Gradienthealth/Segmentation with DicomJson

extensions/ohif-gradienthealth-extension/GRADIENT_README.md

@@ -0,0 +1,68 @@
+# @gradienthealth/ohif-gradienthealth-extension
+
+### Segmentation in DicomJson Series metadata Sample
+
+```json
+{
+  "Modality": "SEG",
+  "SeriesInstanceUID": "2.25.478875556728379505207796619011601982565",
+  "SeriesDescription": "Seg2",
+  "SeriesNumber": 99,
+  "SeriesDate": "20231109",
+  "StudyInstanceUID": "1.2.40.1.13.2.1464541835.1640.1480008284780.704.2.0",
+  "instances": [
+    {
+      "metadata": {
+        "FrameOfReferenceUID": "1.3.46.670589.11.18776.5.0.6996.2016112418000306013",
+        "SOPInstanceUID": "2.25.381554502573666068693329632131787392307",
+        "SOPClassUID": "1.2.840.10008.5.1.4.1.1.66.4",
+        "ReferencedSeriesSequence": {
+          "SeriesInstanceUID": "1.3.46.670589.11.18776.5.0.6088.2016112418015260387",
+          "ReferencedInstanceSequence": [
+            {
+              "ReferencedSOPClassUID": "1.2.840.10008.5.1.4.1.1.4",
+              "ReferencedSOPInstanceUID": "1.3.46.670589.11.18776.5.0.6088.2016112418034896398"
+            },
+            {
+              "ReferencedSOPClassUID": "1.2.840.10008.5.1.4.1.1.4",
+              "ReferencedSOPInstanceUID": "1.3.46.670589.11.18776.5.0.6088.2016112418052378421"
+            },
+            {
+              "ReferencedSOPClassUID": "1.2.840.10008.5.1.4.1.1.4",
+              "ReferencedSOPInstanceUID": "1.3.46.670589.11.18776.5.0.6088.2016112418034934404"
+            },
+            {
+              "ReferencedSOPClassUID": "1.2.840.10008.5.1.4.1.1.4",
+              "ReferencedSOPInstanceUID": "1.3.46.670589.11.18776.5.0.6088.2016112418052326410"
+            }
+          ]
+        },
+        "SharedFunctionalGroupsSequence": {
+          "PlaneOrientationSequence": {
+            "ImageOrientationPatient": [
+              0.06783646345138, 0.99748069047927, 0.02074741572141,
+              -0.0216917078942, 0.02226497046649, -0.9995167255401
+            ]
+          },
+          "PixelMeasuresSequence": {
+            "PixelSpacing": [0.265625, 0.265625],
+            "SliceThickness": 4.099999453351714
+          },
+          "MRImageFrameTypeSequence": {
+            "FrameType": ["ORIGINAL", "PRIMARY", "OTHER", "NONE"],
+            "PixelPresentation": "MONOCHROME",
+            "VolumetricProperties": "VOLUME",
+            "VolumeBasedCalculationTechnique": "NONE",
+            "ComplexImageComponent": "MAGNITUDE",
+            "AcquisitionContrast": "UNKNOWN"
+          }
+        }
+      },
+      "url": "dicomweb:https://storage.googleapis.com/gradient-health-dicomseg/dicomweb/studies/1.2.40.1.13.2.1464541835.1640.1480008284780.704.2.0/series/2.25.478875556728379505207796619011601982565/instances/2.25.381554502573666068693329632131787392307/Seg2.dcm"
+    }
+  ]
+}
+```
+
+Segmentation Series metadata is also retrieved along with other series metadata of the study
+and loaded as Dicom-Seg in the ThumbnailList.

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

@@ -1,3 +1,5 @@
+import dcmjs from 'dcmjs';
+import pako from 'pako'
 import {
   DicomMetadataStore,
   IWebApiDataSource,
@@ -10,6 +12,7 @@ import getImageId from '../DicomWebDataSource/utils/getImageId';
 import _ from 'lodash';
 
 const metadataProvider = classes.MetadataProvider;
+const { datasetToBlob } = dcmjs.data;
 
 const mappings = {
   studyInstanceUid: 'StudyInstanceUID',
@@ -206,6 +209,99 @@ const findStudies = (key, value) => {
   return studies;
 };
 
