feat(multiframe): enhanced support for multiframe dicom (#3164)

* Changes in cswil version and multiframe

* Minor changes

* wip

* Adding support for NM multiframe images

* Applying PR suggestions

* fixing package versions

* Restoring default.js config file

* Check if NM subtype is reconstructable

* Restore default.js values

* refactore code

* feat: add flag for strict zspacing

---------

Co-authored-by: Alireza <ar.sedghi@gmail.com>

platform/core/package.json

@@ -31,7 +31,7 @@
   },
   "peerDependencies": {
     "cornerstone-math": "0.1.9",
-    "cornerstone-wado-image-loader": "^4.10.2",
+    "cornerstone-wado-image-loader": "^4.13.0",
     "dicom-parser": "^1.8.9",
     "@ohif/ui": "^2.0.0"
   },

platform/core/src/classes/MetadataProvider.js

@@ -412,6 +412,34 @@ class MetadataProvider {
     return metadata;
   }
 
+  /**
+   * Retrieves the frameNumber information, depending on the url style
+   * wadors /frames/1
+   * wadouri &frame=1
+   * @param {*} imageId
+   * @returns
+   */
+  getFrameInformationFromURL(imageId) {
+    function getInformationFromURL(informationString, separator) {
+      let result = '';
+      const splittedStr = imageId.split(informationString)[1];
+      if (splittedStr.includes(separator)) {
+        result = splittedStr.split(separator)[0];
+      } else {
+        result = splittedStr;
+      }
+      return result;
+    }
+
+    if (imageId.includes('/frames')) {
+      return getInformationFromURL('/frames', '/');
+    }
+    if (imageId.includes('&frame=')) {
+      return getInformationFromURL('&frame=', '&');
+    }
+    return;
+  }
+
   getUIDsFromImageID(imageId) {
     // TODO: adding csiv here is not really correct. Probably need to use
     // metadataProvider.addImageIdToUIDs(imageId, {
@@ -445,7 +473,7 @@ class MetadataProvider {
     // check if the imageId starts with http:// or https:// using regex
     // Todo: handle non http imageIds
     let imageURI;
-    const urlRegex = /^(http|https):\/\//;
+    const urlRegex = /^(http|https|dicomfile):\/\//;
     if (urlRegex.test(imageId)) {
       imageURI = imageId;
     } else {
@@ -453,7 +481,7 @@ class MetadataProvider {
     }
 
     const uids = this.imageURIToUIDs.get(imageURI);
-    const frameNumber = imageId.split(/\/frames\//)[1];
+    let frameNumber = this.getFrameInformationFromURL(imageId) || '1';
 
     if (uids && frameNumber !== undefined) {
       return { ...uids, frameNumber };

platform/core/src/services/DicomMetadataStore/DicomMetadataStore.ts

@@ -84,9 +84,9 @@ function _getInstance(StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID) {
 }
 
 function _getInstanceByImageId(imageId) {
-  for (let study of _model.studies) {
-    for (let series of study.series) {
-      for (let instance of series.instances) {
+  for (const study of _model.studies) {
+    for (const series of study.series) {
+      for (const instance of series.instances) {
         if (instance.imageId === imageId) {
           return instance;
         }
@@ -236,7 +236,7 @@ const BaseImplementation = {
   addStudy(study) {
     const { StudyInstanceUID } = study;
 
-    let existingStudy = _model.studies.find(
+    const existingStudy = _model.studies.find(
       study => study.StudyInstanceUID === StudyInstanceUID
     );
 

platform/core/src/utils/combineFrameInstance.ts

@@ -30,12 +30,35 @@ const combineFrameInstance = (frame, instance) => {
       .map(it => it[0])
       .filter(it => it !== undefined && typeof it === 'object');
 
