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

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

@@ -53,6 +53,12 @@ const getInstanceUrl = (url, prefix) => {
   return modifiedUrl;
 }
 
+const getProperty = (serieMetadata, property) => {
+  return (
+    serieMetadata[property] || serieMetadata.instances[0].metadata[property]
+  );
+};
+
 const getMetadataFromRows = (rows, prefix, seriesuidArray) => {
   // TODO: bq should not have dups
   let filteredRows = rows.map(row => {
@@ -87,6 +93,7 @@ const getMetadataFromRows = (rows, prefix, seriesuidArray) => {
         SeriesDescription: row['SeriesDescription'] || 'No description',
         StudyInstanceUID: row['StudyInstanceUID'],
         SeriesNumber: row['SeriesNumber'],
+        SeriesDate: row['SeriesDate'],
         SeriesTime: row['SeriesTime'],
         NumInstances: isNaN(parseInt(row['NumInstances']))
           ? 0
@@ -101,16 +108,17 @@ const getMetadataFromRows = (rows, prefix, seriesuidArray) => {
     });
 
     return {
-      StudyInstanceUID: rows[0]['StudyInstanceUID'],
-      PatientName: rows[0]['PatientName'],
-      PatientSex: rows[0]['PatientSex'],
-      AccessionNumber: rows[0]['AccessionNumber'],
-      StudyDate: rows[0]['StudyDate'],
-      PatientID: rows[0]['PatientID'],
-      PatientWeight: rows[0]['PatientWeight'],
-      PatientAge: rows[0]['PatientAge'],
-      StudyDescription: rows[0]['StudyDescription'] || 'No description',
-      StudyTime: rows[0]['StudyTime'],
+      StudyInstanceUID: getProperty(rows[0], 'StudyInstanceUID'),
+      PatientName: getProperty(rows[0], 'PatientName'),
+      PatientSex: getProperty(rows[0], 'PatientSex') || '',
+      AccessionNumber: getProperty(rows[0], 'AccessionNumber'),
+      StudyDate: getProperty(rows[0], 'StudyDate'),
+      PatientID: getProperty(rows[0], 'PatientID'),
+      PatientWeight: getProperty(rows[0], 'PatientWeight') || '',
+      PatientAge: getProperty(rows[0], 'PatientAge') || '',
+      StudyDescription:
+        getProperty(rows[0], 'StudyDescription') || 'No description',
+      StudyTime: getProperty(rows[0], 'StudyTime'),
       NumInstances: studyNumInstances,
       Modalities: `["${rows[0]['Modality']}"]`,
       series: series,
@@ -179,15 +187,15 @@ 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()
@@ -216,23 +224,37 @@ const mapSegSeriesFromDataSet = (dataSet) => {
     SeriesDescription: dataSet.SeriesDescription,
     SeriesNumber: Number(dataSet.SeriesNumber),
     SeriesDate: dataSet.SeriesDate,
+    SeriesTime: dataSet.SeriesTime,
+    StudyDate: dataSet.StudyDate,
+    StudyTime: dataSet.StudyTime,
+    PatientName: dataSet.PatientName,
+    PatientID: dataSet.PatientID,
+    PatientWeight: dataSet.PatientWeight,
+    PatientAge: Number(dataSet.PatientAge),
+    AccessionNumber: Number(dataSet.AccessionNumber),
     StudyInstanceUID: dataSet.StudyInstanceUID,
+    StudyDescription: dataSet.StudyDescription,
     instances: [
       {
         metadata: {
           FrameOfReferenceUID: dataSet.FrameOfReferenceUID,
           SOPInstanceUID: dataSet.SOPInstanceUID,
           SOPClassUID: dataSet.SOPClassUID,
           ReferencedSeriesSequence: dataSet.ReferencedSeriesSequence,
-          SharedFunctionalGroupsSequence: dataSet.SharedFunctionalGroupsSequence,
+          SharedFunctionalGroupsSequence:
+            dataSet.SharedFunctionalGroupsSequence,
+          PerFrameFunctionalGroupsSequence:
+            dataSet.PerFrameFunctionalGroupsSequence,
+          SegmentSequence: dataSet.SegmentSequence,
+          Manufacturer: dataSet.Manufacturer,
         },
         url: dataSet.url,
-      }
+      },
     ],
   };
 };
 
-const storeDicomSeg = async (naturalizedReport, headers) => {
+const storeDicomSeg = async (naturalizedReport, headers, displaySetService) => {
   const {
     StudyInstanceUID,
     SeriesInstanceUID,
@@ -241,24 +263,40 @@ 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
+  let segBucket = params.get('seg-bucket') || bucket
   const segPrefix = params.get('seg-prefix') || prefix
+  const filteredDescription = SeriesDescription.replace(/[/]/g, '');
 
