneByOne = new ViewportStructure('grid', {
-    rows: 1,
-    columns: 1,
+    Rows: 1,
+    Columns: 1,
   });
 
   const viewport = new Viewport();

platform/core/src/hanging-protocols/protocolStore/testProtocols.js

@@ -14,8 +14,8 @@ function getMRTwoByTwoTest() {
   proto.locked = true;
   // Use http://localhost:3000/viewer/1.2.840.113619.2.5.1762583153.215519.978957063.78
 
-  var studyInstanceUid = new ProtocolMatchingRule(
-    'studyInstanceUid',
+  var StudyInstanceUID = new ProtocolMatchingRule(
+    'StudyInstanceUID',
     {
       equals: {
         value: '1.2.840.113619.2.5.1762583153.215519.978957063.78',
@@ -24,30 +24,30 @@ function getMRTwoByTwoTest() {
     true
   );
 
-  proto.addProtocolMatchingRule(studyInstanceUid);
+  proto.addProtocolMatchingRule(StudyInstanceUID);
 
   var oneByTwo = new ViewportStructure('grid', {
-    rows: 1,
-    columns: 2,
+    Rows: 1,
+    Columns: 2,
   });
 
   // Stage 1
   var left = new Viewport();
   var right = new Viewport();
 
-  var firstSeries = new SeriesMatchingRule('seriesNumber', {
+  var firstSeries = new SeriesMatchingRule('SeriesNumber', {
     equals: {
       value: 1,
     },
   });
 
-  var secondSeries = new SeriesMatchingRule('seriesNumber', {
+  var secondSeries = new SeriesMatchingRule('SeriesNumber', {
     equals: {
       value: 2,
     },
   });
 
-  var thirdImage = new ImageMatchingRule('instanceNumber', {
+  var thirdImage = new ImageMatchingRule('InstanceNumber', {
     equals: {
       value: 3,
     },
@@ -67,19 +67,19 @@ function getMRTwoByTwoTest() {
 
   // Stage 2
   var twoByOne = new ViewportStructure('grid', {
-    rows: 2,
-    columns: 1,
+    Rows: 2,
+    Columns: 1,
   });
   var left2 = new Viewport();
   var right2 = new Viewport();
 
-  var fourthSeries = new SeriesMatchingRule('seriesNumber', {
+  var fourthSeries = new SeriesMatchingRule('SeriesNumber', {
     equals: {
       value: 4,
     },
   });
 
-  var fifthSeries = new SeriesMatchingRule('seriesNumber', {
+  var fifthSeries = new SeriesMatchingRule('SeriesNumber', {
     equals: {
       value: 5,
     },
@@ -133,8 +133,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 1,
-            columns: 2,
+            Rows: 1,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -195,8 +195,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 1,
-            columns: 2,
+            Rows: 1,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -257,8 +257,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 2,
-            columns: 2,
+            Rows: 2,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -402,8 +402,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 1,
-            columns: 2,
+            Rows: 1,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -464,8 +464,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 1,
-            columns: 2,
+            Rows: 1,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -548,8 +548,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 2,
-            columns: 2,
+            Rows: 2,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -737,8 +737,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 1,
-            columns: 1,
+            Rows: 1,
+            Columns: 1,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -770,8 +770,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 2,
-            columns: 2,
+            Rows: 2,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -931,8 +931,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 1,
-            columns: 2,
+            Rows: 1,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -993,8 +993,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 1,
-            columns: 2,
+            Rows: 1,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -1044,8 +1044,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 1,
-            columns: 2,
+            Rows: 1,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -1127,8 +1127,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 1,
-            columns: 2,
+            Rows: 1,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -1190,8 +1190,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 1,
-            columns: 2,
+            Rows: 1,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -1275,8 +1275,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 2,
-            columns: 2,
+            Rows: 2,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },
@@ -1386,8 +1386,8 @@ function getDemoProtocols() {
         viewportStructure: {
           type: 'grid',
           properties: {
-            rows: 2,
-            columns: 2,
+            Rows: 2,
+            Columns: 2,
           },
           layoutTemplateName: 'gridLayout',
         },

platform/core/src/lib/cornerstone.js

@@ -21,7 +21,7 @@ function getBoundingBox(context, textLines, x, y, options) {
     // Get the text width in the current font
     const width = context.measureText(text).width;
 