-    return Object.assign(
-      { frameNumber: frameNumber },
-      instance,
-      ...Object.values(shared),
-      ...Object.values(perFrame)
-    );
+    // this is to fix NM multiframe datasets with position and orientation
+    // information inside DetectorInformationSequence
+    if (
+      !instance.ImageOrientationPatient &&
+      instance.DetectorInformationSequence
+    ) {
+      instance.ImageOrientationPatient =
+        instance.DetectorInformationSequence[0].ImageOrientationPatient;
+    }
+    if (
+      !instance.ImagePositionPatient &&
+      instance.DetectorInformationSequence
+    ) {
+      instance.ImagePositionPatient =
+        instance.DetectorInformationSequence[0].ImagePositionPatient;
+    }
+
+    const newInstance = Object.assign(instance, { frameNumber: frameNumber });
+
+    // merge the shared first then the per frame to override
+    [...shared, ...perFrame].forEach(item => {
+      Object.entries(item).forEach(([key, value]) => {
+        newInstance[key] = value;
+      });
+    });
+
+    // Todo: we should cache this combined instance somewhere, maybe add it
+    // back to the dicomMetaStore so we don't have to do this again.
+    return newInstance;
   } else {
     return instance;
   }

platform/core/src/utils/isDisplaySetReconstructable.js

@@ -30,62 +30,98 @@ export default function isDisplaySetReconstructable(instances) {
   }
 
   // Can't reconstruct if all instances don't have the ImagePositionPatient.
-  if (!instances.every(instance => !!instance.ImagePositionPatient)) {
+  if (
+    !isMultiframe &&
+    !instances.every(instance => instance.ImagePositionPatient)
+  ) {
     return { value: false };
   }
 
   const sortedInstances = sortInstancesByPosition(instances);
 
-  if (isMultiframe) {
-    return processMultiframe(sortedInstances[0]);
-  } else {
-    return processSingleframe(sortedInstances);
-  }
+  return isMultiframe
+    ? processMultiframe(sortedInstances[0])
+    : processSingleframe(sortedInstances);
+}
+
+function hasPixelMeasurements(multiFrameInstance) {
+  const perFrameSequence =
+    multiFrameInstance.PerFrameFunctionalGroupsSequence?.[0];
+  const sharedSequence = multiFrameInstance.SharedFunctionalGroupsSequence;
+
+  return (
+    Boolean(perFrameSequence?.PixelMeasuresSequence) ||
+    Boolean(sharedSequence?.PixelMeasuresSequence) ||
+    Boolean(
+      multiFrameInstance.PixelSpacing &&
+        (multiFrameInstance.SliceThickness ||
+          multiFrameInstance.SpacingBetweenFrames)
+    )
+  );
+}
+
+function hasOrientation(multiFrameInstance) {
+  const sharedSequence = multiFrameInstance.SharedFunctionalGroupsSequence;
+  const perFrameSequence =
+    multiFrameInstance.PerFrameFunctionalGroupsSequence?.[0];
+
+  return (
+    Boolean(sharedSequence?.PlaneOrientationSequence) ||
+    Boolean(perFrameSequence?.PlaneOrientationSequence) ||
+    Boolean(
+      multiFrameInstance.ImageOrientationPatient ||
+        multiFrameInstance.DetectorInformationSequence?.[0]
+          ?.ImageOrientationPatient
+    )
+  );
+}
+
+function hasPosition(multiFrameInstance) {
+  const perFrameSequence =
+    multiFrameInstance.PerFrameFunctionalGroupsSequence?.[0];
+
+  return (
+    Boolean(perFrameSequence?.PlanePositionSequence) ||
+    Boolean(perFrameSequence?.CTPositionSequence) ||
+    Boolean(
+      multiFrameInstance.ImagePositionPatient ||
+        multiFrameInstance.DetectorInformationSequence?.[0]
+          ?.ImagePositionPatient
+    )
+  );
+}
+
+function isNMReconstructable(multiFrameInstance) {
+  const imageSubType = multiFrameInstance.ImageType?.[2];
+  return imageSubType === 'RECON TOMO' || imageSubType === 'RECON GATED TOMO';
 }
 
 function processMultiframe(multiFrameInstance) {
-  const {
-    PerFrameFunctionalGroupsSequence,
-    SharedFunctionalGroupsSequence,
-  } = multiFrameInstance;
-
   // If we don't have the PixelMeasuresSequence, then the pixel spacing and
   // slice thickness isn't specified or is changing and we can't reconstruct
   // the dataset.
+  if (!hasPixelMeasurements(multiFrameInstance)) {
+    return { value: false };
+  }
+
+  if (!hasOrientation(multiFrameInstance)) {
+    console.log('No image orientation information, not reconstructable');
+    return { value: false };
+  }
+
+  if (!hasPosition(multiFrameInstance)) {
+    console.log('No image position information, not reconstructable');
+    return { value: false };
+  }
+
   if (
-    !SharedFunctionalGroupsSequence ||
-    !SharedFunctionalGroupsSequence[0].PixelMeasuresSequence
+    multiFrameInstance.Modality.includes('NM') &&
+    !isNMReconstructable(multiFrameInstance)
   ) {
     return { value: false };
   }
 
