Support for multi bucket study loading and sheet integration in segmentation mode.

Author: Adithyan-Dinesh-Trenser

extensions/ohif-gradienthealth-extension/src/DicomJSONDataSource/index.js

@@ -179,15 +179,15 @@ const getBigQueryRows = async (studyuids, seriesuid, access_token) => {
 
 const filesFromStudyInstanceUID = async ({bucketName, prefix, studyuids, headers})=>{
   const studyMetadata = studyuids.map(async (studyuid) => {
-    const folderPath = `${prefix}/${studyuid}/`;
+    const folderPath = `${prefix}/studies/${studyuid}/series/`;
     const delimiter = '/'
     const apiUrl = `https://storage.googleapis.com/storage/v1/b/${bucketName}/o?prefix=${folderPath}&delimiter=${delimiter}`;
     const response = await fetch(apiUrl, { headers });
     const res = await response.json()
     const files = res.items || [];
     const folders = res.prefixes || [];
     const series = folders.map(async (folderPath)=>{
-      const objectName = `${folderPath}metadata.json.gz`;
+      const objectName = `${folderPath}metadata`;
       const apiUrl = `https://storage.googleapis.com/storage/v1/b/${bucketName}/o/${encodeURIComponent(objectName)}?alt=media`;
       const response = await fetch(apiUrl, { headers });
       return response.json()
@@ -241,7 +241,9 @@ const storeDicomSeg = async (naturalizedReport, headers) => {
   } = naturalizedReport;
 
   const params = new URLSearchParams(window.location.search);
-  const bucket = params.get('bucket') || 'gradient-health-search-viewer-links';
+  const buckets = params.getAll('bucket');
+  const bucket =
+    buckets[1] || buckets[0] || 'gradient-health-search-viewer-links';
   const prefix = params.get('bucket-prefix') || 'dicomweb';
   const segBucket = params.get('seg-bucket') || bucket
   const segPrefix = params.get('seg-prefix') || prefix
@@ -275,7 +277,7 @@ const storeDicomSeg = async (naturalizedReport, headers) => {
       const compressedFile = pako.gzip(JSON.stringify(segSeries));
 
       return fetch(
-        `https://storage.googleapis.com/upload/storage/v1/b/${segBucket}/o?uploadType=media&name=${segPrefix}/${StudyInstanceUID}/${SeriesInstanceUID}/metadata.json.gz&contentEncoding=gzip`,
+        `https://storage.googleapis.com/upload/storage/v1/b/${segBucket}/o?uploadType=media&name=${segPrefix}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/metadata&contentEncoding=gzip`,
         {
           method: 'POST',
           headers: {
@@ -320,6 +322,10 @@ function createDicomJSONApi(dicomJsonConfig, servicesManager) {
     },
     initialize: async ({ params, query, url }) => {
       if (!url) url = query.get('url');
+      if (!url) {
+        url = query.toString();
+        query.set('url', url);
+      }
       let metaData = getMetaDataByURL(url);
 
       // if we have already cached the data from this specific url
@@ -331,19 +337,29 @@ function createDicomJSONApi(dicomJsonConfig, servicesManager) {
         });
       }
 
+      const buckets = query.getAll('bucket');
+      if (buckets.length === 0)
+        buckets.push('gradient-health-search-viewer-links');
+
       const { UserAuthenticationService } = servicesManager.services;
-      const studyMetadata = await filesFromStudyInstanceUID({
-        bucketName: query.get('bucket') || 'gradient-health-search-viewer-links',
-        prefix: query.get('bucket-prefix') || 'dicomweb',
-        studyuids: query.getAll('StudyInstanceUID'),
-        headers: UserAuthenticationService.getAuthorizationHeader()
-      });
+
+      const studyMetadata = [];
+      for (let i = 0; i < buckets.length; i++) {
+        const metadataPerBucket = await filesFromStudyInstanceUID({
+          bucketName: buckets[i],
+          prefix: query.get('bucket-prefix') || 'dicomweb',
+          studyuids: query.getAll('StudyInstanceUIDs'),
+          headers: UserAuthenticationService.getAuthorizationHeader(),
+        });
+
+        studyMetadata.push(...metadataPerBucket);
+      }
 
       const data = getMetadataFromRows(
-        _.flatten(studyMetadata), 
-        query.get('prefix'), 
+        _.flatten(studyMetadata),
+        query.get('prefix'),
         query.getAll('SeriesInstanceUID')
-      );      
+      );
 
       let StudyInstanceUID;
       let SeriesInstanceUID;
@@ -422,8 +438,9 @@ function createDicomJSONApi(dicomJsonConfig, servicesManager) {
         console.debug('Not implemented', params)
       },
       series: {
-        metadata: ({
+        metadata: async ({
           StudyInstanceUID,
+          buckets,
           madeInClient = false,
           customSort,
         } = {}) => {
@@ -433,7 +450,20 @@ function createDicomJSONApi(dicomJsonConfig, servicesManager) {
             );
           }
 
-          const study = findStudies('StudyInstanceUID', StudyInstanceUID)[0];
+          let study = findStudies('StudyInstanceUID', StudyInstanceUID)[0];
+
+          if (!study && buckets) {
+            const params = new URLSearchParams(window.location.search);
+            params.set('StudyInstanceUIDs', StudyInstanceUID);
+            params.delete('bucket');
+            buckets.forEach((bucket) => {
+              params.append('bucket', bucket);
+            });
+            await implementation.initialize({ query: params });
+
+            study = findStudies('StudyInstanceUID', StudyInstanceUID)[0];
+          }
+
           let series;
 
           if (customSort) {

extensions/ohif-gradienthealth-extension/src/_shared/FormGeneratorComponent/fields/DisplayValue.tsx