-    // Find the maximum with for all the text rows;
+    // Find the maximum with for all the text Rows;
     maxWidth = Math.max(maxWidth, width);
   });
 

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

@@ -8,9 +8,8 @@ import guid from '../../utils/guid';
 import studyMetadataManager from '../../utils/studyMetadataManager';
 import { measurementApiDefaultConfig } from './../configuration.js';
 
-
 const configuration = {
-  ...measurementApiDefaultConfig
+  ...measurementApiDefaultConfig,
 };
 
 export default class MeasurementApi {
@@ -99,8 +98,8 @@ export default class MeasurementApi {
     const toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.saveToolState();
 
     // Stop here if the metadata for the measurement's study is not loaded yet
-    const { studyInstanceUid } = measurement;
-    const metadata = studyMetadataManager.get(studyInstanceUid);
+    const { StudyInstanceUID } = measurement;
+    const metadata = studyMetadataManager.get(StudyInstanceUID);
     if (!metadata) return;
 
     // Iterate each child tool if the current tool has children
@@ -221,7 +220,7 @@ export default class MeasurementApi {
     this.options.onMeasurementsUpdated(Object.assign({}, this.tools));
   }
 
-  retrieveMeasurements(patientId, timepointIds) {
+  retrieveMeasurements(PatientID, timepointIds) {
     const retrievalFn = configuration.dataExchange.retrieve;
     const { server } = configuration;
     if (typeof retrievalFn !== 'function') {
@@ -297,9 +296,9 @@ export default class MeasurementApi {
       : null;
     const timepoints = this.timepointApi.all(timepointFilter);
     const timepointIds = timepoints.map(t => t.timepointId);
-    const patientId = timepoints[0].patientId;
+    const PatientID = timepoints[0].PatientID;
     const filter = {
-      patientId,
+      PatientID,
       timepointIds,
     };
 
@@ -576,17 +575,17 @@ export default class MeasurementApi {
 
     const toolGroupId = this.toolsGroupsMap[measurementData.toolType];
 
-    // TODO: Remove TrialPatientLocationUid from here and override it somehow
+    // TODO: Remove TrialPatientLocationUID from here and override it somehow
     // by dependant applications. Here we should use the location attribute instead of the uid
     let filter;
     const uid =
       measurementData.additionalData &&
-      measurementData.additionalData.TrialPatientLocationUid;
+      measurementData.additionalData.TrialPatientLocationUID;
     if (uid) {
       filter = tool =>
         tool._id !== measurementData._id &&
         tool.additionalData &&
-        tool.additionalData.TrialPatientLocationUid === uid;
+        tool.additionalData.TrialPatientLocationUID === uid;
     } else {
       filter = tool =>
         tool._id !== measurementData._id &&
@@ -691,8 +690,8 @@ export default class MeasurementApi {
 
     // Get the timepoint
     let timepoint;
-    if (measurement.studyInstanceUid) {
-      timepoint = this.timepointApi.study(measurement.studyInstanceUid)[0];
+    if (measurement.StudyInstanceUID) {
+      timepoint = this.timepointApi.study(measurement.StudyInstanceUID)[0];
     } else {
       const { timepointId } = measurement;
       timepoint = this.timepointApi.timepoints.find(
@@ -760,7 +759,7 @@ export default class MeasurementApi {
       measurement.lesionNamingNumber = found.lesionNamingNumber;
       measurement.measurementNumber = found.measurementNumber;
 
-      // TODO: Remove TrialPatientLocationUid from here and override it somehow
+      // TODO: Remove TrialPatientLocationUID from here and override it somehow
       // by dependant applications
 