-  // Check that the orientation is either shared or with the allowed
-  // difference amount
-  const {
-    PlaneOrientationSequence: sharedOrientation,
-  } = SharedFunctionalGroupsSequence;
-
-  if (!sharedOrientation) {
-    const {
-      PlaneOrientationSequence: firstOrientation,
-    } = PerFrameFunctionalGroupsSequence[0];
-
-    if (!firstOrientation) {
-      console.log('No orientation information');
-      return { value: false };
-    }
-    // TODO - check orientation consistency
-  }
-
-  const frame0 = PerFrameFunctionalGroupsSequence[0];
-  const firstPosition =
-    frame0.PlanePositionSequence || frame0.CTPositionSequence;
-  if (!firstPosition) {
-    console.log('No image position information, not reconstructable');
-    return { value: false };
-  }
   // TODO - check spacing consistency
-
   return { value: true };
 }
 

platform/viewer/package.json

@@ -65,7 +65,7 @@
     "config-point": "^0.4.8",
     "core-js": "^3.16.1",
     "cornerstone-math": "^0.1.9",
-    "cornerstone-wado-image-loader": "^4.10.2",
+    "cornerstone-wado-image-loader": "^4.13.0",
     "dcmjs": "^0.29.4",
     "detect-gpu": "^4.0.16",
     "dicom-parser": "^1.8.9",

platform/viewer/public/config/aws.js

@@ -9,6 +9,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   // filterQueryParam: false,
   dataSources: [
     {

platform/viewer/public/config/default.js

@@ -15,6 +15,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   maxNumRequests: {
     interaction: 100,
     thumbnail: 75,
@@ -34,10 +35,12 @@ window.config = {
         // wadoUriRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/wado',
         // qidoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
         // wadoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
+
         // new server
         wadoUriRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb',
         qidoRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb',
         wadoRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb',
+
         qidoSupportsIncludeField: false,
         supportsReject: false,
         imageRendering: 'wadors',

platform/viewer/public/config/demo.js

@@ -5,6 +5,7 @@ window.config = {
   // below flag is for performance reasons, but it might not work for all servers
   omitQuotationForMultipartRequest: true,
   showWarningMessageForCrossOrigin: true,
+  strictZSpacingForVolumeViewport: true,
   showCPUFallbackMessage: true,
   servers: {
     dicomWeb: [

platform/viewer/public/config/dicomweb-server.js

@@ -9,6 +9,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   // filterQueryParam: false,
   dataSources: [
     {
@@ -29,6 +30,20 @@ window.config = {
         supportsWildcard: false,
       },
     },
+    {
+      friendlyName: 'dicom json',
+      namespace: '@ohif/extension-default.dataSourcesModule.dicomjson',
+      sourceName: 'dicomjson',
+      configuration: {
+        name: 'json',
+      },
+    },
+    {
+      friendlyName: 'dicom local',
+      namespace: '@ohif/extension-default.dataSourcesModule.dicomlocal',
+      sourceName: 'dicomlocal',
+      configuration: {},
+    },
   ],
   defaultDataSourceName: 'dicomweb',
 };

platform/viewer/public/config/dicomweb_relative.js

@@ -10,6 +10,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   // filterQueryParam: false,
   dataSources: [
     {

platform/viewer/public/config/docker_nginx-orthanc.js

@@ -8,6 +8,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   dataSources: [
     {
       friendlyName: 'Orthanc Server',
@@ -23,6 +24,20 @@ window.config = {
         thumbnailRendering: 'wadors',
       },
     },
+    {
+      friendlyName: 'dicom json',
+      namespace: '@ohif/extension-default.dataSourcesModule.dicomjson',
+      sourceName: 'dicomjson',
+      configuration: {
+        name: 'json',
+      },
+    },
+    {
+      friendlyName: 'dicom local',
+      namespace: '@ohif/extension-default.dataSourcesModule.dicomlocal',
+      sourceName: 'dicomlocal',
+      configuration: {},
+    },
   ],
   defaultDataSourceName: 'dicomweb',
 };

