fix(staticwado): SM and RT and update the server with new data (#3422)

* fix bugs for the RT for the new demo

* fix SM with the static-wado server

* remove thumbnail from tmtv

* migration guide

* fix stability for the rt struct

* apply review comments

* add loading indicator to SM

* pdf works

* try to fix relative bulkData

* fix the rest

* fix preflight for the SM

* fix typo

* apply review comments

* yarn lock

extensions/cornerstone-dicom-rt/src/loadRTStruct.js

@@ -7,12 +7,13 @@ async function checkAndLoadContourData(instance, datasource) {
     return Promise.reject('Invalid instance object or ROIContourSequence');
   }
 
-  const promises = [];
+  const promisesMap = new Map();
-  let counter = 0;
 
   for (const ROIContour of instance.ROIContourSequence) {
+    const referencedROINumber = ROIContour.ReferencedROINumber;
     if (!ROIContour || !ROIContour.ContourSequence) {
-      return Promise.reject('Invalid ROIContour or ContourSequence');
+      promisesMap.set(referencedROINumber, [Promise.resolve([])]);
+      continue;
     }
 
     for (const Contour of ROIContour.ContourSequence) {
@@ -21,9 +22,15 @@ async function checkAndLoadContourData(instance, datasource) {
       }
 
       const contourData = Contour.ContourData;
-      counter++;
+
       if (Array.isArray(contourData)) {
-        promises.push(Promise.resolve(contourData));
+        promisesMap.has(referencedROINumber)
+          ? promisesMap
+              .get(referencedROINumber)
+              .push(Promise.resolve(contourData))
+          : promisesMap.set(referencedROINumber, [
+              Promise.resolve(contourData),
+            ]);
       } else if (contourData && contourData.BulkDataURI) {
         const bulkDataURI = contourData.BulkDataURI;
 
@@ -44,53 +51,59 @@ async function checkAndLoadContourData(instance, datasource) {
           SOPInstanceUID: instance.SOPInstanceUID,
         });
 
-        promises.push(bulkDataPromise);
+        promisesMap.has(referencedROINumber)
+          ? promisesMap.get(referencedROINumber).push(bulkDataPromise)
+          : promisesMap.set(referencedROINumber, [bulkDataPromise]);
       } else {
         return Promise.reject(`Invalid ContourData: ${contourData}`);
       }
     }
   }
-  const flattenedPromises = promises.flat();
-  const resolvedPromises = await Promise.allSettled(flattenedPromises);
 
-  // Modify contourData and replace it in its corresponding ROIContourSequence's Contour's contourData
+  const resolvedPromisesMap = new Map();
-  let index = 0;
+  for (const [key, promiseArray] of promisesMap.entries()) {
-  instance.ROIContourSequence.forEach((ROIContour, roiIndex) => {
+    resolvedPromisesMap.set(key, await Promise.allSettled(promiseArray));
-    ROIContour.ContourSequence.forEach((Contour, contourIndex) => {
+  }
-      const promise = resolvedPromises[index++];
 
-      if (promise.status === 'fulfilled') {
+  instance.ROIContourSequence.forEach(ROIContour => {
-        const uint8Array = new Uint8Array(promise.value);
+    try {
-        const textDecoder = new TextDecoder();
+      const referencedROINumber = ROIContour.ReferencedROINumber;
-        const dataUint8Array = textDecoder.decode(uint8Array);
+      const resolvedPromises = resolvedPromisesMap.get(referencedROINumber);
-        if (
-          typeof dataUint8Array === 'string' &&
-          dataUint8Array.includes('\\')
-        ) {
-          const numSlashes = (dataUint8Array.match(/\\/g) || []).length;
-          let startIndex = 0;
-          let endIndex = dataUint8Array.indexOf('\\', startIndex);
-          let numbersParsed = 0;
-          const ContourData = [];
 
