fix(dicom overlay): Handle special cases of ArrayBuffer for various DICOM overlay attributes. (#3684)

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

.circleci/config.yml

@@ -93,43 +93,6 @@ jobs:
           file: '/home/circleci/repo/platform/core/coverage/reports'
           flags: 'core'
 
-  ###
-  # Workflow: PR_OPTIONAL_DOCKER_PUBLISH
-  ###
-  # DOCKER_PR_PUBLISH:
-  #   <<: *defaults
-  #   steps:
-  #     # Enable yarn workspaces
-  #     - run: yarn config set workspaces-experimental true
-
-  #     # Checkout code and ALL Git Tags
-  #     - checkout
-  #     - restore_cache:
-  #         name: Restore Yarn and Cypress Package Cache
-  #         keys:
-  #           # when lock file changes, use increasingly general patterns to restore cache
-  #           - yarn-packages-{{ checksum "yarn.lock" }}
-  #           - yarn-packages-
-
-  #     - run:
-  #         name: Install Dependencies
-  #         command: yarn install --frozen-lockfile
-
-  #     - setup_remote_docker:
-  #         docker_layer_caching: false
-
-  #     - run:
-  #         name: Build and push Docker image
-  #         command: |
-  #           # Remove npm config
-  #           rm -f ./.npmrc
-  #           # Set our version number using vars
-  #           echo $CIRCLE_BUILD_NUM
-  #           # Build our image, auth, and push
-  #           docker build --tag ohif/app:PR_BUILD-$CIRCLE_BUILD_NUM .
-  #           echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
-  #           docker push ohif/app:PR_BUILD-$CIRCLE_BUILD_NUM
-
   ###
   # Workflow: DEPLOY
   ###
@@ -180,6 +143,53 @@ jobs:
             - commit.txt
             - version.json
 
+  # just to make sure later on we can publish them
+  BUILD_PACKAGES_QUICK:
+    <<: *defaults
+    steps:
+      - run: yarn -v
+      # Checkout code and ALL Git Tags
+      - checkout
+      - attach_workspace:
+          at: ~/repo
+      # Use increasingly general patterns to restore cache
+      - restore_cache:
+          name: Restore Yarn and Cypress Package Cache
+          keys:
+            - yarn-packages-{{ checksum "yarn.lock" }}
+            - yarn-packages-
+      - run:
+          name: Install Dependencies
+          command: yarn install --frozen-lockfile
+      - save_cache:
+          name: Save Yarn Package Cache
+          paths:
+            - ~/.cache/yarn
+          key: yarn-packages-{{ checksum "yarn.lock" }}
+      - run:
+          name: Avoid hosts unknown for github
+          command: |
+            rm -rf ~/.ssh
+            mkdir ~/.ssh/
+            echo -e "Host github.com\n\tStrictHostKeyChecking no\n" > ~/.ssh/config
+            git config --global user.email "danny.ri.brown+ohif-bot@gmail.com"
+            git config --global user.name "ohif-bot"
+      - run:
+          name: Authenticate with NPM registry
+          command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
+      - run:
+          name: Increase the event emitter limit
+          command: |
+            node ./increaseEventEmitterLimit.mjs
+      - run:
+          name: build half of the packages (to avoid out of memory in circleci)
+          command: |
+            yarn run build:package-all
+      - run:
+          name: build the other half of the packages
+          command: |
+            yarn run build:package-all-1
+
   ###
   # Workflow: RELEASE
   ###
@@ -406,7 +416,10 @@ jobs:
 workflows:
   PR_CHECKS:
     jobs:
-      - UNIT_TESTS
+      - BUILD_PACKAGES_QUICK
+      - UNIT_TESTS:
+          requires:
+            - BUILD_PACKAGES_QUICK
 
       - CYPRESS_CUSTOM_RUN:
           name: 'Cypress Tests'
@@ -427,7 +440,7 @@ workflows:
               cypress-cache-path:
                 - '~/.cache/Cypress'
           requires:
-            - UNIT_TESTS
+            - BUILD_PACKAGES_QUICK
 
   # PR_OPTIONAL_VISUAL_TESTS:
   #   jobs:

extensions/cornerstone/src/tools/ImageOverlayViewerTool.tsx

@@ -160,6 +160,8 @@ class ImageOverlayViewerTool extends AnnotationDisplayTool {
           let pixelData = null;
           if (overlay.pixelData.Value) {
             pixelData = overlay.pixelData.Value;
+          } else if (overlay.pixelData instanceof Array) {
+            pixelData = overlay.pixelData[0];
           } else if (overlay.pixelData.retrieveBulkData) {
             pixelData = await overlay.pixelData.retrieveBulkData();
           }

modes/basic-test-mode/.webpack/webpack.dev.js

@@ -4,7 +4,7 @@ const SRC_DIR = path.join(__dirname, '../src');
 const DIST_DIR = path.join(__dirname, '../dist');
 
