feat(panel and auth): fix study panel to not rely on priors and add t…

…oken param to url (#3381)

* fix: multiframe

* fix the unnecessary use of prior since some servers dont like it

* add authentication via token in url

* add data citation

* add resources

* upgrade packages

* yarn lock

* apply review comments

DATACITATION.md

@@ -0,0 +1,144 @@
+# OHIF public demo data sets
+
+The OHIF Viewer's public demo page, available at https://viewer.ohif.org/, uses publicly anonymized demo datasets.
+These datasets were mostly obtained from the [NIH NCI Imaging Data Commons](https://datacommons.cancer.gov/repository/imaging-data-commons)
+and [NIH NCI TCIA](https://www.cancerimagingarchive.net/). Before listing the datasets,
+we would like to extend a special thank you to all groups who have made their datasets publicly available.
+Without them, we would not have been able to create this demo page.
+
+Please find below the list of datasets used on the demo page, along with their respective citations.
+
+
+## Platforms
+### NIH NCI IDC
+
+- Fedorov, A., Longabaugh, W.J., Pot, D., Clunie, D.A., Pieper, S., Aerts, H.J., Homeyer, A., Lewis, R., Akbarzadeh, A., Bontempi, D. and Clifford, W., 2021. NCI imaging data commons. Cancer research, 81(16), p.4188.
+
+### NIH NCI TCIA
+
+- Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. Journal of Digital Imaging, 26(6), 1045–1057. https://doi.org/10.1007/s10278-013-9622-7
+
+
+
+
+## Datasets
+Below you can find the StudyInstanceUID of the studies that are used in the demo page along with their citations.
+
+### 1.3.6.1.4.1.14519.5.2.1.267424821384663813780850856506829388886
+
+Segmentation of Vestibular Schwannoma from Magnetic Resonance Imaging: An Open Annotated Dataset and Baseline Algorithm (Vestibular-Schwannoma-SEG)
+
+- Shapey, J., Kujawa, A., Dorent, R., Wang, G., Bisdas, S., Dimitriadis, A., Grishchuck, D., Paddick, I., Kitchen, N., Bradford, R., Saeed, S., Ourselin, S., & Vercauteren, T. (2021). Segmentation of Vestibular Schwannoma from Magnetic Resonance Imaging: An Open Annotated Dataset and Baseline Algorithm [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.9YTJ-5Q73
+
+- Shapey, J., Kujawa, A., Dorent, R., Wang, G., Dimitriadis, A., Grishchuk, D., Paddick, I., Kitchen, N., Bradford, R., Saeed, S. R., Bisdas, S., Ourselin, S., & Vercauteren, T. (2021). Segmentation of vestibular schwannoma from MRI, an open annotated dataset and baseline algorithm. In Scientific Data (Vol. 8, Issue 1). Springer Science and Business Media LLC. https://doi.org/10.1038/s41597-021-01064-w
+
+
+### 1.3.6.1.4.1.14519.5.2.1.7009.2403.334240657131972136850343327463
+### 1.3.6.1.4.1.14519.5.2.1.7009.2403.871108593056125491804754960339
+
+
+ACRIN-NSCLC-FDG-PET (ACRIN 6668)
+
+- Kinahan, P., Muzi, M., Bialecki, B., Herman, B., & Coombs, L. (2019). Data from the ACRIN 6668 Trial NSCLC-FDG-PET (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/tcia.2019.30ilqfcl
+
+- Machtay, M., Duan, F., Siegel, B. A., Snyder, B. S., Gorelick, J. J., Reddin, J. S., Munden, R., Johnson, D. W., Wilf, L. H., DeNittis, A., Sherwin, N., Cho, K. H., Kim, S., Videtic, G., Neumann, D. R., Komaki, R., Macapinlac, H., Bradley, J. D., & Alavi, A. (2013). Prediction of Survival by [18F]Fluorodeoxyglucose Positron Emission Tomography in Patients With Locally Advanced Non–Small-Cell Lung Cancer Undergoing Definitive Chemoradiation Therapy: Results of the ACRIN 6668/RTOG 0235 Trial. In Journal of Clinical Oncology (Vol. 31, Issue 30, pp. 3823–3830). American Society of Clinical Oncology (ASCO). https://doi.org/10.1200/jco.2012.47.5947
+
+
+### 2.25.103659964951665749659160840573802789777
+
+The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM)
+
+- Scarpace, L., Mikkelsen, T., Cha, S., Rao, S., Tekchandani, S., Gutman, D., Saltz, J. H., Erickson, B. J., Pedano, N., Flanders, A. E., Barnholtz-Sloan, J., Ostrom, Q., Barboriak, D., & Pierce, L. J. (2016). The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM) (Version 4) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.RNYFUYE9
+
+
+### 1.3.6.1.4.1.14519.5.2.1.256467663913010332776401703474716742458
+
+Abdominal or pelvic enhanced CT images within 10 days before surgery of 230 patients with stage II colorectal cancer (StageII-Colorectal-CT)
+
+
+- Tong T., Li M. (2022) Abdominal or pelvic enhanced CT images within 10 days before surgery of 230 patients with stage II colorectal cancer (StageII-Colorectal-CT) [Dataset]. The Cancer Imaging Archive. DOI: https://doi.org/10.7937/p5k5-tg43
+
+- Li, M., Gong, J., Bao, Y., Huang, D., Peng, J., & Tong, T. (2022). Special issue “The advance of solid tumor research in China”: Prognosis prediction for stage II colorectal cancer by fusing computed tomography radiomics and deep‐learning features of primary lesions and peripheral lymph nodes. In International Journal of Cancer. Wiley. https://doi.org/10.1002/ijc.34053
+
+
