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["argparse@1.0.10", "", { "dependencies": { "sprintf-js": "~1.0.2" } }, "sha512-o5Roy6tNG4SL/FOkCAN6RzjiakZS25RLYFrcMttJqbdd8BWrnA+fGz57iN5Pb06pvBGvl5gQ0B48dJlslXvoTg=="], + + "texture-compressor/image-size": ["image-size@0.7.5", "", { "bin": { "image-size": "bin/image-size.js" } }, "sha512-Hiyv+mXHfFEP7LzUL/llg9RwFxxY+o9N3JVLIeG5E7iFIFAalxvRU9UZthBdYDEVnzHMgjnKJPPpay5BWf1g9g=="], + "tough-cookie/universalify": ["universalify@0.2.0", "", {}, "sha512-CJ1QgKmNg3CwvAv/kOFmtnEN05f0D/cn9QntgNOQlQF9dgvVTHj3t+8JPdjqawCHk7V/KA+fbUqzZ9XWhcqPUg=="], "trim-repeated/escape-string-regexp": ["escape-string-regexp@1.0.5", "", {}, "sha512-vbRorB5FUQWvla16U8R/qgaFIya2qGzwDrNmCZuYKrbdSUMG6I1ZCGQRefkRVhuOkIGVne7BQ35DSfo1qvJqFg=="], @@ -4083,6 +4367,8 @@ "body-parser/debug/ms": ["ms@2.0.0", "", {}, "sha512-Tpp60P6IUJDTuOq/5Z8cdskzJujfwqfOTkrwIwj7IRISpnkJnT6SyJ4PCPnGMoFjC9ddhal5KVIYtAt97ix05A=="], + "chalk-template/chalk/supports-color": ["supports-color@7.2.0", "", { "dependencies": { "has-flag": "^4.0.0" } }, "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw=="], + "coa/chalk/ansi-styles": ["ansi-styles@3.2.1", "", { "dependencies": { "color-convert": "^1.9.0" } }, "sha512-VT0ZI6kZRdTh8YyJw3SMbYm/u+NqfsAxEpWO0Pf9sq8/e94WxxOpPKx9FR1FlyCtOVDNOQ+8ntlqFxiRc+r5qA=="], "coa/chalk/escape-string-regexp": ["escape-string-regexp@1.0.5", "", {}, "sha512-vbRorB5FUQWvla16U8R/qgaFIya2qGzwDrNmCZuYKrbdSUMG6I1ZCGQRefkRVhuOkIGVne7BQ35DSfo1qvJqFg=="], diff --git a/craco.config.js b/craco.config.js index 1039d728..cbcb67b9 100644 --- a/craco.config.js +++ b/craco.config.js @@ -58,6 +58,20 @@ module.exports = { config.experiments = { asyncWebAssembly: true } + + /* Viv / Deck.gl / Luma ship modern JS; transpile for CRA 5 / webpack 5. */ + config.module.rules.push({ + test: /\.m?js$/, + include: /node_modules[\\/](@deck\.gl|@luma\.gl|@math\.gl|@probe\.gl|@hms-dbmi[\\/]viv)[\\/]/, + use: { + loader: require.resolve('babel-loader'), + options: { + presets: [require.resolve('babel-preset-react-app/dependencies')], + cacheDirectory: true + } + } + }) + return config } }, diff --git a/package.json b/package.json index 67c86ce9..d9ed0556 100644 --- a/package.json +++ b/package.json @@ -38,12 +38,26 @@ ] }, "dependencies": { + "@deck.gl/core": "9.1.15", + "@deck.gl/extensions": "9.1.15", + "@deck.gl/geo-layers": "9.1.15", + "@deck.gl/layers": "9.1.15", + "@deck.gl/mesh-layers": "9.1.15", + "@deck.gl/react": "9.1.15", + "@deck.gl/widgets": "9.1.15", + "@vivjs/layers": "^0.20.0", + "@vivjs/loaders": "^0.20.0", + "@luma.gl/constants": "~9.1.10", + "@luma.gl/core": "~9.1.10", + "@luma.gl/engine": "~9.1.10", + "@luma.gl/shadertools": "~9.1.10", + "@luma.gl/webgl": "~9.1.10", "antd": "^4.22.8", "classnames": "^2.2.6", "dcmjs": "^0.35.0", "detect-browser": "^5.2.1", + "dicomweb-client": "^0.11.2", "dicom-microscopy-viewer": "^0.48.21", - "dicomweb-client": "0.10.3", "oidc-client": "^1.11.5", "react": "^18.2.0", "react-dom": "^18.2.0", @@ -91,7 +105,15 @@ "typescript": "^4.7.4" }, "overrides": { + "@types/minimatch": "5.1.2", "@types/d3-dispatch": "3.0.6", + "@deck.gl/core": "9.1.15", + "@deck.gl/extensions": "9.1.15", + "@deck.gl/geo-layers": "9.1.15", + "@deck.gl/layers": "9.1.15", + "@deck.gl/mesh-layers": "9.1.15", + "@deck.gl/react": "9.1.15", + "@deck.gl/widgets": "9.1.15", "nth-check": "2.0.1", "wrap-ansi": "7.0.0", "make-dir": "3.1.0", diff --git a/src/App.tsx b/src/App.tsx index 70f0cde4..5c31814c 100644 --- a/src/App.tsx +++ b/src/App.tsx @@ -8,6 +8,7 @@ import { Navigate, Route, Routes, + useLocation, useParams, } from 'react-router-dom' @@ -47,6 +48,8 @@ function ParametrizedCaseViewer({ config: AppConfig }): JSX.Element { const { studyInstanceUID } = useParams() + const location = useLocation() + const isVivRoute = location.pathname.startsWith('/viv/') if (studyInstanceUID === undefined) { return @@ -64,6 +67,8 @@ function ParametrizedCaseViewer({ app={app} enableAnnotationTools={enableAnnotationTools} studyInstanceUID={studyInstanceUID} + isVivRoute={isVivRoute} + vivSettings={config.vivSettings} /> ) @@ -462,6 +467,52 @@ class App extends React.Component { this.signIn() } + /** Shared layout for study viewer routes (classic and `/viv/...`). */ + private renderCaseViewerShell( + appInfo: { + name: string + version: string + homepage: string + uid: string + organization?: string + }, + enableWorklist: boolean, + enableServerSelection: boolean, + enableMemoryMonitoring: boolean, + isLogoutPossible: boolean, + onLogout: () => void, + layoutStyle: { height: string }, + layoutContentStyle: { height: string }, + ): JSX.Element { + return ( + + +
+ + + + {enableMemoryMonitoring && ( + + )} + + + ) + } + render(): React.ReactNode { const appInfo = { name: this.props.name, @@ -564,63 +615,55 @@ class App extends React.Component { /> - -
- - - - {enableMemoryMonitoring && ( - - )} - - - } + element={this.renderCaseViewerShell( + appInfo, + enableWorklist, + enableServerSelection, + enableMemoryMonitoring, + isLogoutPossible, + onLogout, + layoutStyle, + layoutContentStyle, + )} /> - -
- - - - {enableMemoryMonitoring && ( - - )} - - - } + element={this.renderCaseViewerShell( + appInfo, + enableWorklist, + enableServerSelection, + enableMemoryMonitoring, + isLogoutPossible, + onLogout, + layoutStyle, + layoutContentStyle, + )} + /> + + + colors?: Array<[number, number, number]> + initialViewState?: { + target: [number, number, number] + zoom?: number + } +} + export default interface AppConfig { /** * Currently, only one server is supported. However, support for multiple @@ -107,4 +124,6 @@ export default interface AppConfig { enableInDevelopment?: boolean } enableMemoryMonitoring?: boolean + /** Optional display overrides for the Viv slide viewer at `/viv/...` routes (channels, contrast, etc.). */ + vivSettings?: VivSettings } diff --git a/src/DicomWebManager.ts b/src/DicomWebManager.ts index df65c6d8..fc40527e 100644 --- a/src/DicomWebManager.ts +++ b/src/DicomWebManager.ts @@ -157,6 +157,20 @@ export default class DicomWebManager implements dwc.api.DICOMwebClient { return this.stores[0].client.headers } + /** + * Run a callback on the primary {@link dwc.api.DICOMwebClient} (the store used for reads). + * Used e.g. to append Viv tile {@link dwc.api.DICOMwebClientOptions.requestHooks} that must + * see the same XHR pipeline as {@link dmv.viewer.VolumeImageViewer}. + */ + applyToPrimaryDicomwebClient( + fn: (client: dwc.api.DICOMwebClient) => void, + ): void { + if (this.stores.length === 0) { + return + } + fn(this.stores[0].client) + } + storeInstances = async ( options: dwc.api.StoreInstancesOptions, ): Promise => { diff --git a/src/components/CaseViewer.tsx b/src/components/CaseViewer.tsx index c9ca3738..907c8c03 100644 --- a/src/components/CaseViewer.tsx +++ b/src/components/CaseViewer.tsx @@ -1,21 +1,37 @@ -import { Layout, Menu } from 'antd' +import type { MenuProps } from 'antd' +import { Layout, Menu, Select, Tag } from 'antd' // skipcq: JS-C1003 import * as dcmjs from 'dcmjs' -import { useEffect, useState } from 'react' +// skipcq: JS-C1003 +import type * as dmv from 'dicom-microscopy-viewer' +import { + Fragment, + type ReactNode, + useCallback, + useEffect, + useState, +} from 