-  const fileName = `${segPrefix}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/instances/${SOPInstanceUID}/${encodeURIComponent(
-    SeriesDescription
+  let fileName = `${segPrefix}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/instances/${SOPInstanceUID}/${encodeURIComponent(
+    filteredDescription
   )}.dcm`;
-  const segUploadUri = `https://storage.googleapis.com/upload/storage/v1/b/${segBucket}/o?uploadType=media&name=${fileName}`;
+
+  const segDisplaySet = displaySetService.getDisplaySetsBy(
+    (ds) =>
+      ds.SeriesInstanceUID === SeriesInstanceUID &&
+      ds.instance.SOPInstanceUID === SOPInstanceUID
+  )[0];
+  if (segDisplaySet) {
+    const url = segDisplaySet.instance.url;
+    segBucket = url.split('https://storage.googleapis.com/')[1].split('/')[0];
+    fileName = url.split(`https://storage.googleapis.com/${segBucket}/`)[1];
+  }
+
+  const segUploadUri = `https://storage.googleapis.com/upload/storage/v1/b/${segBucket}/o?uploadType=media&name=${fileName}&contentEncoding=gzip`;
   const blob = datasetToBlob(naturalizedReport);
+  const compressedFile = pako.gzip(await blob.arrayBuffer());
 
   await fetch(segUploadUri, {
     method: 'POST',
     headers: {
       ...headers,
       'Content-Type': 'application/dicom',
     },
-    body: blob,
+    body: compressedFile,
   })
     .then((response) => response.json())
     .then((data) => {
@@ -275,7 +313,7 @@ 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 +358,10 @@ 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 +373,29 @@ 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('StudyInstanceUID'),
+          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 +474,9 @@ function createDicomJSONApi(dicomJsonConfig, servicesManager) {
         console.debug('Not implemented', params)
       },
       series: {
-        metadata: ({
+        metadata: async ({
           StudyInstanceUID,
+          buckets = [],
           madeInClient = false,
           customSort,
         } = {}) => {
@@ -433,7 +486,22 @@ function createDicomJSONApi(dicomJsonConfig, servicesManager) {
             );
           }
 
-          const study = findStudies('StudyInstanceUID', StudyInstanceUID)[0];
+          let study = findStudies('StudyInstanceUID', StudyInstanceUID)[0];
+
+          if (!study) {
+            // If the study is not found, initialize the study.
+            // If there is no buckets in the url default bucket will be used.
+            const params = new URLSearchParams(window.location.search);
+            params.set('StudyInstanceUID', 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) {
@@ -494,7 +562,11 @@ function createDicomJSONApi(dicomJsonConfig, servicesManager) {
         if (dataset.Modality === 'SEG') {
           const headers = servicesManager.services.UserAuthenticationService.getAuthorizationHeader()
           try {
-            await storeDicomSeg(dataset, headers)
+            await storeDicomSeg(
+              dataset,
+              headers,
+              servicesManager.services.displaySetService
+            );
           } catch (error) {
             throw error
           }

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/getPanelModule.tsx

@@ -2,7 +2,8 @@ import {
   PanelMeasurementTableTracking,
   PanelStudyBrowserTracking,
   PanelForm,
-  PanelFormAndMeasurementTable
+  PanelFormAndMeasurementTable,
+  PanelStudyBrowser,
 } from './panels';
 
 // TODO:
@@ -59,6 +60,17 @@ function getPanelModule({
         servicesManager,
       }),
     },
+    {
+      name: 'seriesList-without-tracking',
+      iconName: 'group-layers',
+      iconLabel: 'Studies',
+      label: 'Studies',
+      component: PanelStudyBrowser.bind(null, {
+        commandsManager,
+        extensionManager,
+        servicesManager,
+      }),
+    },
   ];
 }
 

extensions/ohif-gradienthealth-extension/src/index.tsx

@@ -7,6 +7,7 @@ import { id } from './id.js';
 import GoogleSheetsService from './services/GoogleSheetsService';
 import CropDisplayAreaService from './services/CropDisplayAreaService';
 import CacheAPIService from './services/CacheAPIService';
+import addSegmentationLabelModifier from './utils/addSegmentationLabelModifier';
 
 // import { CornerstoneEventTarget } from '@cornerstonejs/core/CornerstoneEventTarget';
 // import { Events } from '@cornerstonejs/core/Events';
@@ -16,6 +17,9 @@ const gradientHealthExtension = {
    * Only required property. Should be a unique value across all extensions.
    */
   id,
+  onModeEnter({ servicesManager}){
+    addSegmentationLabelModifier(servicesManager)
+  },
   getDataSourcesModule: ({ servicesManager }) => {
     return getDataSourcesModule({ servicesManager });
   },

extensions/ohif-gradienthealth-extension/src/panels/PanelForm/index.tsx

@@ -53,7 +53,7 @@ function PanelForm({ servicesManager, extensionManager }) {
   useEffect(() => {
     if(!firstLoad){
       setLoading(true)
-      GoogleSheetsService.writeFormToRow(formValue).then((values)=>{
+      GoogleSheetsService.updateRow(formValue).then((values)=>{
         setLoading(false)
       })
     }