platform/viewer/public/config/docker_openresty-orthanc-keycloak.js

@@ -6,6 +6,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   servers: {
     // This is an array, but we'll only use the first entry for now
     dicomWeb: [

platform/viewer/public/config/docker_openresty-orthanc.js

@@ -8,6 +8,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   dataSources: [
     {
       friendlyName: 'Orthanc Server',
@@ -23,6 +24,20 @@ window.config = {
         thumbnailRendering: 'wadors',
       },
     },
+    {
+      friendlyName: 'dicom json',
+      namespace: '@ohif/extension-default.dataSourcesModule.dicomjson',
+      sourceName: 'dicomjson',
+      configuration: {
+        name: 'json',
+      },
+    },
+    {
+      friendlyName: 'dicom local',
+      namespace: '@ohif/extension-default.dataSourcesModule.dicomlocal',
+      sourceName: 'dicomlocal',
+      configuration: {},
+    },
   ],
   defaultDataSourceName: 'dicomweb',
 };

platform/viewer/public/config/e2e.js

@@ -8,6 +8,7 @@ window.config = {
   maxNumberOfWebWorkers: 3,
   showWarningMessageForCrossOrigin: false,
   showCPUFallbackMessage: false,
+  strictZSpacingForVolumeViewport: true,
   // filterQueryParam: false,
   dataSources: [
     {

platform/viewer/public/config/google.js

@@ -6,6 +6,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   // This is an array, but we'll only use the first entry for now
   oidc: [
     {

platform/viewer/public/config/idc.js

@@ -6,6 +6,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   servers: {
     // This is an array, but we'll only use the first entry for now
     dicomWeb: [],

platform/viewer/public/config/local_dcm4chee.js

@@ -8,6 +8,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   dataSources: [
     {
       friendlyName: 'DCM4CHEE Server',
@@ -27,6 +28,20 @@ window.config = {
         },
       },
     },
+    {
+      friendlyName: 'dicom json',
+      namespace: '@ohif/extension-default.dataSourcesModule.dicomjson',
+      sourceName: 'dicomjson',
+      configuration: {
+        name: 'json',
+      },
+    },
+    {
+      friendlyName: 'dicom local',
+      namespace: '@ohif/extension-default.dataSourcesModule.dicomlocal',
+      sourceName: 'dicomlocal',
+      configuration: {},
+    },
   ],
   studyListFunctionsEnabled: true,
   defaultDataSourceName: 'dicomweb',

platform/viewer/public/config/local_orthanc.js

@@ -8,6 +8,7 @@ window.config = {
   showLoadingIndicator: true,
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
+  strictZSpacingForVolumeViewport: true,
   // filterQueryParam: false,
   dataSources: [
     {

platform/viewer/public/config/local_static.js

@@ -12,6 +12,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   // filterQueryParam: false,
   dataSources: [
     {

platform/viewer/public/config/multiple.js

@@ -20,6 +20,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   // filterQueryParam: false,
   dataSources: [
     {

platform/viewer/public/config/netlify.js

@@ -9,6 +9,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   // filterQueryParam: false,
   dataSources: [
     {

platform/viewer/public/config/public_dicomweb.js

@@ -6,6 +6,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   servers: {
     dicomWeb: [
       {

platform/viewer/src/routes/buildModeRoutes.tsx

@@ -31,11 +31,6 @@ export default function buildModeRoutes({
   hotkeysManager,
 }) {
   const routes = [];
-
-  // const dataSources = Object.keys(extensionManager.dataSourceMap).map(a =>
-  //   extensionManager.getDataSources(a)
-  // );
-
   const dataSourceNames = [];
 
   dataSources.forEach(dataSource => {
@@ -61,7 +56,6 @@ export default function buildModeRoutes({
           servicesManager={servicesManager}
           commandsManager={commandsManager}
           hotkeysManager={hotkeysManager}
-          commandsManager={commandsManager}
         />
       );
 
@@ -86,7 +80,6 @@ export default function buildModeRoutes({
         servicesManager={servicesManager}
         commandsManager={commandsManager}
         hotkeysManager={hotkeysManager}
-        commandsManager={commandsManager}
       />
     );