-          while (numbersParsed !== numSlashes + 1) {
+      if (ROIContour.ContourSequence) {
-            const str = dataUint8Array.substring(startIndex, endIndex);
+        ROIContour.ContourSequence.forEach((Contour, index) => {
-            let value = parseFloat(str);
+          const promise = resolvedPromises[index];
-
+          if (promise.status === 'fulfilled') {
-            ContourData.push(value);
+            if (
-            startIndex = endIndex + 1;
+              Array.isArray(promise.value) &&
-            endIndex = dataUint8Array.indexOf('\\', startIndex);
+              promise.value.every(Number.isFinite)
-            endIndex === -1 ? (endIndex = dataUint8Array.length) : endIndex;
+            ) {
-            numbersParsed++;
+              // If promise.value is already an array of numbers, use it directly
+              Contour.ContourData = promise.value;
+            } else {
+              // If the resolved promise value is a byte array (Blob), it needs to be decoded
+              const uint8Array = new Uint8Array(promise.value);
+              const textDecoder = new TextDecoder();
+              const dataUint8Array = textDecoder.decode(uint8Array);
+              if (
+                typeof dataUint8Array === 'string' &&
+                dataUint8Array.includes('\\')
+              ) {
+                Contour.ContourData = dataUint8Array
+                  .split('\\')
+                  .map(parseFloat);
+              } else {
+                Contour.ContourData = [];
+              }
+            }
+          } else {
+            console.error(promise.reason);
           }
-          Contour.ContourData = ContourData;
+        });
-        } else {
-          Contour.ContourData = [];
-        }
-      } else {
-        console.error(promise.reason);
       }
-    });
+    } catch (error) {
+      console.error(error);
+    }
   });
 }
 
@@ -104,7 +117,7 @@ export default async function loadRTStruct(
     '@ohif/extension-cornerstone.utilityModule.common'
   );
   const dataSource = extensionManager.getActiveDataSource()[0];
-  const { useBulkDataURI } = dataSource.getConfig?.() || {};
+  const { bulkDataURI } = dataSource.getConfig?.() || {};
 
   const { dicomLoaderService } = utilityModule.exports;
   const imageIdSopInstanceUidPairs = _getImageIdSopInstanceUidPairsForDisplaySet(
@@ -116,7 +129,7 @@ export default async function loadRTStruct(
   rtStructDisplaySet.isLoaded = true;
   let instance = rtStructDisplaySet.instance;
 
-  if (!useBulkDataURI) {
+  if (!bulkDataURI || !bulkDataURI.enabled) {
     const segArrayBuffer = await dicomLoaderService.findDicomDataPromise(
       rtStructDisplaySet,
       null,

extensions/default/src/CustomizableContextMenu/index.ts

@@ -1,11 +1,11 @@
 import ContextMenuController from './ContextMenuController';
 import * as ContextMenuItemsBuilder from './ContextMenuItemsBuilder';
 import defaultContextMenu from './defaultContextMenu';
-import * as CustomizeableContextMenuTypes from './types';
+import * as CustomizableContextMenuTypes from './types';
 
 export {
   ContextMenuController,
-  CustomizeableContextMenuTypes,
+  CustomizableContextMenuTypes,
   ContextMenuItemsBuilder,
   defaultContextMenu,
 };

extensions/default/src/DicomWebDataSource/index.js

@@ -24,6 +24,7 @@ import {
 } from './retrieveStudyMetadata.js';
 import StaticWadoClient from './utils/StaticWadoClient';
 import getDirectURL from '../utils/getDirectURL';
+import { fixBulkDataURI } from './utils/fixBulkDataURI';
 
 const { DicomMetaDictionary, DicomDict } = dcmjs.data;
 
@@ -373,13 +374,23 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) {
        */
       const addRetrieveBulkData = instance => {
         const naturalized = naturalizeDataset(instance);
+
+        // if we konw the server doesn't use bulkDataURI, then don't
+        if (!dicomWebConfig.bulkDataURI?.enabled) {
+          return naturalized;
+        }
+
         Object.keys(naturalized).forEach(key => {
           const value = naturalized[key];
+
           // The value.Value will be set with the bulkdata read value
           // in which case it isn't necessary to re-read this.
           if (value && value.BulkDataURI && !value.Value) {
             // Provide a method to fetch bulkdata
             value.retrieveBulkData = () => {
+              // handle the scenarios where bulkDataURI is relative path
+              fixBulkDataURI(value, naturalized, dicomWebConfig);
+
               const options = {
                 // The bulkdata fetches work with either multipart or
                 // singlepart, so set multipart to false to let the server