 const ENTRY = {
-  app: `${SRC_DIR}/index.js`,
+  app: `${SRC_DIR}/index.ts`,
 };
 
 module.exports = (env, argv) => {

modes/basic-test-mode/.webpack/webpack.prod.js

@@ -11,7 +11,7 @@ const SRC_DIR = path.join(__dirname, '../src');
 const DIST_DIR = path.join(__dirname, '../dist');
 
 const ENTRY = {
-  app: `${SRC_DIR}/index.js`,
+  app: `${SRC_DIR}/index.ts`,
 };
 
 module.exports = (env, argv) => {

platform/core/src/classes/MetadataProvider.ts

@@ -68,7 +68,7 @@ class MetadataProvider {
 
     if (!instance) {
       return;
-  }
+    }
 
     return (frameNumber && combineFrameInstance(frameNumber, instance)) || instance;
   }
@@ -118,16 +118,15 @@ class MetadataProvider {
    * Adds a new handler for the given tag.  The handler will be provided an
    * instance object that it can read values from.
    */
-  public addHandler(
+  public addHandler(wadoImageLoaderTag: string, handler) {
-    wadoImageLoaderTag: string,
-    handler
-  ) {
     WADO_IMAGE_LOADER[wadoImageLoaderTag] = handler;
   }
 
   _getCornerstoneDICOMImageLoaderTag(wadoImageLoaderTag, instance) {
     let metadata = WADO_IMAGE_LOADER[wadoImageLoaderTag]?.(instance);
-    if (metadata) return metadata;
+    if (metadata) {
+      return metadata;
+    }
 
     switch (wadoImageLoaderTag) {
       case WADO_IMAGE_LOADER_TAGS.GENERAL_SERIES_MODULE:
@@ -291,12 +290,42 @@ class MetadataProvider {
           const ROIStandardDeviationTag = `${groupStr}1303`;
           const OverlayOrigin = instance[OverlayOriginTag];
 
+          let rows = 0;
+          if (instance[OverlayRowsTag] instanceof Array) {
+            // The DICOM VR for overlay rows is US (unsigned short).
+            const rowsInt16Array = new Uint16Array(instance[OverlayRowsTag][0]);
+            rows = rowsInt16Array[0];
+          } else {
+            rows = instance[OverlayRowsTag];
+          }
+
+          let columns = 0;
+          if (instance[OverlayColumnsTag] instanceof Array) {
+            // The DICOM VR for overlay columns is US (unsigned short).
+            const columnsInt16Array = new Uint16Array(instance[OverlayColumnsTag][0]);
+            columns = columnsInt16Array[0];
+          } else {
+            columns = instance[OverlayColumnsTag];
+          }
+
+          let x = 0;
+          let y = 0;
+          if (OverlayOrigin.length === 1) {
+            // The DICOM VR for overlay origin is SS (signed short) with a multiplicity of 2.
+            const originInt16Array = new Int16Array(OverlayOrigin[0]);
+            x = originInt16Array[0];
+            y = originInt16Array[1];
+          } else {
+            x = OverlayOrigin[0];
+            y = OverlayOrigin[1];
+          }
+
           const overlay = {
-            rows: instance[OverlayRowsTag],
+            rows: rows,
-            columns: instance[OverlayColumnsTag],
+            columns: columns,
             type: instance[OverlayType],
-            x: OverlayOrigin[0],
+            x,
-            y: OverlayOrigin[1],
+            y,
             pixelData: OverlayData,
             description: instance[OverlayDescriptionTag],
             label: instance[OverlayLabelTag],
@@ -444,7 +473,7 @@ class MetadataProvider {
     imageURI = imageURI.split('&frame=')[0];
 
     const uids = this.imageURIToUIDs.get(imageURI);
-    let frameNumber = this.getFrameInformationFromURL(imageId) || '1';
+    const frameNumber = this.getFrameInformationFromURL(imageId) || '1';
 
     if (uids && frameNumber !== undefined) {
       return { ...uids, frameNumber };
@@ -489,9 +518,7 @@ const WADO_IMAGE_LOADER = {
       imageOrientationPatient: toNumber(ImageOrientationPatient),
       rowCosines: toNumber(rowCosines || [0, 1, 0]),
       columnCosines: toNumber(columnCosines || [0, 0, -1]),
-      imagePositionPatient: toNumber(
+      imagePositionPatient: toNumber(instance.ImagePositionPatient || [0, 0, 0]),
-        instance.ImagePositionPatient || [0, 0, 0]
-      ),
       sliceThickness: toNumber(instance.SliceThickness),
       sliceLocation: toNumber(instance.SliceLocation),
       pixelSpacing: toNumber(PixelSpacing || 1),