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/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
-        //    is a string, not a string array.
-        const imageType =
-          typeof image.ImageType === 'string'
-            ? image.ImageType.split('\\')
-            : image.ImageType;
-        const imageFlavor = imageType[2];
+        const imageFlavor = image.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,
-  topRight,
-  bottomLeft,
-  bottomRight,
-  itemGenerator,
+  topLeft = [],
+  topRight = [],
+  bottomLeft = [],
+  bottomRight = [],
+  itemGenerator = () => {},
 }: {
-  topLeft: OverylayItem[];
-  topRight: OverylayItem[];
-  bottomLeft: OverylayItem[];
-  bottomRight: OverylayItem[];
-  itemGenerator: (props: any) => any;
+  topLeft?: OverlayItem[];
+  topRight?: OverlayItem[];
+  bottomLeft?: OverlayItem[];
+  bottomRight?: OverlayItem[];
+  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({
-  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
-);
+export default generateFromConfig({});

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
  *