extensions/default/src/DicomWebDataSource/utils/fixBulkDataURI.ts

@@ -0,0 +1,56 @@
+/**
+ * Modifies a bulkDataURI to ensure it is absolute based on the DICOMWeb configuration and
+ * instance data. The modification is in-place.
+ *
+ * If the bulkDataURI is relative to the series or study (according to the DICOM standard),
+ * it is made absolute by prepending the relevant paths.
+ *
+ * In scenarios where the bulkDataURI is a server-relative path (starting with '/'), the function
+ * handles two cases:
+ *
+ * 1. If the wado root is absolute (starts with 'http'), it prepends the wado root to the bulkDataURI.
+ * 2. If the wado root is relative, no changes are needed as the bulkDataURI is already correctly relative to the server root.
+ *
+ * @param value - The object containing BulkDataURI to be fixed.
+ * @param instance - The object (DICOM instance data) containing StudyInstanceUID and SeriesInstanceUID.
+ * @param dicomWebConfig - The DICOMWeb configuration object, containing wadoRoot and potentially bulkDataURI.relativeResolution.
+ * @returns The function modifies `value` in-place, it does not return a value.
+ */
+function fixBulkDataURI(value, instance, dicomWebConfig) {
+  // in case of the relative path, make it absolute. The current DICOM standard says
+  // the bulkdataURI is relative to the series. However, there are situations where
+  // it can be relative to the study too
+  if (
+    !value.BulkDataURI.startsWith('http') &&
+    !value.BulkDataURI.startsWith('/')
+  ) {
+    if (dicomWebConfig.bulkDataURI?.relativeResolution === 'studies') {
+      value.BulkDataURI = `${dicomWebConfig.wadoRoot}/studies/${instance.StudyInstanceUID}/${value.BulkDataURI}`;
+    } else if (
+      dicomWebConfig.bulkDataURI?.relativeResolution === 'series' ||
+      !dicomWebConfig.bulkDataURI?.relativeResolution
+    ) {
+      value.BulkDataURI = `${dicomWebConfig.wadoRoot}/studies/${instance.StudyInstanceUID}/series/${instance.SeriesInstanceUID}/${value.BulkDataURI}`;
+    }
+
+    return;
+  }
+
+  // in case it is relative path but starts at the server (e.g., /bulk/1e, note the missing http
+  // in the beginning and the first character is /) There are two scenarios, whether the wado root
+  // is absolute or relative. In case of absolute, we need to prepend the wado root to the bulkdata
+  // uri (e.g., bulkData: /bulk/1e, wado root: http://myserver.com/dicomweb, output: http://myserver.com/bulk/1e)
+  // and in case of relative wado root, we need to prepend the bulkdata uri to the wado root (e.g,. bulkData: /bulk/1e
+  // wado root: /dicomweb, output: /bulk/1e)
+  if (value.BulkDataURI[0] === '/') {
+    if (dicomWebConfig.wadoRoot.startsWith('http')) {
+      // Absolute wado root
+      const url = new URL(dicomWebConfig.wadoRoot);
+      value.BulkDataURI = `${url.origin}${value.BulkDataURI}`;
+    } else {
+      // Relative wado root, we don't need to do anything, bulkdata uri is already correct
+    }
+  }
+}
+
+export { fixBulkDataURI };

extensions/default/src/DicomWebDataSource/utils/index.ts

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

extensions/default/src/commandsModule.ts

@@ -3,14 +3,14 @@ import { ServicesManager, utils, Types } from '@ohif/core';
 import {
   ContextMenuController,
   defaultContextMenu,
-} from './CustomizeableContextMenu';
+} from './CustomizableContextMenu';
 import DicomTagBrowser from './DicomTagBrowser/DicomTagBrowser';
 import reuseCachedLayouts from './utils/reuseCachedLayouts';
 import findViewportsByPosition, {
   findOrCreateViewport as layoutFindOrCreate,
 } from './findViewportsByPosition';
 
-import { ContextMenuProps } from './CustomizeableContextMenu/types';
+import { ContextMenuProps } from './CustomizableContextMenu/types';
 import { NavigateHistory } from './types/commandModuleTypes';
 import { history } from '@ohif/viewer';
 

extensions/default/src/index.ts

@@ -13,8 +13,9 @@ import { id } from './id.js';
 import preRegistration from './init';
 import {
   ContextMenuController,
-  CustomizeableContextMenuTypes,
+  CustomizableContextMenuTypes,
-} from './CustomizeableContextMenu';
+} from './CustomizableContextMenu';
+import * as dicomWebUtils from './DicomWebDataSource/utils';
 
 const defaultExtension: Types.Extensions.Extension = {
   /**
@@ -47,6 +48,7 @@ export default defaultExtension;
 
 export {
   ContextMenuController,
-  CustomizeableContextMenuTypes,
+  CustomizableContextMenuTypes,
   getStudiesForPatientByMRN,
+  dicomWebUtils,
 };

extensions/default/src/utils/getDirectURL.js

@@ -1,10 +1,4 @@
-import {
+import { utils } from '@ohif/core';
-  DicomMetadataStore,
-  IWebApiDataSource,
-  utils,
-  errorHandler,
-  classes,
-} from '@ohif/core';
 