'react' import { Route, Routes, useLocation, useParams } from 'react-router-dom' -import type { AnnotationSettings } from '../AppConfig' +import type { AnnotationSettings, VivSettings } from '../AppConfig' import type { User } from '../auth' import type DicomWebManager from '../DicomWebManager' import type { Slide } from '../data/slides' import { StorageClasses } from '../data/uids' import { useSlides } from '../hooks/useSlides' +import DicomMetadataStore from '../services/DICOMMetadataStore' import { type RouteComponentProps, withRouter } from '../utils/router' +import type { VivBulkAnnotationCatalogPayload } from '../viv/loadBulkAnnotationLayers' +import VivSlideViewport from '../viv/VivSlideViewport' +import { EMPTY_VIV_BULK_LOAD_STATUS } from '../viv/vivBulkLoadStatus' +import AnnotationGroupList from './AnnotationGroupList' import ClinicalTrial from './ClinicalTrial' import Patient from './Patient' import SlideList from './SlideList' import SlideViewer from './SlideViewer' import Study from './Study' +import VivBulkAnnotationLoadIndicator from './VivBulkAnnotationLoadIndicator' +import VivSettingsDrawer from './VivSettingsDrawer' const { naturalizeDataset } = dcmjs.data.DicomMetaDictionary @@ -52,6 +68,66 @@ const findSeriesSlide = ( }) } +/** Non-interactive menu row for custom panel content (avoids invalid DOM props). */ +const menuPanelItemStyle: React.CSSProperties = { + height: 'auto', + cursor: 'default', + padding: 0, + lineHeight: 'normal', +} + +function menuPanelItem( + key: string, + label: ReactNode, +): NonNullable[number] { + return { + key, + label, + disabled: true, + style: menuPanelItemStyle, + } +} + +/** Viv path: main viewport + slim right rail (classic viewer uses ~300px sider). */ +const vivChrome = (main: JSX.Element, rightPanel?: ReactNode): JSX.Element => ( +
+
+ {main} +
+ +
+) + function ParametrizedSlideViewer({ clients, slides, @@ -60,6 +136,8 @@ function ParametrizedSlideViewer({ preload, enableAnnotationTools, annotations, + isVivRoute, + vivSettings, }: { clients: { [key: string]: DicomWebManager } slides: Slide[] @@ -73,6 +151,8 @@ function ParametrizedSlideViewer({ preload: boolean enableAnnotationTools: boolean annotations: AnnotationSettings[] + isVivRoute: boolean + vivSettings?: VivSettings }): JSX.Element | null { const { studyInstanceUID = '', seriesInstanceUID = '' } = useParams<{ studyInstanceUID: string @@ -85,8 +165,126 @@ function ParametrizedSlideViewer({ ) const [derivedDataset, setDerivedDataset] = useState(null) + const [vivBulkCatalog, setVivBulkCatalog] = + useState(null) + const [vivVisibleAnnotationGroupUIDs, setVivVisibleAnnotationGroupUIDs] = + useState>(new Set()) + const [vivAnnotationGroupStyles, setVivAnnotationGroupStyles] = useState< + Record + >({}) + const [vivAnnGroupSeriesSelection, setVivAnnGroupSeriesSelection] = + useState('all') + const [vivIccProfilesAvailable, setVivIccProfilesAvailable] = useState(true) + const [vivBulkLoadStatus, setVivBulkLoadStatus] = useState( + EMPTY_VIV_BULK_LOAD_STATUS, + ) + + const getVivSeriesDescription = (seriesInstanceUID: string): string => { + const study = DicomMetadataStore.getStudy(studyInstanceUID) + if (study?.series != null && study !== undefined) { + const series = study.series.find( + (s) => s.SeriesInstanceUID === seriesInstanceUID, + ) + if ( + series?.SeriesDescription !== undefined && + series.SeriesDescription !