fix(378/327/377/353): DICOM tag browser, worklist (including Modalities in Study when QIDO omits it), overlay colormaps, header badge behavior, and test/tooling updates

bunfig.toml

@@ -0,0 +1,2 @@
+[test]
+preload = ["./src/test/bun-preload.ts"]

package.json

@@ -16,6 +16,7 @@
  "fmt": "biome format --write .",
  "format": "biome format --write .",
  "test": "biome check . && craco test --watchAll=false",
+ "test:bun": "bun test",
  "predeploy": "REACT_APP_CONFIG=demo PUBLIC_URL='https://imagingdatacommons.github.io/slim/' ./scripts/set-git-env.sh craco build",
  "deploy": "gh-pages -d build",
  "clean": "rm -rf ./build ./node_modules",
@@ -52,11 +53,10 @@
  "retry": "^0.13.1"
  },
  "devDependencies": {
- "ajv": "6.12.6",
- "@biomejs/biome": "^2.0.0",
  "@babel/preset-env": "^7.15.0",
  "@babel/preset-react": "^7.17.12",
  "@babel/preset-typescript": "^7.17.12",
+ "@biomejs/biome": "^2.0.0",
  "@craco/craco": "^6.4.0",
  "@semantic-release/changelog": "^6.0.3",
  "@semantic-release/commit-analyzer": "^12.0.0",
@@ -67,6 +67,7 @@
  "@testing-library/jest-dom": "^5.16.4",
  "@testing-library/react": "^14.0.0",
  "@testing-library/user-event": "^7.1.2",
+ "@types/d3-dispatch": "3.0.6",
  "@types/jest": "^28.1.3",
  "@types/lodash": "^4.17.20",
  "@types/node": "^14.14.9",
@@ -75,11 +76,13 @@
  "@types/react-router-dom": "^5.3.3",
  "@types/retry": "^0.12.1",
  "@types/uuid": "^8.3.0",
+ "ajv": "6.12.6",
  "copy-webpack-plugin": "9.1.0",
  "craco-less": "^2.0.0",
  "eslint": "^8.57.0",
  "eslint-plugin-sonarjs": "^0.25.0",
  "gh-pages": "^5.0.0",
+ "happy-dom": "^20.8.7",
  "husky": "^9.1.7",
  "react-scripts": "5.0.0",
  "react-test-renderer": "^18.2.0",
@@ -88,6 +91,7 @@
  "typescript": "^4.7.4"
  },
  "overrides": {
+ "@types/d3-dispatch": "3.0.6",
  "nth-check": "2.0.1",
  "wrap-ansi": "7.0.0",
  "make-dir": "3.1.0",

src/__mocks__/dicomMicroscopyViewerMock.js

@@ -14,6 +14,7 @@ const TAG_TO_KEYWORD = {
  '00201206': 'NumberOfStudyRelatedSeries',
  '00201208': 'NumberOfStudyRelatedInstances',
  '00080061': 'ModalitiesInStudy',
+ '00080060': 'Modality',
  '00080090': 'ReferringPhysicianName',
  '0020000E': 'SeriesInstanceUID'
 }

src/components/DicomTagBrowser/DicomTagBrowser.tsx

@@ -13,6 +13,7 @@ import DicomMetadataStore, {
  type Study,
 } from '../../services/DICOMMetadataStore'
 import { formatDicomDate } from '../../utils/formatDicomDate'
+import { logger } from '../../utils/logger'
 import { getSortedTags, type TagInfo } from './dicomTagUtils'
 
 const { Option } = Select
@@ -43,6 +44,16 @@ interface DicomTagBrowserProps {
  seriesInstanceUID?: string
 }
 
+function bucketContainsSopInstance(bucket: unknown[], sop: string): boolean {
+ if (sop === '') return false
+ for (const existing of bucket) {
+ if ((existing as Record<string, unknown>).SOPInstanceUID === sop) {
+ return true
+ }
+ }
+ return false
+}
+
 const DicomTagBrowser = ({
  clients,
  studyInstanceUID,
@@ -109,50 +120,65 @@ const DicomTagBrowser = ({
  if (slides.length > 0) {
  displaySets = slides
  .flatMap((slide): DisplaySet[] => {
- const slideDisplaySets: DisplaySet[] = []
+ /** One row per SeriesInstanceUID; volume/overview/label often share a series. */
+ const imagesBySeries = new Map<string, unknown[]>()
 