+### 1.3.6.1.4.1.14519.5.2.1.3023.4024.215308722288168917637555384485
+
+The Cancer Genome Atlas Sarcoma Collection (TCGA-SARC)
+
+- Roche, C., Bonaccio, E., & Filippini, J. (2016). The Cancer Genome Atlas Sarcoma Collection (TCGA-SARC) (Version 3) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.CX6YLSUX
+
+
+
+### 1.3.6.1.4.1.14519.5.2.1.4792.2001.105216574054253895819671475627
+
+BREAST-DIAGNOSIS
+
+
+- Bloch, B. Nicolas, Jain, Ashali, & Jaffe, C. Carl. (2015). BREAST-DIAGNOSIS [Data set]. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2015.SDNRQXXR
+
+
+
+
+### 1.3.6.1.4.1.14519.5.2.1.1706.8374.643249677828306008300337414785
+
+Multimodality annotated HCC cases with and without advanced imaging segmentation (HCC-TACE-Seg)
+
+
+- Moawad, A. W., Fuentes, D., Morshid, A., Khalaf, A. M., Elmohr, M. M., Abusaif, A., Hazle, J. D., Kaseb, A. O., Hassan, M., Mahvash, A., Szklaruk, J., Qayyom, A., & Elsayes, K. (2021). Multimodality annotated HCC cases with and without advanced imaging segmentation [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.5FNA-0924
+
+- Morshid, A., Elsayes, K. M., Khalaf, A. M., Elmohr, M. M., Yu, J., Kaseb, A. O., Hassan, M., Mahvash, A., Wang, Z., Hazle, J. D., & Fuentes, D. (2019). A Machine Learning Model to Predict Hepatocellular Carcinoma Response to Transcatheter Arterial Chemoembolization. Radiology: Artificial Intelligence, 1(5), e180021. https://doi.org/10.1148/ryai.2019180021
+
+
+
+### 1.3.6.1.4.1.14519.5.2.1.1188.2803.137585363493444318569098508293
+
+Ultrasound data of a variety of liver masses (B-mode-and-CEUS-Liver)
+
+- Eisenbrey, J., Lyshchik, A., & Wessner, C. (2021). Ultrasound data of a variety of liver masses [Data set]. The Cancer Imaging Archive.  DOI: https://doi.org/10.7937/TCIA.2021.v4z7-tc39
+
+
+
+### 1.3.6.1.4.1.32722.99.99.62087908186665265759322018723889952421
+
+NSCLC-Radiomics
+
+- Aerts, H. J. W. L., Wee, L., Rios Velazquez, E., Leijenaar, R. T. H., Parmar, C., Grossmann, P., Carvalho, S., Bussink, J., Monshouwer, R., Haibe-Kains, B., Rietveld, D., Hoebers, F., Rietbergen, M. M., Leemans, C. R., Dekker, A., Quackenbush, J., Gillies, R. J., Lambin, P. (2019). Data From NSCLC-Radiomics (version 4) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2015.PF0M9REI
+
+
+- Aerts, H. J. W. L., Velazquez, E. R., Leijenaar, R. T. H., Parmar, C., Grossmann, P., Carvalho, S., Bussink, J., Monshouwer, R., Haibe-Kains, B., Rietveld, D., Hoebers, F., Rietbergen, M. M., Leemans, C. R., Dekker, A., Quackenbush, J., Gillies, R. J., Lambin, P. (2014, June 3). Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms5006  (link)
+
+
+### 1.3.6.1.4.1.14519.5.2.1.3671.4754.298665348758363466150039312520
+
+QIN-PROSTATE-Repeatability
+
+- Fedorov, A; Schwier, M; Clunie, D; Herz, C; Pieper, S; Kikinis, R; Tempany, C; Fennessy, F. (2018). Data From QIN-PROSTATE-Repeatability. The Cancer Imaging Archive. DOI: 10.7937/K9/TCIA.2018.MR1CKGND
+
+
+- Fedorov A, Vangel MG, Tempany CM, Fennessy FM. Multiparametric Magnetic Resonance Imaging of the Prostate: Repeatability of Volume and Apparent Diffusion Coefficient Quantification. Investigative Radiology. 52, 538–546 (2017). DOI: 10.1097/RLI.0000000000000382
+
+- Fedorov, A., Schwier, M., Clunie, D., Herz, C., Pieper, S., Kikinis,R., Tempany, C. & Fennessy, F. An annotated test-retest collection of prostate multiparametric MRI. Scientific Data 5, 180281 (2018). DOI:
+
+### 2.25.141277760791347900862109212450152067508
+
+The Clinical Proteomic Tumor Analysis Consortium Clear Cell Renal Cell Carcinoma Collection (CPTAC-CCRCC)
+
+- National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Clear Cell Renal Cell Carcinoma Collection (CPTAC-CCRCC) (Version 10) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.OBLAMN27
+
+- The CPTAC program requests that publications using data from this program include the following statement: “Data used in this publication were generated by the National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC).”
+
+
+### 2.25.275741864483510678566144889372061815320
+
+National Lung Screening Trial
+
+-  National Lung Screening Trial Research Team. (2013). Data from the National Lung Screening Trial (NLST) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.HMQ8-J677
+
+- National Lung Screening Trial Research Team*; Aberle DR, Adams AM, Berg CD, Black WC, Clapp JD, Fagerstrom RM, Gareen IF, Gatsonis C, Marcus PM, Sicks JD (2011). Reduced Lung-Cancer Mortality with Low-Dose Computed Tomographic Screening. New England Journal of Medicine, 365(5), 395–409. https://doi.org/10.1056/nejmoa1102873
+
+
+### 1.3.6.1.4.1.14519.5.2.1.99.1071.26968527900428638961173806140069
+
+Stony Brook University COVID-19 Positive Cases (COVID-19-NY-SBU)
+
+- Saltz, J., Saltz, M., Prasanna, P., Moffitt, R., Hajagos, J., Bremer, E., Balsamo, J., & Kurc, T. (2021). Stony Brook University COVID-19 Positive Cases [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.BBAG-2923