       // Change the update object to set the same number, additionalData,
@@ -768,8 +767,8 @@ export default class MeasurementApi {
       updateObject.lesionNamingNumber = found.lesionNamingNumber;
       updateObject.measurementNumber = found.measurementNumber;
       updateObject.additionalData = measurement.additionalData || {};
-      updateObject.additionalData.TrialPatientLocationUid =
-        found.additionalData && found.additionalData.TrialPatientLocationUid;
+      updateObject.additionalData.TrialPatientLocationUID =
+        found.additionalData && found.additionalData.TrialPatientLocationUID;
       updateObject.location = found.location;
       updateObject.label = found.label;
       updateObject.description = found.description;
@@ -807,7 +806,7 @@ export default class MeasurementApi {
         toolId: toolType,
         toolItemId: addedMeasurement._id,
         timepointId: timepoint.timepointId,
-        studyInstanceUid: addedMeasurement.studyInstanceUid,
+        StudyInstanceUID: addedMeasurement.StudyInstanceUID,
         createdAt: addedMeasurement.createdAt,
         lesionNamingNumber: addedMeasurement.lesionNamingNumber,
         measurementNumber: addedMeasurement.measurementNumber,

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

@@ -55,7 +55,7 @@ export default class TimepointApi {
     });
     const filteredTimepoints = sortedTimepoints.find(
       tp =>
-        tp.patientId === timepoint.patientId &&
+        tp.PatientID === timepoint.PatientID &&
         tp.timepointType === timepoint.timepointType
     );
 
@@ -129,14 +129,14 @@ export default class TimepointApi {
     );
   }
 
-  disassociateStudy(timepointIds, studyInstanceUid) {
+  disassociateStudy(timepointIds, StudyInstanceUID) {
     const disassociateFn = configuration.dataExchange.disassociate;
     if (typeof disassociateFn !== 'function') {
       log.error('Study disassociate function has not been configured.');
       return;
     }
 
-    disassociateFn(timepointIds, studyInstanceUid).then(() => {
+    disassociateFn(timepointIds, StudyInstanceUID).then(() => {
       log.info('Disassociation completed');
 
       this.timepoints = [];
@@ -510,9 +510,9 @@ export default class TimepointApi {
   }
 
   // Return only the timepoints for the given study
-  study(studyInstanceUid) {
+  study(StudyInstanceUID) {
     return this.all().filter(timepoint =>
-      timepoint.studyInstanceUids.includes(studyInstanceUid)
+      timepoint.studyInstanceUIDs.includes(StudyInstanceUID)
     );
   }
 

platform/core/src/measurements/conformance/ConformanceCriteria.js

@@ -21,12 +21,12 @@ class ConformanceCriteria {
     this.options = options;
   }
 
-  loadStudy(studyInstanceUid) {
+  loadStudy(StudyInstanceUID) {
     if (typeof this.options.loadStudy !== 'function') {
       throw new Error('loadStudy callback is not defined');
     }
 
-    return this.options.loadStudy(null, studyInstanceUid);
+    return this.options.loadStudy(null, StudyInstanceUID);
   }
 
   async validate(trialCriteriaType) {
@@ -181,7 +181,7 @@ class ConformanceCriteria {
       const measurements = this.measurementApi.fetch(measurementType);
 
       measurements.forEach(measurement => {
-        const { studyInstanceUid } = measurement;
+        const { StudyInstanceUID } = measurement;
 
         const timepointId = measurement.timepointId;
         const timepoint =
@@ -195,7 +195,7 @@ class ConformanceCriteria {
           return;
         }
 
-        const promise = this.loadStudy(studyInstanceUid);
+        const promise = this.loadStudy(StudyInstanceUID);
         promise.then(
           studyMetadata => {
             data[measurementType].push({

platform/core/src/measurements/conformance/criteria/MeasurementsLength.js

@@ -65,7 +65,7 @@ export const MeasurementsLengthSchema = {
     },
     isNodal: {
       label: 'Filter to evaluate only nodal or extranodal measurements',
-      type: 'boolean'
+      type: 'boolean',
     },
     message: {
       label: 'Message to be displayed in case of nonconformity',
@@ -119,19 +119,24 @@ export class MeasurementsLengthCriterion extends BaseCriterion {
         shortestDiameter = (child && child.shortestDiameter) || 0;
       }
 
-      const { sliceThickness } = metadata;
-      const modality = (metadata.getRawValue('x00080060') || '').toUpperCase();
+      const { SliceThickness } = metadata;
 