 /**
  * Generates a URL that can be used for direct retrieve of the bulkdata
@@ -57,31 +51,19 @@ const getDirectURL = (config, params) => {
   const BulkDataURI =
     (value && value.BulkDataURI) ||
     `series/${SeriesInstanceUID}/instances/${SOPInstanceUID}${defaultPath}`;
-  const hasQuery = BulkDataURI.indexOf('?') != -1;
+  const hasQuery = BulkDataURI.indexOf('?') !== -1;
-  const hasAccept = BulkDataURI.indexOf('accept=') != -1;
+  const hasAccept = BulkDataURI.indexOf('accept=') !== -1;
   const acceptUri =
     BulkDataURI +
     (hasAccept ? '' : (hasQuery ? '&' : '?') + `accept=${defaultType}`);
-  if (BulkDataURI.indexOf('http') === 0) {
+
-    if (tag === 'PixelData' || tag === 'EncapsulatedDocument') {
+  if (tag === 'PixelData' || tag === 'EncapsulatedDocument') {
-      return `${wadoRoot}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/instances/${SOPInstanceUID}/rendered`;
+    return `${wadoRoot}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/instances/${SOPInstanceUID}/rendered`;
-    } else {
-      return acceptUri;
-    }
   }
-  if (BulkDataURI.indexOf('/') === 0) {
+
-    return wadoRoot + acceptUri;
+  // The DICOMweb standard states that the default is multipart related, and then
-  }
+  // separately states that the accept parameter is the URL parameter equivalent of the accept header.
-  if (BulkDataURI.indexOf('series/') == 0) {
+  return acceptUri;
-    return `${wadoRoot}/studies/${StudyInstanceUID}/${acceptUri}`;
-  }
-  if (BulkDataURI.indexOf('instances/') === 0) {
-    return `${wadoRoot}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/${acceptUri}`;
-  }
-  if (BulkDataURI.indexOf('bulkdata/') === 0) {
-    return `${wadoRoot}/studies/${StudyInstanceUID}/${acceptUri}`;
-  }
-  throw new Error('BulkDataURI in unknown format:' + BulkDataURI);
 };
 
 export default getDirectURL;

extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx

@@ -2,6 +2,7 @@ import React, { Component } from 'react';
 import ReactResizeDetector from 'react-resize-detector';
 import PropTypes from 'prop-types';
 import debounce from 'lodash.debounce';
+import { LoadingIndicatorProgress } from '@ohif/ui';
 
 import './DicomMicroscopyViewport.css';
 import ViewportOverlay from './components/ViewportOverlay';
@@ -10,9 +11,20 @@ import dcmjs from 'dcmjs';
 import cleanDenaturalizedDataset from './utils/cleanDenaturalizedDataset';
 import MicroscopyService from './services/MicroscopyService';
 
+function transformImageTypeUnnaturalized(entry) {
+  if (entry.vr === 'CS') {
+    return {
+      vr: 'US',
+      Value: entry.Value[0].split('\\'),
+    };
+  }
+  return entry;
+}
+
 class DicomMicroscopyViewport extends Component {
   state = {
     error: null as any,
+    isLoaded: false,
   };
 
   microscopyService: MicroscopyService;
@@ -132,6 +144,10 @@ class DicomMicroscopyViewport extends Component {
       //       );
       //       m['00200052'].Value[0] = volumeImages[0].FrameOfReferenceUID;
       //     }
+      //     NOTE: depending on different data source, image.ImageType sometimes
+      //     is a string, not a string array.
+      //     m['00080008'] = transformImageTypeUnnaturalized(m['00080008']);
+
       //     const image = new metadataUtils.VLWholeSlideMicroscopyImage({
       //       metadata: m,
       //     });
@@ -143,8 +159,20 @@ class DicomMicroscopyViewport extends Component {
       // }
 