== '' + ) { + return series.SeriesDescription + } + } + return `Series ${seriesInstanceUID.slice(0, 8)}…` + } + + const handleVivIccAvailability = useCallback((hasIccProfiles: boolean) => { + setVivIccProfilesAvailable(hasIccProfiles) + }, []) + + const handleVivBulkCatalogChange = useCallback( + (c: VivBulkAnnotationCatalogPayload | null) => { + setVivBulkCatalog(c) + if (c == null) { + setVivBulkLoadStatus(EMPTY_VIV_BULK_LOAD_STATUS) + } + if (c != null && c.annotationGroups.length > 0) { + setVivAnnGroupSeriesSelection('all') + setVivVisibleAnnotationGroupUIDs(new Set()) + setVivAnnotationGroupStyles({ ...c.defaultStylesByGroupUID }) + } else if (c != null) { + setVivVisibleAnnotationGroupUIDs(new Set()) + setVivAnnotationGroupStyles({}) + } else { + setVivVisibleAnnotationGroupUIDs(new Set()) + setVivAnnotationGroupStyles({}) + setVivAnnGroupSeriesSelection('all') + } + }, + [], + ) + + const handleVivAnnotationGroupVisibilityChange = useCallback( + ({ + annotationGroupUID, + isVisible, + }: { + annotationGroupUID: string + isVisible: boolean + }) => { + setVivVisibleAnnotationGroupUIDs((prev) => { + const next = new Set(prev) + if (isVisible) { + next.add(annotationGroupUID) + } else { + next.delete(annotationGroupUID) + } + return next + }) + }, + [], + ) + + const handleVivAnnotationGroupStyleChange = useCallback( + ({ + uid, + styleOptions, + }: { + uid: string + styleOptions: { + opacity?: number + color?: number[] + measurement?: dcmjs.sr.coding.CodedConcept + limitValues?: number[] + } + }) => { + setVivAnnotationGroupStyles((prev) => { + const base = prev[uid] ?? + vivBulkCatalog?.defaultStylesByGroupUID[uid] ?? { + opacity: 1, + color: [220, 60, 60], + } + return { + ...prev, + [uid]: { + opacity: styleOptions.opacity ?? base.opacity, + color: styleOptions.color ?? base.color, + }, + } + }) + }, + [vivBulkCatalog], + ) + + const handleVivAnnotationGroupSeriesSelect = useCallback((value: string) => { + setVivVisibleAnnotationGroupUIDs(new Set()) + setVivAnnGroupSeriesSelection(value) + }, []) + + const handleVivAnnotationGroupClick = useCallback((_uid: string) => { + /* Viv preview: no VolumeImageViewer.zoomToROI equivalent yet */ + }, []) useEffect(() => { + setVivIccProfilesAvailable(true) + const currentSlideMatchesSeries = selectedSlide?.seriesInstanceUIDs.some( (uid: string) => uid === seriesInstanceUID, @@ -171,21 +369,261 @@ function ParametrizedSlideViewer({ let viewer = null if (selectedSlide != null && selectedSlide !== undefined) { - viewer = ( - - ) + if (isVivRoute) { + const microscopyClient = + clients[StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE] ?? + clients.default + if (microscopyClient === undefined) { + return null + } + const bulkAnnotationClient = + clients[StorageClasses.MICROSCOPY_BULK_SIMPLE_ANNOTATION] ?? + microscopyClient + + let vivAnnotationGroupListSection: ReactNode = null + if ( + vivBulkCatalog != null && + vivBulkCatalog.annotationGroups.length > 0 + ) { + const annotationGroups = vivBulkCatalog.annotationGroups + const annotationGroupsBySeries: { + [seriesInstanceUID: string]: dmv.annotation.AnnotationGroup[] + } = {} + for (const ag of annotationGroups) { + const seriesUID = ag.seriesInstanceUID + if (!(seriesUID in annotationGroupsBySeries)) { + annotationGroupsBySeries[seriesUID] = [] + } + annotationGroupsBySeries[seriesUID]?.push(ag) + } + const dropdownOptions = [ + { value: 'all', label: 'All' }, + ...Object.keys(annotationGroupsBySeries).map((seriesUID) => ({ + value: seriesUID, + label: `${getVivSeriesDescription(seriesUID)} (${annotationGroupsBySeries[seriesUID]?.length ?? 0} groups)`, + })), + ] + const selectedSeriesAnnotationGroups = + vivAnnGroupSeriesSelection === 'all' + ? annotationGroups + : (annotationGroupsBySeries[vivAnnGroupSeriesSelection] ?? []) + + vivAnnotationGroupListSection = ( + <> +
+