extensions/cornerstone-dicom-sr/package.json

@@ -46,7 +46,7 @@
     "@babel/runtime": "^7.20.13",
     "classnames": "^2.3.2",
     "@cornerstonejs/adapters": "^0.6.0",
-    "@cornerstonejs/core": "^0.44.2",
-    "@cornerstonejs/tools": "^0.66.2"
+    "@cornerstonejs/core": "^0.46.2",
+    "@cornerstonejs/tools": "^0.67.2"
   }
 }

extensions/cornerstone/package.json

@@ -34,7 +34,7 @@
   "peerDependencies": {
     "@ohif/core": "^3.0.0",
     "@ohif/ui": "^2.0.0",
-    "@cornerstonejs/dicom-image-loader": "^0.4.0",
+    "@cornerstonejs/dicom-image-loader": "^0.6.4",
     "@cornerstonejs/codec-charls": "^1.2.3",
     "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
     "@cornerstonejs/codec-openjpeg": "^1.2.2",
@@ -53,9 +53,9 @@
   "dependencies": {
     "@babel/runtime": "^7.20.13",
     "@cornerstonejs/adapters": "^0.6.0",
-    "@cornerstonejs/core": "^0.44.2",
-    "@cornerstonejs/streaming-image-volume-loader": "^0.19.2",
-    "@cornerstonejs/tools": "^0.66.2",
+    "@cornerstonejs/core": "^0.46.2",
+    "@cornerstonejs/streaming-image-volume-loader": "^0.20.2",
+    "@cornerstonejs/tools": "^0.67.2",
     "@kitware/vtk.js": "27.3.1",
     "html2canvas": "^1.4.1",
     "lodash.debounce": "4.0.8",