+const mapSegSeriesFromDataSet = (dataSet) => {
+  return {
+    Modality: dataSet.Modality,
+    SeriesInstanceUID: dataSet.SeriesInstanceUID,
+    SeriesDescription: dataSet.SeriesDescription,
+    SeriesNumber: Number(dataSet.SeriesNumber),
+    SeriesDate: dataSet.SeriesDate,
+    StudyInstanceUID: dataSet.StudyInstanceUID,
+    instances: [
+      {
+        metadata: {
+          FrameOfReferenceUID: dataSet.FrameOfReferenceUID,
+          SOPInstanceUID: dataSet.SOPInstanceUID,
+          SOPClassUID: dataSet.SOPClassUID,
+          ReferencedSeriesSequence: dataSet.ReferencedSeriesSequence,
+          SharedFunctionalGroupsSequence: dataSet.SharedFunctionalGroupsSequence,
+        },
+        url: dataSet.url,
+      }
+    ],
+  };
+};
+
+const storeDicomSeg = async (naturalizedReport, headers) => {
+  const {
+    StudyInstanceUID,
+    SeriesInstanceUID,
+    SOPInstanceUID,
+    SeriesDescription,
+  } = naturalizedReport;
+
+  const params = new URLSearchParams(window.location.search);
+  const bucket = params.get('bucket') || '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
+
+  const fileName = `${segPrefix}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/instances/${SOPInstanceUID}/${encodeURIComponent(
+    SeriesDescription
+  )}.dcm`;
+  const segUploadUri = `https://storage.googleapis.com/upload/storage/v1/b/${segBucket}/o?uploadType=media&name=${fileName}`;
+  const blob = datasetToBlob(naturalizedReport);
+
+  await fetch(segUploadUri, {
+    method: 'POST',
+    headers: {
+      ...headers,
+      'Content-Type': 'application/dicom',
+    },
+    body: blob,
+  })
+    .then((response) => response.json())
+    .then((data) => {
+      if (data.error) {
+        throw new Error(
+          `${data.error.code}: ${data.error.message}`
+        );
+      }
+
+      const segUri = `dicomweb:https://storage.googleapis.com/${segBucket}/${data.name}`;
+      // We are storing the imageId so that when naturalizedReport is made to displayset we can get url to DicomSeg file.
+      naturalizedReport.url = segUri
+      const segSeries = mapSegSeriesFromDataSet(naturalizedReport);
+      const compressedFile = pako.gzip(JSON.stringify(segSeries));
+
+      return fetch(
+        `https://storage.googleapis.com/upload/storage/v1/b/${segBucket}/o?uploadType=media&name=${segPrefix}/${StudyInstanceUID}/${SeriesInstanceUID}/metadata.json.gz&contentEncoding=gzip`,
+        {
+          method: 'POST',
+          headers: {
+            ...headers,
+            'Content-Type': 'application/json',
+          },
+          body: compressedFile,
+        }
+      )
+        .then((response) => response.json())
+        .then((data) => {
+          if (data.error) {
+            throw new Error(
+              `${data.error.code}: ${data.error.message}`
+            );
+          }
+        })
+        .catch((error) => {
+          throw new Error(error.message || 'Failed to store DicomSeg metadata')
+        })
+    })
+    .catch((error) => {
+      throw new Error(error.message || 'Failed to store DicomSeg file')
+    })
+};
+
 let _dicomJsonConfig = null;
 
 function createDicomJSONApi(dicomJsonConfig, servicesManager) {
@@ -394,8 +490,17 @@ function createDicomJSONApi(dicomJsonConfig, servicesManager) {
       },
     },
     store: {
-      dicom: () => {
-        console.debug(' DICOMJson store dicom');
+      dicom: async (dataset) => {
+        if (dataset.Modality === 'SEG') {
+          const headers = servicesManager.services.UserAuthenticationService.getAuthorizationHeader()
+          try {
+            await storeDicomSeg(dataset, headers)
+          } catch (error) {
+            throw error
+          }
+        } else {
+          console.debug(' DICOMJson store dicom');
+        }
       },
     },
     getImageIdsForDisplaySet(displaySet) {

extensions/ohif-gradienthealth-extension/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx

@@ -7,6 +7,7 @@ import {
   useViewportGrid,
   Dialog,
 } from '@ohif/ui';
+import { useNavigate } from 'react-router-dom';
 
 const { formatDate } = utils;
 
@@ -20,7 +21,7 @@ function PanelStudyBrowserTracking({
   UIDialogService,
   UINotificationService,
   getImageSrc,
-  getStudiesForPatientByStudyInstanceUID,
+  getStudiesForPatientByMRN,
   requestDisplaySetCreationForStudy,
   dataSource,
 }) {
@@ -32,6 +33,7 @@ function PanelStudyBrowserTracking({
     { activeViewportId, viewports, numCols, numRows },
     viewportGridService,
   ] = useViewportGrid();
+  const navigate=useNavigate()
 
   const [activeTabName, setActiveTabName] = useState('primary');
   const [expandedStudyInstanceUIDs, setExpandedStudyInstanceUIDs] = useState([
@@ -50,7 +52,7 @@ function PanelStudyBrowserTracking({
   };
 
   const activeViewportDisplaySetInstanceUIDs =
-    viewports[activeViewportId]?.displaySetInstanceUIDs;
+    viewports.get(activeViewportId)?.displaySetInstanceUIDs;
 
   const isSingleViewport = numCols === 1 && numRows === 1;
 
