feat(multiframe): enhanced support for multiframe dicom (OHIF#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 <[email protected]>
webxzy · Apr 1, 2023 · 8ed75b1 · 8ed75b1
1 parent e667496
commit 8ed75b1
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Showing 28 changed files with 228 additions and 62 deletions.
diff --git a/extensions/cornerstone/package.json b/extensions/cornerstone/package.json
@@ -29,7 +29,7 @@
   "peerDependencies": {
     "@ohif/core": "^3.0.0",
     "@ohif/ui": "^2.0.0",
-    "cornerstone-wado-image-loader": "^4.10.2",
+    "cornerstone-wado-image-loader": "^4.13.0",
     "dcmjs": "^0.29.4",
     "dicom-parser": "^1.8.9",
     "hammerjs": "^2.0.8",

diff --git a/extensions/cornerstone/src/init.tsx b/extensions/cornerstone/src/init.tsx
@@ -43,6 +43,14 @@ export default async function init({
 
   // For debugging e2e tests that are failing on CI
   cornerstone.setUseCPURendering(Boolean(appConfig.useCPURendering));
+  cornerstone.setConfiguration({
+    ...cornerstone.getConfiguration(),
+    rendering: {
+      ...cornerstone.getConfiguration().rendering,
+      strictZSpacingForVolumeViewport:
+        appConfig.strictZSpacingForVolumeViewport,
+    },
+  });
 
   // For debugging large datasets
   const MAX_CACHE_SIZE_1GB = 1073741824;

diff --git a/extensions/default/src/DicomLocalDataSource/index.js b/extensions/default/src/DicomLocalDataSource/index.js
@@ -138,7 +138,9 @@ function createDicomLocalApi(dicomLocalConfig) {
           study.series.forEach(aSeries => {
             const { SeriesInstanceUID } = aSeries;
 
-            aSeries.instances.forEach(instance => {
+            const isMultiframe = aSeries.instances[0].NumberOfFrames > 1;
+
+            aSeries.instances.forEach((instance, index) => {
               const {
                 url: imageId,
                 StudyInstanceUID,
@@ -153,6 +155,7 @@ function createDicomLocalApi(dicomLocalConfig) {
                 StudyInstanceUID,
                 SeriesInstanceUID,
                 SOPInstanceUID,
+                frameIndex: isMultiframe ? index : 1,
               });
             });
 
@@ -185,7 +188,7 @@ function createDicomLocalApi(dicomLocalConfig) {
       displaySet.images.forEach(instance => {
         const NumberOfFrames = instance.NumberOfFrames;
         if (NumberOfFrames > 1) {
-          for (let i = 0; i < NumberOfFrames; i++) {
+          for (let i = 1; i <= NumberOfFrames; i++) {
             const imageId = this.getImageIdsForInstance({
               instance,
               frame: i,

diff --git a/extensions/default/src/DicomWebDataSource/index.js b/extensions/default/src/DicomWebDataSource/index.js
@@ -104,7 +104,7 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) {
     query: {
       studies: {
         mapParams: mapParams.bind(),
-        search: async function (origParams) {
+        search: async function(origParams) {
           const headers = userAuthenticationService.getAuthorizationHeader();
           if (headers) {
             qidoDicomWebClient.headers = headers;
@@ -129,7 +129,7 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) {
       },
       series: {
         // mapParams: mapParams.bind(),
-        search: async function (studyInstanceUid) {
+        search: async function(studyInstanceUid) {
           const headers = userAuthenticationService.getAuthorizationHeader();
           if (headers) {
             qidoDicomWebClient.headers = headers;

diff --git a/platform/core/package.json b/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"
   },

diff --git a/platform/core/src/classes/MetadataProvider.js b/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, {
@@ -454,15 +482,15 @@ 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 {
       imageURI = imageIdToURI(imageId);
     }
 
     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 };

diff --git a/platform/core/src/services/DicomMetadataStore/DicomMetadataStore.ts b/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
     );
 

diff --git a/platform/core/src/utils/combineFrameInstance.ts b/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;
   }

diff --git a/platform/core/src/utils/isDisplaySetReconstructable.js b/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 processMultiframe(multiFrameInstance) {
-  const {
-    PerFrameFunctionalGroupsSequence,
-    SharedFunctionalGroupsSequence,
-  } = multiFrameInstance;
+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) {
   // 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 (
-    !SharedFunctionalGroupsSequence ||
-    !SharedFunctionalGroupsSequence[0].PixelMeasuresSequence
-  ) {
+  if (!hasPixelMeasurements(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
+  if (!hasOrientation(multiFrameInstance)) {
+    console.log('No image orientation information, not reconstructable');
+    return { value: false };
   }
 
-  const frame0 = PerFrameFunctionalGroupsSequence[0];
-  const firstPosition =
-    frame0.PlanePositionSequence || frame0.CTPositionSequence;
-  if (!firstPosition) {
+  if (!hasPosition(multiFrameInstance)) {
     console.log('No image position information, not reconstructable');
     return { value: false };
   }
-  // TODO - check spacing consistency
 
+  if (
+    multiFrameInstance.Modality.includes('NM') &&
+    !isNMReconstructable(multiFrameInstance)
+  ) {
+    return { value: false };
+  }
+
+  // TODO - check spacing consistency
   return { value: true };
 }
 

diff --git a/platform/viewer/package.json b/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",

diff --git a/platform/viewer/public/config/aws.js b/platform/viewer/public/config/aws.js
@@ -9,6 +9,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   // filterQueryParam: false,
   dataSources: [
     {

diff --git a/platform/viewer/public/config/default.js b/platform/viewer/public/config/default.js
@@ -26,6 +26,7 @@ window.config = {
   showWarningMessageForCrossOrigin: true,
   showCPUFallbackMessage: true,
   showLoadingIndicator: true,
+  strictZSpacingForVolumeViewport: true,
   maxNumRequests: {
     interaction: 100,
     thumbnail: 75,
@@ -45,10 +46,12 @@ 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',

diff --git a/platform/viewer/public/config/demo.js b/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: [