extensions/cornerstone/src/index.tsx

@@ -23,6 +23,7 @@ import * as CornerstoneExtensionTypes from './types';
 import { toolNames } from './initCornerstoneTools';
 import { getEnabledElement, reset as enabledElementReset } from './state';
 import dicomLoaderService from './utils/dicomLoaderService';
+import getActiveViewportEnabledElement from './utils/getActiveViewportEnabledElement';
 import { registerColormap } from './utils/colormap/transferFunctionHelpers';
 
 import { id } from './id';
@@ -141,5 +142,5 @@ const cornerstoneExtension: Types.Extensions.Extension = {
 };
 
 export type { PublicViewportOptions };
-export { measurementMappingUtils, CornerstoneExtensionTypes, toolNames };
+export { measurementMappingUtils, CornerstoneExtensionTypes, toolNames , getActiveViewportEnabledElement};
 export default cornerstoneExtension;

extensions/default/src/DicomLocalDataSource/index.js

@@ -200,6 +200,7 @@ function createDicomLocalApi(dicomLocalConfig) {
       displaySet.images.forEach(instance => {
         const NumberOfFrames = instance.NumberOfFrames;
         if (NumberOfFrames > 1) {
+          // in multiframe we start at frame 1
           for (let i = 1; i <= NumberOfFrames; i++) {
             const imageId = this.getImageIdsForInstance({
               instance,

extensions/default/src/Panels/PanelStudyBrowser.tsx

@@ -12,7 +12,7 @@ const { sortStudyInstances, formatDate } = utils;
 function PanelStudyBrowser({
   servicesManager,
   getImageSrc,
-  getStudiesForPatientByStudyInstanceUID,
+  getStudiesForPatientByMRN,
   requestDisplaySetCreationForStudy,
   dataSource,
 }) {
@@ -64,42 +64,52 @@ function PanelStudyBrowser({
   useEffect(() => {
     // Fetch all studies for the patient in each primary study
     async function fetchStudiesForPatient(StudyInstanceUID) {
-      const qidoStudiesForPatient =
-        (await getStudiesForPatientByStudyInstanceUID(StudyInstanceUID)) || [];
+      // current study qido
+      const qidoForStudyUID = await dataSource.query.studies.search({
+        studyInstanceUid: StudyInstanceUID,
+      });
 
-      // TODO: This should be "naturalized DICOM JSON" studies
-      const mappedStudies = _mapDataSourceStudies(qidoStudiesForPatient);
+      let qidoStudiesForPatient = qidoForStudyUID;
+
+      // try to fetch the prior studies based on the patientID if the
+      // server can respond.
+      try {
+        qidoStudiesForPatient = await getStudiesForPatientByMRN(
+          qidoForStudyUID
+        );
+      } catch (error) {
+        console.warn(error);
+      }
 
+      const mappedStudies = _mapDataSourceStudies(qidoStudiesForPatient);
       const actuallyMappedStudies = mappedStudies.map(qidoStudy => {
         return {
           studyInstanceUid: qidoStudy.StudyInstanceUID,
           date: formatDate(qidoStudy.StudyDate),
           description: qidoStudy.StudyDescription,
           modalities: qidoStudy.ModalitiesInStudy,
           numInstances: qidoStudy.NumInstances,
-          // displaySets: []
         };
       });
-      if (isMounted.current) {
-        setStudyDisplayList(prevArray => {
-          const ret = [...prevArray];
-          for (const study of actuallyMappedStudies) {
-            if (
-              !prevArray.find(
-                it => it.studyInstanceUid === study.studyInstanceUid
-              )
-            ) {
-              ret.push(study);
-            }
+
+      setStudyDisplayList(prevArray => {
+        const ret = [...prevArray];
+        for (const study of actuallyMappedStudies) {
+          if (
+            !prevArray.find(
+              it => it.studyInstanceUid === study.studyInstanceUid
+            )
+          ) {
+            ret.push(study);
           }
-          return ret;
-        });
-      }
+        }
+        return ret;
+      });
     }
 
     StudyInstanceUIDs.forEach(sid => fetchStudiesForPatient(sid));
     // eslint-disable-next-line react-hooks/exhaustive-deps
-  }, [StudyInstanceUIDs, getStudiesForPatientByStudyInstanceUID]);
+  }, [StudyInstanceUIDs, getStudiesForPatientByMRN]);
 