       metadata.forEach(m => {
+        // NOTE: depending on different data source, image.ImageType sometimes
+        //    is a string, not a string array.
+        m.ImageType =
+          typeof m.ImageType === 'string'
+            ? m.ImageType.split('\\')
+            : m.ImageType;
+
         const inst = cleanDenaturalizedDataset(
-          dcmjs.data.DicomMetaDictionary.denaturalizeDataset(m)
+          dcmjs.data.DicomMetaDictionary.denaturalizeDataset(m),
+          {
+            StudyInstanceUID: m.StudyInstanceUID,
+            SeriesInstanceUID: m.SeriesInstanceUID,
+            dataSourceConfig: this.props.dataSource.getConfig(),
+          }
         );
         if (!inst['00480105']) {
           // Optical Path Sequence, no OpticalPathIdentifier?
@@ -165,13 +193,7 @@ class DicomMicroscopyViewport extends Component {
           metadata: inst,
         });
 
-        // NOTE: depending on different data source, image.ImageType sometimes
+        const imageFlavor = image.ImageType[2];
-        //    is a string, not a string array.
-        const imageType =
-          typeof image.ImageType === 'string'
-            ? image.ImageType.split('\\')
-            : image.ImageType;
-        const imageFlavor = imageType[2];
         if (imageFlavor === 'VOLUME' || imageFlavor === 'THUMBNAIL') {
           volumeImages.push(image);
         }
@@ -182,7 +204,7 @@ class DicomMicroscopyViewport extends Component {
         client,
         metadata: volumeImages,
         retrieveRendered: false,
-        controls: ['overview', 'position', 'zoom'],
+        controls: ['overview', 'position'],
       };
 
       this.viewer = new microscopyViewer(options);
@@ -237,7 +259,11 @@ class DicomMicroscopyViewport extends Component {
   componentDidMount() {
     const { displaySets, viewportIndex } = this.props;
     const displaySet = displaySets[viewportIndex];
-    this.installOpenLayersRenderer(this.container.current, displaySet);
+    this.installOpenLayersRenderer(this.container.current, displaySet).then(
+      () => {
+        this.setState({ isLoaded: true });
+      }
+    );
   }
 
   componentDidUpdate(
@@ -316,6 +342,9 @@ class DicomMicroscopyViewport extends Component {
         ) : (
           <div style={style} ref={this.container} />
         )}
+        {this.state.isLoaded ? null : (
+          <LoadingIndicatorProgress className={'w-full h-full bg-black'} />
+        )}
       </div>
     );
   }

extensions/dicom-microscopy/src/components/ViewportOverlay/index.tsx

@@ -1,6 +1,5 @@
 import React from 'react';
 import classnames from 'classnames';
-import ConfigPoint from 'config-point';
 
 import listComponentGenerator from './listComponentGenerator';
 import './ViewportOverlay.css';
@@ -11,7 +10,7 @@ import {
   formatPN,
 } from './utils';
 
-interface OverylayItem {
+interface OverlayItem {
   id: string;
   title: string;
   value?: (props: any) => string;
@@ -28,17 +27,17 @@ interface OverylayItem {
  * @returns
  */
 export const generateFromConfig = ({
-  topLeft,
+  topLeft = [],
-  topRight,
+  topRight = [],
-  bottomLeft,
+  bottomLeft = [],
-  bottomRight,
+  bottomRight = [],
-  itemGenerator,
+  itemGenerator = () => {},
 }: {
-  topLeft: OverylayItem[];
+  topLeft?: OverlayItem[];
-  topRight: OverylayItem[];
+  topRight?: OverlayItem[];
-  bottomLeft: OverylayItem[];
+  bottomLeft?: OverlayItem[];
-  bottomRight: OverylayItem[];
+  bottomRight?: OverlayItem[];
-  itemGenerator: (props: any) => any;
+  itemGenerator?: (props: any) => any;
 }) => {
   return (props: any) => {
     const topLeftClass = 'top-viewport left-viewport text-primary-light';
@@ -127,29 +126,4 @@ const itemGenerator = (props: any) => {
   );
 };
 