@@ -8,7 +8,7 @@ export default function DisplayValue({formIndex, name, value, defaultValue, opti
         <Typography sx={{ fontSize: 14, marginRight: 1 }} color="text.secondary" gutterBottom>
           { name }:
         </Typography>
-        <Typography variant="body2">
+        <Typography variant="body2" className="overflow-auto invisible-scrollbar">
           { value !== null ? value.toString() : defaultValue !== null ? defaultValue.toString() : '' } 
         </Typography>
     </Paper>

extensions/ohif-gradienthealth-extension/src/_shared/FormGeneratorComponent/fields/Textarea.tsx

@@ -1,18 +1,21 @@
-import * as React from 'react';
-import { useMemo } from 'react';
+import React, { useState, useMemo, useEffect } from 'react';
 import Paper from '@mui/material/Paper';
 import TextField from '@mui/material/TextField';
 import debounce from 'lodash.debounce';
 
 export default function Textarea({formIndex, name, value, defaultValue, options, onChange}) {
-  const [val, setVal] = React.useState(value !== null ? value : (defaultValue !== null ? defaultValue : ''));  
+  const [val, setVal] = useState(value ?? defaultValue ?? '');
   const { rows } = options
   const debouncedOnChange = useMemo(
     () => debounce((formIndex, value) => {
-      onChange({formIndex, value})
-    }, 600), [onChange]
+        onChange({formIndex, value})
+      }, 600), [onChange]
   );
 
+  useEffect(() => {
+    setVal(value ?? defaultValue ?? '');
+  }, [value, defaultValue]);
+
   const handleChange = (event: React.ChangeEvent<HTMLInputElement>) => {
     setVal(event.target.value);
     debouncedOnChange(formIndex, event.target.value)

extensions/ohif-gradienthealth-extension/src/services/CacheAPIService/CacheAPIService.ts

@@ -119,12 +119,23 @@ export default class CacheAPIService {
     });
   }
 
-  public async cacheStudy(StudyInstanceUID) {
-    await this.dataSource.retrieve.series.metadata({ StudyInstanceUID });
+  public async cacheStudy(StudyInstanceUID, buckets = undefined) {
+    const { sopClassUids: segSOPClassUIDs } =
+      this.extensionManager.getModuleEntry(
+        '@ohif/extension-cornerstone-dicom-seg.sopClassHandlerModule.dicom-seg'
+      );
+    await this.dataSource.retrieve.series.metadata({
+      StudyInstanceUID,
+      buckets,
+    });
     const study = DicomMetadataStore.getStudy(StudyInstanceUID);
-    const imageIds = study.series.flatMap((serie) =>
-      serie.instances.flatMap((instance) => instance.imageId)
-    );
+    const imageIds = study.series
+      .filter(
+        (serie) => !segSOPClassUIDs.includes(serie.instances[0].SOPClassUID)
+      )
+      .flatMap((serie) =>
+        serie.instances.flatMap((instance) => instance.imageId)
+      );
     this.cacheImageIds(imageIds);
   }
 

extensions/ohif-gradienthealth-extension/src/services/GoogleSheetsService/GoogleSheetsService.js

@@ -57,7 +57,7 @@ export default class GoogleSheetsService {
       const url = row[urlIndex];
       const params = new URLSearchParams('?' + url.split('?')[1]);
       const StudyInstanceUID = params.get('StudyInstanceUIDs');
-      CacheAPIService.cacheStudy(StudyInstanceUID);
+      CacheAPIService.cacheStudy(StudyInstanceUID, params.getAll('bucket'));
     });
   }
 
@@ -254,12 +254,16 @@ export default class GoogleSheetsService {
       const url = rowValues[index];
       const params = new URLSearchParams('?' + url.split('?')[1]);
       const StudyInstanceUID = params.get('StudyInstanceUIDs');
+      const buckets = params.getAll('bucket');
       if (!StudyInstanceUID) {
         window.location.href = `https://docs.google.com/spreadsheets/d/${this.sheetId}`;
       }
       const dataSource = this.extensionManager.getActiveDataSource()[0];
-      await dataSource.retrieve.series.metadata({ StudyInstanceUID });
+      await dataSource.retrieve.series.metadata({ StudyInstanceUID, buckets });
       const studies = [DicomMetadataStore.getStudy(StudyInstanceUID)];
+      const activeProtocolId =
+        HangingProtocolService.getActiveProtocol().protocol.id;
+      HangingProtocolService.reset()
       HangingProtocolService.run(
         {
           studies,
@@ -270,11 +274,17 @@ export default class GoogleSheetsService {
             }
           ),
         },
-        'breast'
+        activeProtocolId
       );
 
       const nextParams = new URLSearchParams(window.location.search);
       nextParams.set('StudyInstanceUIDs', StudyInstanceUID);
+      if (buckets.length) {
+        nextParams.delete('bucket');
+        buckets.forEach((bucket) => {
+          nextParams.append('bucket', bucket);
+        });
+      }
       const nextURL =
         window.location.href.split('?')[0] + '?' + nextParams.toString();
       window.history.replaceState({}, null, nextURL);