   // // ~~ Initial Thumbnails
   useEffect(() => {
@@ -254,7 +264,7 @@ PanelStudyBrowser.propTypes = {
     getImageIdsForDisplaySet: PropTypes.func.isRequired,
   }).isRequired,
   getImageSrc: PropTypes.func.isRequired,
-  getStudiesForPatientByStudyInstanceUID: PropTypes.func.isRequired,
+  getStudiesForPatientByMRN: PropTypes.func.isRequired,
   requestDisplaySetCreationForStudy: PropTypes.func.isRequired,
 };
 

extensions/default/src/Panels/WrappedPanelStudyBrowser.tsx

@@ -3,7 +3,7 @@ import PropTypes from 'prop-types';
 //
 import PanelStudyBrowser from './PanelStudyBrowser';
 import getImageSrcFromImageId from './getImageSrcFromImageId';
-import getStudiesForPatientByStudyInstanceUID from './getStudiesForPatientByStudyInstanceUID';
+import getStudiesForPatientByMRN from './getStudiesForPatientByMRN';
 import requestDisplaySetCreationForStudy from './requestDisplaySetCreationForStudy';
 
 /**
@@ -21,7 +21,7 @@ function WrappedPanelStudyBrowser({
   // TODO: This should be made available a different way; route should have
   // already determined our datasource
   const dataSource = extensionManager.getDataSources()[0];
-  const _getStudiesForPatientByStudyInstanceUID = getStudiesForPatientByStudyInstanceUID.bind(
+  const _getStudiesForPatientByMRN = getStudiesForPatientByMRN.bind(
     null,
     dataSource
   );
@@ -38,9 +38,7 @@ function WrappedPanelStudyBrowser({
       servicesManager={servicesManager}
       dataSource={dataSource}
       getImageSrc={_getImageSrcFromImageId}
-      getStudiesForPatientByStudyInstanceUID={
-        _getStudiesForPatientByStudyInstanceUID
-      }
+      getStudiesForPatientByMRN={_getStudiesForPatientByMRN}
       requestDisplaySetCreationForStudy={_requestDisplaySetCreationForStudy}
     />
   );

extensions/default/src/Panels/getImageSrcFromImageId.js

@@ -6,7 +6,7 @@ function getImageSrcFromImageId(cornerstone, imageId) {
   return new Promise((resolve, reject) => {
     const canvas = document.createElement('canvas');
     cornerstone.utilities
-      .loadImageToCanvas(canvas, imageId)
+      .loadImageToCanvas({ canvas, imageId })
       .then(imageId => {
         resolve(canvas.toDataURL());
       })

extensions/default/src/Panels/getStudiesForPatientByMRN.js

@@ -0,0 +1,11 @@
+async function getStudiesForPatientByMRN(dataSource, qidoForStudyUID) {
+  if (qidoForStudyUID && qidoForStudyUID.length && qidoForStudyUID[0].mrn) {
+    return dataSource.query.studies.search({
+      patientId: qidoForStudyUID[0].mrn,
+    });
+  }
+  console.log('No mrn found for', qidoForStudyUID);
+  return qidoForStudyUID;
+}
+
+export default getStudiesForPatientByMRN;

extensions/default/src/index.ts

@@ -7,7 +7,7 @@ import getSopClassHandlerModule from './getSopClassHandlerModule.js';
 import getToolbarModule from './getToolbarModule';
 import getCommandsModule from './commandsModule';
 import getHangingProtocolModule from './getHangingProtocolModule';
-import getStudiesForPatientByStudyInstanceUID from './Panels/getStudiesForPatientByStudyInstanceUID';
+import getStudiesForPatientByMRN from './Panels/getStudiesForPatientByMRN';
 import getCustomizationModule from './getCustomizationModule';
 import { id } from './id.js';
 import preRegistration from './init';
@@ -34,7 +34,7 @@ const defaultExtension: Types.Extensions.Extension = {
       {
         name: 'common',
         exports: {
-          getStudiesForPatientByStudyInstanceUID,
+          getStudiesForPatientByMRN,
         },
       },
     ];
@@ -45,4 +45,8 @@ const defaultExtension: Types.Extensions.Extension = {
 
 export default defaultExtension;
 
-export { ContextMenuController, CustomizeableContextMenuTypes };
+export {
+  ContextMenuController,
+  CustomizeableContextMenuTypes,
+  getStudiesForPatientByMRN,
+};