-const { MicroscopyViewportOverlay } = ConfigPoint.register({
+export default generateFromConfig({});
-  MicroscopyViewportOverlay: {
-    configBase: {
-      topLeft: [
-        // {
-        //   id: 'sm-overlay-patient-name',
-        //   title: 'PatientName',
-        //   condition: ({ instance }) =>
-        //     instance && instance.PatientName && instance.PatientName.Alphabetic,
-        //   value: ({ instance }) =>
-        //     instance.PatientName && instance.PatientName.Alphabetic,
-        // } as OverylayItem,
-      ],
-      topRight: [] as OverylayItem[],
-      bottomLeft: [] as OverylayItem[],
-      bottomRight: [] as OverylayItem[],
-      itemGenerator,
-      generateFromConfig,
-    },
-    ...(window.config?.MicroscopyViewportOverlay || {}),
-  },
-});
-
-export default MicroscopyViewportOverlay.generateFromConfig(
-  MicroscopyViewportOverlay
-);

extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts

@@ -1,3 +1,5 @@
+import { dicomWebUtils } from '@ohif/extension-default';
+
 function isPrimitive(v: any) {
   return !(typeof v == 'object' || Array.isArray(v));
 }
@@ -24,10 +26,17 @@ const vrNumerics = [
  * @param obj
  * @returns
  */
-export default function cleanDenaturalizedDataset(obj: any): any {
+export default function cleanDenaturalizedDataset(
+  obj: any,
+  options: {
+    StudyInstanceUID: string;
+    SeriesInstanceUID: string;
+    dataSourceConfig: unknown;
+  }
+): any {
   if (Array.isArray(obj)) {
     const newAry = obj.map(o =>
-      isPrimitive(o) ? o : cleanDenaturalizedDataset(o)
+      isPrimitive(o) ? o : cleanDenaturalizedDataset(o, options)
     );
     return newAry;
   } else if (isPrimitive(obj)) {
@@ -38,7 +47,11 @@ export default function cleanDenaturalizedDataset(obj: any): any {
         delete obj[key].Value;
       } else if (Array.isArray(obj[key].Value) && obj[key].vr) {
         if (obj[key].Value.length === 1 && obj[key].Value[0].BulkDataURI) {
-          obj[key].BulkDataURI = obj[key].Value[0].BulkDataURI;
+          obj[key].Value[0] = dicomWebUtils.fixBulkDataURI(
+            obj[key].Value[0],
+            options,
+            options.dataSourceConfig
+          );
 
           // prevent mixed-content blockage
           if (
@@ -54,7 +67,9 @@ export default function cleanDenaturalizedDataset(obj: any): any {
         } else if (vrNumerics.includes(obj[key].vr)) {
           obj[key].Value = obj[key].Value.map(v => +v);
         } else {
-          obj[key].Value = obj[key].Value.map(cleanDenaturalizedDataset);
+          obj[key].Value = obj[key].Value.map(entry =>
+            cleanDenaturalizedDataset(entry, options)
+          );
         }
       }
     });

extensions/dicom-microscopy/src/utils/dicomWebClient.ts

@@ -1,6 +1,12 @@
 import { api } from 'dicomweb-client';
 import { errorHandler, DicomMetadataStore } from '@ohif/core';
 
+const { DICOMwebClient } = api;
+
+DICOMwebClient._buildMultipartAcceptHeaderFieldValue = () => {
+  return '*/*';
+};
+
 /**
  * create a DICOMwebClient object to be used by Dicom Microscopy Viewer
  *

extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx

@@ -1,6 +1,6 @@
 import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
-import { HangingProtocolService, utils } from '@ohif/core';
+import { utils } from '@ohif/core';
 import {
   StudyBrowser,
   useImageViewer,

modes/tmtv/src/index.js

@@ -189,16 +189,26 @@ function modeFactory({ modeConfiguration }) {
       study: [],
       series: [],
     },
-    isValidMode: ({ modalities }) => {
+    isValidMode: ({ modalities, study }) => {
       const modalities_list = modalities.split('\\');
       const invalidModalities = ['SM'];
 
-      // there should be both CT and PT modalities and the modality should not be SM
+      const isValid =
-      return (
         modalities_list.includes('CT') &&
         modalities_list.includes('PT') &&
-        !invalidModalities.some(modality => modalities_list.includes(modality))
+        !invalidModalities.some(modality =>
-      );
+          modalities_list.includes(modality)
+        ) &&
+        // This is study is a 4D study with PT and CT and not a 3D study for the tmtv
+        // mode, until we have a better way to identify 4D studies we will use the
+        // StudyInstanceUID to identify the study
+        // Todo: when we add the 4D mode which comes with a mechanism to identify
+        // 4D studies we can use that
+        study.studyInstanceUid !==
+          '1.3.6.1.4.1.12842.1.1.14.3.20220915.105557.468.2963630849';
+
+      // there should be both CT and PT modalities and the modality should not be SM
+      return isValid;
     },
     routes: [
       {

platform/docs/docs/configuration/dataSources/dicom-web.md

@@ -179,6 +179,24 @@ See the [`singlepart`](#singlepart) data source configuration option.
 ### DICOM Video
 See the [`singlepart`](#singlepart) data source configuration option.
 