- // Helper function to process any image type
- const processImageType = (
+ const addImages = (
  images: unknown[] | undefined,
  imageType: string,
  ): void => {
- if (images?.[0] !== undefined) {
- console.info(
- `Found ${images.length} ${imageType} image(s) for slide ${slide.containerIdentifier}`,
- )
-
- const img = images[0] as Record<string, unknown>
- const {
- SeriesDate,
- SeriesTime,
- SeriesNumber,
- SeriesInstanceUID,
- SeriesDescription,
- Modality,
- } = img
-
- processedSeries.push(SeriesInstanceUID as string)
-
- const ds: DisplaySet = {
- displaySetInstanceUID: index,
- SeriesDate: SeriesDate as string | undefined,
- SeriesTime: SeriesTime as string | undefined,
- SeriesInstanceUID: SeriesInstanceUID as string,
- SeriesNumber: String(SeriesNumber),
- SeriesDescription: SeriesDescription as string | undefined,
- Modality: Modality as string,
- images,
+ if (images?.[0] === undefined) return
+ logger.debug(
+ `Found ${images.length} ${imageType} image(s) for slide ${slide.containerIdentifier}`,
+ )
+ for (const image of images) {
+ const img = image as Record<string, unknown>
+ const seriesUID = img.SeriesInstanceUID as string | undefined
+ if (seriesUID === undefined || seriesUID === '') continue
+
+ let bucket = imagesBySeries.get(seriesUID)
+ if (bucket === undefined) {
+ processedSeries.push(seriesUID)
+ bucket = []
+ imagesBySeries.set(seriesUID, bucket)
+ }
+
+ const sop =
+ typeof img.SOPInstanceUID === 'string' ? img.SOPInstanceUID : ''
+ if (!bucketContainsSopInstance(bucket, sop)) {
+ bucket.push(image)
  }
- slideDisplaySets.push(ds)
- index++
  }
  }
 
- // Process all image types
- processImageType(slide.volumeImages, 'volume')
- processImageType(slide.overviewImages, 'overview')
- processImageType(slide.labelImages, 'label')
+ addImages(slide.volumeImages, 'volume')
+ addImages(slide.overviewImages, 'overview')
+ addImages(slide.labelImages, 'label')
 
+ const slideDisplaySets: DisplaySet[] = []
+ for (const images of imagesBySeries.values()) {
+ if (images[0] === undefined) continue
+ const img = images[0] as Record<string, unknown>
+ const {
+ SeriesDate,
+ SeriesTime,
+ SeriesNumber,
+ SeriesInstanceUID,
+ SeriesDescription,
+ Modality,
+ } = img
+ slideDisplaySets.push({
+ displaySetInstanceUID: index,
+ SeriesDate: SeriesDate as string | undefined,
+ SeriesTime: SeriesTime as string | undefined,
+ SeriesInstanceUID: SeriesInstanceUID as string,
+ SeriesNumber: String(SeriesNumber),
+ SeriesDescription: SeriesDescription as string | undefined,
+ Modality: Modality as string,
+ images,
+ })
+ index++
+ }
  return slideDisplaySets
  })
  .filter((set): set is DisplaySet => set !== null && set !== undefined)
@@ -372,12 +398,10 @@ const DicomTagBrowser = ({
  matchingPaths.push(currentPath)
  }
 
- if (node.children != null) {
- node.children.forEach((child) => {
- const childPaths = findMatchingPaths(child, currentPath)
- matchingPaths = [...matchingPaths, ...childPaths]
- })
- }
+ node.children?.forEach((child) => {
+ const childPaths = findMatchingPaths(child, currentPath)
+ matchingPaths = [...matchingPaths, ...childPaths]
+ })
 
  return matchingPaths
  }