@@ -81,9 +83,26 @@ function PanelStudyBrowserTracking({
   useEffect(() => {
     // Fetch all studies for the patient in each primary study
     async function fetchStudiesForPatient(StudyInstanceUID) {
-      const qidoStudiesForPatient =
-        (await getStudiesForPatientByStudyInstanceUID(StudyInstanceUID)) || [];
-      // TODO: This should be "naturalized DICOM JSON" studies
+      // current study qido
+      const qidoForStudyUID = await dataSource.query.studies.search({
+        studyInstanceUid: StudyInstanceUID,
+      });
+
+      if (!qidoForStudyUID?.length) {
+        navigate('/notfoundstudy', '_self');
+        throw new Error('Invalid study URL');
+      }
+
+      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 {
@@ -92,16 +111,22 @@ function PanelStudyBrowserTracking({
           description: qidoStudy.StudyDescription,
           modalities: qidoStudy.ModalitiesInStudy,
           numInstances: qidoStudy.NumInstances,
-          // displaySets: []
         };
       });
 
-      setStudyDisplayList(actuallyMappedStudies);
+      setStudyDisplayList(prevArray => {
+        const ret = [...prevArray];
+        for (const study of actuallyMappedStudies) {
+          if (!prevArray.find(it => it.studyInstanceUid === study.studyInstanceUid)) {
+            ret.push(study);
+          }
+        }
+        return ret;
+      });
     }
 
     StudyInstanceUIDs.forEach(sid => fetchStudiesForPatient(sid));
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-  }, [StudyInstanceUIDs, getStudiesForPatientByStudyInstanceUID]);
+  }, [StudyInstanceUIDs, dataSource, getStudiesForPatientByMRN, navigate]);
 
   // ~~ Initial Thumbnails
   useEffect(() => {
@@ -328,7 +353,7 @@ PanelStudyBrowserTracking.propTypes = {
     getImageIdsForDisplaySet: PropTypes.func.isRequired,
   }).isRequired,
   getImageSrc: PropTypes.func.isRequired,
-  getStudiesForPatientByStudyInstanceUID: PropTypes.func.isRequired,
+  getStudiesForPatientByMRN: PropTypes.func.isRequired,
   requestDisplaySetCreationForStudy: PropTypes.func.isRequired,
 };
 
@@ -373,7 +398,7 @@ function _mapDisplaySets(
     const componentType = _getComponentType(ds.Modality);
     const viewportIdentificator = isSingleViewport
       ? []
-      : viewports.reduce((acc, viewportData, index) => {
+      : Object.values(viewports).reduce((acc, viewportData, index) => {
           if (
             viewportData?.displaySetInstanceUIDs?.includes(
               ds.displaySetInstanceUID

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

@@ -10,8 +10,8 @@ function _getStudyForPatientUtility(extensionManager) {
     '@ohif/extension-default.utilityModule.common'
   );
 
-  const { getStudiesForPatientByStudyInstanceUID } = utilityModule.exports;
-  return getStudiesForPatientByStudyInstanceUID;
+  const { getStudiesForPatientByMRN } = utilityModule.exports;
+  return getStudiesForPatientByMRN;
 }
 
 /**
@@ -28,10 +28,10 @@ function WrappedPanelStudyBrowserTracking({
 }) {
   const dataSource = extensionManager.getActiveDataSource()[0];
 
-  const getStudiesForPatientByStudyInstanceUID = _getStudyForPatientUtility(
+  const getStudiesForPatientByMRN = _getStudyForPatientUtility(
     extensionManager
   );
-  const _getStudiesForPatientByStudyInstanceUID = getStudiesForPatientByStudyInstanceUID.bind(
+  const _getStudiesForPatientByMRN = getStudiesForPatientByMRN.bind(
     null,
     dataSource
   );
@@ -51,8 +51,8 @@ function WrappedPanelStudyBrowserTracking({
       UINotificationService={servicesManager.services.UINotificationService}
       dataSource={dataSource}
       getImageSrc={_getImageSrcFromImageId}
-      getStudiesForPatientByStudyInstanceUID={
-        _getStudiesForPatientByStudyInstanceUID
+      getStudiesForPatientByMRN={
+        _getStudiesForPatientByMRN
       }
       requestDisplaySetCreationForStudy={_requestDisplaySetCreationForStudy}
     />