+### BulkDataURI
+
+The `bulkDataURI` configuration option allows the datasource to use the
+bulkdata end points for retrieving metadata if originally was not included in the
+response from the server. This is useful for the metadata information that
+are big and can/should be retrieved in a separate request. In case the bulkData URI
+is relative (instead of absolute) the `relativeResolution` option can be used to
+specify the resolution of the relative URI. The possible values are `studies`, `series` and `instances`.
+Certainly the knowledge of how the server is configured is required to use this option.
+
+```js
+bulkDataURI: {
+  enabled: true,
+  relativeResolution: 'series',
+},
+```
+
+
 ### Running DCM4CHEE
 
 dcm4che is a collection of open source applications for healthcare enterprise

platform/docs/docs/migration-guide.md

@@ -209,6 +209,13 @@ see [custom routes](./platform/services/ui/customization-service.md#customroutes
 </details>
 
 
+## DICOM Endpoints
+
+In OHIF v3 there is a new end point that your DICOM server should be able to respond to
+`WADO-RS GET studies/{studyInstanceUid}/series`
+
+This is used in the viewer for fetching the series list for a study to use for the hanging protocol.
+
 ## LifeCycle Hooks
 
 OHIF v2 had `preRegistration` hook for extensions for initialization. In OHIF v3 you have

platform/docs/docs/platform/services/ui/customization-service.md

@@ -490,7 +490,7 @@ are specific to the context used for where the menu is displayed.
 The default cornerstone context menu can be customized by setting the
 `cornerstoneContextMenu`.  For a full example, see `findingsContextMenu`.
 
-## Customizeable Cornerstone Viewport Click Behaviour
+## Customizable Cornerstone Viewport Click Behaviour
 
 The behaviour on clicking on the cornerstone viewport can be customized
 by setting the `cornerstoneViewportClickCommands`.  This is intended to

platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.tsx

@@ -19,7 +19,7 @@ function LoadingIndicatorProgress({ className, textBlock, progress }) {
     >
       <Icon name="loading-ohif-mark" className="text-white w-12 h-12" />
       <div className="w-48">
-        <ProgressLoadingBar></ProgressLoadingBar>
+        <ProgressLoadingBar progress={progress} />
       </div>
       {textBlock}
     </div>

platform/viewer/package.json

@@ -65,7 +65,6 @@
     "@ohif/ui": "^2.0.0",
     "@types/react": "^17.0.38",
     "classnames": "^2.3.2",
-    "config-point": "^0.4.8",
     "core-js": "^3.16.1",
     "cornerstone-math": "^0.1.9",
     "@cornerstonejs/dicom-image-loader": "^0.6.8",

platform/viewer/public/config/default.js

@@ -48,9 +48,9 @@ window.config = {
         // wadoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
 
         // new server
-        wadoUriRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb',
+        wadoUriRoot: 'https://d33do7qe4w26qo.cloudfront.net/dicomweb',
-        qidoRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb',
+        qidoRoot: 'https://d33do7qe4w26qo.cloudfront.net/dicomweb',
-        wadoRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb',
+        wadoRoot: 'https://d33do7qe4w26qo.cloudfront.net/dicomweb',
 
         qidoSupportsIncludeField: false,
         supportsReject: false,
@@ -60,8 +60,14 @@ window.config = {
         supportsFuzzyMatching: false,
         supportsWildcard: true,
         staticWado: true,
-        singlepart: 'bulkdata,video,pdf',
+        singlepart: 'bulkdata,video',
-        useBulkDataURI: false,
+        // whether the data source should use retrieveBulkData to grab metadata,
+        // and in case of relative path, what would it be relative to, options
+        // are in the series level or study level (some servers like series some study)
+        bulkDataURI: {
+          enabled: true,
+          relativeResolution: 'studies',
+        },
       },
     },
     {