-      // Stop here if the measurement does not match the modality and location filters
-      if (typeof isNodal === 'boolean' && typeof options.isNodal === 'boolean' && options.isNodal !== isNodal)
+      const Modality = metadata.getTagValue('Modality') || '';
+
+      // Stop here if the measurement does not match the Modality and location filters
+      if (
+        typeof isNodal === 'boolean' &&
+        typeof options.isNodal === 'boolean' &&
+        options.isNodal !== isNodal
+      )
         return;
       if (options.locationIn && options.locationIn.indexOf(location) === -1)
         return;
-      if (options.modalityIn && options.modalityIn.indexOf(modality) === -1)
+      if (options.modalityIn && options.modalityIn.indexOf(Modality) === -1)
         return;
       if (options.locationNotIn && options.locationNotIn.indexOf(location) > -1)
         return;
-      if (options.modalityNotIn && options.modalityNotIn.indexOf(modality) > -1)
+      if (options.modalityNotIn && options.modalityNotIn.indexOf(Modality) > -1)
         return;
 
       // Check the measurement length
@@ -139,11 +144,11 @@ export class MeasurementsLengthCriterion extends BaseCriterion {
         (options.longAxis && longestDiameter < options.longAxis) ||
         (options.shortAxis && shortestDiameter < options.shortAxis) ||
         (longMultiplier &&
-          !isNaN(sliceThickness) &&
-          longestDiameter < longMultiplier * sliceThickness) ||
+          !isNaN(SliceThickness) &&
+          longestDiameter < longMultiplier * SliceThickness) ||
         (shortMultiplier &&
-          !isNaN(sliceThickness) &&
-          shortestDiameter < shortMultiplier * sliceThickness);
+          !isNaN(SliceThickness) &&
+          shortestDiameter < shortMultiplier * SliceThickness);
 
       // Mark this measurement as invalid if some of the checks have failed
       if (failed) {

platform/core/src/measurements/conformance/criteria/Modality.js

@@ -32,7 +32,7 @@ export const ModalitySchema = {
 
 /*
  * ModalityCriteria
- *   Check if a modality is allowed or denied
+ *   Check if a Modality is allowed or denied
  * Options:
  *   method (string): Specify if it\'s goinig to "allow" or "deny" the modalities
  *   measurementTypes (string[]): List of measurement types that will be evaluated
@@ -56,16 +56,14 @@ export class ModalityCriterion extends BaseCriterion {
 
       items.forEach(item => {
         const { measurement, metadata } = item;
-        const modality = (
-          metadata.getRawValue('x00080060') || ''
-        ).toUpperCase();
+        const Modality = metadata.getTagValue('Modality') || '';
 
         if (
-          (validationMethod === 'allow' && !modalitiesSet.has(modality)) ||
-          (validationMethod === 'deny' && modalitiesSet.has(modality))
+          (validationMethod === 'allow' && !modalitiesSet.has(Modality)) ||
+          (validationMethod === 'deny' && modalitiesSet.has(Modality))
         ) {
           measurements.push(measurement);
-          invalidModalities.add(modality);
+          invalidModalities.add(Modality);
         }
       });
     });
@@ -74,7 +72,7 @@ export class ModalityCriterion extends BaseCriterion {
       const uniqueModalities = Array.from(invalidModalities);
       const uniqueModalitiesText = uniqueModalities.join(', ');
       const modalityText =
-        uniqueModalities.length > 1 ? 'modalities' : 'modality';
+        uniqueModalities.length > 1 ? 'modalities' : 'Modality';
 
       message = `The ${modalityText} ${uniqueModalitiesText} should not be used as a method of measurement`;
     }

platform/core/src/measurements/dataExchange.js

@@ -1,6 +1,6 @@
 import log from '../log';
 
-export const retrieveMeasurements = (patientId, timepointIds) => {
+export const retrieveMeasurements = (PatientID, timepointIds) => {
   log.error('retrieveMeasurements');
   return Promise.resolve();
 };
@@ -30,7 +30,7 @@ export const removeTimepoint = timepointId => {
   return Promise.resolve();
 };
 
-export const disassociateStudy = (timepointIds, studyInstanceUid) => {
+export const disassociateStudy = (timepointIds, StudyInstanceUID) => {
   log.error('disassociateStudy');
   return Promise.resolve();
 };