platform/viewer/public/config/demo.js

@@ -22,7 +22,9 @@ window.config = {
         qidoSupportsIncludeField: true,
         imageRendering: 'wadors',
         enableStudyLazyLoad: true,
-        useBulkDataURI: false,
+        bulkDataURI: {
+          enabled: false,
+        },
       },
     },
   ],

platform/viewer/public/config/local_dcm4chee.js

@@ -33,6 +33,12 @@ window.config = {
         },
         dicomUploadEnabled: true,
         singlepart: 'pdf,video',
+        // whether the data source should use retrieveBulkData to grab metadata,
+        // and in case of relative path, what would it be relative to, options
+        // are in the series level or study level (some servers like series some study)
+        bulkDataURI: {
+          enabled: true,
+        },
       },
     },
     {

platform/viewer/public/config/local_orthanc.js

@@ -29,10 +29,12 @@ window.config = {
         imageRendering: 'wadors',
         thumbnailRendering: 'wadors',
         enableStudyLazyLoad: true,
-        useBulkDataURI: false,
         supportsFuzzyMatching: true,
         supportsWildcard: true,
         dicomUploadEnabled: true,
+        bulkDataURI: {
+          enabled: false,
+        },
       },
     },
     {

platform/viewer/src/routes/WorkList/WorkList.tsx

@@ -343,6 +343,7 @@ function WorkList({
 
             const isValidMode = mode.isValidMode({
               modalities: modalitiesToCheck,
+              study,
             });
             // TODO: Modes need a default/target route? We mostly support a single one for now.
             // We should also be using the route path, but currently are not

yarn.lock

@@ -1302,7 +1302,7 @@
     core-js-pure "^3.25.1"
     regenerator-runtime "^0.13.11"
 
-"@babel/runtime@7.17.9", "@babel/runtime@^7.0.0", "@babel/runtime@^7.1.2", "@babel/runtime@^7.10.3", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.13", "@babel/runtime@^7.12.5", "@babel/runtime@^7.14.6", "@babel/runtime@^7.17.8", "@babel/runtime@^7.18.6", "@babel/runtime@^7.20.13", "@babel/runtime@^7.20.6", "@babel/runtime@^7.20.7", "@babel/runtime@^7.21.0", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.2", "@babel/runtime@^7.7.4", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.4", "@babel/runtime@^7.9.2":
+"@babel/runtime@7.17.9", "@babel/runtime@^7.0.0", "@babel/runtime@^7.1.2", "@babel/runtime@^7.10.3", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.13", "@babel/runtime@^7.12.5", "@babel/runtime@^7.17.8", "@babel/runtime@^7.18.6", "@babel/runtime@^7.20.13", "@babel/runtime@^7.20.6", "@babel/runtime@^7.20.7", "@babel/runtime@^7.21.0", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.2", "@babel/runtime@^7.7.4", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.4", "@babel/runtime@^7.9.2":
   version "7.21.0"
   resolved "https://registry.npmjs.org/@babel/runtime/-/runtime-7.21.0.tgz#5b55c9d394e5fcf304909a8b00c07dc217b56673"
   integrity sha512-xwII0//EObnq89Ji5AKYQaRYiW/nZ3llSv29d49IuxPhKbtJoLP+9QUUZ4nVragQVtaVGeZrpB+ZtG/Pdy/POw==
@@ -7461,14 +7461,6 @@ config-chain@^1.1.11:
     ini "^1.3.4"
     proto-list "~1.2.1"
 
-config-point@^0.4.8:
-  version "0.4.9"
-  resolved "https://registry.npmjs.org/config-point/-/config-point-0.4.9.tgz#ec4594d04235438d5852e5ab33bde60aeffd18db"
-  integrity sha512-2QyqD2eb2iURURZNW6MAcNcT2e1Pr1VXwCaMgEQM0f/i+WaUCLZOdPjFtqF7oIT1rzPXNoMfl3KK2hbNcy5dXw==
-  dependencies:
-    "@babel/runtime" "^7.14.6"
-    json5 "^2.2.0"
-
 configstore@^5.0.1:
   version "5.0.1"
   resolved "https://registry.npmjs.org/configstore/-/configstore-5.0.1.tgz#d365021b5df4b98cdd187d6a3b0e3f6a7cc5ed96"